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Sample records for genome informatics advances

  1. Genome Informatics

    PubMed Central

    Winslow, Raimond L.; Boguski, Mark S.

    2005-01-01

    This article reviews recent advances in genomics and informatics relevant to cardiovascular research. In particular, we review the status of (1) whole genome sequencing efforts in human, mouse, rat, zebrafish, and dog; (2) the development of data mining and analysis tools; (3) the launching of the National Heart, Lung, and Blood Institute Programs for Genomics Applications and Proteomics Initiative; (4) efforts to characterize the cardiac transcriptome and proteome; and (5) the current status of computational modeling of the cardiac myocyte. In each instance, we provide links to relevant sources of information on the World Wide Web and critical appraisals of the promises and the challenges of an expanding and diverse information landscape. PMID:12750305

  2. Creating advanced health informatics certification.

    PubMed

    Gadd, Cynthia S; Williamson, Jeffrey J; Steen, Elaine B; Fridsma, Douglas B

    2016-07-01

    In 2005, AMIA leaders and members concluded that certification of advanced health informatics professionals would offer value to individual practitioners, organizations that hire them, and society at large. AMIA's work to create advanced informatics certification began by leading a successful effort to create the clinical informatics subspecialty for American Board of Medical Specialties board-certified physicians. Since 2012, AMIA has been working to establish advanced health informatics certification (AHIC) for all health informatics practitioners regardless of their primary discipline. In November 2015, AMIA completed the first of 3 key tasks required to establish AHIC, with the AMIA Board of Directors' endorsement of proposed eligibility requirements. This AMIA Board white paper describes efforts to establish AHIC, reports on the current status of AHIC components, and provides a context for the proposed AHIC eligibility requirements. PMID:27358327

  3. Farm animal genomics and informatics: an update

    PubMed Central

    Fadiel, Ahmed; Anidi, Ifeanyi; Eichenbaum, Kenneth D.

    2005-01-01

    Farm animal genomics is of interest to a wide audience of researchers because of the utility derived from understanding how genomics and proteomics function in various organisms. Applications such as xenotransplantation, increased livestock productivity, bioengineering new materials, products and even fabrics are several reasons for thriving farm animal genome activity. Currently mined in rapidly growing data warehouses, completed genomes of chicken, fish and cows are available but are largely stored in decentralized data repositories. In this paper, we provide an informatics primer on farm animal bioinformatics and genome project resources which drive attention to the most recent advances in the field. We hope to provide individuals in biotechnology and in the farming industry with information on resources and updates concerning farm animal genome projects. PMID:16275782

  4. Eligibility requirements for advanced health informatics certification.

    PubMed

    Gadd, Cynthia S; Williamson, Jeffrey J; Steen, Elaine B; Andriole, Katherine P; Delaney, Connie; Gumpper, Karl; LaVenture, Martin; Rosendale, Doug; Sittig, Dean F; Thyvalikakath, Thankam; Turner, Peggy; Fridsma, Douglas B

    2016-07-01

    AMIA is leading the effort to strengthen the health informatics profession by creating an advanced health informatics certification (AHIC) for individuals whose informatics work directly impacts the practice of health care, public health, or personal health. The AMIA Board of Directors has endorsed a set of proposed AHIC eligibility requirements that will be presented to the future AHIC certifying entity for adoption. These requirements specifically establish who will be eligible to sit for the AHIC examination and more generally signal the depth and breadth of knowledge and experience expected from certified individuals. They also inform the development of the accreditation process and provide guidance to graduate health informatics programs as well as individuals interested in pursuing AHIC. AHIC eligibility will be determined by practice focus, education in primary field and health informatics, and significant health informatics experience. PMID:27358328

  5. Mapping the Materials Genome through Combinatorial Informatics

    NASA Astrophysics Data System (ADS)

    Rajan, Krishna

    2012-02-01

    The recently announced White House Materials Genome Initiative provides an exciting challenge to the materials science community. To meet that challenge one needs to address a critical question, namely what is the materials genome? Some guide on how to the answer this question can be gained by recognizing that a ``gene'' is a carrier of information. In the biological sciences, discovering how to manipulate these genes has generated exciting discoveries in fundamental molecular biology as well as significant advances in biotechnology. Scaling that up to molecular, cellular length scales and beyond, has spawned from genomics, fields such as proteomics, metabolomics and essentially systems biology. The ``omics'' approach requires that one needs to discover and track these ``carriers of information'' and then correlate that information to predict behavior. A similar challenge lies in materials science, where there is a diverse array of modalities of materials ``discovery'' ranging from new materials chemistries and molecular arrangements with novel properties, to the development and design of new micro- and mesoscale structures. Hence to meaningfully adapt the spirit of ``genomics'' style research in materials science, we need to first identify and map the ``genes'' across different materials science applications On the experimental side, combinatorial experiments have opened a new approach to generate data in a high throughput manner, but without a clear way to link that to models, the full value of that data is not realized. Hence along with experimental and computational materials science, we need to add a ``third leg'' to our toolkit to make the ``Materials Genome'' a reality, the science of Materials Informatics. In this presentation we provide an overview of how information science coupled to materials science can in fact achieve the goal of mapping the ``Materials Genome''.

  6. Advanced Extravehicular Mobility Unit Informatics Software Design

    NASA Technical Reports Server (NTRS)

    Wright, Theodore

    2014-01-01

    This is a description of the software design for the 2013 edition of the Advanced Extravehicular Mobility Unit (AEMU) Informatics computer assembly. The Informatics system is an optional part of the space suit assembly. It adds a graphical interface for displaying suit status, timelines, procedures, and caution and warning information. In the future it will display maps with GPS position data, and video and still images captured by the astronaut.

  7. Applications of the pipeline environment for visual informatics and genomics computations

    PubMed Central

    2011-01-01

    Background Contemporary informatics and genomics research require efficient, flexible and robust management of large heterogeneous data, advanced computational tools, powerful visualization, reliable hardware infrastructure, interoperability of computational resources, and detailed data and analysis-protocol provenance. The Pipeline is a client-server distributed computational environment that facilitates the visual graphical construction, execution, monitoring, validation and dissemination of advanced data analysis protocols. Results This paper reports on the applications of the LONI Pipeline environment to address two informatics challenges - graphical management of diverse genomics tools, and the interoperability of informatics software. Specifically, this manuscript presents the concrete details of deploying general informatics suites and individual software tools to new hardware infrastructures, the design, validation and execution of new visual analysis protocols via the Pipeline graphical interface, and integration of diverse informatics tools via the Pipeline eXtensible Markup Language syntax. We demonstrate each of these processes using several established informatics packages (e.g., miBLAST, EMBOSS, mrFAST, GWASS, MAQ, SAMtools, Bowtie) for basic local sequence alignment and search, molecular biology data analysis, and genome-wide association studies. These examples demonstrate the power of the Pipeline graphical workflow environment to enable integration of bioinformatics resources which provide a well-defined syntax for dynamic specification of the input/output parameters and the run-time execution controls. Conclusions The LONI Pipeline environment http://pipeline.loni.ucla.edu provides a flexible graphical infrastructure for efficient biomedical computing and distributed informatics research. The interactive Pipeline resource manager enables the utilization and interoperability of diverse types of informatics resources. The Pipeline client

  8. The Epilepsy Phenome/Genome Project (EPGP) informatics platform

    PubMed Central

    Nesbitt, Gerry; McKenna, Kevin; Mays, Vickie; Carpenter, Alan; Miller, Kevin; Williams, Michael

    2013-01-01

    Background The Epilepsy Phenome/Genome Project (EPGP) is a large-scale, multi-institutional, collaborative network of 27 epilepsy centers throughout the U.S., Australia, and Argentina, with the objective of collecting detailed phenotypic and genetic data on a large number of epilepsy participants. The goals of EPGP are (1) to perform detailed phenotyping on 3750 participants with specific forms of non-acquired epilepsy and 1500 parents without epilepsy, (2) to obtain DNA samples on these individuals, and (3) to ultimately genotype the samples in order to discover novel genes that cause epilepsy. To carry out the project, a reliable and robust informatics platform was needed for standardized electronic data collection and storage, data quality review, and phenotypic analysis involving cases from multiple sites. Methods EPGP developed its own suite of web-based informatics applications for participant tracking, electronic data collection (using electronic case report forms/surveys), data management, phenotypic data review and validation, specimen tracking, electroencephalograph and neuroimaging storage, and issue tracking. We implemented procedures to train and support end-users at each clinical site. Results Thus far, 3780 study participants have been enrolled and 20,957 web-based study activities have been completed using this informatics platform. Over 95% of respondents to an end-user satisfaction survey felt that the informatics platform was successful almost always or most of the time. Conclusions The EPGP informatics platform has successfully and effectively allowed study management and efficient and reliable collection of phenotypic data. Our novel informatics platform met the requirements of a large, multicenter research project. The platform has had a high level of end-user acceptance by principal investigators and study coordinators, and can serve as a model for new tools to support future large scale, collaborative research projects collecting extensive

  9. Introduction to Metagenomics at DOE JGI: Program Overview and Program Informatics (Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    SciTech Connect

    Tringe, Susannah

    2011-10-12

    Susannah Tringe of the DOE Joint Genome Institute talks about the Program Overview and Program Informatics at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011

  10. Introduction to Metagenomics at DOE JGI: Program Overview and Program Informatics (Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    ScienceCinema

    Tringe, Susannah [DOE JGI

    2013-01-22

    Susannah Tringe of the DOE Joint Genome Institute talks about the Program Overview and Program Informatics at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011

  11. Informatics Infrastructure for the Materials Genome Initiative

    NASA Astrophysics Data System (ADS)

    Dima, Alden; Bhaskarla, Sunil; Becker, Chandler; Brady, Mary; Campbell, Carelyn; Dessauw, Philippe; Hanisch, Robert; Kattner, Ursula; Kroenlein, Kenneth; Newrock, Marcus; Peskin, Adele; Plante, Raymond; Li, Sheng-Yen; Rigodiat, Pierre-François; Amaral, Guillaume Sousa; Trautt, Zachary; Schmitt, Xavier; Warren, James; Youssef, Sharief

    2016-07-01

    A materials data infrastructure that enables the sharing and transformation of a wide range of materials data is an essential part of achieving the goals of the Materials Genome Initiative. We describe two high-level requirements of such an infrastructure as well as an emerging open-source implementation consisting of the Materials Data Curation System and the National Institute of Standards and Technology Materials Resource Registry.

  12. Directions for clinical research and genomic research into the next decade: implications for informatics.

    PubMed

    Rindfleisch, T C; Brutlag, D L

    1998-01-01

    Medical informatics is defined largely by its host disciplines in clinical and biological medicine, and to project the agenda for informatics into the next decade, the health community must envision the broad context of biomedical research. This paper is a sketch of this vision, taking into account pressures from changes in the U.S. health care system, the need for more objective information on which to base health care decisions, and the accelerating progress and clinical impact of genomics research. The lessons of modern genomics research demonstrate the power of computing and communication tools to facilitate rapid progress through the adoption of open community standards for information exchange and collaboration. While aspects of this vision are speculative, it seems clear that the core agenda for informatics must be the development of interoperating systems that can facilitate the secure gathering, interchange, and analysis of high-quality information and can gain leverage from worldwide collaboration in advancing and applying new medical knowledge. PMID:9760387

  13. Clinical Research Informatics: Recent Advances and Future Directions

    PubMed Central

    2015-01-01

    Summary Objectives To summarize significant developments in Clinical Research Informatics (CRI) over the past two years and discuss future directions. Methods Survey of advances, open problems and opportunities in this field based on exploration of current literature. Results Recent advances are structured according to three use cases of clinical research: Protocol feasibility, patient identification/recruitment and clinical trial execution. Discussion CRI is an evolving, dynamic field of research. Global collaboration, open metadata, content standards with semantics and computable eligibility criteria are key success factors for future developments in CRI. PMID:26293865

  14. The mouse genome informatics and the mouse genome database

    SciTech Connect

    Maltais, L.J.; Blackburn, R.E.; Bradt, D.W.

    1994-09-01

    The Mouse Genome Database (MGD) is a centralized, comprehensive database of the mouse genome that includes genetic mapping data, comparative mapping data, gene descriptions, mutant phenotype descriptions, strains and allelic polymorphism data, inbred strain characteristics, physical mapping data, and molecular probes and clones data. Data in MGD are obtained from the published literature and by electronic transfer from laboratories working on large backcross panels of mice. MGD provides tools that enable the user to search the database, retrieve data, generate reports, analyze data, annotate records, and build genetic maps. The Encyclopedia of the Mouse Genome provides a graphic user interface to mouse genome data. It consists of software tools including: LinkMap, a graphic display of genetic linkage maps with the ability to magnify regions of high locus density: CytoMap, a graphic display of cytogenetic maps showing banded chromosomes with cytogenetic locations of genes and chromosomal aberrations; CATS, a catalog searching tool for text retrieval of mouse locus descriptions. These software tools provide access to the following data sets: Chromosome Committee Reports, MIT Genome Center data, GBASE reports, Mouse Locus Catalog (MLC), and Mouse Cytogenetic Mapping Data. The MGD is available to the scientific community through the World Wide Web (WWW) and Gopher. In addition GBASE can be accessed via the Internet.

  15. Sequencing Single Cell Microbial Genomes with Microfluidic Amplifications Tools (MICW - Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    SciTech Connect

    Quake, Steve

    2011-10-12

    Stanford University's Steve Quake on "Sequencing Single Cell Microbial Genomes with Microfluidic Amplification Tools" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

  16. Genome Assembly Forensics: Metrics for Assessing Assembly Correctness (Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    SciTech Connect

    Pop, Mihai

    2011-10-13

    University of Maryland's Mihai Pop on "Genome Assembly Forensics: Metrics for Assessing Assembly Correctness" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

  17. Sequencing Single Cell Microbial Genomes with Microfluidic Amplifications Tools (MICW - Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    ScienceCinema

    Quake, Steve [University of Stanford

    2013-01-22

    Stanford University's Steve Quake on "Sequencing Single Cell Microbial Genomes with Microfluidic Amplification Tools" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

  18. Genome Assembly Forensics: Metrics for Assessing Assembly Correctness (Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    ScienceCinema

    Pop, Mihai [University of Maryland

    2013-01-22

    University of Maryland's Mihai Pop on "Genome Assembly Forensics: Metrics for Assessing Assembly Correctness" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

  19. Perspectives on Clinical Informatics: Integrating Large-Scale Clinical, Genomic, and Health Information for Clinical Care

    PubMed Central

    Choi, In Young; Kim, Tae-Min; Kim, Myung Shin; Mun, Seong K.

    2013-01-01

    The advances in electronic medical records (EMRs) and bioinformatics (BI) represent two significant trends in healthcare. The widespread adoption of EMR systems and the completion of the Human Genome Project developed the technologies for data acquisition, analysis, and visualization in two different domains. The massive amount of data from both clinical and biology domains is expected to provide personalized, preventive, and predictive healthcare services in the near future. The integrated use of EMR and BI data needs to consider four key informatics areas: data modeling, analytics, standardization, and privacy. Bioclinical data warehouses integrating heterogeneous patient-related clinical or omics data should be considered. The representative standardization effort by the Clinical Bioinformatics Ontology (CBO) aims to provide uniquely identified concepts to include molecular pathology terminologies. Since individual genome data are easily used to predict current and future health status, different safeguards to ensure confidentiality should be considered. In this paper, we focused on the informatics aspects of integrating the EMR community and BI community by identifying opportunities, challenges, and approaches to provide the best possible care service for our patients and the population. PMID:24465229

  20. Perspectives on clinical informatics: integrating large-scale clinical, genomic, and health information for clinical care.

    PubMed

    Choi, In Young; Kim, Tae-Min; Kim, Myung Shin; Mun, Seong K; Chung, Yeun-Jun

    2013-12-01

    The advances in electronic medical records (EMRs) and bioinformatics (BI) represent two significant trends in healthcare. The widespread adoption of EMR systems and the completion of the Human Genome Project developed the technologies for data acquisition, analysis, and visualization in two different domains. The massive amount of data from both clinical and biology domains is expected to provide personalized, preventive, and predictive healthcare services in the near future. The integrated use of EMR and BI data needs to consider four key informatics areas: data modeling, analytics, standardization, and privacy. Bioclinical data warehouses integrating heterogeneous patient-related clinical or omics data should be considered. The representative standardization effort by the Clinical Bioinformatics Ontology (CBO) aims to provide uniquely identified concepts to include molecular pathology terminologies. Since individual genome data are easily used to predict current and future health status, different safeguards to ensure confidentiality should be considered. In this paper, we focused on the informatics aspects of integrating the EMR community and BI community by identifying opportunities, challenges, and approaches to provide the best possible care service for our patients and the population. PMID:24465229

  1. Advancing Nursing Informatics in the Next Decade: Recommendations from an International Survey.

    PubMed

    Topaz, Maxim; Ronquillo, Charlene; Peltonen, Laura-Maria; Pruinelli, Lisiane; Sarmiento, Raymond Francis; Badger, Martha K; Ali, Samira; Lewis, Adrienne; Georgsson, Mattias; Jeon, Eunjoo; Tayaben, Jude L; Kuo, Chiu-Hsiang; Islam, Tasneem; Sommer, Janine; Jung, Hyunggu; Eler, Gabrielle Jacklin; Alhuwail, Dari

    2016-01-01

    In the summer of 2015, the International Medical Informatics Association Nursing Informatics Special Interest Group (IMIA NISIG) Student Working Group developed and distributed an international survey of current and future trends in nursing informatics. The survey was developed based on current literature on nursing informatics trends and translated into six languages. Respondents were from 31 different countries in Asia, Africa, North and Central America, South America, Europe, and Australia. This paper presents the results of responses to the survey question: "What should be done (at a country or organizational level) to advance nursing informatics in the next 5-10 years?" (n responders = 272). Using thematic qualitative analysis, responses were grouped into five key themes: 1) Education and training; 2) Research; 3) Practice; 4) Visibility; and 5) Collaboration and integration. We also provide actionable recommendations for advancing nursing informatics in the next decade. PMID:27332175

  2. Introducing National Center for Genome Resources (NCGR) Informatics (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

    ScienceCinema

    Crow, John [National Center for Genome Resources

    2013-01-25

    John Crow from the National Center for Genome Resources discusses his organization's informatics at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

  3. Advancing Climate Change and Impacts Science Through Climate Informatics

    NASA Astrophysics Data System (ADS)

    Lenhardt, W.; Pouchard, L. C.; King, A. W.; Branstetter, M. L.; Kao, S.; Wang, D.

    2010-12-01

    This poster will outline the work to date on developing a climate informatics capability at Oak Ridge National Laboratory (ORNL). The central proposition of this effort is that the application of informatics and information science to the domain of climate change science is an essential means to bridge the realm of high performance computing (HPC) and domain science. The goal is to facilitate knowledge capture and the creation of new scientific insights. For example, a climate informatics capability will help with the understanding and use of model results in domain sciences that were not originally in the scope. From there, HPC can also benefit from feedback as the new approaches may lead to better parameterization in the models. In this poster we will summarize the challenges associated with climate change science that can benefit from the systematic application of informatics and we will highlight our work to date in creating the climate informatics capability to address these types of challenges. We have identified three areas that are particularly challenging in the context of climate change science: 1) integrating model and observational data across different spatial and temporal scales, 2) model linkages, i.e. climate models linked to other models such as hydrologic models, and 3) model diagnostics. Each of these has a methodological component and an informatics component. Our project under way at ORNL seeks to develop new approaches and tools in the context of linking climate change and water issues. We are basing our work on the following four use cases: 1) Evaluation/test of CCSM4 biases in hydrology (precipitation, soil water, runoff, river discharge) over the Rio Grande Basin. User: climate modeler. 2) Investigation of projected changes in hydrology of Rio Grande Basin using the VIC (Variable Infiltration Capacity Macroscale) Hydrologic Model. User: watershed hydrologist/modeler. 3) Impact of climate change on agricultural productivity of the Rio Grande

  4. Allele, phenotype and disease data at Mouse Genome Informatics: improving access and analysis.

    PubMed

    Bello, Susan M; Smith, Cynthia L; Eppig, Janan T

    2015-08-01

    A core part of the Mouse Genome Informatics (MGI) resource is the collection of mouse mutations and the annotation phenotypes and diseases displayed by mice carrying these mutations. These data are integrated with the rest of data in MGI and exported to numerous other resources. The use of mouse phenotype data to drive translational research into human disease has expanded rapidly with the improvements in sequencing technology. MGI has implemented many improvements in allele and phenotype data annotation, search, and display to facilitate access to these data through multiple avenues. For example, the description of alleles has been modified to include more detailed categories of allele attributes. This allows improved discrimination between mutation types. Further, connections have been created between mutations involving multiple genes and each of the genes overlapping the mutation. This allows users to readily find all mutations affecting a gene and see all genes affected by a mutation. In a similar manner, the genes expressed by transgenic or knock-in alleles are now connected to these alleles. The advanced search forms and public reports have been updated to take advantage of these improvements. These search forms and reports are used by an expanding number of researchers to identify novel human disease genes and mouse models of human disease. PMID:26162703

  5. Eco-informatics for decision makers advancing a research agenda

    USGS Publications Warehouse

    Cushing, J.B.; Wilson, T.; Brandt, L.; Gregg, V.; Spengler, S.; Borning, A.; Delcambre, L.; Bowker, G.; Frame, M.; Fulop, J.; Hert, C.; Hovy, E.; Jones, J.; Landis, E.; Schnase, J.L.; Schweik, C.; Sonntag, W.

    2005-01-01

    Resource managers often face significant information technology (IT) problems when integrating ecological or environmental information to make decisions. At a workshop sponsored by the NSF and USGS in December 2004, university researchers, natural resource managers, and information managers met to articulate IT problems facing ecology and environmental decision makers. Decision making IT problems were identified in five areas: 1) policy, 2) data presentation, 3) data gaps, 4) tools, and 5) indicators. To alleviate those problems, workshop participants recommended specific informatics research in modeling and simulation, data quality, information integration and ontologies, and social and human aspects. This paper reports the workshop findings, and briefly compares these with research that traditionally falls under the emerging eco-informatics rubric. ?? Springer-Verlag Berlin Heidelberg 2005.

  6. Evaluation of the Cow Rumen Metagenome; Assembly by Single Copy Gene Analysis and Single Cell Genome Assemblies(Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    SciTech Connect

    Sczyrba, Alex

    2011-10-13

    DOE JGI's Alex Sczyrba on "Evaluation of the Cow Rumen Metagenome" and "Assembly by Single Copy Gene Analysis and Single Cell Genome Assemblies" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

  7. Evaluation of the Cow Rumen Metagenome; Assembly by Single Copy Gene Analysis and Single Cell Genome Assemblies(Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    ScienceCinema

    Sczyrba, Alex [DOE JGI

    2013-01-22

    DOE JGI's Alex Sczyrba on "Evaluation of the Cow Rumen Metagenome" and "Assembly by Single Copy Gene Analysis and Single Cell Genome Assemblies" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

  8. Clinical Microbiology Informatics

    PubMed Central

    Sintchenko, Vitali; Rauch, Carol A.; Pantanowitz, Liron

    2014-01-01

    SUMMARY The clinical microbiology laboratory has responsibilities ranging from characterizing the causative agent in a patient's infection to helping detect global disease outbreaks. All of these processes are increasingly becoming partnered more intimately with informatics. Effective application of informatics tools can increase the accuracy, timeliness, and completeness of microbiology testing while decreasing the laboratory workload, which can lead to optimized laboratory workflow and decreased costs. Informatics is poised to be increasingly relevant in clinical microbiology, with the advent of total laboratory automation, complex instrument interfaces, electronic health records, clinical decision support tools, and the clinical implementation of microbial genome sequencing. This review discusses the diverse informatics aspects that are relevant to the clinical microbiology laboratory, including the following: the microbiology laboratory information system, decision support tools, expert systems, instrument interfaces, total laboratory automation, telemicrobiology, automated image analysis, nucleic acid sequence databases, electronic reporting of infectious agents to public health agencies, and disease outbreak surveillance. The breadth and utility of informatics tools used in clinical microbiology have made them indispensable to contemporary clinical and laboratory practice. Continued advances in technology and development of these informatics tools will further improve patient and public health care in the future. PMID:25278581

  9. Sharing intellectual and social capital: A partnership to advance informatics and foster consumer centric care.

    PubMed

    Skiba, Diane J; Barton, Amy J; Norton, Michele; McCasky, Teresa; Kimmel, Kathleen

    2006-01-01

    The need to educate the nursing workforce about using informatics tools to provide safe, quality consumer centric care is of utmost importance. A unique and strategic partnership was established to address this challenge. The informatics specialty option at the University of Colorado at Denver and Health Sciences Center School of Nursing has joined forces with McKesson Corporation. The overall goal of this partnership is to provide leadership in the field of nursing informatics and the further development of nursing informatics as a discipline. This paper describes the converging forces that serve as a foundation for the partnership. There are also descriptions of the two partners and their shared goals. This partnership was designed to share intellectual and social capital to advance nursing informatics through educational and research opportunities. The partnership also allows for the use of intellectual capital to brainstorm new developments, designs and to test the usability of new products. This paper reports on the various projects underway in the area of education, scholarship, research and development. PMID:17102253

  10. Genomes to natural products PRediction Informatics for Secondary Metabolomes (PRISM).

    PubMed

    Skinnider, Michael A; Dejong, Chris A; Rees, Philip N; Johnston, Chad W; Li, Haoxin; Webster, Andrew L H; Wyatt, Morgan A; Magarvey, Nathan A

    2015-11-16

    Microbial natural products are an invaluable source of evolved bioactive small molecules and pharmaceutical agents. Next-generation and metagenomic sequencing indicates untapped genomic potential, yet high rediscovery rates of known metabolites increasingly frustrate conventional natural product screening programs. New methods to connect biosynthetic gene clusters to novel chemical scaffolds are therefore critical to enable the targeted discovery of genetically encoded natural products. Here, we present PRISM, a computational resource for the identification of biosynthetic gene clusters, prediction of genetically encoded nonribosomal peptides and type I and II polyketides, and bio- and cheminformatic dereplication of known natural products. PRISM implements novel algorithms which render it uniquely capable of predicting type II polyketides, deoxygenated sugars, and starter units, making it a comprehensive genome-guided chemical structure prediction engine. A library of 57 tailoring reactions is leveraged for combinatorial scaffold library generation when multiple potential substrates are consistent with biosynthetic logic. We compare the accuracy of PRISM to existing genomic analysis platforms. PRISM is an open-source, user-friendly web application available at http://magarveylab.ca/prism/. PMID:26442528

  11. Genomes to natural products PRediction Informatics for Secondary Metabolomes (PRISM)

    PubMed Central

    Skinnider, Michael A.; Dejong, Chris A.; Rees, Philip N.; Johnston, Chad W.; Li, Haoxin; Webster, Andrew L. H.; Wyatt, Morgan A.; Magarvey, Nathan A.

    2015-01-01

    Microbial natural products are an invaluable source of evolved bioactive small molecules and pharmaceutical agents. Next-generation and metagenomic sequencing indicates untapped genomic potential, yet high rediscovery rates of known metabolites increasingly frustrate conventional natural product screening programs. New methods to connect biosynthetic gene clusters to novel chemical scaffolds are therefore critical to enable the targeted discovery of genetically encoded natural products. Here, we present PRISM, a computational resource for the identification of biosynthetic gene clusters, prediction of genetically encoded nonribosomal peptides and type I and II polyketides, and bio- and cheminformatic dereplication of known natural products. PRISM implements novel algorithms which render it uniquely capable of predicting type II polyketides, deoxygenated sugars, and starter units, making it a comprehensive genome-guided chemical structure prediction engine. A library of 57 tailoring reactions is leveraged for combinatorial scaffold library generation when multiple potential substrates are consistent with biosynthetic logic. We compare the accuracy of PRISM to existing genomic analysis platforms. PRISM is an open-source, user-friendly web application available at http://magarveylab.ca/prism/. PMID:26442528

  12. Exploring novel candidate genes from the Mouse Genome Informatics database: Potential implications for avian migration research.

    PubMed

    Contina, Andrea; Bridge, Eli S; Kelly, Jeffrey F

    2016-07-01

    To search for genes associated with migratory phenotypes in songbirds, we selected candidate genes through annotations from the Mouse Genome Informatics database and assembled an extensive candidate-gene library. Then, we implemented a next-generation sequencing approach to obtain DNA sequences from the Painted Bunting genome. We focused on those sequences that were conserved across avian species and that aligned with candidate genes in our mouse library. We genotyped short sequence repeats from the following candidate genes: ADRA1d, ANKRD17, CISH and MYH7. We studied the possible correlations between allelic variations occurring in these novel candidate migration genes and avian migratory phenotypes available from the published literature. We found that allele variation at MYH7 correlated with a calculated index of speed of migration (km/day) across 11 species of songbirds. We highlight the potential of the Mouse Genome Informatics database in providing new candidate genes that might play a crucial role in regulating migration in birds and possibly in other taxa. Our research effort shows the benefits and limitations of working with extensive genomic datasets and offers a snapshot of the challenges related to cross-species validation in behavioral and molecular ecology studies. PMID:27061206

  13. Whole-genome CNV analysis: advances in computational approaches

    PubMed Central

    Pirooznia, Mehdi; Goes, Fernando S.; Zandi, Peter P.

    2015-01-01

    Accumulating evidence indicates that DNA copy number variation (CNV) is likely to make a significant contribution to human diversity and also play an important role in disease susceptibility. Recent advances in genome sequencing technologies have enabled the characterization of a variety of genomic features, including CNVs. This has led to the development of several bioinformatics approaches to detect CNVs from next-generation sequencing data. Here, we review recent advances in CNV detection from whole genome sequencing. We discuss the informatics approaches and current computational tools that have been developed as well as their strengths and limitations. This review will assist researchers and analysts in choosing the most suitable tools for CNV analysis as well as provide suggestions for new directions in future development. PMID:25918519

  14. Sequencing quality assessment tools to enable data-driven informatics for high throughput genomics

    PubMed Central

    Leggett, Richard M.; Ramirez-Gonzalez, Ricardo H.; Clavijo, Bernardo J.; Waite, Darren; Davey, Robert P.

    2013-01-01

    The processes of quality assessment and control are an active area of research at The Genome Analysis Centre (TGAC). Unlike other sequencing centers that often concentrate on a certain species or technology, TGAC applies expertise in genomics and bioinformatics to a wide range of projects, often requiring bespoke wet lab and in silico workflows. TGAC is fortunate to have access to a diverse range of sequencing and analysis platforms, and we are at the forefront of investigations into library quality and sequence data assessment. We have developed and implemented a number of algorithms, tools, pipelines and packages to ascertain, store, and expose quality metrics across a number of next-generation sequencing platforms, allowing rapid and in-depth cross-platform Quality Control (QC) bioinformatics. In this review, we describe these tools as a vehicle for data-driven informatics, offering the potential to provide richer context for downstream analysis and to inform experimental design. PMID:24381581

  15. Advances in Genome Biology & Technology

    SciTech Connect

    Thomas J. Albert, Jon R. Armstrong, Raymond K. Auerback, W. Brad Barbazuk, et al.

    2007-12-01

    This year's meeting focused on the latest advances in new DNA sequencing technologies and the applications of genomics to disease areas in biology and biomedicine. Daytime plenary sessions highlighted cutting-edge research in areas such as complex genetic diseases, comparative genomics, medical sequencing, massively parallel DNA sequencing, and synthetic biology. Technical approaches being developed and utilized in contemporary genomics research were presented during evening concurrent sessions. Also, as in previous years, poster sessions bridged the morning and afternoon plenary sessions. In addition, for the third year in a row, the Advances in Genome Biology and Technology (AGBT) meeting was preceded by a pre-meeting workshop that aimed to provide an introductory overview for trainees and other meeting attendees. This year, speakers at the workshop focused on next-generation sequencing technologies, including their experiences, findings, and helpful advise for others contemplating using these platforms in their research. Speakers from genome centers and core sequencing facilities were featured and the workshop ended with a roundtable discussion, during which speakers fielded questions from the audience.

  16. Using Informatics-, Bioinformatics- and Genomics-Based Approaches for the Molecular Surveillance and Detection of Biothreat Agents

    NASA Astrophysics Data System (ADS)

    Seto, Donald

    The convergence and wealth of informatics, bioinformatics and genomics methods and associated resources allow a comprehensive and rapid approach for the surveillance and detection of bacterial and viral organisms. Coupled with the continuing race for the fastest, most cost-efficient and highest-quality DNA sequencing technology, that is, "next generation sequencing", the detection of biological threat agents by `cheaper and faster' means is possible. With the application of improved bioinformatic tools for the understanding of these genomes and for parsing unique pathogen genome signatures, along with `state-of-the-art' informatics which include faster computational methods, equipment and databases, it is feasible to apply new algorithms to biothreat agent detection. Two such methods are high-throughput DNA sequencing-based and resequencing microarray-based identification. These are illustrated and validated by two examples involving human adenoviruses, both from real-world test beds.

  17. Infusing informatics into interprofessional education: the iTEAM (Interprofessional Technology Enhanced Advanced practice Model) project.

    PubMed

    Skiba, Diane J; Barton, Amy J; Knapfel, Sarah; Moore, Gina; Trinkley, Katy

    2014-01-01

    The iTEAM goal is to prepare advanced practice nurses, physicians and pharmacists with the interprofessional (IP) core competencies (informatics, patient centric, quality-focused, evidence based care) to provide technology enhanced collaborative care by: offering technology enhanced learning opportunities through a required informatics course, advanced practice courses (team based experiences with both standardized and virtual patients) and team based clinical experiences including e-health experiences. The innovative features of iTEAM project will be achieved through use of social media strategies, a web accessible Electronic Health Records (EHRs) system, a Virtual Clinic/Hospital in Second Life, various e-health applications including traditional telehealth tools and consumer oriented tools such as patient portals, social media consumer groups and mobile health (m-health) applications for health and wellness functions. It builds upon the schools' rich history of IP education and includes clinical partners, such as the VA and other clinical sites focused on care for underserved patient populations. PMID:24943525

  18. Bridging the Gap from Bench to Bedside--An Informatics Infrastructure for Integrating Clinical, Genomics and Environmental Data (ICGED).

    PubMed

    2015-01-01

    The abundance of heterogeneous biomedical data from a variety of sources demands the development of strategies to address data integration and management issues, so that the data can be used effectively in clinical practices and biomedical research. This research presents an Informatics Infrastructure for Integrating Clinical, Genomics and Environmental Data (ICGED) and provides a roadmap that envisions utilizing the clinical and biomedical resources in our case study. This work describes a data integration approach, proposed by ICGED, with a two-fold purpose: personalized medicine and biomedical data storage and sharing platform. It describes our experiences integrating disease specific clinical and genomics datasets with Data Integration and Analysis Tools (DIAT)--using Informatics for Integrating Biology and the Bedside, and discusses work in progress and future work for extending DIAT, and the development of Risk Assessment and Prediction Tools, Clinical Decision Support Systems and a Bioinformatics Data Warehouse. PMID:26262353

  19. Bioimage informatics for experimental biology

    PubMed Central

    Swedlow, Jason R.; Goldberg, Ilya G.; Eliceiri, Kevin W.

    2012-01-01

    Over the last twenty years there have been great advances in light microscopy with the result that multi-dimensional imaging has driven a revolution in modern biology. The development of new approaches of data acquisition are reportedly frequently, and yet the significant data management and analysis challenges presented by these new complex datasets remains largely unsolved. Like the well-developed field of genome bioinformatics, central repositories are and will be key resources, but there is a critical need for informatics tools in individual laboratories to help manage, share, visualize, and analyze image data. In this article we present the recent efforts by the bioimage informatics community to tackle these challenges and discuss our own vision for future development of bioimage informatics solution. PMID:19416072

  20. Integrating Genome-based Informatics to Modernize Global Disease Monitoring, Information Sharing, and Response

    PubMed Central

    Brown, Eric W.; Detter, Chris; Gerner-Smidt, Peter; Gilmour, Matthew W.; Harmsen, Dag; Hendriksen, Rene S.; Hewson, Roger; Heymann, David L.; Johansson, Karin; Ijaz, Kashef; Keim, Paul S.; Koopmans, Marion; Kroneman, Annelies; Wong, Danilo Lo Fo; Lund, Ole; Palm, Daniel; Sawanpanyalert, Pathom; Sobel, Jeremy; Schlundt, Jørgen

    2012-01-01

    The rapid advancement of genome technologies holds great promise for improving the quality and speed of clinical and public health laboratory investigations and for decreasing their cost. The latest generation of genome DNA sequencers can provide highly detailed and robust information on disease-causing microbes, and in the near future these technologies will be suitable for routine use in national, regional, and global public health laboratories. With additional improvements in instrumentation, these next- or third-generation sequencers are likely to replace conventional culture-based and molecular typing methods to provide point-of-care clinical diagnosis and other essential information for quicker and better treatment of patients. Provided there is free-sharing of information by all clinical and public health laboratories, these genomic tools could spawn a global system of linked databases of pathogen genomes that would ensure more efficient detection, prevention, and control of endemic, emerging, and other infectious disease outbreaks worldwide. PMID:23092707

  1. Genome informatics and vaccine targets in Corynebacterium urealyticum using two whole genomes, comparative genomics, and reverse vaccinology

    PubMed Central

    2015-01-01

    Background Corynebacterium urealyticum is an opportunistic pathogen that normally lives on skin and mucous membranes in humans. This high Gram-positive bacteria can cause acute or encrusted cystitis, encrusted pyelitis, and pyelonephritis in immunocompromised patients. The bacteria is multi-drug resistant, and knowledge about the genes that contribute to its virulence is very limited. Two complete genome sequences were used in this comparative genomic study: C. urealyticum DSM 7109 and C. urealyticum DSM 7111. Results We used comparative genomics strategies to compare the two strains, DSM 7109 and DSM 7111, and to analyze their metabolic pathways, genome plasticity, and to predict putative antigenic targets. The genomes of these two strains together encode 2,115 non-redundant coding sequences, 1,823 of which are common to both genomes. We identified 188 strain-specific genes in DSM 7109 and 104 strain-specific genes in DSM 7111. The high number of strain-specific genes may be a result of horizontal gene transfer triggered by the large number of transposons in the genomes of these two strains. Screening for virulence factors revealed the presence of the spaDEF operon that encodes pili forming proteins. Therefore, spaDEF may play a pivotal role in facilitating the adhesion of the pathogen to the host tissue. Application of the reverse vaccinology method revealed 19 putative antigenic proteins that may be used in future studies as candidate drug or vaccine targets. Conclusions The genome features and the presence of virulence factors in genomic islands in the two strains of C. urealyticum provide insights in the lifestyle of this opportunistic pathogen and may be useful in developing future therapeutic strategies. PMID:26041051

  2. Big heart data: advancing health informatics through data sharing in cardiovascular imaging.

    PubMed

    Suinesiaputra, Avan; Medrano-Gracia, Pau; Cowan, Brett R; Young, Alistair A

    2015-07-01

    The burden of heart disease is rapidly worsening due to the increasing prevalence of obesity and diabetes. Data sharing and open database resources for heart health informatics are important for advancing our understanding of cardiovascular function, disease progression and therapeutics. Data sharing enables valuable information, often obtained at considerable expense and effort, to be reused beyond the specific objectives of the original study. Many government funding agencies and journal publishers are requiring data reuse, and are providing mechanisms for data curation and archival. Tools and infrastructure are available to archive anonymous data from a wide range of studies, from descriptive epidemiological data to gigabytes of imaging data. Meta-analyses can be performed to combine raw data from disparate studies to obtain unique comparisons or to enhance statistical power. Open benchmark datasets are invaluable for validating data analysis algorithms and objectively comparing results. This review provides a rationale for increased data sharing and surveys recent progress in the cardiovascular domain. We also highlight the potential of recent large cardiovascular epidemiological studies enabling collaborative efforts to facilitate data sharing, algorithms benchmarking, disease modeling and statistical atlases. PMID:25415993

  3. Big Heart Data: Advancing Health Informatics through Data Sharing in Cardiovascular Imaging

    PubMed Central

    Suinesiaputra, Avan; Medrano-Gracia, Pau; Cowan, Brett R.; Young, Alistair A.

    2015-01-01

    The burden of heart disease is rapidly worsening due to increasing prevalence of obesity and diabetes. Data sharing and open database resources for heart health informatics are important for advancing our understanding of cardiovascular function, disease progression and therapeutics. Data sharing enables valuable information, often obtained at considerable expense and effort, to be re-used beyond the specific objectives of the original study. Many government funding agencies and journal publishers are requiring data re-use, and are providing mechanisms for data curation and archival. Tools and infrastructure are available to archive anonymous data from a wide range of studies, from descriptive epidemiological data to gigabytes of imaging data. Meta-analyses can be performed to combine raw data from disparate studies to obtain unique comparisons or to enhance statistical power. Open benchmark datasets are invaluable for validating data analysis algorithms and objectively comparing results. This review provides a rationale for increased data sharing and surveys recent progress in the cardiovascular domain. We also highlight the potential of recent large cardiovascular epidemiological studies enabling collaborative efforts to facilitate data sharing, algorithms benchmarking, disease modeling and statistical atlases. PMID:25415993

  4. Advances in plant chromosome genomics.

    PubMed

    Doležel, Jaroslav; Vrána, Jan; Cápal, Petr; Kubaláková, Marie; Burešová, Veronika; Simková, Hana

    2014-01-01

    Next generation sequencing (NGS) is revolutionizing genomics and is providing novel insights into genome organization, evolution and function. The number of plant genomes targeted for sequencing is rising. For the moment, however, the acquisition of full genome sequences in large genome species remains difficult, largely because the short reads produced by NGS platforms are inadequate to cope with repeat-rich DNA, which forms a large part of these genomes. The problem of sequence redundancy is compounded in polyploids, which dominate the plant kingdom. An approach to overcoming some of these difficulties is to reduce the full nuclear genome to its individual chromosomes using flow-sorting. The DNA acquired in this way has proven to be suitable for many applications, including PCR-based physical mapping, in situ hybridization, forming DNA arrays, the development of DNA markers, the construction of BAC libraries and positional cloning. Coupling chromosome sorting with NGS offers opportunities for the study of genome organization at the single chromosomal level, for comparative analyses between related species and for the validation of whole genome assemblies. Apart from the primary aim of reducing the complexity of the template, taking a chromosome-based approach enables independent teams to work in parallel, each tasked with the analysis of a different chromosome(s). Given that the number of plant species tractable for chromosome sorting is increasing, the likelihood is that chromosome genomics - the marriage of cytology and genomics - will make a significant contribution to the field of plant genetics. PMID:24406816

  5. Global health informatics education.

    PubMed

    Hovenga, E J

    2000-01-01

    Health informatics education has evolved since the 1960s with a strong research foundation primarily in medical schools across the USA and Europe. By 1989 health informatics education was provided in some form by at least 20 countries representing five continents. This continues to progress, in Europe with the help of a number of special projects, via the integration of informatics into pre registration health professional courses, undergraduate and post graduate course work and research degree programs. Each program is unique in terms or content and structure reflecting the many foundation disciplines which contribute or are incorporated in the health informatics discipline. Nursing informatics education is not as widespread. Indeed the evidence suggests a poor uptake of informatics by this profession. Advances in computer based educational technologies are making innovative modes of educational delivery possible and are facilitating a shift towards learner centred, flexible and life long learning. Greater cooperation between Universities is recommended. PMID:10947666

  6. Metagenome Assembly at the DOE JGI (Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    ScienceCinema

    Chain, Patrick [DOE JGI at LANL

    2013-01-22

    Patrick Chain of DOE JGI at LANL, Co-Chair of the Metagenome-specific Assembly session, on "Metagenome Assembly at the DOE JGI" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

  7. Metagenome Assembly at the DOE JGI (Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    SciTech Connect

    Chain, Patrick

    2011-10-13

    Patrick Chain of DOE JGI at LANL, Co-Chair of the Metagenome-specific Assembly session, on "Metagenome Assembly at the DOE JGI" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

  8. Recent advance in carrot genomics

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In recent years there has been an effort towards the development of genomic resources in carrot. The number of available sequences for carrot in public databases has increased recently. This has allowed the design of SSRs markers, COS markers and a high-throughput SNP assay for genotyping. Additiona...

  9. Imaging Informatics: 25 Years of Progress.

    PubMed

    Agrawal, J P; Erickson, B J; Kahn, C E

    2016-01-01

    The science and applications of informatics in medical imaging have advanced dramatically in the past 25 years. This article provides a selective overview of key developments in medical imaging informatics. Advances in standards and technologies for compression and transmission of digital images have enabled Picture Archiving and Communications Systems (PACS) and teleradiology. Research in speech recognition, structured reporting, ontologies, and natural language processing has improved the ability to generate and analyze the reports of imaging procedures. Informatics has provided tools to address workflow and ergonomic issues engendered by the growing volume of medical image information. Research in computeraided detection and diagnosis of abnormalities in medical images has opened new avenues to improve patient care. The growing number of medical-imaging examinations and their large volumes of information create a natural platform for "big data" analytics, particularly when joined with high-dimensional genomic data. Radiogenomics investigates relationships between a disease's genetic and gene-expression characteristics and its imaging phenotype; this emerging field promises to help us better understand disease biology, prognosis, and treatment options. The next 25 years offer remarkable opportunities for informatics and medical imaging together to lead to further advances in both disciplines and to improve health. PMID:27362590

  10. Genome engineering in cattle: recent technological advancements.

    PubMed

    Wang, Zhongde

    2015-02-01

    Great strides in technological advancements have been made in the past decade in cattle genome engineering. First, the success of cloning cattle by somatic cell nuclear transfer (SCNT) or chromatin transfer (CT) is a significant advancement that has made obsolete the need for using embryonic stem (ES) cells to conduct cell-mediated genome engineering, whereby site-specific genetic modifications can be conducted in bovine somatic cells via DNA homologous recombination (HR) and whereby genetically engineered cattle can subsequently be produced by animal cloning from the genetically modified cells. With this approach, a chosen bovine genomic locus can be precisely modified in somatic cells, such as to knock out (KO) or knock in (KI) a gene via HR, a gene-targeting strategy that had almost exclusively been used in mouse ES cells. Furthermore, by the creative application of embryonic cloning to rejuvenate somatic cells, cattle genome can be sequentially modified in the same line of somatic cells and complex genetic modifications have been achieved in cattle. Very recently, the development of designer nucleases-such as zinc finger nucleases (ZFNs) and transcription activator-like effector nuclease (TALENs), and clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9)-has enabled highly efficient and more facile genome engineering in cattle. Most notably, by employing such designer nucleases, genomes can be engineered at single-nucleotide precision; this process is now often referred to as genome or gene editing. The above achievements are a drastic departure from the traditional methods of creating genetically modified cattle, where foreign DNAs are randomly integrated into the animal genome, most often along with the integrations of bacterial or viral DNAs. Here, I review the most recent technological developments in cattle genome engineering by highlighting some of the major achievements in creating genetically engineered

  11. Biomedical informatics and translational medicine

    PubMed Central

    2010-01-01

    Biomedical informatics involves a core set of methodologies that can provide a foundation for crossing the "translational barriers" associated with translational medicine. To this end, the fundamental aspects of biomedical informatics (e.g., bioinformatics, imaging informatics, clinical informatics, and public health informatics) may be essential in helping improve the ability to bring basic research findings to the bedside, evaluate the efficacy of interventions across communities, and enable the assessment of the eventual impact of translational medicine innovations on health policies. Here, a brief description is provided for a selection of key biomedical informatics topics (Decision Support, Natural Language Processing, Standards, Information Retrieval, and Electronic Health Records) and their relevance to translational medicine. Based on contributions and advancements in each of these topic areas, the article proposes that biomedical informatics practitioners ("biomedical informaticians") can be essential members of translational medicine teams. PMID:20187952

  12. Advances in Arachis through genomics and biotechnology

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The 5th International Conference of the peanut research community met in Brasilia, Brazil from June 13 through 16, 2011 to discuss “Advances in Arachis through genomics and biotechnology”. Over 100 participated from many countries such as United States, Japan, China, India, Brazil, Argentina, with ...

  13. Advances in Maize Genomics and Their Value for Enhancing Genetic Gains from Breeding

    PubMed Central

    Xu, Yunbi; Skinner, Debra J.; Wu, Huixia; Palacios-Rojas, Natalia; Araus, Jose Luis; Yan, Jianbing; Gao, Shibin; Warburton, Marilyn L.; Crouch, Jonathan H.

    2009-01-01

    Maize is an important crop for food, feed, forage, and fuel across tropical and temperate areas of the world. Diversity studies at genetic, molecular, and functional levels have revealed that, tropical maize germplasm, landraces, and wild relatives harbor a significantly wider range of genetic variation. Among all types of markers, SNP markers are increasingly the marker-of-choice for all genomics applications in maize breeding. Genetic mapping has been developed through conventional linkage mapping and more recently through linkage disequilibrium-based association analyses. Maize genome sequencing, initially focused on gene-rich regions, now aims for the availability of complete genome sequence. Conventional insertion mutation-based cloning has been complemented recently by EST- and map-based cloning. Transgenics and nutritional genomics are rapidly advancing fields targeting important agronomic traits including pest resistance and grain quality. Substantial advances have been made in methodologies for genomics-assisted breeding, enhancing progress in yield as well as abiotic and biotic stress resistances. Various genomic databases and informatics tools have been developed, among which MaizeGDB is the most developed and widely used by the maize research community. In the future, more emphasis should be given to the development of tools and strategic germplasm resources for more effective molecular breeding of tropical maize products. PMID:19688107

  14. Advances in Genomics of Entomopathogenic Fungi.

    PubMed

    Wang, J B; St Leger, R J; Wang, C

    2016-01-01

    Fungi are the commonest pathogens of insects and crucial regulators of insect populations. The rapid advance of genome technologies has revolutionized our understanding of entomopathogenic fungi with multiple Metarhizium spp. sequenced, as well as Beauveria bassiana, Cordyceps militaris, and Ophiocordyceps sinensis among others. Phylogenomic analysis suggests that the ancestors of many of these fungi were plant endophytes or pathogens, with entomopathogenicity being an acquired characteristic. These fungi now occupy a wide range of habitats and hosts, and their genomes have provided a wealth of information on the evolution of virulence-related characteristics, as well as the protein families and genomic structure associated with ecological and econutritional heterogeneity, genome evolution, and host range diversification. In particular, their evolutionary transition from plant pathogens or endophytes to insect pathogens provides a novel perspective on how new functional mechanisms important for host switching and virulence are acquired. Importantly, genomic resources have helped make entomopathogenic fungi ideal model systems for answering basic questions in parasitology, entomology, and speciation. At the same time, identifying the selective forces that act upon entomopathogen fitness traits could underpin both the development of new mycoinsecticides and further our understanding of the natural roles of these fungi in nature. These roles frequently include mutualistic relationships with plants. Genomics has also facilitated the rapid identification of genes encoding biologically useful molecules, with implications for the development of pharmaceuticals and the use of these fungi as bioreactors. PMID:27131323

  15. Advances in Climate Informatics: Accelerating Discovery in Climate Science with Machine Learning

    NASA Astrophysics Data System (ADS)

    Monteleoni, C.

    2015-12-01

    Despite the scientific consensus on climate change, drastic uncertainties remain. The climate system is characterized by complex phenomena that are imperfectly observed and even more imperfectly simulated. Climate data is Big Data, yet the magnitude of data and climate model output increasingly overwhelms the tools currently used to analyze them. Computational innovation is therefore needed. Machine learning is a cutting-edge research area at the intersection of computer science and statistics, focused on developing algorithms for big data analytics. Machine learning has revolutionized scientific discovery (e.g. Bioinformatics), and spawned new technologies (e.g. Web search). The impact of machine learning on climate science promises to be similarly profound. The goal of the novel interdisciplinary field of Climate Informatics is to accelerate discovery in climate science with machine learning, in order to shed light on urgent questions about climate change. In this talk, I will survey my research group's progress in the emerging field of climate informatics. Our work includes algorithms to improve the combined predictions of the IPCC multi-model ensemble, applications to seasonal and subseasonal prediction, and a data-driven technique to detect and define extreme events.

  16. The future of health informatics.

    PubMed

    Cesnik, B

    1999-07-01

    Whatever a future vision for health informatics entails, it must take into account the evolving nature of the field, a growing trend towards primary and preventive care and the explosive growth in global networking as exemplified by the Internet. While, historically, storage and retrieval of data has been the main target for information systems development, the need to capture knowledge itself is becoming the focus for development. In parallel, education in health informatics for tomorrow's healthcare professionals is now essential. The Asia Pacific Association for Medical Informatics (APAMI) is a regional group of the International Medical Informatics Association (IMIA). While the newest of the IMIA regional organizations, its growth and activities in the Asia Pacific region aim to advance health informatics. Its triennial conferences act as a means of promoting and monitoring the growth of our field in this region, APAMI itself is a part of the future of health informatics. PMID:10471244

  17. Use of a wiki as an interactive teaching tool in pathology residency education: Experience with a genomics, research, and informatics in pathology course

    PubMed Central

    Park, Seung; Parwani, Anil; MacPherson, Trevor; Pantanowitz, Liron

    2012-01-01

    Background: The need for informatics and genomics training in pathology is critical, yet limited resources for such training are available. In this study we sought to critically test the hypothesis that the incorporation of a wiki (a collaborative writing and publication tool with roots in “Web 2.0”) in a combined informatics and genomics course could both (1) serve as an interactive, collaborative educational resource and reference and (2) actively engage trainees by requiring the creation and sharing of educational materials. Materials and Methods: A 2-week full-time course at our institution covering genomics, research, and pathology informatics (GRIP) was taught by 36 faculty to 18 second- and third-year pathology residents. The course content included didactic lectures and hands-on demonstrations of technology (e.g., whole-slide scanning, telepathology, and statistics software). Attendees were given pre- and posttests. Residents were trained to use wiki technology (MediaWiki) and requested to construct a wiki about the GRIP course by writing comprehensive online review articles on assigned lectures. To gauge effectiveness, pretest and posttest scores for our course were compared with scores from the previous 7 years from the predecessor course (limited to informatics) given at our institution that did not utilize wikis. Results: Residents constructed 59 peer-reviewed collaborative wiki articles. This group showed a 25% improvement (standard deviation 12%) in test scores, which was greater than the 16% delta recorded in the prior 7 years of our predecessor course (P = 0.006). Conclusions: Our use of wiki technology provided a wiki containing high-quality content that will form the basis of future pathology informatics and genomics courses and proved to be an effective teaching tool, as evidenced by the significant rise in our resident posttest scores. Data from this project provide support for the notion that active participation in content creation is an

  18. Advancing Eucalyptus Genomics: Cytogenomics Reveals Conservation of Eucalyptus Genomes.

    PubMed

    Ribeiro, Teresa; Barrela, Ricardo M; Bergès, Hélène; Marques, Cristina; Loureiro, João; Morais-Cecílio, Leonor; Paiva, Jorge A P

    2016-01-01

    The genus Eucalyptus encloses several species with high ecological and economic value, being the subgenus Symphyomyrtus one of the most important. Species such as E. grandis and E. globulus are well characterized at the molecular level but knowledge regarding genome and chromosome organization is very scarce. Here we characterized and compared the karyotypes of three economically important species, E. grandis, E. globulus, and E. calmadulensis, and three with ecological relevance, E. pulverulenta, E. cornuta, and E. occidentalis, through an integrative approach including genome size estimation, fluorochrome banding, rDNA FISH, and BAC landing comprising genes involved in lignin biosynthesis. All karyotypes show a high degree of conservation with pericentromeric 35S and 5S rDNA loci in the first and third pairs, respectively. GC-rich heterochromatin was restricted to the 35S rDNA locus while the AT-rich heterochromatin pattern was species-specific. The slight differences in karyotype formulas and distribution of AT-rich heterochromatin, along with genome sizes estimations, support the idea of Eucalyptus genome evolution by local expansions of heterochromatin clusters. The unusual co-localization of both rDNA with AT-rich heterochromatin was attributed mainly to the presence of silent transposable elements in those loci. The cinnamoyl CoA reductase gene (CCR1) previously assessed to linkage group 10 (LG10) was clearly localized distally at the long arm of chromosome 9 establishing an unexpected correlation between the cytogenetic chromosome 9 and the LG10. Our work is novel and contributes to the understanding of Eucalyptus genome organization which is essential to develop successful advanced breeding strategies for this genus. PMID:27148332

  19. Advancing Eucalyptus Genomics: Cytogenomics Reveals Conservation of Eucalyptus Genomes

    PubMed Central

    Ribeiro, Teresa; Barrela, Ricardo M.; Bergès, Hélène; Marques, Cristina; Loureiro, João; Morais-Cecílio, Leonor; Paiva, Jorge A. P.

    2016-01-01

    The genus Eucalyptus encloses several species with high ecological and economic value, being the subgenus Symphyomyrtus one of the most important. Species such as E. grandis and E. globulus are well characterized at the molecular level but knowledge regarding genome and chromosome organization is very scarce. Here we characterized and compared the karyotypes of three economically important species, E. grandis, E. globulus, and E. calmadulensis, and three with ecological relevance, E. pulverulenta, E. cornuta, and E. occidentalis, through an integrative approach including genome size estimation, fluorochrome banding, rDNA FISH, and BAC landing comprising genes involved in lignin biosynthesis. All karyotypes show a high degree of conservation with pericentromeric 35S and 5S rDNA loci in the first and third pairs, respectively. GC-rich heterochromatin was restricted to the 35S rDNA locus while the AT-rich heterochromatin pattern was species-specific. The slight differences in karyotype formulas and distribution of AT-rich heterochromatin, along with genome sizes estimations, support the idea of Eucalyptus genome evolution by local expansions of heterochromatin clusters. The unusual co-localization of both rDNA with AT-rich heterochromatin was attributed mainly to the presence of silent transposable elements in those loci. The cinnamoyl CoA reductase gene (CCR1) previously assessed to linkage group 10 (LG10) was clearly localized distally at the long arm of chromosome 9 establishing an unexpected correlation between the cytogenetic chromosome 9 and the LG10. Our work is novel and contributes to the understanding of Eucalyptus genome organization which is essential to develop successful advanced breeding strategies for this genus. PMID:27148332

  20. Advances in genomics of bony fish

    PubMed Central

    Jansen, Hans J.; Dirks, Ron P.

    2014-01-01

    In this review, we present an overview of the recent advances of genomic technologies applied to studies of fish species belonging to the superclass of Osteichthyes (bony fish) with a major emphasis on the infraclass of Teleostei, also called teleosts. This superclass that represents more than 50% of all known vertebrate species has gained considerable attention from genome researchers in the last decade. We discuss many examples that demonstrate that this highly deserved attention is currently leading to new opportunities for answering important biological questions on gene function and evolutionary processes. In addition to giving an overview of the technologies that have been applied for studying various fish species we put the recent advances in genome research on the model species zebrafish and medaka in the context of its impact for studies of all fish of the superclass of Osteichthyes. We thereby want to illustrate how the combined value of research on model species together with a broad angle perspective on all bony fish species will have a huge impact on research in all fields of fundamental science and will speed up applications in many societally important areas such as the development of new medicines, toxicology test systems, environmental sensing systems and sustainable aquaculture strategies. PMID:24291769

  1. Informatics Moments

    ERIC Educational Resources Information Center

    Williams, Kate

    2012-01-01

    The informatics moment is the moment when a person seeks help in using some digital technology that is new to him or her. This article examines the informatics moment in people's everyday lives as they sought help at a branch public library. Four types of literacy were involved: basic literacy (reading and writing), computer literacy (use of a…

  2. Informatic nephrology.

    PubMed

    Musso, Carlos; Aguilera, Jerónimo; Otero, Carlos; Vilas, Manuel; Luna, Daniel; de Quirós, Fernán González Bernaldo

    2013-08-01

    Biomedical informatics in Health (BIH) is the discipline in charge of capturing, handling and using information in health and biomedicine in order to improve the processes involved with assistance and management. Informatic nephrology has appeared as a product of the combination between conventional nephrology with BIH and its development has been considerable in the assistance as well as in the academic field. Regarding the former, there is increasing evidence that informatics technology can make nephrological assistance be better in quality (effective, accessible, safe and satisfying), improve patient's adherence, optimize patient's and practitioner's time, improve physical space and achieve health cost reduction. Among its main elements, we find electronic medical and personal health records, clinical decision support system, tele-nephrology, and recording and monitoring devices. Additionally, regarding the academic field, informatics and Internet contribute to education and research in the nephrological field. In conclusion, informatics nephrology represents a new field which will influence the future of nephrology. PMID:23065430

  3. Introduction to Metagenomics at DOE JGI (Opening Remarks for the Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    ScienceCinema

    Kyrpides, Nikos [DOE JGI

    2013-01-22

    After a quick introduction by DOE JGI Director Eddy Rubin, DOE JGI's Nikos Kyrpides delivers the opening remarks at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011

  4. Scalability of Comparative Analysis, Novel Algorithms and Tools (MICW - Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    SciTech Connect

    Mavrommatis, Kostas

    2011-10-12

    DOE JGI's Kostas Mavrommatis, chair of the Scalability of Comparative Analysis, Novel Algorithms and Tools panel, at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

  5. Introduction to Metagenomics at DOE JGI (Opening Remarks for the Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    SciTech Connect

    Kyrpides, Nikos

    2011-10-12

    After a quick introduction by DOE JGI Director Eddy Rubin, DOE JGI's Nikos Kyrpides delivers the opening remarks at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011

  6. Metagenomics, metaMicrobesOnline and Kbase Data Integration (MICW - Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    ScienceCinema

    Dehal, Paramvir [LBNL

    2013-01-22

    Berkeley Lab's Paramvir Dehal on "Managing and Storing large Datasets in MicrobesOnline, metaMicrobesOnline and the DOE Knowledgebase" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

  7. Memory Efficient Sequence Analysis Using Compressed Data Structures (Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    ScienceCinema

    Simpson, Jared [Wellcome Trust Sanger Institute

    2013-01-22

    Wellcome Trust Sanger Institute's Jared Simpson on "Memory efficient sequence analysis using compressed data structures" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011

  8. Scalability of Comparative Analysis, Novel Algorithms and Tools (MICW - Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    ScienceCinema

    Mavrommatis, Kostas [JGI

    2013-01-22

    DOE JGI's Kostas Mavrommatis, chair of the Scalability of Comparative Analysis, Novel Algorithms and Tools panel, at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

  9. Memory Efficient Sequence Analysis Using Compressed Data Structures (Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    SciTech Connect

    Simpson, Jared

    2011-10-13

    Wellcome Trust Sanger Institute's Jared Simpson on "Memory efficient sequence analysis using compressed data structures" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011

  10. Metagenomics, metaMicrobesOnline and Kbase Data Integration (MICW - Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    SciTech Connect

    Dehal, Paramvir

    2011-10-12

    Berkeley Lab's Paramvir Dehal on "Managing and Storing large Datasets in MicrobesOnline, metaMicrobesOnline and the DOE Knowledgebase" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

  11. Fish T cells: recent advances through genomics

    USGS Publications Warehouse

    Laing, Kerry J.; Hansen, John D.

    2011-01-01

    This brief review is intended to provide a concise overview of the current literature concerning T cells, advances in identifying distinct T cell functional subsets, and in distinguishing effector cells from memory cells. We compare and contrast a wealth of recent progress made in T cell immunology of teleost, elasmobranch, and agnathan fish, to knowledge derived from mammalian T cell studies. From genome studies, fish clearly have most components associated with T cell function and we can speculate on the presence of putative T cell subsets, and the ability to detect their differentiation to form memory cells. Some recombinant proteins for T cell associated cytokines and antibodies for T cell surface receptors have been generated that will facilitate studying the functional roles of teleost T cells during immune responses. Although there is still a long way to go, major advances have occurred in recent years for investigating T cell responses, thus phenotypic and functional characterization is on the near horizon.

  12. Virus-epitope vaccine design: informatic matching the HLA-I polymorphism to the virus genome.

    PubMed

    Vider-Shalit, Tal; Raffaeli, Shai; Louzoun, Yoram

    2007-02-01

    Attempts to develop peptide vaccines, based on a limited number of peptides face two problems: HLA polymorphism and the high mutation rate of viral epitopes. We have developed a new genomic method that ensures maximal coverage and thus maximal applicability of the peptide vaccine. The same method also promises a large number of epitopes per HLA to prevent escape via mutations. Our design can be applied swiftly in order to face rapidly emerging viral diseases. We use a genomic scan of all candidate peptides and join them optimally. For a given virus, we use algorithms computing: peptide cleavage probability, transfer through TAP and MHC binding for a large number of HLA alleles. The resulting peptide libraries are pruned for peptides that are not conserved or are too similar to self peptides. We then use a genetic algorithm to produce an optimal protein composed of peptides from this list properly ordered for cleavage. The selected peptides represent an optimal combination to cover all HLA alleles and all viral proteins. We have applied this method to HCV and found that some HCV proteins (mainly envelope proteins) represent much less peptide than expected. A more detailed analysis of the peptide variability shows a balance between the attempts of the immune system to detect less mutating peptides, and the attempts of viruses to mutate peptides and avoid detection by the immune system. In order to show the applicability of our method, we have further used it on HIV-I, Influenza H3N2 and the Avian Flu Viruses. PMID:16930710

  13. Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology

    PubMed Central

    Paley, Suzanne M.; Krummenacker, Markus; Latendresse, Mario; Dale, Joseph M.; Lee, Thomas J.; Kaipa, Pallavi; Gilham, Fred; Spaulding, Aaron; Popescu, Liviu; Altman, Tomer; Paulsen, Ian; Keseler, Ingrid M.; Caspi, Ron

    2010-01-01

    Pathway Tools is a production-quality software environment for creating a type of model-organism database called a Pathway/Genome Database (PGDB). A PGDB such as EcoCyc integrates the evolving understanding of the genes, proteins, metabolic network and regulatory network of an organism. This article provides an overview of Pathway Tools capabilities. The software performs multiple computational inferences including prediction of metabolic pathways, prediction of metabolic pathway hole fillers and prediction of operons. It enables interactive editing of PGDBs by DB curators. It supports web publishing of PGDBs, and provides a large number of query and visualization tools. The software also supports comparative analyses of PGDBs, and provides several systems biology analyses of PGDBs including reachability analysis of metabolic networks, and interactive tracing of metabolites through a metabolic network. More than 800 PGDBs have been created using Pathway Tools by scientists around the world, many of which are curated DBs for important model organisms. Those PGDBs can be exchanged using a peer-to-peer DB sharing system called the PGDB Registry. PMID:19955237

  14. Earth Science Informatics - Overview

    NASA Technical Reports Server (NTRS)

    Ramapriyan, H. K.

    2015-01-01

    Over the last 10-15 years, significant advances have been made in information management, there are an increasing number of individuals entering the field of information management as it applies to Geoscience and Remote Sensing data, and the field of informatics has come to its own. Informatics is the science and technology of applying computers and computational methods to the systematic analysis, management, interchange, and representation of science data, information, and knowledge. Informatics also includes the use of computers and computational methods to support decision making and applications. Earth Science Informatics (ESI, a.k.a. geoinformatics) is the application of informatics in the Earth science domain. ESI is a rapidly developing discipline integrating computer science, information science, and Earth science. Major national and international research and infrastructure projects in ESI have been carried out or are on-going. Notable among these are: the Global Earth Observation System of Systems (GEOSS), the European Commissions INSPIRE, the U.S. NSDI and Geospatial One-Stop, the NASA EOSDIS, and the NSF DataONE, EarthCube and Cyberinfrastructure for Geoinformatics. More than 18 departments and agencies in the U.S. federal government have been active in Earth science informatics. All major space agencies in the world, have been involved in ESI research and application activities. In the United States, the Federation of Earth Science Information Partners (ESIP), whose membership includes nearly 150 organizations (government, academic and commercial) dedicated to managing, delivering and applying Earth science data, has been working on many ESI topics since 1998. The Committee on Earth Observation Satellites (CEOS)s Working Group on Information Systems and Services (WGISS) has been actively coordinating the ESI activities among the space agencies. Remote Sensing; Earth Science Informatics, Data Systems; Data Services; Metadata

  15. Museum Informatics.

    ERIC Educational Resources Information Center

    Marty, Paul F.; Rayward, W. Boyd; Twidale, Michael B.

    2003-01-01

    Discusses museum informatics that studies how information science and technology affect the museum environment. Examines digital technology; information organization and access; digitization, personal computers, and the Internet; data sharing; standards; social impacts of new technologies; collaboration; consortia; multimedia exhibits; virtual…

  16. Exploiting HPC Platforms for Metagenomics: Challenges and Opportunities (MICW - Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    ScienceCinema

    Canon, Shane [LBNL

    2013-01-22

    DOE JGI's Zhong Wang, chair of the High-performance Computing session, gives a brief introduction before Berkeley Lab's Shane Canon talks about "Exploiting HPC Platforms for Metagenomics: Challenges and Opportunities" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

  17. Exploiting HPC Platforms for Metagenomics: Challenges and Opportunities (MICW - Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    SciTech Connect

    Canon, Shane

    2011-10-12

    DOE JGI's Zhong Wang, chair of the High-performance Computing session, gives a brief introduction before Berkeley Lab's Shane Canon talks about "Exploiting HPC Platforms for Metagenomics: Challenges and Opportunities" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

  18. Informatics and the clinical laboratory.

    PubMed

    Jones, Richard G; Johnson, Owen A; Batstone, Gifford

    2014-08-01

    The nature of pathology services is changing under the combined pressures of increasing workloads, cost constraints and technological advancement. In the face of this, laboratory systems need to meet new demands for data exchange with clinical electronic record systems for test requesting and results reporting. As these needs develop, new challenges are emerging especially with respect to the format and content of the datasets which are being exchanged. If the potential for the inclusion of intelligent systems in both these areas is to be realised, the continued dialogue between clinicians and laboratory information specialists is of paramount importance. Requirements of information technology (IT) in pathology, now extend well beyond the provision of purely analytical data. With the aim of achieving seamless integration of laboratory data into the total clinical pathway, 'Informatics' - the art and science of turning data into useful information - is becoming increasingly important in laboratory medicine. Informatics is a powerful tool in pathology - whether in implementing processes for pathology modernisation, introducing new diagnostic modalities (e.g. proteomics, genomics), providing timely and evidence-based disease management, or enabling best use of limited and often costly resources. Providing appropriate information to empowered and interested patients - which requires critical assessment of the ever-increasing volume of information available - can also benefit greatly from appropriate use of informatics in enhancing self-management of long term conditions. The increasing demands placed on pathology information systems in the context of wider developmental change in healthcare delivery are explored in this review. General trends in medical informatics are reflected in current priorities for laboratory medicine, including the need for unified electronic records, computerised order entry, data security and recovery, and audit. We conclude that there is a

  19. Health Informatics.

    ERIC Educational Resources Information Center

    Russell, Marie; Brittain, J. Michael

    2002-01-01

    Identifies current trends and issues in health informatics with examples of applications, particularly in English-speaking countries. Topics include health systems, professionals, and patients; consumer health information; electronic medical records; nursing; privacy and confidentiality; finding and using information; the Internet; e-mail;…

  20. Health Informatics.

    ERIC Educational Resources Information Center

    MacDougall, Jennifer; Brittain, J. Michael

    1994-01-01

    Examines recent developments in health informatics from a historical and global perspective relating to information management through the interdisciplinary application of information science and technology for the benefits of patients, staff, scientists, managers, and caregivers. Highlights include competition; the World Health Organization;…

  1. Advancing Crop Transformation in the Era of Genome Editing

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Plant transformation has enabled fundamental insights into plant biology and revolutionized commercial agriculture. Unfortunately, for most crops, transformation and regeneration remain arduous even after more than thirty years of technological advances. Genome editing provides new opportunities to...

  2. Advances in Genetics and Genomics for Sustainable Peanut Production

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Plant breeding, genetics, and genomics have a critical role to play in sustainable agriculture. These technologies are contributing to rapid progress in improving crop productivity, quality, and resistance to pests and diseases. The advances in genetics and genomics are opening new frontiers in pean...

  3. [Advances in Genomics Studies for Coronary Artery Disease].

    PubMed

    Wang, Ying; Zhu, Hui-juan; Zeng, Yong

    2015-08-01

    Coronary artery disease (CAD) is one of the major life-threatening diseases. In addition to traditional risk factors including age, sex, smoking, hypertension,and diabetes, genomic studies have shown that CAD has obvious genetic predisposition. In recent years, the rapid advances in genomics shed new light on early diagnosis, risk stratification and new treatment targets. PMID:26564468

  4. Climate Informatics

    NASA Technical Reports Server (NTRS)

    Monteleoni, Claire; Schmidt, Gavin A.; Alexander, Francis J.; Niculescu-Mizil, Alexandru; Steinhaeuser, Karsten; Tippett, Michael; Banerjee, Arindam; Blumenthal, M. Benno; Ganguly, Auroop R.; Smerdon, Jason E.; Tedesco, Marco

    2013-01-01

    The impacts of present and potential future climate change will be one of the most important scientific and societal challenges in the 21st century. Given observed changes in temperature, sea ice, and sea level, improving our understanding of the climate system is an international priority. This system is characterized by complex phenomena that are imperfectly observed and even more imperfectly simulated. But with an ever-growing supply of climate data from satellites and environmental sensors, the magnitude of data and climate model output is beginning to overwhelm the relatively simple tools currently used to analyze them. A computational approach will therefore be indispensable for these analysis challenges. This chapter introduces the fledgling research discipline climate informatics: collaborations between climate scientists and machine learning researchers in order to bridge this gap between data and understanding. We hope that the study of climate informatics will accelerate discovery in answering pressing questions in climate science.

  5. Health Informatics

    PubMed Central

    Stead, William W.; Lorenzi, Nancy M.

    1999-01-01

    Informatics and information technology do not appear to be valued by the health industry to the degree that they are in other industries. The agenda for health informatics should be presented so that value to the health system is linked directly to required investment. The agenda should acknowledge the foundation provided by the current health system and the role of financial issues, system impediments, policy, and knowledge in effecting change. The desired outcomes should be compelling, such as improved public health, improved quality as perceived by consumers, and lower costs. Strategies to achieve these outcomes should derive from the differentia of health, opportunities to leverage other efforts, and lessons from successes inside and outside the health industry. Examples might include using logistics to improve quality, mass customization to adapt to individual values, and system thinking to change the game to one that can be won. The justification for the informatics infrastructure of a virtual health care data bank, a national health care knowledge base, and a personal clinical health record flows naturally from these strategies. PMID:10495093

  6. Polymer Informatics

    NASA Astrophysics Data System (ADS)

    Adams, Nico

    Polymers are arguably the most important set of materials in common use. The increasing adoption of both combinatorial as well as high-throughput approaches, coupled with an increasing amount of interdisciplinarity, has wrought tremendous change in the field of polymer science. Yet the informatics tools required to support and further enhance these changes are almost completely absent. In the first part of the chapter, a critical analysis of the challenges facing modern polymer informatics is provided. It is argued, that most of the problems facing the field today are rooted in the current scholarly communication process and the way in which chemists and polymer scientists handle and publish data. Furthermore, the chapter reviews existing modes of representing and communicating polymer information and discusses the impact, which the emergence of semantic technologies will have on the way in which scientific and polymer data is published and transmitted. In the second part, a review of the use of informatics tools for the prediction of polymer properties and in silico design of polymers is offered.

  7. Advances in Miniaturized Instruments for Genomics

    PubMed Central

    2014-01-01

    In recent years, a lot of demonstrations of the miniaturized instruments were reported for genomic applications. They provided the advantages of miniaturization, automation, sensitivity, and specificity for the development of point-of-care diagnostics. The aim of this paper is to report on recent developments on miniaturized instruments for genomic applications. Based on the mature development of microfabrication, microfluidic systems have been demonstrated for various genomic detections. Since one of the objectives of miniaturized instruments is for the development of point-of-care device, impedimetric detection is found to be a promising technique for this purpose. An in-depth discussion of the impedimetric circuits and systems will be included to provide total consideration of the miniaturized instruments and their potential application towards real-time portable imaging in the “-omics” era. The current excellent demonstrations suggest a solid foundation for the development of practical and widespread point-of-care genomic diagnostic devices. PMID:25114919

  8. The Human Genome Project, and recent advances in personalized genomics.

    PubMed

    Wilson, Brenda J; Nicholls, Stuart G

    2015-01-01

    The language of "personalized medicine" and "personal genomics" has now entered the common lexicon. The idea of personalized medicine is the integration of genomic risk assessment alongside other clinical investigations. Consistent with this approach, testing is delivered by health care professionals who are not medical geneticists, and where results represent risks, as opposed to clinical diagnosis of disease, to be interpreted alongside the entirety of a patient's health and medical data. In this review we consider the evidence concerning the application of such personalized genomics within the context of population screening, and potential implications that arise from this. We highlight two general approaches which illustrate potential uses of genomic information in screening. The first is a narrowly targeted approach in which genetic profiling is linked with standard population-based screening for diseases; the second is a broader targeting of variants associated with multiple single gene disorders, performed opportunistically on patients being investigated for unrelated conditions. In doing so we consider the organization and evaluation of tests and services, the challenge of interpretation with less targeted testing, professional confidence, barriers in practice, and education needs. We conclude by discussing several issues pertinent to health policy, namely: avoiding the conflation of genetics with biological determinism, resisting the "technological imperative", due consideration of the organization of screening services, the need for professional education, as well as informed decision making and public understanding. PMID:25733939

  9. Informatics and the Clinical Laboratory

    PubMed Central

    Jones, Richard G; Johnson, Owen A; Batstone, Gifford

    2014-01-01

    The nature of pathology services is changing under the combined pressures of increasing workloads, cost constraints and technological advancement. In the face of this, laboratory systems need to meet new demands for data exchange with clinical electronic record systems for test requesting and results reporting. As these needs develop, new challenges are emerging especially with respect to the format and content of the datasets which are being exchanged. If the potential for the inclusion of intelligent systems in both these areas is to be realised, the continued dialogue between clinicians and laboratory information specialists is of paramount importance. Requirements of information technology (IT) in pathology, now extend well beyond the provision of purely analytical data. With the aim of achieving seamless integration of laboratory data into the total clinical pathway, ‘Informatics’ – the art and science of turning data into useful information – is becoming increasingly important in laboratory medicine. Informatics is a powerful tool in pathology – whether in implementing processes for pathology modernisation, introducing new diagnostic modalities (e.g. proteomics, genomics), providing timely and evidence-based disease management, or enabling best use of limited and often costly resources. Providing appropriate information to empowered and interested patients – which requires critical assessment of the ever-increasing volume of information available – can also benefit greatly from appropriate use of informatics in enhancing self-management of long term conditions. The increasing demands placed on pathology information systems in the context of wider developmental change in healthcare delivery are explored in this review. General trends in medical informatics are reflected in current priorities for laboratory medicine, including the need for unified electronic records, computerised order entry, data security and recovery, and audit. We conclude that

  10. The Human Genome Project, and recent advances in personalized genomics

    PubMed Central

    Wilson, Brenda J; Nicholls, Stuart G

    2015-01-01

    The language of “personalized medicine” and “personal genomics” has now entered the common lexicon. The idea of personalized medicine is the integration of genomic risk assessment alongside other clinical investigations. Consistent with this approach, testing is delivered by health care professionals who are not medical geneticists, and where results represent risks, as opposed to clinical diagnosis of disease, to be interpreted alongside the entirety of a patient’s health and medical data. In this review we consider the evidence concerning the application of such personalized genomics within the context of population screening, and potential implications that arise from this. We highlight two general approaches which illustrate potential uses of genomic information in screening. The first is a narrowly targeted approach in which genetic profiling is linked with standard population-based screening for diseases; the second is a broader targeting of variants associated with multiple single gene disorders, performed opportunistically on patients being investigated for unrelated conditions. In doing so we consider the organization and evaluation of tests and services, the challenge of interpretation with less targeted testing, professional confidence, barriers in practice, and education needs. We conclude by discussing several issues pertinent to health policy, namely: avoiding the conflation of genetics with biological determinism, resisting the “technological imperative”, due consideration of the organization of screening services, the need for professional education, as well as informed decision making and public understanding. PMID:25733939

  11. Recent Advances in Medicago truncatula Genomics

    PubMed Central

    Ané, Jean-Michel; Zhu, Hongyan; Frugoli, Julia

    2008-01-01

    Legume rotation has allowed a consistent increase in crop yield and consequently in human population since the antiquity. Legumes will also be instrumental in our ability to maintain the sustainability of our agriculture while facing the challenges of increasing food and biofuel demand. Medicago truncatula and Lotus japonicus have emerged during the last decade as two major model systems for legume biology. Initially developed to dissect plant-microbe symbiotic interactions and especially legume nodulation, these two models are now widely used in a variety of biological fields from plant physiology and development to population genetics and structural genomics. This review highlights the genetic and genomic tools available to the M. truncatula community. Comparative genomic approaches to transfer biological information between model systems and legume crops are also discussed. PMID:18288239

  12. Recent advances in malaria genomics and epigenomics.

    PubMed

    Kirchner, Sebastian; Power, B Joanne; Waters, Andrew P

    2016-01-01

    Malaria continues to impose a significant disease burden on low- and middle-income countries in the tropics. However, revolutionary progress over the last 3 years in nucleic acid sequencing, reverse genetics, and post-genome analyses has generated step changes in our understanding of malaria parasite (Plasmodium spp.) biology and its interactions with its host and vector. Driven by the availability of vast amounts of genome sequence data from Plasmodium species strains, relevant human populations of different ethnicities, and mosquito vectors, researchers can consider any biological component of the malarial process in isolation or in the interactive setting that is infection. In particular, considerable progress has been made in the area of population genomics, with Plasmodium falciparum serving as a highly relevant model. Such studies have demonstrated that genome evolution under strong selective pressure can be detected. These data, combined with reverse genetics, have enabled the identification of the region of the P. falciparum genome that is under selective pressure and the confirmation of the functionality of the mutations in the kelch13 gene that accompany resistance to the major frontline antimalarial, artemisinin. Furthermore, the central role of epigenetic regulation of gene expression and antigenic variation and developmental fate in P. falciparum is becoming ever clearer. This review summarizes recent exciting discoveries that genome technologies have enabled in malaria research and highlights some of their applications to healthcare. The knowledge gained will help to develop surveillance approaches for the emergence or spread of drug resistance and to identify new targets for the development of antimalarial drugs and perhaps vaccines. PMID:27605022

  13. Advances in Arachis genomics for peanut improvement

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Peanut genomics is very challenging due to its inherent problem of genetic architecture. Blockage of gene flow from diploid wild relatives to tetraploid cultivated peanut, recent polyploidization combined with self pollination and narrow genetic base of primary gene pool resulted in low genetic dive...

  14. Advances in Swine biomedical Model Genomics

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This manuscript is a short update on the diversity of swine biomedical models and the importance of genomics in their continued development. The swine has been used as a major mammalian model for human studies because of the similarity in size and physiology, and in organ development and disease pro...

  15. Bioinformatics and genomic medicine.

    PubMed

    Kim, Ju Han

    2002-01-01

    Bioinformatics is a rapidly emerging field of biomedical research. A flood of large-scale genomic and postgenomic data means that many of the challenges in biomedical research are now challenges in computational science. Clinical informatics has long developed methodologies to improve biomedical research and clinical care by integrating experimental and clinical information systems. The informatics revolution in both bioinformatics and clinical informatics will eventually change the current practice of medicine, including diagnostics, therapeutics, and prognostics. Postgenome informatics, powered by high-throughput technologies and genomic-scale databases, is likely to transform our biomedical understanding forever, in much the same way that biochemistry did a generation ago. This paper describes how these technologies will impact biomedical research and clinical care, emphasizing recent advances in biochip-based functional genomics and proteomics. Basic data preprocessing with normalization and filtering, primary pattern analysis, and machine-learning algorithms are discussed. Use of integrative biochip informatics technologies, including multivariate data projection, gene-metabolic pathway mapping, automated biomolecular annotation, text mining of factual and literature databases, and the integrated management of biomolecular databases, are also discussed. PMID:12544491

  16. Advances in Faba Bean Genetics and Genomics.

    PubMed

    O'Sullivan, Donal M; Angra, Deepti

    2016-01-01

    Vicia faba L, is a globally important grain legume whose main centers of diversity are the Fertile Crescent and Mediterranean basin. Because of its small number (six) of exceptionally large and easily observed chromosomes it became a model species for plant cytogenetics the 70s and 80s. It is somewhat ironic therefore, that the emergence of more genomically tractable model plant species such as Arabidopsis and Medicago coincided with a marked decline in genome research on the formerly favored plant cytogenetic model. Thus, as ever higher density molecular marker coverage and dense genetic and even complete genome sequence maps of key crop and model species emerged through the 1990s and early 2000s, genetic and genome knowledge of Vicia faba lagged far behind other grain legumes such as soybean, common bean and pea. However, cheap sequencing technologies have stimulated the production of deep transcriptome coverage from several tissue types and numerous distinct cultivars in recent years. This has permitted the reconstruction of the faba bean meta-transcriptome and has fueled development of extensive sets of Simple Sequence Repeat and Single Nucleotide Polymorphism (SNP) markers. Genetics of faba bean stretches back to the 1930s, but it was not until 1993 that DNA markers were used to construct genetic maps. A series of Random Amplified Polymorphic DNA-based genetic studies mainly targeted at quantitative loci underlying resistance to a series of biotic and abiotic stresses were conducted during the 1990's and early 2000s. More recently, SNP-based genetic maps have permitted chromosome intervals of interest to be aligned to collinear segments of sequenced legume genomes such as the model legume Medicago truncatula, which in turn opens up the possibility for hypotheses on gene content, order and function to be translated from model to crop. Some examples of where knowledge of gene content and function have already been productively exploited are discussed. The

  17. Advances in Faba Bean Genetics and Genomics

    PubMed Central

    O'Sullivan, Donal M.; Angra, Deepti

    2016-01-01

    Vicia faba L, is a globally important grain legume whose main centers of diversity are the Fertile Crescent and Mediterranean basin. Because of its small number (six) of exceptionally large and easily observed chromosomes it became a model species for plant cytogenetics the 70s and 80s. It is somewhat ironic therefore, that the emergence of more genomically tractable model plant species such as Arabidopsis and Medicago coincided with a marked decline in genome research on the formerly favored plant cytogenetic model. Thus, as ever higher density molecular marker coverage and dense genetic and even complete genome sequence maps of key crop and model species emerged through the 1990s and early 2000s, genetic and genome knowledge of Vicia faba lagged far behind other grain legumes such as soybean, common bean and pea. However, cheap sequencing technologies have stimulated the production of deep transcriptome coverage from several tissue types and numerous distinct cultivars in recent years. This has permitted the reconstruction of the faba bean meta-transcriptome and has fueled development of extensive sets of Simple Sequence Repeat and Single Nucleotide Polymorphism (SNP) markers. Genetics of faba bean stretches back to the 1930s, but it was not until 1993 that DNA markers were used to construct genetic maps. A series of Random Amplified Polymorphic DNA-based genetic studies mainly targeted at quantitative loci underlying resistance to a series of biotic and abiotic stresses were conducted during the 1990's and early 2000s. More recently, SNP-based genetic maps have permitted chromosome intervals of interest to be aligned to collinear segments of sequenced legume genomes such as the model legume Medicago truncatula, which in turn opens up the possibility for hypotheses on gene content, order and function to be translated from model to crop. Some examples of where knowledge of gene content and function have already been productively exploited are discussed. The

  18. Informatics Workup.

    PubMed Central

    Naeymi-Rad, F.; Trace, D.; Shoults, K.; Suico, J.; O'Brien, M.; Evens, M.; Carmony, L.; Roberts, R.; Zelanski, R.

    1992-01-01

    We introduce the concept of a Medical Informatics Workup performed by fourth year medical students working in a busy inner-city Emergency Room. These students use portable computers (Macintosh PowerBook 170s connected to a removable cartridge hard drive and CD-ROM drive) to do the patient workups. The PowerBook 170 contains the automated medical record entry software (IMR-E), five expert system software packages, and a program that allows the PowerBook to emulate a PC-compatible computer. With this configuration the student has a portable system that allows for the creation of a computerized medical record at the patient's bedside, along with the ability to analyze the data and generate a list of differential diagnoses. PMID:1482933

  19. Advances in biotechnology and genomics of switchgrass

    PubMed Central

    2013-01-01

    Switchgrass (Panicum virgatum L.) is a C4 perennial warm season grass indigenous to the North American tallgrass prairie. A number of its natural and agronomic traits, including adaptation to a wide geographical distribution, low nutrient requirements and production costs, high water use efficiency, high biomass potential, ease of harvesting, and potential for carbon storage, make it an attractive dedicated biomass crop for biofuel production. We believe that genetic improvements using biotechnology will be important to realize the potential of the biomass and biofuel-related uses of switchgrass. Tissue culture techniques aimed at rapid propagation of switchgrass and genetic transformation protocols have been developed. Rapid progress in genome sequencing and bioinformatics has provided efficient strategies to identify, tag, clone and manipulate many economically-important genes, including those related to higher biomass, saccharification efficiency, and lignin biosynthesis. Application of the best genetic tools should render improved switchgrass that will be more economically and environmentally sustainable as a lignocellulosic bioenergy feedstock. PMID:23663491

  20. Integrative clinical genomics of advanced prostate cancer.

    PubMed

    Robinson, Dan; Van Allen, Eliezer M; Wu, Yi-Mi; Schultz, Nikolaus; Lonigro, Robert J; Mosquera, Juan-Miguel; Montgomery, Bruce; Taplin, Mary-Ellen; Pritchard, Colin C; Attard, Gerhardt; Beltran, Himisha; Abida, Wassim; Bradley, Robert K; Vinson, Jake; Cao, Xuhong; Vats, Pankaj; Kunju, Lakshmi P; Hussain, Maha; Feng, Felix Y; Tomlins, Scott A; Cooney, Kathleen A; Smith, David C; Brennan, Christine; Siddiqui, Javed; Mehra, Rohit; Chen, Yu; Rathkopf, Dana E; Morris, Michael J; Solomon, Stephen B; Durack, Jeremy C; Reuter, Victor E; Gopalan, Anuradha; Gao, Jianjiong; Loda, Massimo; Lis, Rosina T; Bowden, Michaela; Balk, Stephen P; Gaviola, Glenn; Sougnez, Carrie; Gupta, Manaswi; Yu, Evan Y; Mostaghel, Elahe A; Cheng, Heather H; Mulcahy, Hyojeong; True, Lawrence D; Plymate, Stephen R; Dvinge, Heidi; Ferraldeschi, Roberta; Flohr, Penny; Miranda, Susana; Zafeiriou, Zafeiris; Tunariu, Nina; Mateo, Joaquin; Perez-Lopez, Raquel; Demichelis, Francesca; Robinson, Brian D; Schiffman, Marc; Nanus, David M; Tagawa, Scott T; Sigaras, Alexandros; Eng, Kenneth W; Elemento, Olivier; Sboner, Andrea; Heath, Elisabeth I; Scher, Howard I; Pienta, Kenneth J; Kantoff, Philip; de Bono, Johann S; Rubin, Mark A; Nelson, Peter S; Garraway, Levi A; Sawyers, Charles L; Chinnaiyan, Arul M

    2015-05-21

    Toward development of a precision medicine framework for metastatic, castration-resistant prostate cancer (mCRPC), we established a multi-institutional clinical sequencing infrastructure to conduct prospective whole-exome and transcriptome sequencing of bone or soft tissue tumor biopsies from a cohort of 150 mCRPC affected individuals. Aberrations of AR, ETS genes, TP53, and PTEN were frequent (40%-60% of cases), with TP53 and AR alterations enriched in mCRPC compared to primary prostate cancer. We identified new genomic alterations in PIK3CA/B, R-spondin, BRAF/RAF1, APC, β-catenin, and ZBTB16/PLZF. Moreover, aberrations of BRCA2, BRCA1, and ATM were observed at substantially higher frequencies (19.3% overall) compared to those in primary prostate cancers. 89% of affected individuals harbored a clinically actionable aberration, including 62.7% with aberrations in AR, 65% in other cancer-related genes, and 8% with actionable pathogenic germline alterations. This cohort study provides clinically actionable information that could impact treatment decisions for these affected individuals. PMID:26000489

  1. Integrative clinical genomics of advanced prostate cancer

    PubMed Central

    Dan, Robinson; Van Allen, Eliezer M.; Wu, Yi-Mi; Schultz, Nikolaus; Lonigro, Robert J.; Mosquera, Juan-Miguel; Montgomery, Bruce; Taplin, Mary-Ellen; Pritchard, Colin C; Attard, Gerhardt; Beltran, Himisha; Abida, Wassim M.; Bradley, Robert K.; Vinson, Jake; Cao, Xuhong; Vats, Pankaj; Kunju, Lakshmi P.; Hussain, Maha; Feng, Felix Y.; Tomlins, Scott A.; Cooney, Kathleen A.; Smith, David C.; Brennan, Christine; Siddiqui, Javed; Mehra, Rohit; Chen, Yu; Rathkopf, Dana E.; Morris, Michael J.; Solomon, Stephen B.; Durack, Jeremy C.; Reuter, Victor E.; Gopalan, Anuradha; Gao, Jianjiong; Loda, Massimo; Lis, Rosina T.; Bowden, Michaela; Balk, Stephen P.; Gaviola, Glenn; Sougnez, Carrie; Gupta, Manaswi; Yu, Evan Y.; Mostaghel, Elahe A.; Cheng, Heather H.; Mulcahy, Hyojeong; True, Lawrence D.; Plymate, Stephen R.; Dvinge, Heidi; Ferraldeschi, Roberta; Flohr, Penny; Miranda, Susana; Zafeiriou, Zafeiris; Tunariu, Nina; Mateo, Joaquin; Lopez, Raquel Perez; Demichelis, Francesca; Robinson, Brian D.; Schiffman, Marc A.; Nanus, David M.; Tagawa, Scott T.; Sigaras, Alexandros; Eng, Kenneth W.; Elemento, Olivier; Sboner, Andrea; Heath, Elisabeth I.; Scher, Howard I.; Pienta, Kenneth J.; Kantoff, Philip; de Bono, Johann S.; Rubin, Mark A.; Nelson, Peter S.; Garraway, Levi A.; Sawyers, Charles L.; Chinnaiyan, Arul M.

    2015-01-01

    SUMMARY Toward development of a precision medicine framework for metastatic, castration resistant prostate cancer (mCRPC), we established a multi-institutional clinical sequencing infrastructure to conduct prospective whole exome and transcriptome sequencing of bone or soft tissue tumor biopsies from a cohort of 150 mCRPC affected individuals. Aberrations of AR, ETS genes, TP53 and PTEN were frequent (40–60% of cases), with TP53 and AR alterations enriched in mCRPC compared to primary prostate cancer. We identified novel genomic alterations in PIK3CA/B, R-spondin, BRAF/RAF1, APC, β-catenin and ZBTB16/PLZF. Aberrations of BRCA2, BRCA1 and ATM were observed at substantially higher frequencies (19.3% overall) than seen in primary prostate cancers. 89% of affected individuals harbored a clinically actionable aberration including 62.7% with aberrations in AR, 65% in other cancer-related genes, and 8% with actionable pathogenic germline alterations. This cohort study provides evidence that clinical sequencing in mCRPC is feasible and could impact treatment decisions in significant numbers of affected individuals. PMID:26000489

  2. Advances in genomics for the improvement of quality in coffee.

    PubMed

    Tran, Hue Tm; Lee, L Slade; Furtado, Agnelo; Smyth, Heather; Henry, Robert J

    2016-08-01

    Coffee is an important crop that provides a livelihood to millions of people living in developing countries. Production of genotypes with improved coffee quality attributes is a primary target of coffee genetic improvement programmes. Advances in genomics are providing new tools for analysis of coffee quality at the molecular level. The recent report of a genomic sequence for robusta coffee, Coffea canephora, is a major development. However, a reference genome sequence for the genetically more complex arabica coffee (C. arabica) will also be required to fully define the molecular determinants controlling quality in coffee produced from this high quality coffee species. Genes responsible for control of the levels of the major biochemical components in the coffee bean that are known to be important in determining coffee quality can now be identified by association analysis. However, the narrow genetic base of arabica coffee suggests that genomics analysis of the wild relatives of coffee (Coffea spp.) may be required to find the phenotypic diversity required for effective association genetic analysis. The genomic resources available for the study of coffee quality are described and the potential for the application of next generation sequencing and association genetic analysis to advance coffee quality research are explored. © 2016 Society of Chemical Industry. PMID:26919810

  3. MetaVelvet: An Extension of Velvet Assembler to de novo Metagenome Assembly from Short Sequence Reads (Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    SciTech Connect

    Sakakibara, Yasumbumi

    2011-10-13

    Keio University's Yasumbumi Sakakibara on "MetaVelvet: An Extension of Velvet Assembler to de novo Metagenome Assembly from Short Sequence Reads" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

  4. Comparison of Normalized and Unnormalized Single Cell and Population Assemblies (MICW - Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    SciTech Connect

    Hugenholtz, Phil

    2011-10-12

    University of Queensland's Phil Hugenholtz on "Comparison of Normalized and Unnormalized Single Cell and Population Assemblies" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

  5. MetaVelvet: An Extension of Velvet Assembler to de novo Metagenome Assembly from Short Sequence Reads (Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    ScienceCinema

    Sakakibara, Yasumbumi [Keio University

    2013-01-22

    Keio University's Yasumbumi Sakakibara on "MetaVelvet: An Extension of Velvet Assembler to de novo Metagenome Assembly from Short Sequence Reads" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

  6. Comparison of Normalized and Unnormalized Single Cell and Population Assemblies (MICW - Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    ScienceCinema

    Hugenholtz, Phil [University of Queensland

    2013-01-22

    University of Queensland's Phil Hugenholtz on "Comparison of Normalized and Unnormalized Single Cell and Population Assemblies" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

  7. Effective Analysis of NGS Metagenomic Data with Ultra-Fast Clustering Algorithms (MICW - Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    ScienceCinema

    Li, Weizhong [San Diego Supercomputer Center

    2013-01-22

    San Diego Supercomputer Center's Weizhong Li on "Effective Analysis of NGS Metagenomic Data with Ultra-fast Clustering Algorithms" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

  8. Effective Analysis of NGS Metagenomic Data with Ultra-Fast Clustering Algorithms (MICW - Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    SciTech Connect

    Li, Weizhong

    2011-10-12

    San Diego Supercomputer Center's Weizhong Li on "Effective Analysis of NGS Metagenomic Data with Ultra-fast Clustering Algorithms" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

  9. Advancing Crop Transformation in the Era of Genome Editing.

    PubMed

    Altpeter, Fredy; Springer, Nathan M; Bartley, Laura E; Blechl, Ann E; Brutnell, Thomas P; Citovsky, Vitaly; Conrad, Liza J; Gelvin, Stanton B; Jackson, David P; Kausch, Albert P; Lemaux, Peggy G; Medford, June I; Orozco-Cárdenas, Martha L; Tricoli, David M; Van Eck, Joyce; Voytas, Daniel F; Walbot, Virginia; Wang, Kan; Zhang, Zhanyuan J; Stewart, C Neal

    2016-07-01

    Plant transformation has enabled fundamental insights into plant biology and revolutionized commercial agriculture. Unfortunately, for most crops, transformation and regeneration remain arduous even after more than 30 years of technological advances. Genome editing provides novel opportunities to enhance crop productivity but relies on genetic transformation and plant regeneration, which are bottlenecks in the process. Here, we review the state of plant transformation and point to innovations needed to enable genome editing in crops. Plant tissue culture methods need optimization and simplification for efficiency and minimization of time in culture. Currently, specialized facilities exist for crop transformation. Single-cell and robotic techniques should be developed for high-throughput genomic screens. Plant genes involved in developmental reprogramming, wound response, and/or homologous recombination should be used to boost the recovery of transformed plants. Engineering universal Agrobacterium tumefaciens strains and recruiting other microbes, such as Ensifer or Rhizobium, could facilitate delivery of DNA and proteins into plant cells. Synthetic biology should be employed for de novo design of transformation systems. Genome editing is a potential game-changer in crop genetics when plant transformation systems are optimized. PMID:27335450

  10. Recent Advances in Genome Editing Using CRISPR/Cas9

    PubMed Central

    Ding, Yuduan; Li, Hong; Chen, Ling-Ling; Xie, Kabin

    2016-01-01

    The CRISPR (clustered regularly interspaced short palindromic repeat)-Cas9 (CRISPR-associated nuclease 9) system is a versatile tool for genome engineering that uses a guide RNA (gRNA) to target Cas9 to a specific sequence. This simple RNA-guided genome-editing technology has become a revolutionary tool in biology and has many innovative applications in different fields. In this review, we briefly introduce the Cas9-mediated genome-editing method, summarize the recent advances in CRISPR/Cas9 technology, and discuss their implications for plant research. To date, targeted gene knockout using the Cas9/gRNA system has been established in many plant species, and the targeting efficiency and capacity of Cas9 has been improved by optimizing its expression and that of its gRNA. The CRISPR/Cas9 system can also be used for sequence-specific mutagenesis/integration and transcriptional control of target genes. We also discuss off-target effects and the constraint that the protospacer-adjacent motif (PAM) puts on CRISPR/Cas9 genome engineering. To address these problems, a number of bioinformatic tools are available to help design specific gRNAs, and new Cas9 variants and orthologs with high fidelity and alternative PAM specificities have been engineered. Owing to these recent efforts, the CRISPR/Cas9 system is becoming a revolutionary and flexible tool for genome engineering. Adoption of the CRISPR/Cas9 technology in plant research would enable the investigation of plant biology at an unprecedented depth and create innovative applications in precise crop breeding. PMID:27252719

  11. Pharmacogenomics and Nanotechnology Toward Advancing Personalized Medicine

    NASA Astrophysics Data System (ADS)

    Vizirianakis, Ioannis S.; Amanatiadou, Elsa P.

    The target of personalized medicine to achieve major benefits for all patients in terms of diagnosis and drug delivery can be facilitated by creating a sincere multidisciplinary information-based infrastructure in health care. To this end, nanotechnology, pharmacogenomics, and informatics can advance the utility of personalized medicine, enable clinical translation of genomic knowledge, empower healthcare environment, and finally improve clinical outcomes.

  12. Earth Science Informatics Comes of Age

    NASA Technical Reports Server (NTRS)

    Jodha, Siri; Khalsa, S.; Ramachandran, Rahul

    2014-01-01

    The volume and complexity of Earth science data have steadily increased, placing ever-greater demands on researchers, software developers and data managers tasked with handling such data. Additional demands arise from requirements being levied by funding agencies and governments to better manage, preserve and provide open access to data. Fortunately, over the past 10-15 years significant advances in information technology, such as increased processing power, advanced programming languages, more sophisticated and practical standards, and near-ubiquitous internet access have made the jobs of those acquiring, processing, distributing and archiving data easier. These advances have also led to an increasing number of individuals entering the field of informatics as it applies to Geoscience and Remote Sensing. Informatics is the science and technology of applying computers and computational methods to the systematic analysis, management, interchange, and representation of data, information, and knowledge. Informatics also encompasses the use of computers and computational methods to support decisionmaking and other applications for societal benefits.

  13. DOE JGI Quality Metrics; Approaches to Scaling and Improving Metagenome Assembly (Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    SciTech Connect

    Copeland, Alex; Brown, C Titus

    2011-10-13

    DOE JGI's Alex Copeland on "DOE JGI Quality Metrics" and Michigan State University's C. Titus Brown on "Approaches to Scaling and Improving Metagenome Assembly" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

  14. Single Cell and Metagenomic Assemblies: Biology Drives Technical Choices and Goals (Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    SciTech Connect

    Stepanauskas, Ramunas

    2011-10-13

    DOE JGI's Tanja Woyke, chair of the Single Cells and Metagenomes session, delivers an introduction, followed by Bigelow Laboratory's Ramunas Stepanauskas on "Single Cell and Metagenomic Assemblies: Biology Drives Technical Choices and Goals" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

  15. Single Cell and Metagenomic Assemblies: Biology Drives Technical Choices and Goals (Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    ScienceCinema

    Stepanauskas, Ramunas [Bigelow Laboratory

    2013-01-22

    DOE JGI's Tanja Woyke, chair of the Single Cells and Metagenomes session, delivers an introduction, followed by Bigelow Laboratory's Ramunas Stepanauskas on "Single Cell and Metagenomic Assemblies: Biology Drives Technical Choices and Goals" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

  16. DOE JGI Quality Metrics; Approaches to Scaling and Improving Metagenome Assembly (Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    ScienceCinema

    Copeland, Alex [DOE JGI]; Brown, C Titus [Michigan State University

    2013-01-22

    DOE JGI's Alex Copeland on "DOE JGI Quality Metrics" and Michigan State University's C. Titus Brown on "Approaches to Scaling and Improving Metagenome Assembly" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

  17. Translational informatics: an industry perspective

    PubMed Central

    2012-01-01

    Translational informatics (TI) is extremely important for the pharmaceutical industry, especially as the bar for regulatory approval of new medications is set higher and higher. This paper will explore three specific areas in the drug development lifecycle, from tools developed by precompetitive consortia to standardized clinical data collection to the effective delivery of medications using clinical decision support, in which TI has a major role to play. Advancing TI will require investment in new tools and algorithms, as well as ensuring that translational issues are addressed early in the design process of informatics projects, and also given higher weight in funding or publication decisions. Ultimately, the source of translational tools and differences between academia and industry are secondary, as long as they move towards the shared goal of improving health. PMID:22237867

  18. Enzyme Informatics

    PubMed Central

    Alderson, Rosanna G.; Ferrari, Luna De; Mavridis, Lazaros; McDonagh, James L.; Mitchell, John B. O.; Nath, Neetika

    2012-01-01

    Over the last 50 years, sequencing, structural biology and bioinformatics have completely revolutionised biomolecular science, with millions of sequences and tens of thousands of three dimensional structures becoming available. The bioinformatics of enzymes is well served by, mostly free, online databases. BRENDA describes the chemistry, substrate specificity, kinetics, preparation and biological sources of enzymes, while KEGG is valuable for understanding enzymes and metabolic pathways. EzCatDB, SFLD and MACiE are key repositories for data on the chemical mechanisms by which enzymes operate. At the current rate of genome sequencing and manual annotation, human curation will never finish the functional annotation of the ever-expanding list of known enzymes. Hence there is an increasing need for automated annotation, though it is not yet widespread for enzyme data. In contrast, functional ontologies such as the Gene Ontology already profit from automation. Despite our growing understanding of enzyme structure and dynamics, we are only beginning to be able to design novel enzymes. One can now begin to trace the functional evolution of enzymes using phylogenetics. The ability of enzymes to perform secondary functions, albeit relatively inefficiently, gives clues as to how enzyme function evolves. Substrate promiscuity in enzymes is one example of imperfect specificity in protein-ligand interactions. Similarly, most drugs bind to more than one protein target. This may sometimes result in helpful polypharmacology as a drug modulates plural targets, but also often leads to adverse side-effects. Many cheminformatics approaches can be used to model the interactions between druglike molecules and proteins in silico. We can even use quantum chemical techniques like DFT and QM/MM to compute the structural and energetic course of enzyme catalysed chemical reaction mechanisms, including a full description of bond making and breaking. PMID:23116471

  19. Nursing informatics: the future now.

    PubMed

    Mamta

    2014-01-01

    Technological advancements in the health care field have always impacted the health care practices. Nursing practice has also been greatly influenced by the technology. In the recent years, use of information technology including computers, handheld digital devices, internet has advanced the nursing by bridging the gap from nursing as an art to nursing as science. In every sphere of nursing practice, nursing research, nursing education and nursing informatics play a very important role. If used properly it is a way to save time, helping to provide quality nursing care and increases the proficiency of nursing personnel. PMID:25924417

  20. Consumer Health Informatics: Health Information Technology for Consumers.

    ERIC Educational Resources Information Center

    Jimison, Holly Brugge; Sher, Paul Phillip

    1995-01-01

    Explains consumer health informatics and describes the technology advances, the computer programs that are currently available, and the basic research that addresses both the effectiveness of computer health informatics and its impact on the future direction of health care. Highlights include commercial computer products for consumers and…

  1. Office of Biological Informatics and Outreach geospatial technology activities

    USGS Publications Warehouse

    U.S. Geological Survey

    1998-01-01

    The U.S. Geological Survey (USGS) Office of Biological Informatics and Outreach (OBIO) in Reston, Virginia, and its Center for Biological Informatics (CBI) in Denver, Colorado, provide leadership in the development and use of geospatial technologies to advance the Nation's biological science activities.

  2. What Is Nursing Informatics?

    ERIC Educational Resources Information Center

    McGonigle, D.; And Others

    Information technology has developed to the point of providing a means to manage nursing and related health-care data effectively for nursing administrators, educators, practitioners, and researchers. Therefore, the newly recognized area of nursing informatics is important to the nursing profession as a whole. Nursing informatics is defined as the…

  3. Health Informatics: An Overview.

    ERIC Educational Resources Information Center

    MacDougall, Jennifer; And Others

    1996-01-01

    Reviews literature related to health informatics and health information management. Provides examples covering types of information, library and information services outcomes, training of informatics professionals, areas of application, the impact of evidence based medicine, professional issues, integrated information systems, and the needs of the…

  4. Emerging Vaccine Informatics

    PubMed Central

    He, Yongqun; Rappuoli, Rino; De Groot, Anne S.; Chen, Robert T.

    2010-01-01

    Vaccine informatics is an emerging research area that focuses on development and applications of bioinformatics methods that can be used to facilitate every aspect of the preclinical, clinical, and postlicensure vaccine enterprises. Many immunoinformatics algorithms and resources have been developed to predict T- and B-cell immune epitopes for epitope vaccine development and protective immunity analysis. Vaccine protein candidates are predictable in silico from genome sequences using reverse vaccinology. Systematic transcriptomics and proteomics gene expression analyses facilitate rational vaccine design and identification of gene responses that are correlates of protection in vivo. Mathematical simulations have been used to model host-pathogen interactions and improve vaccine production and vaccination protocols. Computational methods have also been used for development of immunization registries or immunization information systems, assessment of vaccine safety and efficacy, and immunization modeling. Computational literature mining and databases effectively process, mine, and store large amounts of vaccine literature and data. Vaccine Ontology (VO) has been initiated to integrate various vaccine data and support automated reasoning. PMID:21772787

  5. Advances in exercise, fitness, and performance genomics in 2012.

    PubMed

    Pérusse, Louis; Rankinen, Tuomo; Hagberg, James M; Loos, Ruth J F; Roth, Stephen M; Sarzynski, Mark A; Wolfarth, Bernd; Bouchard, Claude

    2013-05-01

    A small number of excellent articles on exercise genomics issues were published in 2012. A new PYGM knock-in mouse model will provide opportunities to investigate the exercise intolerance and very low activity level of people with McArdle disease. New reports on variants in ACTN3 and ACE have increased the level of uncertainty regarding their true role in skeletal muscle metabolism and strength traits. The evidence continues to accumulate on the positive effects of regular physical activity on body mass index or adiposity in individuals at risk of obesity as assessed by their FTO genotype or by the number of risk alleles they carry at multiple obesity-susceptibility loci. The serum levels of triglycerides and the risk of hypertriglyceridemia were shown to be influenced by the interactions between a single nucleotide polymorphism (SNP) in the NOS3 gene and physical activity level. Allelic variation at nine SNPs was shown to account for the heritable component of the changes in submaximal exercise heart rate induced by the HERITAGE Family Study exercise program. SNPs at the RBPMS, YWHAQ, and CREB1 loci were found to be particularly strong predictors of the changes in submaximal exercise heart rate. The 2012 review ends with comments on the importance of relying more on experimental data, the urgency of identifying panels of genomic predictors of the response to regular exercise and particularly of adverse responses, and the exciting opportunities offered by recent advances in our understanding of the global architecture of the human genome as reported by the Encyclopedia of DNA Elements project. PMID:23470294

  6. Prospects for advancing defense to cereal rusts through genetical genomics.

    PubMed

    Ballini, Elsa; Lauter, Nick; Wise, Roger

    2013-01-01

    Rusts are one of the most severe threats to cereal crops because new pathogen races emerge regularly, resulting in infestations that lead to large yield losses. In 1999, a new race of stem rust, Puccinia graminis f. sp. tritici (Pgt TTKSK or Ug99), was discovered in Uganda. Most of the wheat and barley cultivars grown currently worldwide are susceptible to this new race. Pgt TTKSK has already spread northward into Iran and will likely spread eastward throughout the Indian subcontinent in the near future. This scenario is not unique to stem rust; new races of leaf rust (Puccinia triticina) and stripe rust (Puccinia striiformis) have also emerged recently. One strategy for countering the persistent adaptability of these pathogens is to stack complete- and partial-resistance genes, which requires significant breeding efforts in order to reduce deleterious effects of linkage drag. These varied resistance combinations are typically more difficult for the pathogen to defeat, since they would be predicted to apply lower selection pressure. Genetical genomics or expression Quantitative Trait Locus (eQTL) analysis enables the identification of regulatory loci that control the expression of many to hundreds of genes. Integrated deployment of these technologies coupled with efficient phenotyping offers significant potential to elucidate the regulatory nodes in genetic networks that orchestrate host defense responses. The focus of this review will be to present advances in genetical genomic experimental designs and analysis, particularly as they apply to the prospects for discovering partial disease resistance alleles in cereals. PMID:23641250

  7. Advances in genome-wide DNA methylation analysis

    PubMed Central

    Gupta, Romi; Nagarajan, Arvindhan; Wajapeyee, Narendra

    2013-01-01

    The covalent DNA modification of cytosine at position 5 (5-methylcytosine; 5mC) has emerged as an important epigenetic mark most commonly present in the context of CpG dinucleotides in mammalian cells. In pluripotent stem cells and plants, it is also found in non-CpG and CpNpG contexts, respectively. 5mC has important implications in a diverse set of biological processes, including transcriptional regulation. Aberrant DNA methylation has been shown to be associated with a wide variety of human ailments and thus is the focus of active investigation. Methods used for detecting DNA methylation have revolutionized our understanding of this epigenetic mark and provided new insights into its role in diverse biological functions. Here we describe recent technological advances in genome-wide DNA methylation analysis and discuss their relative utility and drawbacks, providing specific examples from studies that have used these technologies for genome-wide DNA methylation analysis to address important biological questions. Finally, we discuss a newly identified covalent DNA modification, 5-hydroxymethylcytosine (5hmC), and speculate on its possible biological function, as well as describe a new methodology that can distinguish 5hmC from 5mC. PMID:20964631

  8. Recent advances in Echinococcus genomics and stem cell research.

    PubMed

    Koziol, U; Brehm, K

    2015-10-30

    Alveolar and cystic echinococcosis, caused by the metacestode larval stages of the tapeworms Echinococcus multilocularis and Echinococcus granulosus, respectively, are life-threatening diseases and very difficult to treat. The introduction of benzimidazole-based chemotherapy, which targets parasite β-tubulin, has significantly improved the life-span and prognosis of echinococcosis patients. However, benzimidazoles show only parasitostatic activity, are associated with serious adverse side effects and have to be administered for very long time periods, underlining the need for new drugs. Very recently, the nuclear genomes of E. multilocularis and E. granulosus have been characterised, revealing a plethora of data for gaining a deeper understanding of host-parasite interaction, parasite development and parasite evolution. Combined with extensive transcriptome analyses of Echinococcus life cycle stages these investigations also yielded novel clues for targeted drug design. Recent years also witnessed significant advancements in the molecular and cellular characterisation of the Echinococcus 'germinative cell' population, which forms a unique stem cell system that differs from stem cells of other organisms in the expression of several genes associated with the maintenance of pluripotency. As the only parasite cell type capable of undergoing mitosis, the germinative cells are central to all developmental transitions of Echinococcus within the host and to parasite expansion via asexual proliferation. In the present article, we will briefly introduce and discuss recent advances in Echinococcus genomics and stem cell research in the context of drug design and development. Interestingly, it turns out that benzimidazoles seem to have very limited effects on Echinococcus germinative cells, which could explain the high recurrence rates observed after chemotherapeutic treatment of echinococcosis patients. This clearly indicates that future efforts into the development of

  9. Perspective: Materials informatics across the product lifecycle: Selection, manufacturing, and certification

    NASA Astrophysics Data System (ADS)

    Mulholland, Gregory J.; Paradiso, Sean P.

    2016-05-01

    The process of taking a new material from invention to deployment can take 20 years or more. Since the announcement of the Materials Genome Initiative in 2011, new attention has been paid to accelerating this timeframe to address key challenges in industries from energy, to biomedical materials, to catalysis, to polymers, particularly in the development of new materials discovery techniques. Materials informatics, or algorithmically analyzing materials data at scale to gain novel insight, has been lauded as a path forward in this regard. An equal challenge to discovery, however, is the acceleration from discovery to market. In this paper, we address application of an informatics approach to materials selection, manufacturing, and qualification and identify key opportunities and challenges in each of these areas with a focus on reducing time to market for new advanced materials technologies.

  10. Chapter 17: bioimage informatics for systems pharmacology.

    PubMed

    Li, Fuhai; Yin, Zheng; Jin, Guangxu; Zhao, Hong; Wong, Stephen T C

    2013-04-01

    Recent advances in automated high-resolution fluorescence microscopy and robotic handling have made the systematic and cost effective study of diverse morphological changes within a large population of cells possible under a variety of perturbations, e.g., drugs, compounds, metal catalysts, RNA interference (RNAi). Cell population-based studies deviate from conventional microscopy studies on a few cells, and could provide stronger statistical power for drawing experimental observations and conclusions. However, it is challenging to manually extract and quantify phenotypic changes from the large amounts of complex image data generated. Thus, bioimage informatics approaches are needed to rapidly and objectively quantify and analyze the image data. This paper provides an overview of the bioimage informatics challenges and approaches in image-based studies for drug and target discovery. The concepts and capabilities of image-based screening are first illustrated by a few practical examples investigating different kinds of phenotypic changes caEditorsused by drugs, compounds, or RNAi. The bioimage analysis approaches, including object detection, segmentation, and tracking, are then described. Subsequently, the quantitative features, phenotype identification, and multidimensional profile analysis for profiling the effects of drugs and targets are summarized. Moreover, a number of publicly available software packages for bioimage informatics are listed for further reference. It is expected that this review will help readers, including those without bioimage informatics expertise, understand the capabilities, approaches, and tools of bioimage informatics and apply them to advance their own studies. PMID:23633943

  11. Genomic Advances to Improve Biomass for Biofuels (LBNL Science at the Theater)

    ScienceCinema

    Rokhsar, Daniel

    2011-04-28

    Lawrence Berkeley National Lab bioscientist Daniel Rokhsar discusses genomic advances to improve biomass for biofuels. He presented his talk Feb. 11, 2008 in Berkeley, California as part of Berkeley Lab's community lecture series. Rokhsar works with the U.S. Department of Energy's Joint Genome Institute and Berkeley Lab's Genomics Division.

  12. Genome Reshuffling for Advanced Intercross Permutation (GRAIP): Simulation and permutation for advanced intercross population analysis

    SciTech Connect

    Pierce, Jeremy; Broman, Karl; Lu, Lu; Chesler, Elissa J; Zhou, Guomin; Airey, David; Birmingham, Amanda; Williams, Robert

    2008-04-01

    Background: Advanced intercross lines (AIL) are segregating populations created using a multi-generation breeding protocol for fine mapping complex trait loci (QTL) in mice and other organisms. Applying QTL mapping methods for intercross and backcross populations, often followed by na ve permutation of individuals and phenotypes, does not account for the effect of AIL family structure in which final generations have been expanded and leads to inappropriately low significance thresholds. The critical problem with na ve mapping approaches in AIL populations is that the individual is not an exchangeable unit. Methodology/Principal Findings: The effect of family structure has immediate implications for the optimal AIL creation (many crosses, few animals per cross, and population expansion before the final generation) and we discuss these and the utility of AIL populations for QTL fine mapping. We also describe Genome Reshuffling for Advanced Intercross Permutation, (GRAIP) a method for analyzing AIL data that accounts for family structure. GRAIP permutes a more interchangeable unit in the final generation crosses - the parental genome - and simulating regeneration of a permuted AIL population based on exchanged parental identities. GRAIP determines appropriate genome-wide significance thresholds and locus-specific Pvalues for AILs and other populations with similar family structures. We contrast GRAIP with na ve permutation using a large densely genotyped mouse AIL population (1333 individuals from 32 crosses). A na ve permutation using coat color as a model phenotype demonstrates high false-positive locus identification and uncertain significance levels, which are corrected using GRAIP. GRAIP also detects an established hippocampus weight locus and a new locus, Hipp9a. Conclusions and Significance: GRAIP determines appropriate genome-wide significance thresholds and locus-specific Pvalues for AILs and other populations with similar family structures. The effect of

  13. The i5K Initiative: advancing arthropod genomics for knowledge, human health, agriculture, and the environment.

    PubMed

    2013-01-01

    Insects and their arthropod relatives including mites, spiders, and crustaceans play major roles in the world's terrestrial, aquatic, and marine ecosystems. Arthropods compete with humans for food and transmit devastating diseases. They also comprise the most diverse and successful branch of metazoan evolution, with millions of extant species. Here, we describe an international effort to guide arthropod genomic efforts, from species prioritization to methodology and informatics. The 5000 arthropod genomes initiative (i5K) community met formally in 2012 to discuss a roadmap for sequencing and analyzing 5000 high-priority arthropods and is continuing this effort via pilot projects, the development of standard operating procedures, and training of students and career scientists. With university, governmental, and industry support, the i5K Consortium aspires to deliver sequences and analytical tools for each of the arthropod branches and each of the species having beneficial and negative effects on humankind. PMID:23940263

  14. The i5K Initiative: Advancing Arthropod Genomics for Knowledge, Human Health, Agriculture, and the Environment

    PubMed Central

    2013-01-01

    Insects and their arthropod relatives including mites, spiders, and crustaceans play major roles in the world’s terrestrial, aquatic, and marine ecosystems. Arthropods compete with humans for food and transmit devastating diseases. They also comprise the most diverse and successful branch of metazoan evolution, with millions of extant species. Here, we describe an international effort to guide arthropod genomic efforts, from species prioritization to methodology and informatics. The 5000 arthropod genomes initiative (i5K) community met formally in 2012 to discuss a roadmap for sequencing and analyzing 5000 high-priority arthropods and is continuing this effort via pilot projects, the development of standard operating procedures, and training of students and career scientists. With university, governmental, and industry support, the i5K Consortium aspires to deliver sequences and analytical tools for each of the arthropod branches and each of the species having beneficial and negative effects on humankind. PMID:23940263

  15. Origins of Medical Informatics

    PubMed Central

    Collen, Morris F.

    1986-01-01

    Medical informatics is a new knowledge domain of computer and information science, engineering and technology in all fields of health and medicine, including research, education and practice. Medical informatics has evolved over the past 30 years as medicine learned to exploit the extraordinary capabilities of the electronic digital computer to better meet its complex information needs. The first articles on this subject appeared in the 1950s, the number of publications rapidly increased in the 1960s and medical informatics was identified as a new specialty in the 1970s. PMID:3544507

  16. MRSQ informatics education columns: passing the baton.

    PubMed

    Hasman, Linda; Hoberecht, Toni; Pullen, Kimberly

    2012-01-01

    This is the last Informatics Education column under the current editors. The outgoing co-editor identifies several key themes that describe the column during her tenure. The main theme discovered while reviewing the columns published over the last five years is technology. Technological changes and advances have affected the way in which librarians conduct instruction, such as incorporating e-learning with traditional workshops and in-class sessions. Technology plays a key role in all of the themes that emerged. The incoming editors imagine what the future themes will be for the Informatics Education column. PMID:23092421

  17. Informatics in Turkey

    NASA Technical Reports Server (NTRS)

    Cakir, Serhat

    1994-01-01

    In the last twenty years the rapid change in the informatics sector has had economic and social impact on private and government activities. The Supreme Council for Science and Technology of Turkey assigned highest priority to the informatics in its meeting in February 1993. With this advice TUBITAK (The Scientific and Technical Research Council of Turkey) intends to give a strong impulse to development of a research policy in this field.

  18. Impact of medical informatics on medical education.

    PubMed

    Hou, S M

    1999-11-01

    In recent years, medical informatics has become a well-recognized branch of medicine. It is a multidisciplinary science that combines information technology and various specialties of medicine. The impact of medical informatics on medical education is advancing along with the rapid developments in computer science. Departments of medical informatics or similar divisions have appeared in schools of medicine in Taiwan in the past 5 years. At National Taiwan University College of Medicine, we offer curricula in basic computer concepts, network concepts, operating systems, word processing, database and data processing, computer media resources, multimedia computer statistics, intelligent health information systems, medical diagnostic support systems, and electronic medical record systems. Distance learning has also been favorably accepted on this campus. Recently, we proposed the concept of a virtual medical campus, which will break the physical barriers of time and space. We expect this revolution to influence every aspect of medicine, especially medical education. PMID:10705693

  19. What is biomedical informatics?

    PubMed Central

    Bernstam, Elmer V.; Smith, Jack W.; Johnson, Todd R.

    2009-01-01

    Biomedical informatics lacks a clear and theoretically grounded definition. Many proposed definitions focus on data, information, and knowledge, but do not provide an adequate definition of these terms. Leveraging insights from the philosophy of information, we define informatics as the science of information, where information is data plus meaning. Biomedical informatics is the science of information as applied to or studied in the context of biomedicine. Defining the object of study of informatics as data plus meaning clearly distinguishes the field from related fields, such as computer science, statistics and biomedicine, which have different objects of study. The emphasis on data plus meaning also suggests that biomedical informatics problems tend to be difficult when they deal with concepts that are hard to capture using formal, computational definitions. In other words, problems where meaning must be considered are more difficult than problems where manipulating data without regard for meaning is sufficient. Furthermore, the definition implies that informatics research, teaching, and service should focus on biomedical information as data plus meaning rather than only computer applications in biomedicine. PMID:19683067

  20. Ciceromics: Advancement in Genomics and Recent Molecular Techniques

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genomics is a branch of science that decodes the encrypted information in DNA and reveals information such as the number of genes, genome organization and content. This information has tremendous application in agriculture, evolutionary biology and other areas of science. Although genomics has allow...

  1. The Saccharomyces Genome Database: Advanced Searching Methods and Data Mining.

    PubMed

    Cherry, J Michael

    2015-12-01

    At the core of the Saccharomyces Genome Database (SGD) are chromosomal features that encode a product. These include protein-coding genes and major noncoding RNA genes, such as tRNA and rRNA genes. The basic entry point into SGD is a gene or open-reading frame name that leads directly to the locus summary information page. A keyword describing function, phenotype, selective condition, or text from abstracts will also provide a door into the SGD. A DNA or protein sequence can be used to identify a gene or a chromosomal region using BLAST. Protein and DNA sequence identifiers, PubMed and NCBI IDs, author names, and function terms are also valid entry points. The information in SGD has been gathered and is maintained by a group of scientific biocurators and software developers who are devoted to providing researchers with up-to-date information from the published literature, connections to all the major research resources, and tools that allow the data to be explored. All the collected information cannot be represented or summarized for every possible question; therefore, it is necessary to be able to search the structured data in the database. This protocol describes the YeastMine tool, which provides an advanced search capability via an interactive tool. The SGD also archives results from microarray expression experiments, and a strategy designed to explore these data using the SPELL (Serial Pattern of Expression Levels Locator) tool is provided. PMID:26631124

  2. Massive Open Online Course for Health Informatics Education

    PubMed Central

    2014-01-01

    Objectives This paper outlines a new method of teaching health informatics to large numbers of students from around the world through a Massive Open Online Course (MOOC). Methods The Health Informatics Forum is one of examples of MOOCs through a social networking site for educating health informatics students and professionals. It is running a MOOC for students from around the world that uses creative commons licenced content funded by the US government and developed by five US universities. The content is delivered through narrated lectures with slides that can be viewed online with discussion threads on the forum for class interactions. Students can maintain a professional profile, upload photos and files, write their own blog posts and post discussion threads on the forum. Results The Health Informatics Forum MOOC has been accessed by 11,316 unique users from 127 countries from August 2, 2012 to January 24, 2014. Most users accessed the MOOC via a desktop computer, followed by tablets and mobile devices and 55% of users were female. Over 400,000 unique users have now accessed the wider Health Informatics Forum since it was established in 2008. Conclusions Advances in health informatics and educational technology have both created a demand for online learning material in health informatics and a solution for providing it. By using a MOOC delivered through a social networking platform it is hoped that high quality health informatics education will be able to be delivered to a large global audience of future health informaticians without cost. PMID:24872906

  3. Pathology informatics fellowship training: Focus on molecular pathology

    PubMed Central

    Mandelker, Diana; Lee, Roy E.; Platt, Mia Y.; Riedlinger, Gregory; Quinn, Andrew; Rao, Luigi K. F.; Klepeis, Veronica E.; Mahowald, Michael; Lane, William J.; Beckwith, Bruce A.; Baron, Jason M.; McClintock, David S.; Kuo, Frank C.; Lebo, Matthew S.; Gilbertson, John R.

    2014-01-01

    Background: Pathology informatics is both emerging as a distinct subspecialty and simultaneously becoming deeply integrated within the breadth of pathology practice. As specialists, pathology informaticians need a broad skill set, including aptitude with information fundamentals, information systems, workflow and process, and governance and management. Currently, many of those seeking training in pathology informatics additionally choose training in a second subspecialty. Combining pathology informatics training with molecular pathology is a natural extension, as molecular pathology is a subspecialty with high potential for application of modern biomedical informatics techniques. Methods and Results: Pathology informatics and molecular pathology fellows and faculty evaluated the current fellowship program's core curriculum topics and subtopics for relevance to molecular pathology. By focusing on the overlap between the two disciplines, a structured curriculum consisting of didactics, operational rotations, and research projects was developed for those fellows interested in both pathology informatics and molecular pathology. Conclusions: The scope of molecular diagnostics is expanding dramatically as technology advances and our understanding of disease extends to the genetic level. Here, we highlight many of the informatics challenges facing molecular pathology today, and outline specific informatics principles necessary for the training of future molecular pathologists. PMID:24843823

  4. Genome Reshuffling for Advanced Intercross Permutation (GRAIP): Simulation and permutation for advanced intercross population analysis

    SciTech Connect

    Pierce, Jeremy; Broman, Karl; Chesler, Elissa J; Zhou, Guomin; Airey, David; Birmingham, Amanda; Williams, Robert

    2008-01-01

    Abstract Background Advanced intercross lines (AIL) are segregating populations created using a multigeneration breeding protocol for fine mapping complex traits in mice and other organisms. Applying quantitative trait locus (QTL) mapping methods for intercross and backcross populations, often followed by na ve permutation of individuals and phenotypes, does not account for the effect of family structure in AIL populations in which final generations have been expanded and leads to inappropriately low significance thresholds. The critical problem with a na ve mapping approach in such AIL populations is that the individual is not an exchangeable unit given the family structure. Methodology/Principal Findings The effect of family structure has immediate implications for the optimal AIL creation (many crosses, few animals per cross, and population expansion before the final generation) and we discuss these and the utility of AIL populations for QTL fine mapping. We also describe Genome Reshuffling for Advanced Intercross Permutation, (GRAIP) a method for analyzing AIL data that accounts for family structure. RAIP permutes a more interchangeable unit in the final generation crosses - the parental genome - and simulating regeneration of a permuted AIL population based on exchanged parental identities. GRAIP determines appropriate genome- ide significance thresholds and locus-specific P-values for AILs and other populations with similar family structures. We contrast GRAIP with na ve permutation using a large densely genotyped mouse AIL population (1333 individuals from 32 crosses). A na ve permutation using coat color as a model phenotype demonstrates high false-positive locus identification and uncertain significance levels in our AIL population, which are corrected by use of GRAIP. We also show that GRAIP detects an established hippocampus weight locus and a new locus, Hipp9a. Conclusions and Significance GRAIP determines appropriate genome-wide significance thresholds

  5. Mouse genome database 2016

    PubMed Central

    Bult, Carol J.; Eppig, Janan T.; Blake, Judith A.; Kadin, James A.; Richardson, Joel E.

    2016-01-01

    The Mouse Genome Database (MGD; http://www.informatics.jax.org) is the primary community model organism database for the laboratory mouse and serves as the source for key biological reference data related to mouse genes, gene functions, phenotypes and disease models with a strong emphasis on the relationship of these data to human biology and disease. As the cost of genome-scale sequencing continues to decrease and new technologies for genome editing become widely adopted, the laboratory mouse is more important than ever as a model system for understanding the biological significance of human genetic variation and for advancing the basic research needed to support the emergence of genome-guided precision medicine. Recent enhancements to MGD include new graphical summaries of biological annotations for mouse genes, support for mobile access to the database, tools to support the annotation and analysis of sets of genes, and expanded support for comparative biology through the expansion of homology data. PMID:26578600

  6. Mouse genome database 2016.

    PubMed

    Bult, Carol J; Eppig, Janan T; Blake, Judith A; Kadin, James A; Richardson, Joel E

    2016-01-01

    The Mouse Genome Database (MGD; http://www.informatics.jax.org) is the primary community model organism database for the laboratory mouse and serves as the source for key biological reference data related to mouse genes, gene functions, phenotypes and disease models with a strong emphasis on the relationship of these data to human biology and disease. As the cost of genome-scale sequencing continues to decrease and new technologies for genome editing become widely adopted, the laboratory mouse is more important than ever as a model system for understanding the biological significance of human genetic variation and for advancing the basic research needed to support the emergence of genome-guided precision medicine. Recent enhancements to MGD include new graphical summaries of biological annotations for mouse genes, support for mobile access to the database, tools to support the annotation and analysis of sets of genes, and expanded support for comparative biology through the expansion of homology data. PMID:26578600

  7. Multi-Sensory Informatics Education

    ERIC Educational Resources Information Center

    Katai, Zoltan; Toth, Laszlo; Adorjani, Alpar Karoly

    2014-01-01

    A recent report by the joint Informatics Europe & ACM Europe Working Group on Informatics Education emphasizes that: (1) computational thinking is an important ability that all people should possess; (2) informatics-based concepts, abilities and skills are teachable, and must be included in the primary and particularly in the secondary school…

  8. Advances and Challenges in Genomic Selection for Disease Resistance.

    PubMed

    Poland, Jesse; Rutkoski, Jessica

    2016-08-01

    Breeding for disease resistance is a central focus of plant breeding programs, as any successful variety must have the complete package of high yield, disease resistance, agronomic performance, and end-use quality. With the need to accelerate the development of improved varieties, genomics-assisted breeding is becoming an important tool in breeding programs. With marker-assisted selection, there has been success in breeding for disease resistance; however, much of this work and research has focused on identifying, mapping, and selecting for major resistance genes that tend to be highly effective but vulnerable to breakdown with rapid changes in pathogen races. In contrast, breeding for minor-gene quantitative resistance tends to produce more durable varieties but is a more challenging breeding objective. As the genetic architecture of resistance shifts from single major R genes to a diffused architecture of many minor genes, the best approach for molecular breeding will shift from marker-assisted selection to genomic selection. Genomics-assisted breeding for quantitative resistance will therefore necessitate whole-genome prediction models and selection methodology as implemented for classical complex traits such as yield. Here, we examine multiple case studies testing whole-genome prediction models and genomic selection for disease resistance. In general, whole-genome models for disease resistance can produce prediction accuracy suitable for application in breeding. These models also largely outperform multiple linear regression as would be applied in marker-assisted selection. With the implementation of genomic selection for yield and other agronomic traits, whole-genome marker profiles will be available for the entire set of breeding lines, enabling genomic selection for disease at no additional direct cost. In this context, the scope of implementing genomics selection for disease resistance, and specifically for quantitative resistance and quarantined pathogens

  9. Molecular Pathology Informatics.

    PubMed

    Roy, Somak

    2015-06-01

    Molecular informatics (MI) is an evolving discipline that will support the dynamic landscape of molecular pathology and personalized medicine. MI provides a fertile ground for development of clinical solutions to bridge the gap between clinical informatics and bioinformatics. Rapid adoption of next generation sequencing (NGS) in the clinical arena has triggered major endeavors in MI that are expected to bring a paradigm shift in the practice of pathology. This brief review presents a broad overview of various aspects of MI, particularly in the context of NGS based testing. PMID:26065793

  10. Informatics in Infection Control.

    PubMed

    Lin, Michael Y; Trick, William E

    2016-09-01

    Informatics tools are becoming integral to routine infection control activities. Informatics has the potential to improve infection control outcomes in surveillance, prevention, and connections with public health. Surveillance activities include fully or semiautomated surveillance of infections, surveillance of device use, and hospital/ward outbreak investigation. Prevention activities include awareness of multidrug-resistant organism carriage on admission, enhanced interfacility communication, identifying inappropriate infection precautions, reducing device use, and antimicrobial stewardship. Public health activities include electronic communicable disease reporting, syndromic surveillance, and regional outbreak detection. The challenge for infection control personnel is in translating the knowledge gained from electronic surveillance systems into action. PMID:27515146

  11. Current and future trends in imaging informatics for oncology

    PubMed Central

    Levy, Mia A.; Rubin, Daniel L.

    2014-01-01

    Clinical imaging plays an essential role in cancer care and research for diagnosis, prognosis and treatment response assessment. Major advances have been made over the last several decades in imaging informatics to support medical imaging. More recent informatics advances focus on the special needs of oncologic imaging, yet gaps still remain. We review the current state, limitations, and future trends in imaging informatics for oncology care including clinical and clinical research systems. We review information systems to support cancer clinical workflows including oncologist ordering of radiology studies, radiologist review and reporting of image findings, and oncologist review and integration of imaging information for clinical decision making. We discuss informatics approaches to oncologic imaging including but not limited to controlled terminologies, image annotation, and image processing algorithms. With the ongoing development of novel imaging modalities and imaging biomarkers, we expect these systems will continue to evolve and mature. PMID:21799326

  12. Whole genome amplification - Review of applications and advances

    SciTech Connect

    Hawkins, Trevor L.; Detter, J.C.; Richardson, Paul

    2001-11-15

    The concept of Whole Genome Amplification is something that has arisen in the past few years as modifications to the polymerase chain reaction (PCR) have been adapted to replicate regions of genomes which are of biological interest. The applications here are many--forensics, embryonic disease diagnosis, bio terrorism genome detection, ''imoralization'' of clinical samples, microbial diversity, and genotyping. The key question is if DNA can be replicated a genome at a time without bias or non random distribution of the target. Several papers published in the last year and currently in preparation may lead to the conclusion that whole genome amplification may indeed be possible and therefore open up a new avenue to molecular biology.

  13. From bacterial genomics to metagenomics: concept, tools and recent advances.

    PubMed

    Sharma, Pooja; Kumari, Hansi; Kumar, Mukesh; Verma, Mansi; Kumari, Kirti; Malhotra, Shweta; Khurana, Jitendra; Lal, Rup

    2008-06-01

    In the last 20 years, the applications of genomics tools have completely transformed the field of microbial research. This has primarily happened due to revolution in sequencing technologies that have become available today. This review therefore, first describes the discoveries, upgradation and automation of sequencing techniques in a chronological order, followed by a brief discussion on microbial genomics. Some of the recently sequenced bacterial genomes are described to explain how complete genome data is now being used to derive interesting findings. Apart from the genomics of individual microbes, the study of unculturable microbiota from different environments is increasingly gaining importance. The second section is thus dedicated to the concept of metagenomics describing environmental DNA isolation, metagenomic library construction and screening methods to look for novel and potentially important genes, enzymes and biomolecules. It also deals with the pioneering studies in the area of metagenomics that are offering new insights into the previously unappreciated microbial world. PMID:23100712

  14. Case-based medical informatics

    PubMed Central

    Pantazi, Stefan V; Arocha, José F; Moehr, Jochen R

    2004-01-01

    Background The "applied" nature distinguishes applied sciences from theoretical sciences. To emphasize this distinction, we begin with a general, meta-level overview of the scientific endeavor. We introduce the knowledge spectrum and four interconnected modalities of knowledge. In addition to the traditional differentiation between implicit and explicit knowledge we outline the concepts of general and individual knowledge. We connect general knowledge with the "frame problem," a fundamental issue of artificial intelligence, and individual knowledge with another important paradigm of artificial intelligence, case-based reasoning, a method of individual knowledge processing that aims at solving new problems based on the solutions to similar past problems. We outline the fundamental differences between Medical Informatics and theoretical sciences and propose that Medical Informatics research should advance individual knowledge processing (case-based reasoning) and that natural language processing research is an important step towards this goal that may have ethical implications for patient-centered health medicine. Discussion We focus on fundamental aspects of decision-making, which connect human expertise with individual knowledge processing. We continue with a knowledge spectrum perspective on biomedical knowledge and conclude that case-based reasoning is the paradigm that can advance towards personalized healthcare and that can enable the education of patients and providers. We center the discussion on formal methods of knowledge representation around the frame problem. We propose a context-dependent view on the notion of "meaning" and advocate the need for case-based reasoning research and natural language processing. In the context of memory based knowledge processing, pattern recognition, comparison and analogy-making, we conclude that while humans seem to naturally support the case-based reasoning paradigm (memory of past experiences of problem-solving and

  15. Recent advances in genomics and transcriptomics of cnidarians.

    PubMed

    Technau, Ulrich; Schwaiger, Michaela

    2015-12-01

    The advent of the genomic era has provided important and surprising insights into the deducted genetic composition of the common ancestor of cnidarians and bilaterians. This has changed our view of how genomes of metazoans evolve and when crucial gene families arose and diverged in animal evolution. Sequencing of several cnidarian genomes showed that cnidarians share a great part of their gene repertoire as well as genome synteny with vertebrates, with less gene losses in the anthozoan cnidarian lineage than for example in ecdysozoans like Drosophila melanogaster or Caenorhabditis elegans. The Hydra genome on the other hand has evolved more rapidly indicated by more divergent sequences, more cases of gene losses and many taxonomically restricted genes. Cnidarian genomes also contain a rich repertoire of transcription factors, including those that in bilaterian model organisms regulate the development of key bilaterian traits such as mesoderm, nervous system development and bilaterality. The sea anemone Nematostella vectensis, and possibly cnidarians in general, does not only share its complex gene repertoire with bilaterians, but also the regulation of crucial developmental regulatory genes via distal enhancer elements. In addition, epigenetic modifications on DNA and chromatin are shared among eumetazoans. This suggests that most conserved genes present in our genomes today, as well as the mechanisms guiding their expression, evolved before the divergence of cnidarians and bilaterians about 600 Myr ago. PMID:26421490

  16. Informatics: A Brief Survey.

    ERIC Educational Resources Information Center

    He, Shaoyi

    2003-01-01

    Provides a brief survey of informatics, defined as the application of information technology to various fields, with respect to its historical background, disciplinary identity, fundamental aspects, applications, and challenges. Highlights include biological, clinical, dental, environmental, geomatics, health, legal, management, medical, museum,…

  17. Emerging technologies advancing forage and turf grass genomics.

    PubMed

    Kopecký, David; Studer, Bruno

    2014-01-01

    Grassland is of major importance for agricultural production and provides valuable ecosystem services. Its impact is likely to rise in changing socio-economic and climatic environments. High yielding forage grass species are major components of sustainable grassland production. Understanding the genome structure and function of grassland species provides opportunities to accelerate crop improvement and thus to mitigate the future challenges of increased feed and food demand, scarcity of natural resources such as water and nutrients, and high product qualities. In this review, we will discuss a selection of technological developments that served as main drivers to generate new insights into the structure and function of nuclear genomes. Many of these technologies were originally developed in human or animal science and are now increasingly applied in plant genomics. Our main goal is to highlight the benefits of using these technologies for forage and turf grass genome research, to discuss their potentials and limitations as well as their relevance for future applications. PMID:24309540

  18. Recent advances in microbial single cell genomics technology and applications

    NASA Astrophysics Data System (ADS)

    Stepanauskas, R.

    2015-12-01

    Single cell genomics is increasingly utilized as a powerful tool to decipher the metabolic potential, evolutionary histories and in situ interactions of environmental microorganisms. I will present several new developments of this exciting technology, which improve genomic data recovery from individual cells and allow its integration with cell's phenotypic properties. I will also demonstrate how these new technical capabilities help understanding the biology of the "microbial dark matter" inhabiting marine and terrestrial subsurface environments.

  19. Advancing Genomic Research and Reducing Health Disparities: What Can Nurse Scholars Do?

    PubMed Central

    Jaja, Cheedy; Gibson, Robert; Quarles, Shirley

    2012-01-01

    Purpose Advances in genomic research are improving our understanding of human diseases and evoking promise of an era of genomic medicine. It is unclear whether genomic medicine may exacerbate or attenuate extant racial group health disparities. We delineate how nurse scholars could engage in the configuration of an equitable genomic medicine paradigm. Organizing Construct We identify as legitimate subjects for nursing scholarship the scientific relevance, ethical, and public policy implications for employing racial categories in genomic research in the context of reducing extant health disparities. Findings Since genomic research is largely population specific, current classification of genomic data will center on racial and ethnic groups. Nurse scholars should be involved in clarifying how putative racial group differences should be elucidated in light of the current orthodoxy that genomic solutions may alleviate racial health disparities. Conclusions Nurse scholars are capable of employing their expertise in concept analysis to elucidate how race is used as a variable in scientific research, and to use knowledge brokering to delineate how race variables that imply human ancestry could be utilized in genomic research pragmatically in the context of health disparities. Clinical Relevance In an era of genomic medicine, nurse scholars should recognize and understand the challenges and complexities of genomics and race and their relevance to health care and health disparities. PMID:23452096

  20. The life aquatic: advances in marine vertebrate genomics.

    PubMed

    Kelley, Joanna L; Brown, Anthony P; Therkildsen, Nina Overgaard; Foote, Andrew D

    2016-07-01

    The ocean is hypothesized to be where life on earth originated, and subsequent evolutionary transitions between marine and terrestrial environments have been key events in the origin of contemporary biodiversity. Here, we review how comparative genomic approaches are an increasingly important aspect of understanding evolutionary processes, such as physiological and morphological adaptation to the diverse habitats within the marine environment. In addition, we highlight how population genomics has provided unprecedented resolution for population structuring, speciation and adaptation in marine environments, which can have a low cost of dispersal and few physical barriers to gene flow, and can thus support large populations. Building upon this work, we outline the applications of genomics tools to conservation and their relevance to assessing the wide-ranging impact of fisheries and climate change on marine species. PMID:27376488

  1. Advances in therapeutic CRISPR/Cas9 genome editing.

    PubMed

    Savić, Nataša; Schwank, Gerald

    2016-02-01

    Targeted nucleases are widely used as tools for genome editing. Two years ago the clustered regularly interspaced short palindromic repeat (CRISPR)-associated Cas9 nuclease was used for the first time, and since then has largely revolutionized the field. The tremendous success of the CRISPR/Cas9 genome editing tool is powered by the ease design principle of the guide RNA that targets Cas9 to the desired DNA locus, and by the high specificity and efficiency of CRISPR/Cas9-generated DNA breaks. Several studies recently used CRISPR/Cas9 to successfully modulate disease-causing alleles in vivo in animal models and ex vivo in somatic and induced pluripotent stem cells, raising hope for therapeutic genome editing in the clinics. In this review, we will summarize and discuss such preclinical CRISPR/Cas9 gene therapy reports. PMID:26470680

  2. Patient-controlled encrypted genomic data: an approach to advance clinical genomics

    PubMed Central

    2012-01-01

    Background The revolution in DNA sequencing technologies over the past decade has made it feasible to sequence an individual’s whole genome at a relatively low cost. The potential value of the information generated by genomic technologies for medicine and society is enormous. However, in order for exome sequencing, and eventually whole genome sequencing, to be implemented clinically, a number of major challenges need to be overcome. For instance, obtaining meaningful informed-consent, managing incidental findings and the great volume of data generated (including multiple findings with uncertain clinical significance), re-interpreting the genomic data and providing additional counselling to patients as genetic knowledge evolves are issues that need to be addressed. It appears that medical genetics is shifting from the present “phenotype-first” medical model to a “data-first” model which leads to multiple complexities. Discussion This manuscript discusses the different challenges associated with integrating genomic technologies into clinical practice and describes a “phenotype-first” approach, namely, “Individualized Mutation-weighed Phenotype Search”, and its benefits. The proposed approach allows for a more efficient prioritization of the genes to be tested in a clinical lab based on both the patient’s phenotype and his/her entire genomic data. It simplifies “informed-consent” for clinical use of genomic technologies and helps to protect the patient’s autonomy and privacy. Overall, this approach could potentially render widespread use of genomic technologies, in the immediate future, practical, ethical and clinically useful. Summary The “Individualized Mutation-weighed Phenotype Search” approach allows for an incremental integration of genomic technologies into clinical practice. It ensures that we do not over-medicalize genomic data but, rather, continue our current medical model which is based on serving the patient’s concerns

  3. Parallel computing in genomic research: advances and applications

    PubMed Central

    Ocaña, Kary; de Oliveira, Daniel

    2015-01-01

    Today’s genomic experiments have to process the so-called “biological big data” that is now reaching the size of Terabytes and Petabytes. To process this huge amount of data, scientists may require weeks or months if they use their own workstations. Parallelism techniques and high-performance computing (HPC) environments can be applied for reducing the total processing time and to ease the management, treatment, and analyses of this data. However, running bioinformatics experiments in HPC environments such as clouds, grids, clusters, and graphics processing unit requires the expertise from scientists to integrate computational, biological, and mathematical techniques and technologies. Several solutions have already been proposed to allow scientists for processing their genomic experiments using HPC capabilities and parallelism techniques. This article brings a systematic review of literature that surveys the most recently published research involving genomics and parallel computing. Our objective is to gather the main characteristics, benefits, and challenges that can be considered by scientists when running their genomic experiments to benefit from parallelism techniques and HPC capabilities. PMID:26604801

  4. Advances in exercise, fitness, and performance genomics in 2013.

    PubMed

    Wolfarth, Bernd; Rankinen, Tuomo; Hagberg, James M; Loos, Ruth J F; Pérusse, Louis; Roth, Stephen M; Sarzynski, Mark A; Bouchard, Claude

    2014-01-01

    The most significant and scientifically sound articles in exercise genomics that were published in 2013 are reviewed in this report. No article on the genetic basis of sedentary behavior or physical activity level was identified. A calcineurin- and alpha actinin-2-based mechanism has been identified as the potential molecular basis for the observed lower muscular strength and power in alpha actinin-3-deficient individuals. Although baseline muscle transcriptomic signatures were found to be associated with strength training-induced muscle hypertrophy, no predictive genomic variants could be identified as of yet. One study found no clear evidence that the inverse relation between physical activity level and incident CHD events was influenced by 58 genomic variants clustered into four genetic scores. Lower physical activity level in North American populations may be driving the apparent risk of obesity in fat mass- and obesity-associated gene (FTO)-susceptible individuals compared with more active populations. Two large studies revealed that common genetic variants associated with baseline levels of plasma HDL cholesterol and triglycerides are not clear predictors of changes induced by interventions focused on weight loss, diet, and physical activity behavior. One large study from Japan reported that a higher fitness level attenuated the arterial stiffness-promoting effect of the Ala54 allele at the fatty acid binding protein 2 locus, which is a controversial finding because previous studies have suggested that Thr54 was the risk allele. Using transcriptomics to generate genomic targets in an unbiased manner for subsequent DNA sequence variants studies appears to be a growing trend. Moreover, exercise genomics is rapidly embracing gene and pathway analysis to better define the underlying biology and provide a foundation for the study of human variation. PMID:24743105

  5. Tools for medical informatics.

    PubMed

    Hindel, R

    1992-05-01

    Informatics uses words, terms and expressions of various scientific disciplines. The proposed tools, hermeneutics and phenomenology, generate a basis for quality control by establishing the authenticity and validity of such expressions. Without such tools there is the danger that poorly defined expressions obscure true meaning and prevent progress. The method is demonstrated on "objects" as used in "object oriented programming" and on "open systems" as used in the International Standards Organization model for "open system interconnection." PMID:1623046

  6. Systematic genomic identification of colorectal cancer genes delineating advanced from early clinical stage and metastasis

    PubMed Central

    2013-01-01

    Background Colorectal cancer is the third leading cause of cancer deaths in the United States. The initial assessment of colorectal cancer involves clinical staging that takes into account the extent of primary tumor invasion, determining the number of lymph nodes with metastatic cancer and the identification of metastatic sites in other organs. Advanced clinical stage indicates metastatic cancer, either in regional lymph nodes or in distant organs. While the genomic and genetic basis of colorectal cancer has been elucidated to some degree, less is known about the identity of specific cancer genes that are associated with advanced clinical stage and metastasis. Methods We compiled multiple genomic data types (mutations, copy number alterations, gene expression and methylation status) as well as clinical meta-data from The Cancer Genome Atlas (TCGA). We used an elastic-net regularized regression method on the combined genomic data to identify genetic aberrations and their associated cancer genes that are indicators of clinical stage. We ranked candidate genes by their regression coefficient and level of support from multiple assay modalities. Results A fit of the elastic-net regularized regression to 197 samples and integrated analysis of four genomic platforms identified the set of top gene predictors of advanced clinical stage, including: WRN, SYK, DDX5 and ADRA2C. These genetic features were identified robustly in bootstrap resampling analysis. Conclusions We conducted an analysis integrating multiple genomic features including mutations, copy number alterations, gene expression and methylation. This integrated approach in which one considers all of these genomic features performs better than any individual genomic assay. We identified multiple genes that robustly delineate advanced clinical stage, suggesting their possible role in colorectal cancer metastatic progression. PMID:24308539

  7. Collaborative Research to Advance Precision Medicine in the Post-Genomic World | Office of Cancer Genomics

    Cancer.gov

    My name is Subhashini Jagu, and I am the Scientific Program Manager for the Cancer Target Discovery and Development (CTD2) Network at the Office of Cancer Genomics (OCG). In my new role, I help CTD2 work toward its mission, which is to develop new scientific approaches to accelerate the translation of genomic discoveries into new treatments. Collaborative efforts that bring together a variety of expertise and infrastructure are needed to understand and successfully treat cancer, a highly complex disease.

  8. Development and implementation of a multitiered health informatics curriculum in a college of pharmacy.

    PubMed

    Breeden, Elizabeth A; Clauson, Kevin A

    2016-07-01

    Standards requiring education in informatics in pharmacy curricula were introduced in the last 10 years by the Accreditation Council for Pharmacy Education. Mirroring difficulties faced by other health professions educators, implementation of these requirements remains fragmented and somewhat limited across colleges of pharmacy in the US. Clinical practice and workforce metrics underline a pronounced need for clinicians with varying competencies in health informatics. In response to these challenges, a multitiered health informatics curriculum was developed and implemented at a college of pharmacy in the Southeast. The multitiered approach is structured to ensure that graduating pharmacists possess core competencies in health informatics, while providing specialized and advanced training opportunities for pharmacy students, health professions students, and working professionals interested in a career path in informatics. The approach described herein offers institutions, administrators, faculty, residents, and students an adaptable model for selected or comprehensive adoption and integration of a multitiered health informatics curriculum. PMID:27121611

  9. Advances in sarcoma genomics and new therapeutic targets

    PubMed Central

    Taylor, Barry S.; Barretina, Jordi; Maki, Robert G.; Antonescu, Cristina R.; Singer, Samuel; Ladanyi, Marc

    2012-01-01

    Preface Increasingly, human mesenchymal malignancies are classified by the abnormalities that drive their pathogenesis. While many of these aberrations are highly prevalent within particular sarcoma subtypes, few are currently targeted therapeutically. Indeed, most subtypes of sarcoma are still treated with traditional therapeutic modalities and in many cases are resistant to adjuvant therapies. In this Review, we discuss the core molecular determinants of sarcomagenesis and emphasize the emerging genomic and functional genetic approaches that, coupled to novel therapeutic strategies, have the potential to transform the care of patients with sarcoma. PMID:21753790

  10. Next generation informatics for big data in precision medicine era.

    PubMed

    Zhang, Yuji; Zhu, Qian; Liu, Hongfang

    2015-01-01

    The rise of data-intensive biology, advances in informatics technology, and changes in the way health care is delivered has created an compelling opportunity to allow us investigate biomedical questions in the context of "big data" and develop knowledge systems to support precision medicine. To promote such data mining and informatics technology development in precision medicine, we hosted two international informatics workshops in 2014: 1) the first workshop on Data Mining in Biomedical informatics and Healthcare, in conjunction with the 18th Pacific-Asia Conference on Knowledge Discovery and Data Mining (PAKDD 2014), and 2) the first workshop on Translational biomedical and clinical informatics, in conjunction with the 8th International Conference on Systems Biology and the 4th Translational Bioinformatics Conference (ISB/TBC 2014). This thematic issue of BioData Mining presents a series of selected papers from these two international workshops, aiming to address the data mining needs in the informatics field due to the deluge of "big data" generated by next generation biotechnologies such as next generation sequencing, metabolomics, and proteomics, as well as the structured and unstructured biomedical and healthcare data from electronic health records. We are grateful for the BioData Mining's willingness to produce this forward-looking thematic issue. PMID:26539249

  11. Consumer Health Informatics--integrating patients, providers, and professionals online.

    PubMed

    Klein-Fedyshin, Michele S

    2002-01-01

    Consumer Health Informatics (CHI) means different things to patients, health professionals, and health care systems. A broader perspective on this new and rapidly developing field will enable us to understand and better apply its advances. This article provides an overview of CHI discussing its evolution and driving forces, along with advanced applications such as Personal Health Records, Internet transmission of personal health data, clinical e-mail, online pharmacies, and shared decision-making tools. Consumer Health Informatics will become integrated with medical care, electronic medical records, and patient education to impact the whole process and business of health care. PMID:12238015

  12. Training Residents in Medical Informatics.

    ERIC Educational Resources Information Center

    Jerant, Anthony F.

    1999-01-01

    Describes an eight-step process for developing or refining a family-medicine informatics curriculum: needs assessment, review of expert recommendations, enlisting faculty and local institutional support, espousal of a human-centered approach, integrating informatics into the larger curriculum, easy access to computers, practical training, and…

  13. The 2005 Australian Informatics Competition

    ERIC Educational Resources Information Center

    Clark, David

    2006-01-01

    This article describes the Australian Informatics Competition (AIC), a non-programming competition aimed at identifying students with potential in programming and algorithmic design. It is the first step in identifying students to represent Australia at the International Olympiad in Informatics. The main aim of the AIC is to increase awareness of…

  14. Latvian Education Informatization System LIIS

    ERIC Educational Resources Information Center

    Bicevskis, Janis; Andzans, Agnis; Ikaunieks, Evalds; Medvedis, Inga; Straujums, Uldis; Vezis, Viesturs

    2004-01-01

    The Latvian Education Informatization System LIIS project covers the whole information grid: education content, management, information services, infrastructure and user training at several levels--schools, school boards and Ministry of Education and Science. Informatization is the maintained process of creating the technical, economical and…

  15. Informatics applied to cytology

    PubMed Central

    Hornish, Maryanne; Goulart, Robert A.

    2008-01-01

    Automation and emerging information technologies are being adopted by cytology laboratories to augment Pap test screening and improve diagnostic accuracy. As a result, informatics, the application of computers and information systems to information management, has become essential for the successful operation of the cytopathology laboratory. This review describes how laboratory information management systems can be used to achieve an automated and seamless workflow process. The utilization of software, electronic databases and spreadsheets to perform necessary quality control measures are discussed, as well as a Lean production system and Six Sigma approach, to reduce errors in the cytopathology laboratory. PMID:19495402

  16. Nursing informatics competencies: bibliometric analysis.

    PubMed

    Kokol, Peter; Blažun, Helena; Vošner, Janez; Saranto, Kaija

    2014-01-01

    Information and communication technology is developing rapidly and it is incorporated in many health care processes, but in spite of that fact we can still notice that nursing informatics competencies had received limited attention in basic nursing education curricula in Europe and especially in Eastern European countries. The purpose of the present paper is to present the results of a bibliometric analysis of the nursing informatics competencies scientific literature production. We applied the bibliometrics analysis to the corpus of 332 papers found in SCOPUS, related to nursing informatics competencies. The results showed that there is a positive trend in the number of published papers per year, indicating the increased research interest in nursing informatics competencies. Despite the fact that the first paper was published in Denmark, the most prolific country regarding the research in nursing informatics competencies is United States as are their institutions and authors. PMID:24943565

  17. Advances in Exercise, Fitness, and Performance Genomics in 2014

    PubMed Central

    Loos, Ruth J. F.; Hagberg, James M.; Pérusse, Louis; Roth, Stephen M.; Sarzynski, Mark A.; Wolfarth, Bernd; Rankinen, Tuomo; Bouchard, Claude

    2015-01-01

    This is the annual review of the exercise genomics literature in which we report on the highest quality papers published in 2014. We identified a number of noteworthy papers across a number of fields. In 70 to 89 years old, only 19% of ACE II homozygotes exhibited significant improvement in gait speed in response to a year-long physical activity program compared to 30% of ACE D-allele carriers. New studies continue to support the notion that the genetic susceptibility to obesity, as evidenced by a genomic risk score (GRS; based on multiple SNPs), is attenuated by 40-50% in individuals who are physically active, compare to those who are sedentary. One study reported that the polygenic risk for hypertriglyceridemia was reduced by 30-40% in individuals with high cardiorespiratory fitness. One report showed that there was a significant interaction of a type 2 diabetes GRS with physical activity, with active individuals having the lowest risk of developing diabetes. The protective effect of was most pronounced in the low GRS tertile (HR=0.82). The interaction observed with the diabetes GRS appeared to be dependent on a genetic susceptibility to insulin resistance and not insulin secretion. A significant interaction between PPARα sequence variants and physical activity levels on cardiometabolic risk was observed, with higher activity levels associated with lower risk only in carriers of specific genotypes and haplotypes. The review concludes with a discussion of the importance of replication studies when very large population or intervention discovery studies are not feasible or are cost prohibitive. PMID:25706296

  18. Advances in exercise, fitness, and performance genomics in 2014.

    PubMed

    Loos, Ruth J F; Hagberg, James M; Pérusse, Louis; Roth, Stephen M; Sarzynski, Mark A; Wolfarth, Bernd; Rankinen, Tuomo; Bouchard, Claude

    2015-06-01

    This is the annual review of the exercise genomics literature in which we report on the highest quality papers published in 2014. We identified a number of noteworthy papers across a number of fields. In 70-89 yr olds, only 19% of angiotensin-converting enzyme (ACE) II homozygotes exhibited significant improvement in gait speed in response to a yearlong physical activity program compared to 30% of ACE D-allele carriers. New studies continue to support the notion that the genetic susceptibility to obesity, as evidenced by a genomic risk score (GRS; based on multiple single nucleotide polymorphisms), is attenuated by 40%-50% in individuals who are physically active, compared to those who are sedentary. One study reported that the polygenic risk for hypertriglyceridemia was reduced by 30%-40% in individuals with high cardiorespiratory fitness. One report showed that there was a significant interaction of a type 2 diabetes GRS with physical activity, with active individuals having the lowest risk of developing diabetes. The protective effect of physical activity was most pronounced in the low GRS tertile (hazard ratio, 0.82). The interaction observed with the diabetes GRS seemed to be dependent on a genetic susceptibility to insulin resistance and not insulin secretion. A significant interaction between PPARα sequence variants and physical activity levels on cardiometabolic risk was observed, with higher activity levels associated with lower risk only in carriers of specific genotypes and haplotypes. The review concludes with a discussion of the importance of replication studies when very large population or intervention discovery studies are not feasible or are cost prohibitive. PMID:25706296

  19. 78 FR 8546 - National Center for Advancing Translational Sciences (NCATS) and National Human Genome Research...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-02-06

    ...The National Center for Advancing Translational Sciences (NCATS) and the National Human Genome Research Institute (NHGRI), the National Institutes of Health (NIH), are seeking Cooperative Research and Development Agreement (CRADA) partners to collaborate in the final stages of lead optimization, evaluation and preclinical development of a novel selective series of non-inhibitory chaperones of......

  20. Genomic Data Commons and Genomic Cloud Pilots - Google Hangout

    Cancer.gov

    Join us for a live, moderated discussion about two NCI efforts to expand access to cancer genomics data: the Genomic Data Commons and Genomic Cloud Pilots. NCI subject matters experts will include Louis M. Staudt, M.D., Ph.D., Director Center for Cancer Genomics, Warren Kibbe, Ph.D., Director, NCI Center for Biomedical Informatics and Information Technology, and moderated by Anthony Kerlavage, Ph.D., Chief, Cancer Informatics Branch, Center for Biomedical Informatics and Information Technology. We welcome your questions before and during the Hangout on Twitter using the hashtag #AskNCI.

  1. Innovation in transformative nursing leadership: nursing informatics competencies and roles.

    PubMed

    Remus, Sally; Kennedy, Margaret Ann

    2012-12-01

    In a recent brief to the Canadian Nurses Association's National Expert Commission on the Health of Our Nation, the Academy of Canadian Executive Nurses (ACEN) discussed leadership needs in the Canadian healthcare system, and promoted the pivotal role of nursing executives in transforming Canada's healthcare system into an integrated patient-centric system. Included among several recommendations was the need to develop innovative leadership competencies that enable nurse leaders to lead and advance transformative health system change. This paper focuses on an emerging "avant-garde executive leadership competency" recommended for today's health leaders to guide health system transformation. Specifically, this competency is articulated as "state of the art communication and technology savvy," and it implies linkages between nursing informatics competencies and transformational leadership roles for nurse executive. The authors of this paper propose that distinct nursing informatics competencies are required to augment traditional executive skills to support transformational outcomes of safe, integrated, high-quality care delivery through knowledge-driven care. International trends involving nursing informatics competencies and the evolution of new corporate informatics roles, such as chief nursing informatics officers (CNIOs), are demonstrating value and advanced transformational leadership as nursing executive roles that are informed by clinical data. PMID:23803423

  2. The pathology informatics curriculum wiki: Harnessing the power of user-generated content

    PubMed Central

    Kim, Ji Yeon; Gudewicz, Thomas M.; Dighe, Anand S.; Gilbertson, John R.

    2010-01-01

    Background: The need for informatics training as part of pathology training has never been so critical, but pathology informatics is a wide and complex field and very few programs currently have the resources to provide comprehensive educational pathology informatics experiences to their residents. In this article, we present the “pathology informatics curriculum wiki”, an open, on-line wiki that indexes the pathology informatics content in a larger public wiki, Wikipedia, (and other online content) and organizes it into educational modules based on the 2003 standard curriculum approved by the Association for Pathology Informatics (API). Methods and Results: In addition to implementing the curriculum wiki at http://pathinformatics.wikispaces.com, we have evaluated pathology informatics content in Wikipedia. Of the 199 non-duplicate terms in the API curriculum, 90% have at least one associated Wikipedia article. Furthermore, evaluation of articles on a five-point Likert scale showed high scores for comprehensiveness (4.05), quality (4.08), currency (4.18), and utility for the beginner (3.85) and advanced (3.93) learners. These results are compelling and support the thesis that Wikipedia articles can be used as the foundation for a basic curriculum in pathology informatics. Conclusions: The pathology informatics community now has the infrastructure needed to collaboratively and openly create, maintain and distribute the pathology informatics content worldwide (Wikipedia) and also the environment (the curriculum wiki) to draw upon its own resources to index and organize this content as a sustainable basic pathology informatics educational resource. The remaining challenges are numerous, but largest by far will be to convince the pathologists to take the time and effort required to build pathology informatics content in Wikipedia and to index and organize this content for education in the curriculum wiki. PMID:20805963

  3. Functional genomics of seed dormancy in wheat: advances and prospects.

    PubMed

    Gao, Feng; Ayele, Belay T

    2014-01-01

    Seed dormancy is a mechanism underlying the inability of viable seeds to germinate under optimal environmental conditions. To achieve rapid and uniform germination, wheat and other cereal crops have been selected against dormancy. As a result, most of the modern commercial cultivars have low level of seed dormancy and are susceptible to preharvest sprouting when wet and moist conditions occur prior to harvest. As it causes substantial loss in grain yield and quality, preharvest sprouting is an ever-present major constraint to the production of wheat. The significance of the problem emphasizes the need to incorporate an intermediate level of dormancy into elite wheat cultivars, and this requires detailed dissection of the mechanisms underlying the regulation of seed dormancy and preharvest sprouting. Seed dormancy research in wheat often involves after-ripening, a period of dry storage during which seeds lose dormancy, or comparative analysis of seeds derived from dormant and non-dormant cultivars. The increasing development in wheat genomic resources along with the application of transcriptomics, proteomics, and metabolomics approaches in studying wheat seed dormancy have extended our knowledge of the mechanisms acting at transcriptional and post-transcriptional levels. Recent progresses indicate that some of the molecular mechanisms are associated with hormonal pathways, epigenetic regulations, targeted oxidative modifications of seed mRNAs and proteins, redox regulation of seed protein thiols, and modulation of translational activities. Given that preharvest sprouting is closely associated with seed dormancy, these findings will significantly contribute to the designing of efficient strategies for breeding preharvest sprouting tolerant wheat. PMID:25309557

  4. The Awakening of an Advanced Malignant Cancer: An Insult to the Mitochondrial Genome

    PubMed Central

    Cook, Cody C.; Higuchi, Masahiro

    2011-01-01

    Background In only months-to-years a primary cancer can progress to an advanced phenotype that is metastatic and resistant to clinical treatments. As early as the 1900s, it was discovered that the progression of a cancer to the advanced phenotype is often associated with a shift in the metabolic profile of the disease from a state of respiration to anaerobic fermentation – a phenomenon denoted as the Warburg Effect. Scope of Review Reports in the literature strongly suggest that the Warburg Effect is generated as a response to a loss in the integrity of the sequence and/or copy number of the mitochondrial genome content within a cancer. Multiple studies regarding the progression of cancer indicate that mutation, and/or, a flux in the copy number, of the mitochondrial genome content can support the early development of a cancer, until; the mutational load and/or the reduction-to-depletion of the copy number of the mitochondrial genome content induces the progression of the disease to an advanced phenotype. General Significance Collectively, evidence has revealed that the human cell has incorporated the mitochondrial genome content into a cellular mechanism that, when pathologically actuated, can de (un)differentiate a cancer from the parental tissue of origin into an autonomous disease that disrupts the hierarchical structure-and-function of the human body. PMID:21920409

  5. Bioimage Informatics for Big Data.

    PubMed

    Peng, Hanchuan; Zhou, Jie; Zhou, Zhi; Bria, Alessandro; Li, Yujie; Kleissas, Dean Mark; Drenkow, Nathan G; Long, Brian; Liu, Xiaoxiao; Chen, Hanbo

    2016-01-01

    Bioimage informatics is a field wherein high-throughput image informatics methods are used to solve challenging scientific problems related to biology and medicine. When the image datasets become larger and more complicated, many conventional image analysis approaches are no longer applicable. Here, we discuss two critical challenges of large-scale bioimage informatics applications, namely, data accessibility and adaptive data analysis. We highlight case studies to show that these challenges can be tackled based on distributed image computing as well as machine learning of image examples in a multidimensional environment. PMID:27207370

  6. Recent advances in genome mining of secondary metabolites in Aspergillus terreus

    PubMed Central

    Guo, Chun-Jun; Wang, Clay C. C.

    2014-01-01

    Filamentous fungi are rich resources of secondary metabolites (SMs) with a variety of interesting biological activities. Recent advances in genome sequencing and techniques in genetic manipulation have enabled researchers to study the biosynthetic genes of these SMs. Aspergillus terreus is the well-known producer of lovastatin, a cholesterol-lowering drug. This fungus also produces other SMs, including acetylaranotin, butyrolactones, and territram, with interesting bioactivities. This review will cover recent progress in genome mining of SMs identified in this fungus. The identification and characterization of the gene cluster for these SMs, as well as the proposed biosynthetic pathways, will be discussed in depth. PMID:25566227

  7. Identifying contamination with advanced visualization and analysis practices: metagenomic approaches for eukaryotic genome assemblies

    PubMed Central

    Delmont, Tom O.

    2016-01-01

    High-throughput sequencing provides a fast and cost-effective mean to recover genomes of organisms from all domains of life. However, adequate curation of the assembly results against potential contamination of non-target organisms requires advanced bioinformatics approaches and practices. Here, we re-analyzed the sequencing data generated for the tardigrade Hypsibius dujardini, and created a holistic display of the eukaryotic genome assembly using DNA data originating from two groups and eleven sequencing libraries. By using bacterial single-copy genes, k-mer frequencies, and coverage values of scaffolds we could identify and characterize multiple near-complete bacterial genomes from the raw assembly, and curate a 182 Mbp draft genome for H. dujardini supported by RNA-Seq data. Our results indicate that most contaminant scaffolds were assembled from Moleculo long-read libraries, and most of these contaminants have differed between library preparations. Our re-analysis shows that visualization and curation of eukaryotic genome assemblies can benefit from tools designed to address the needs of today’s microbiologists, who are constantly challenged by the difficulties associated with the identification of distinct microbial genomes in complex environmental metagenomes. PMID:27069789

  8. The origins of informatics.

    PubMed Central

    Collen, M F

    1994-01-01

    This article summarizes the origins of informatics, which is based on the science, engineering, and technology of computer hardware, software, and communications. In just four decades, from the 1950s to the 1990s, computer technology has progressed from slow, first-generation vacuum tubes, through the invention of the transistor and its incorporation into microprocessor chips, and ultimately, to fast, fourth-generation very-large-scale-integrated silicon chips. Programming has undergone a parallel transformation, from cumbersome, first-generation, machine languages to efficient, fourth-generation application-oriented languages. Communication has evolved from simple copper wires to complex fiberoptic cables in computer-linked networks. The digital computer has profound implications for the development and practice of clinical medicine. PMID:7719803

  9. Building Informatics Environment

    Energy Science and Technology Software Center (ESTSC)

    2008-06-02

    The Building Informatics Environment is a modeling environment based on the Modelica language. The environment allows users to create a computer model of a building and its energy systems with various time scales and physical resolutions. The environment can be used for rapid development of, e.g., demand controls algorithms, new HVAC system solutions and new operational strategies (controls, fault detection and diagnostics). Models for building energy and control systems are made available in the environment.more » The models can be used as provided, or they can be changed and/or linked with each other in order to model the effects that a particular user is interested in.« less

  10. BING: biomedical informatics pipeline for Next Generation Sequencing.

    PubMed

    Kriseman, Jeffrey; Busick, Christopher; Szelinger, Szabolcs; Dinu, Valentin

    2010-06-01

    High throughput parallel genomic sequencing (Next Generation Sequencing, NGS) shifts the bottleneck in sequencing processes from experimental data production to computationally intensive informatics-based data analysis. This manuscript introduces a biomedical informatics pipeline (BING) for the analysis of NGS data that offers several novel computational approaches to 1. image alignment, 2. signal correlation, compensation, separation, and pixel-based cluster registration, 3. signal measurement and base calling, 4. quality control and accuracy measurement. These approaches address many of the informatics challenges, including image processing, computational performance, and accuracy. These new algorithms are benchmarked against the Illumina Genome Analysis Pipeline. BING is the one of the first software tools to perform pixel-based analysis of NGS data. When compared to the Illumina informatics tool, BING's pixel-based approach produces a significant increase in the number of sequence reads, while reducing the computational time per experiment and error rate (<2%). This approach has the potential of increasing the density and throughput of NGS technologies. PMID:19925883

  11. Spreading Informatics in Educational Technology.

    ERIC Educational Resources Information Center

    Hauser, Zoltan; Kis-Toth, Lajos

    1995-01-01

    Examines developments in information dissemination and educational technology. Highlights include telecommunications, audiovisual media and programmed education, pedagogical technology, advantages of computer-based learning, instructional materials, applied informatics, teacher training, and future perspectives. (AEF)

  12. Informatics — EDRN Public Portal

    Cancer.gov

    The EDRN provides a comprehensive informatics activity which includes a number of tools and an integrated knowledge environment for capturing, managing, integrating, and sharing results from across EDRN's cancer biomarker research network.

  13. Translational Bioinformatics and Healthcare Informatics: Computational and Ethical Challenges

    PubMed Central

    Sethi, Prerna; Theodos, Kimberly

    2009-01-01

    Exponentially growing biological and bioinformatics data sets present a challenge and an opportunity for researchers to contribute to the understanding of the genetic basis of phenotypes. Due to breakthroughs in microarray technology, it is possible to simultaneously monitor the expressions of thousands of genes, and it is imperative that researchers have access to the clinical data to understand the genetics and proteomics of the diseased tissue. This technology could be a landmark in personalized medicine, which will provide storage for clinical and genetic data in electronic health records (EHRs). In this paper, we explore the computational and ethical challenges that emanate from the intersection of bioinformatics and healthcare informatics research. We describe the current situation of the EHR and its capabilities to store clinical and genetic data and then discuss the Genetic Information Nondiscrimination Act. Finally, we posit that the synergy obtained from the collaborative efforts between the genomics, clinical, and healthcare disciplines has potential to enhance and promote faster and more advanced breakthroughs in healthcare. PMID:20169020

  14. Dental Informatics in India: Time to Embrace the Change.

    PubMed

    Chhabra, Kumar Gaurav; Mulla, Salma H; Deolia, Shravani Govind; Chhabra, Chaya; Singh, Jagjeet; Marwaha, Baldeep Singh

    2016-03-01

    Dental informatics is comparatively a juvenile and new field that has noteworthy potential for supporting clinical care, research, education and management. This field utilizes computer science, information sciences and the application of same to espouse dentistry. However, in the under-developed and developing countries almost most of the dentists are unacquainted about dental informatics, its goals, what it is capable of achieving and by what means they can get involved into it. Despite of emerging advances, certain conflicts also go along with it such as, professional under representation, security issues of the stored information due to universal access to computers high speed internet connections. Endnote software was used as resource material to collect literature which was carefully arranged in a synchronized way. Hence, the purpose of this review was to give an overall scenario of dental informatics, its applications, challenges and recommendations for further enhancement in this area. PMID:27135022

  15. Dental Informatics in India: Time to Embrace the Change

    PubMed Central

    Mulla, Salma H.; Deolia, Shravani Govind; Chhabra, Chaya; Singh, Jagjeet; Marwaha, Baldeep Singh

    2016-01-01

    Dental informatics is comparatively a juvenile and new field that has noteworthy potential for supporting clinical care, research, education and management. This field utilizes computer science, information sciences and the application of same to espouse dentistry. However, in the under-developed and developing countries almost most of the dentists are unacquainted about dental informatics, its goals, what it is capable of achieving and by what means they can get involved into it. Despite of emerging advances, certain conflicts also go along with it such as, professional under representation, security issues of the stored information due to universal access to computers high speed internet connections. Endnote software was used as resource material to collect literature which was carefully arranged in a synchronized way. Hence, the purpose of this review was to give an overall scenario of dental informatics, its applications, challenges and recommendations for further enhancement in this area. PMID:27135022

  16. Plasma genetic and genomic abnormalities predict treatment response and clinical outcome in advanced prostate cancer.

    PubMed

    Xia, Shu; Kohli, Manish; Du, Meijun; Dittmar, Rachel L; Lee, Adam; Nandy, Debashis; Yuan, Tiezheng; Guo, Yongchen; Wang, Yuan; Tschannen, Michael R; Worthey, Elizabeth; Jacob, Howard; See, William; Kilari, Deepak; Wang, Xuexia; Hovey, Raymond L; Huang, Chiang-Ching; Wang, Liang

    2015-06-30

    Liquid biopsies, examinations of tumor components in body fluids, have shown promise for predicting clinical outcomes. To evaluate tumor-associated genomic and genetic variations in plasma cell-free DNA (cfDNA) and their associations with treatment response and overall survival, we applied whole genome and targeted sequencing to examine the plasma cfDNAs derived from 20 patients with advanced prostate cancer. Sequencing-based genomic abnormality analysis revealed locus-specific gains or losses that were common in prostate cancer, such as 8q gains, AR amplifications, PTEN losses and TMPRSS2-ERG fusions. To estimate tumor burden in cfDNA, we developed a Plasma Genomic Abnormality (PGA) score by summing the most significant copy number variations. Cox regression analysis showed that PGA scores were significantly associated with overall survival (p < 0.04). After androgen deprivation therapy or chemotherapy, targeted sequencing showed significant mutational profile changes in genes involved in androgen biosynthesis, AR activation, DNA repair, and chemotherapy resistance. These changes may reflect the dynamic evolution of heterozygous tumor populations in response to these treatments. These results strongly support the feasibility of using non-invasive liquid biopsies as potential tools to study biological mechanisms underlying therapy-specific resistance and to predict disease progression in advanced prostate cancer. PMID:25915538

  17. Insert, remove or replace: A highly advanced genome editing system using CRISPR/Cas9.

    PubMed

    Ceasar, S Antony; Rajan, Vinothkumar; Prykhozhij, Sergey V; Berman, Jason N; Ignacimuthu, S

    2016-09-01

    The clustered, regularly interspaced, short palindromic repeat (CRISPR) and CRISPR associated protein 9 (Cas9) system discovered as an adaptive immunity mechanism in prokaryotes has emerged as the most popular tool for the precise alterations of the genomes of diverse species. CRISPR/Cas9 system has taken the world of genome editing by storm in recent years. Its popularity as a tool for altering genomes is due to the ability of Cas9 protein to cause double-stranded breaks in DNA after binding with short guide RNA molecules, which can be produced with dramatically less effort and expense than required for production of transcription-activator like effector nucleases (TALEN) and zinc-finger nucleases (ZFN). This system has been exploited in many species from prokaryotes to higher animals including human cells as evidenced by the literature showing increasing sophistication and ease of CRISPR/Cas9 as well as increasing species variety where it is applicable. This technology is poised to solve several complex molecular biology problems faced in life science research including cancer research. In this review, we highlight the recent advancements in CRISPR/Cas9 system in editing genomes of prokaryotes, fungi, plants and animals and provide details on software tools available for convenient design of CRISPR/Cas9 targeting plasmids. We also discuss the future prospects of this advanced molecular technology. PMID:27350235

  18. Plasma genetic and genomic abnormalities predict treatment response and clinical outcome in advanced prostate cancer

    PubMed Central

    Du, Meijun; Dittmar, Rachel L.; Lee, Adam; Nandy, Debashis; Yuan, Tiezheng; Guo, Yongchen; Wang, Yuan; Tschannen, Michael R.; Worthey, Elizabeth; Jacob, Howard; See, William; Kilari, Deepak; Wang, Xuexia; Hovey, Raymond L.; Huang, Chiang-Ching; Wang, Liang

    2015-01-01

    Liquid biopsies, examinations of tumor components in body fluids, have shown promise for predicting clinical outcomes. To evaluate tumor-associated genomic and genetic variations in plasma cell-free DNA (cfDNA) and their associations with treatment response and overall survival, we applied whole genome and targeted sequencing to examine the plasma cfDNAs derived from 20 patients with advanced prostate cancer. Sequencing-based genomic abnormality analysis revealed locus-specific gains or losses that were common in prostate cancer, such as 8q gains, AR amplifications, PTEN losses and TMPRSS2-ERG fusions. To estimate tumor burden in cfDNA, we developed a Plasma Genomic Abnormality (PGA) score by summing the most significant copy number variations. Cox regression analysis showed that PGA scores were significantly associated with overall survival (p < 0.04). After androgen deprivation therapy or chemotherapy, targeted sequencing showed significant mutational profile changes in genes involved in androgen biosynthesis, AR activation, DNA repair, and chemotherapy resistance. These changes may reflect the dynamic evolution of heterozygous tumor populations in response to these treatments. These results strongly support the feasibility of using non-invasive liquid biopsies as potential tools to study biological mechanisms underlying therapy-specific resistance and to predict disease progression in advanced prostate cancer. PMID:25915538

  19. Evaluating the AMIA-OHSU 10x10 Program to Train Healthcare Professionals in Medical Informatics

    PubMed Central

    Feldman, Sue S.; Hersh, William

    2008-01-01

    The promise of health information technology (HIT) has led to calls for a larger and better trained work-force in medical informatics. University programs in applied health and biomedical informatics have been evolving in an effort to address the need for health-care professionals to be trained in informatics. One such evolution is the American Medical Informatics Association’s (AMIA) 10x10 program. To assess current delivery and content models, participant satisfaction, and how graduates have benefited from the program in career or education advancement, all students who completed the Oregon Health & Science University (OHSU) offering of the AMIA 10x10 course through the end of 2006 were surveyed. We found that the 10x10 program is approaching AMIA’s goals, and that there are potential areas for content and delivery modifications. Further research in defining the optimal competencies of the medical informatics workforce and its optimal education is needed. PMID:18999199

  20. Clinical research informatics: a conceptual perspective

    PubMed Central

    Weng, Chunhua

    2012-01-01

    Clinical research informatics is the rapidly evolving sub-discipline within biomedical informatics that focuses on developing new informatics theories, tools, and solutions to accelerate the full translational continuum: basic research to clinical trials (T1), clinical trials to academic health center practice (T2), diffusion and implementation to community practice (T3), and ‘real world’ outcomes (T4). We present a conceptual model based on an informatics-enabled clinical research workflow, integration across heterogeneous data sources, and core informatics tools and platforms. We use this conceptual model to highlight 18 new articles in the JAMIA special issue on clinical research informatics. PMID:22523344

  1. Advances in the translational genomics of neuroblastoma: From improving risk stratification and revealing novel biology to identifying actionable genomic alterations.

    PubMed

    Bosse, Kristopher R; Maris, John M

    2016-01-01

    Neuroblastoma is an embryonal malignancy that commonly affects young children and is remarkably heterogenous in its malignant potential. Recently, the genetic basis of neuroblastoma has come into focus and not only has catalyzed a more comprehensive understanding of neuroblastoma tumorigenesis but also has revealed novel oncogenic vulnerabilities that are being therapeutically leveraged. Neuroblastoma is a model pediatric solid tumor in its use of recurrent genomic alterations, such as high-level MYCN (v-myc avian myelocytomatosis viral oncogene neuroblastoma-derived homolog) amplification, for risk stratification. Given the relative paucity of recurrent, activating, somatic point mutations or gene fusions in primary neuroblastoma tumors studied at initial diagnosis, innovative treatment approaches beyond small molecules targeting mutated or dysregulated kinases will be required moving forward to achieve noticeable improvements in overall patient survival. However, the clonally acquired, oncogenic aberrations in relapsed neuroblastomas are currently being defined and may offer an opportunity to improve patient outcomes with molecularly targeted therapy directed toward aberrantly regulated pathways in relapsed disease. This review summarizes the current state of knowledge about neuroblastoma genetics and genomics, highlighting the improved prognostication and potential therapeutic opportunities that have arisen from recent advances in understanding germline predisposition, recurrent segmental chromosomal alterations, somatic point mutations and translocations, and clonal evolution in relapsed neuroblastoma. PMID:26539795

  2. Development of a high-throughput SNP resource to advance genomic, genetic and breeding research in carrot (Daucus carota L.)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The rapid advancement in high-throughput SNP genotyping technologies along with next generation sequencing (NGS) platforms has decreased the cost, improved the quality of large-scale genome surveys, and allowed specialty crops with limited genomic resources such as carrot (Daucus carota) to access t...

  3. The Impact of Imaging Informatics Fellowships.

    PubMed

    Liao, Geraldine J; Nagy, Paul G; Cook, Tessa S

    2016-08-01

    Imaging informatics (II) is an area within clinical informatics that is particularly important in the field of radiology. Provider groups have begun employing dedicated radiologist-informaticists to bridge medical, information technology and administrative functions, and academic institutions are meeting this demand through formal II fellowships. However, little is known about how these programs influence graduates' careers and perceptions about professional development. We electronically surveyed 26 graduates from US II fellowships and consensus leaders in the II community-many of whom were subspecialty diagnostic radiologists (68%) employed within academic institutions (48%)-about the perceived impact of II fellowships on career development and advancement. All graduates felt that II fellowship made them more valuable to employers, with the majority of reporting ongoing II roles (78%) and continued used of competencies (61%) and skills (56%) gained during fellowship in their current jobs. Other key benefits included access to mentors, protected time for academic work, networking opportunities, and positive impacts of annual compensation. Of respondents without II fellowship training, all would recommend fellowships to current trainees given the ability to gain a "still rare" but "essential skill set" that is "critical for future leaders in radiology" and "better job opportunities." While some respondents felt that II fellowships needed further formalization and standardization, most (85%) disagreed with requiring a 2-year II fellowship in order to qualify for board certification in clinical informatics. Instead, most believed that fellowships should be integrated with clinical residency or fellowship training while preserving formal didactics and unstructured project time. More work is needed to understand existing variations in II fellowship training structure and identify the optimal format for programs targeted at radiologists. PMID:26831474

  4. Using informatics to capture older adults’ wellness

    PubMed Central

    Demiris, George; Thompson, Hilaire J.; Reeder, Blaine; Wilamowska, Katarzyna; Zaslavsky, Oleg

    2014-01-01

    Purpose The aim of this paper is to demonstrate how informatics applications can support the assessment and visualization of older adults’ wellness. A theoretical framework is presented that informs the design of a technology enhanced screening platform for wellness. We highlight an ongoing pilot demonstration in an assisted living facility where a community room has been converted into a living laboratory for the use of diverse technologies (including a telehealth component to capture vital signs and customized questionnaires, a gait analysis component and cognitive assessment software) to assess the multiple aspects of wellness of older adults. Methods A demonstration project was introduced in an independent retirement community to validate our theoretical framework of informatics and wellness assessment for older adults. Subjects are being recruited to attend a community room and engage in the use of diverse technologies to assess cognitive performance, physiological and gait variables as well as psychometrics pertaining to social and spiritual components of wellness for a period of eight weeks. Data are integrated from various sources into one study database and different visualization approaches are pursued to efficiently display potential correlations between different parameters and capture overall trends of wellness. Results Preliminary findings indicate that older adults are willing to participate in technology-enhanced interventions and embrace different information technology applications given appropriate and customized training and hardware and software features that address potential functional limitations and inexperience with computers. Conclusion Informatics can advance health care for older adults and support a holistic assessment of older adults’ wellness. The described framework can support decision making, link formal and informal caregiving networks and identify early trends and patterns that if addressed could reduce adverse health events

  5. Advancing Crop Transformation in the Era of Genome Editing[OPEN

    PubMed Central

    Blechl, Ann E.; Brutnell, Thomas P.; Conrad, Liza J.; Gelvin, Stanton B.; Jackson, David P.; Kausch, Albert P.; Lemaux, Peggy G.; Medford, June I.; Orozco-Cárdenas, Martha L.; Tricoli, David M.; Van Eck, Joyce; Voytas, Daniel F.

    2016-01-01

    Plant transformation has enabled fundamental insights into plant biology and revolutionized commercial agriculture. Unfortunately, for most crops, transformation and regeneration remain arduous even after more than 30 years of technological advances. Genome editing provides novel opportunities to enhance crop productivity but relies on genetic transformation and plant regeneration, which are bottlenecks in the process. Here, we review the state of plant transformation and point to innovations needed to enable genome editing in crops. Plant tissue culture methods need optimization and simplification for efficiency and minimization of time in culture. Currently, specialized facilities exist for crop transformation. Single-cell and robotic techniques should be developed for high-throughput genomic screens. Plant genes involved in developmental reprogramming, wound response, and/or homologous recombination should be used to boost the recovery of transformed plants. Engineering universal Agrobacterium tumefaciens strains and recruiting other microbes, such as Ensifer or Rhizobium, could facilitate delivery of DNA and proteins into plant cells. Synthetic biology should be employed for de novo design of transformation systems. Genome editing is a potential game-changer in crop genetics when plant transformation systems are optimized. PMID:27335450

  6. Recent Advances in Understanding the Role of Nutrition in Human Genome Evolution12

    PubMed Central

    Ye, Kaixiong; Gu, Zhenglong

    2011-01-01

    Dietary transitions in human history have been suggested to play important roles in the evolution of mankind. Genetic variations caused by adaptation to diet during human evolution could have important health consequences in current society. The advance of sequencing technologies and the rapid accumulation of genome information provide an unprecedented opportunity to comprehensively characterize genetic variations in human populations and unravel the genetic basis of human evolution. Series of selection detection methods, based on various theoretical models and exploiting different aspects of selection signatures, have been developed. Their applications at the species and population levels have respectively led to the identification of human specific selection events that distinguish human from nonhuman primates and local adaptation events that contribute to human diversity. Scrutiny of candidate genes has revealed paradigms of adaptations to specific nutritional components and genome-wide selection scans have verified the prevalence of diet-related selection events and provided many more candidates awaiting further investigation. Understanding the role of diet in human evolution is fundamental for the development of evidence-based, genome-informed nutritional practices in the era of personal genomics. PMID:22332091

  7. The Evolution of Data-Information-Knowledge-Wisdom in Nursing Informatics.

    PubMed

    Ronquillo, Charlene; Currie, Leanne M; Rodney, Paddy

    2016-01-01

    The data-information-knowledge-wisdom (DIKW) model has been widely adopted in nursing informatics. In this article, we examine the evolution of DIKW in nursing informatics while incorporating critiques from other disciplines. This includes examination of assumptions of linearity and hierarchy and an exploration of the implicit philosophical grounding of the model. Two guiding questions are considered: (1) Does DIKW serve clinical information systems, nurses, or both? and (2) What level of theory does DIKW occupy? The DIKW model has been valuable in advancing the independent field of nursing informatics. We offer that if the model is to continue to move forward, its role and functions must be explicitly addressed. PMID:26836997

  8. Advances in genetics and genomics: use and limitations in achieving malaria elimination goals

    PubMed Central

    Gunawardena, Sharmini; Karunaweera, Nadira D.

    2015-01-01

    Success of the global research agenda towards eradication of malaria will depend on the development of new tools, including drugs, vaccines, insecticides and diagnostics. Genetic and genomic information now available for the malaria parasites, their mosquito vectors and human host, can be harnessed to both develop these tools and monitor their effectiveness. Here we review and provide specific examples of current technological advances and how these genetic and genomic tools have increased our knowledge of host, parasite and vector biology in relation to malaria elimination and in turn enhanced the potential to reach that goal. We then discuss limitations of these tools and future prospects for the successful achievement of global malaria elimination goals. PMID:25943157

  9. Monitoring of Ebola Virus Makona Evolution through Establishment of Advanced Genomic Capability in Liberia.

    PubMed

    Kugelman, Jeffrey R; Wiley, Michael R; Mate, Suzanne; Ladner, Jason T; Beitzel, Brett; Fakoli, Lawrence; Taweh, Fahn; Prieto, Karla; Diclaro, Joseph W; Minogue, Timothy; Schoepp, Randal J; Schaecher, Kurt E; Pettitt, James; Bateman, Stacey; Fair, Joseph; Kuhn, Jens H; Hensley, Lisa; Park, Daniel J; Sabeti, Pardis C; Sanchez-Lockhart, Mariano; Bolay, Fatorma K; Palacios, Gustavo

    2015-07-01

    To support Liberia's response to the ongoing Ebola virus (EBOV) disease epidemic in Western Africa, we established in-country advanced genomic capabilities to monitor EBOV evolution. Twenty-five EBOV genomes were sequenced at the Liberian Institute for Biomedical Research, which provided an in-depth view of EBOV diversity in Liberia during September 2014-February 2015. These sequences were consistent with a single virus introduction to Liberia; however, shared ancestry with isolates from Mali indicated at least 1 additional instance of movement into or out of Liberia. The pace of change is generally consistent with previous estimates of mutation rate. We observed 23 nonsynonymous mutations and 1 nonsense mutation. Six of these changes are within known binding sites for sequence-based EBOV medical countermeasures; however, the diagnostic and therapeutic impact of EBOV evolution within Liberia appears to be low. PMID:26079255

  10. Monitoring of Ebola Virus Makona Evolution through Establishment of Advanced Genomic Capability in Liberia

    PubMed Central

    Kugelman, Jeffrey R.; Wiley, Michael R.; Mate, Suzanne; Ladner, Jason T.; Beitzel, Brett; Fakoli, Lawrence; Taweh, Fahn; Prieto, Karla; Diclaro, Joseph W.; Minogue, Timothy; Schoepp, Randal J.; Schaecher, Kurt E.; Pettitt, James; Bateman, Stacey; Fair, Joseph; Kuhn, Jens H.; Hensley, Lisa; Park, Daniel J.; Sabeti, Pardis C.; Sanchez-Lockhart, Mariano; Bolay, Fatorma K.

    2015-01-01

    To support Liberia’s response to the ongoing Ebola virus (EBOV) disease epidemic in Western Africa, we established in-country advanced genomic capabilities to monitor EBOV evolution. Twenty-five EBOV genomes were sequenced at the Liberian Institute for Biomedical Research, which provided an in-depth view of EBOV diversity in Liberia during September 2014–February 2015. These sequences were consistent with a single virus introduction to Liberia; however, shared ancestry with isolates from Mali indicated at least 1 additional instance of movement into or out of Liberia. The pace of change is generally consistent with previous estimates of mutation rate. We observed 23 nonsynonymous mutations and 1 nonsense mutation. Six of these changes are within known binding sites for sequence-based EBOV medical countermeasures; however, the diagnostic and therapeutic impact of EBOV evolution within Liberia appears to be low. PMID:26079255

  11. A nursing informatics research agenda for 2008-18: contextual influences and key components.

    PubMed

    Bakken, Suzanne; Stone, Patricia W; Larson, Elaine L

    2008-01-01

    The context for nursing informatics research has changed significantly since the National Institute of Nursing Research-funded Nursing Informatics Research Agenda was published in 1993 and the Delphi study of nursing informatics research priorities reported a decade ago. The authors focus on 3 specific aspects of context--genomic health care, shifting research paradigms, and social (Web 2.0) technologies--that must be considered in formulating a nursing informatics research agenda. These influences are illustrated using the significant issue of healthcare associated infections (HAI). A nursing informatics research agenda for 2008-18 must expand users of interest to include interdisciplinary researchers; build upon the knowledge gained in nursing concept representation to address genomic and environmental data; guide the reengineering of nursing practice; harness new technologies to empower patients and their caregivers for collaborative knowledge development; develop user-configurable software approaches that support complex data visualization, analysis, and predictive modeling; facilitate the development of middle-range nursing informatics theories; and encourage innovative evaluation methodologies that attend to human-computer interface factors and organizational context. PMID:18922269

  12. A Nursing Informatics Research Agenda for 2008–18: Contextual Influences and Key Components

    PubMed Central

    Bakken, Suzanne; Stone, Patricia W.; Larson, Elaine L.

    2008-01-01

    The context for nursing informatics research has changed significantly since the National Institute of Nursing Research-funded Nursing Informatics Research Agenda was published in 1993 and the Delphi study of nursing informatics research priorities reported a decade ago. The authors focus on three specific aspects of context - genomic health care, shifting research paradigms, and social (Web 2.0) technologies - that must be considered in formulating a nursing informatics research agenda. These influences are illustrated using the significant issue of healthcare associated infections (HAI). A nursing informatics research agenda for 2008–18 must expand users of interest to include interdisciplinary researchers; build upon the knowledge gained in nursing concept representation to address genomic and environmental data; guide the reengineering of nursing practice; harness new technologies to empower patients and their caregivers for collaborative knowledge development; develop user-configurable software approaches that support complex data visualization, analysis, and predictive modeling; facilitate the development of middle-range nursing informatics theories; and encourage innovative evaluation methodologies that attend to human-computer interface factors and organizational context. PMID:18922269

  13. Advances in induced pluripotent stem cells, genomics, biomarkers, and antiplatelet therapy highlights of the year in JCTR 2013.

    PubMed

    Barbato, Emanuele; Lara-Pezzi, Enrique; Stolen, Craig; Taylor, Angela; Barton, Paul J; Bartunek, Jozef; Iaizzo, Paul; Judge, Daniel P; Kirshenbaum, Lorrie; Blaxall, Burns C; Terzic, Andre; Hall, Jennifer L

    2014-07-01

    The Journal provides the clinician and scientist with the latest advances in discovery research, emerging technologies, preclinical research design and testing, and clinical trials. We highlight advances in areas of induced pluripotent stem cells, genomics, biomarkers, multimodality imaging, and antiplatelet biology and therapy. The top publications are critically discussed and presented along with anatomical reviews and FDA insight to provide context. PMID:24659088

  14. Informatics for multi-disciplinary ocean sciences

    NASA Astrophysics Data System (ADS)

    Pearlman, Jay; Delory, Eric; Pissierssens, Peter; Raymond, Lisa; Simpson, Pauline; Waldmann, Christoph; Williams 3rd, Albert; Yoder, Jim

    2014-05-01

    Ocean researchers must work across disciplines to provide clear and understandable assessments of the state of the ocean. With advances in technology, not only in observation, but also communication and computer science, we are in a new era where we can answer questions at the time and space scales that are relevant to our state of the art research needs. This presentation will address three areas of the informatics of the end-to-end process: sensors and information extraction in the sensing environment; using diverse data for understanding selected ocean processes; and supporting open data initiatives. A National Science Foundation funded Ocean Observations Research Coordination Network (RCN) is addressing these areas from the perspective of improving interdisciplinary research. The work includes an assessment of Open Data Access with a paper in preparation. Interoperability and sensors is a new activity that couples with European projects, COOPEUS and NeXOS, in looking at sensors and related information systems for a new generation of measurement capability. A working group on synergies of in-situ and satellite remote sensing is analyzing approaches for more effective use of these measurements. This presentation will examine the steps forward for data exchange and for addressing gaps in communication and informatics.

  15. Inferring Genome-Wide Recombination Landscapes from Advanced Intercross Lines: Application to Yeast Crosses

    PubMed Central

    Illingworth, Christopher J. R.; Parts, Leopold; Bergström, Anders; Liti, Gianni; Mustonen, Ville

    2013-01-01

    Accurate estimates of recombination rates are of great importance for understanding evolution. In an experimental genetic cross, recombination breaks apart and rejoins genetic material, such that the genomes of the resulting isolates are comprised of distinct blocks of differing parental origin. We here describe a method exploiting this fact to infer genome-wide recombination profiles from sequenced isolates from an advanced intercross line (AIL). We verified the accuracy of the method against simulated data. Next, we sequenced 192 isolates from a twelve-generation cross between West African and North American yeast Saccharomyces cerevisiae strains and inferred the underlying recombination landscape at a fine genomic resolution (mean segregating site distance 0.22 kb). Comparison was made with landscapes inferred for a similar cross between four yeast strains, and with a previous single-generation, intra-strain cross (Mancera et al., Nature 2008). Moderate congruence was identified between landscapes (correlation 0.58–0.77 at 5 kb resolution), albeit with variance between mean genome-wide recombination rates. The multiple generations of mating undergone in the AILs gave more precise inference of recombination rates than could be achieved from a single-generation cross, in particular in identifying recombination cold-spots. The recombination landscapes we describe have particular utility; both AILs are part of a resource to study complex yeast traits (see e.g. Parts et al., Genome Res 2011). Our results will enable future applications of this resource to take better account of local linkage structure heterogeneities. Our method has general applicability to other crossing experiments, including a variety of experimental designs. PMID:23658715

  16. Recent advances in soybean transformation and their application to molecular breeding and genomic analysis

    PubMed Central

    Yamada, Tetsuya; Takagi, Kyoko; Ishimoto, Masao

    2012-01-01

    Herbicide-resistant transgenic soybean plants hold a leading market share in the USA and other countries, but soybean has been regarded as recalcitrant to transformation for many years. The cumulative and, at times, exponential advances in genetic manipulation have made possible further choices for soybean transformation. The most widely and routinely used transformation systems are cotyledonary node–Agrobacterium-mediated transformation and somatic embryo–particle-bombardment-mediated transformation. These ready systems enable us to improve seed qualities and agronomic characteristics by transgenic approaches. In addition, with the accumulation of soybean genomic resources, convenient or promising approaches will be requisite for the determination and use of gene function in soybean. In this article, we describe recent advances in and problems of soybean transformation, and survey the current transgenic approaches for applied and basic research in Japan. PMID:23136488

  17. Personal Chemical Exposure informatics

    EPA Science Inventory

    Chemical Exposure science is the study of human contact with chemicals (from manufacturing facilities, everyday products, waste) occurring in their environments and advances knowledge of the mechanisms and dynamics of events that cause or prevent adverse health outcomes. (adapted...

  18. Policy Implications of Education Informatics

    ERIC Educational Resources Information Center

    Carr, Jo Ann; O'Brien, Nancy P.

    2010-01-01

    Background/Context: This concluding article identifies the policy implications of education informatics and explores impacts of current copyright laws, legislative structures, publishing practices, and education organizations. Synthesizing the discussions in the preceding articles, this article highlights the importance of designing information…

  19. An advanced draft genome assembly of a desi type chickpea (Cicer arietinum L.)

    PubMed Central

    Parween, Sabiha; Nawaz, Kashif; Roy, Riti; Pole, Anil K.; Venkata Suresh, B.; Misra, Gopal; Jain, Mukesh; Yadav, Gitanjali; Parida, Swarup K.; Tyagi, Akhilesh K.; Bhatia, Sabhyata; Chattopadhyay, Debasis

    2015-01-01

    Chickpea (Cicer arietinum L.) is an important pulse legume crop. We previously reported a draft genome assembly of the desi chickpea cultivar ICC 4958. Here we report an advanced version of the ICC 4958 genome assembly (version 2.0) generated using additional sequence data and an improved genetic map. This resulted in 2.7-fold increase in the length of the pseudomolecules and substantial reduction of sequence gaps. The genome assembly covered more than 94% of the estimated gene space and predicted the presence of 30,257 protein-coding genes including 2230 and 133 genes encoding potential transcription factors (TF) and resistance gene homologs, respectively. Gene expression analysis identified several TF and chickpea-specific genes with tissue-specific expression and displayed functional diversification of the paralogous genes. Pairwise comparison of pseudomolecules in the desi (ICC 4958) and the earlier reported kabuli (CDC Frontier) chickpea assemblies showed an extensive local collinearity with incongruity in the placement of large sequence blocks along the linkage groups, apparently due to use of different genetic maps. Single nucleotide polymorphism (SNP)-based mining of intra-specific polymorphism identified more than four thousand SNPs differentiating a desi group and a kabuli group of chickpea genotypes. PMID:26259924

  20. Advancing our understanding of functional genome organisation through studies in the fission yeast

    PubMed Central

    Olsson, Ida

    2010-01-01

    Significant progress has been made in understanding the functional organisation of the cell nucleus. Still many questions remain to be answered about the relationship between the spatial organisation of the nucleus and the regulation of the genome function. There are many conflicting data in the field making it very difficult to merge published results on mammalian cells into one model on subnuclear chromatin organisation. The fission yeast, Schizosaccharomyces pombe, over the last decades has emerged as a valuable model organism in understanding basic biological mechanisms, especially the cell cycle and chromosome biology. In this review we describe and compare the nuclear organisation in mammalian and fission yeast cells. We believe that fission yeast is a good tool to resolve at least some of the contradictions and unanswered questions concerning functional nuclear architecture, since S. pombe has chromosomes structurally similar to that of human. S. pombe also has the advantage over higher eukaryotes in that the genome can easily be manipulated via homologous recombination making it possible to integrate the tools needed for visualisation of chromosomes using live-cell microscopy. Classical genetic experiments can be used to elucidate what factors are involved in a certain mechanism. The knowledge we have gained during the last few years indicates similarities between the genome organisation in fission yeast and mammalian cells. We therefore propose the use of fission yeast for further advancement of our understanding of functional nuclear organisation. PMID:21113595

  1. Exploiting the genome

    SciTech Connect

    Block, S.; Cornwall, J.; Dyson, F.; Koonin, S.; Lewis, N.; Schwitters, R.

    1998-09-11

    In 1997, JASON conducted a DOE-sponsored study of the human genome project with special emphasis on the areas of technology, quality assurance and quality control, and informatics. The present study has two aims: first, to update the 1997 Report in light of recent developments in genome sequencing technology, and second, to consider possible roles for the DOE in the ''post-genomic" era, following acquisition of the complete human genome sequence.

  2. Partnership to promote interprofessional education and practice for population and public health informatics: A case study.

    PubMed

    Rajamani, Sripriya; Westra, Bonnie L; Monsen, Karen A; LaVenture, Martin; Gatewood, Laël Cranmer

    2015-01-01

    Team-based healthcare delivery models, which emphasize care coordination, patient engagement, and utilization of health information technology, are emerging. To achieve these models, expertise in interprofessional education, collaborative practice across professions, and informatics is essential. This case study from informatics programs in the Academic Health Center (AHC) at the University of Minnesota and the Office of Health Information Technology (OHIT) at the Minnesota Department of Health presents an academic-practice partnership, which focuses on both interprofessionalism and informatics. Outcomes include the Minnesota Framework for Interprofessional Biomedical Health Informatics, comprising collaborative curriculum development, teaching and research, practicums to promote competencies, service to advance biomedical health informatics, and collaborative environments to facilitate a learning health system. Details on these Framework categories are presented. Partnership success is due to interprofessional connections created with emphasis on informatics and to committed leadership across partners. A limitation of this collaboration is the need for formal agreements outlining resources and roles, which are vital for sustainability. This partnership addresses a recommendation on the future of interprofessionalism: that both education and practice sectors be attuned to each other's expectations and evolving trends. Success strategies and lessons learned from collaborations, such as that of the AHC-OHIT that promote both interprofessionalism and informatics, need to be shared. PMID:26120895

  3. Advances in genetic engineering of the avian genome: "Realising the promise".

    PubMed

    Doran, Timothy J; Cooper, Caitlin A; Jenkins, Kristie A; Tizard, Mark L V

    2016-06-01

    This review provides an historic perspective of the key steps from those reported at the 1st Transgenic Animal Research Conference in 1997 through to the very latest developments in avian transgenesis. Eighteen years later, on the occasion of the 10th conference in this series, we have seen breakthrough advances in the use of viral vectors and transposons to transform the germline via the direct manipulation of the chicken embryo, through to the establishment of PGC cultures allowing in vitro modification, expansion into populations to analyse the genetic modifications and then injection of these cells into embryos to create germline chimeras. We have now reached an unprecedented time in the history of chicken transgenic research where we have the technology to introduce precise, targeted modifications into the chicken genome, ranging from; new transgenes that provide improved phenotypes such as increased resilience to economically important diseases; the targeted disruption of immunoglobulin genes and replacement with human sequences to generate transgenic chickens that express "humanised" antibodies for biopharming; and the deletion of specific nucleotides to generate targeted gene knockout chickens for functional genomics. The impact of these advances is set to be realised through applications in chickens, and other bird species as models in scientific research, for novel biotechnology and to protect and improve agricultural productivity. PMID:26820412

  4. Postcards from the imaging informatics road. Despite policy complexities, diagnostic imaging informatics makes progress on multiple fronts.

    PubMed

    Hagland, Mark

    2011-11-01

    The current strategic landscape for imaging informatics is one filled with great contrasts and paradoxes. On the one hand, because imaging informatics was not explicitly addressed in Stage 1 of the meaningful use requirements under the American Recovery and Reinvestment Act/Health Information Technology for Economic and Clinical Health Act (ARRA-HITECH) legislation, it instantly lost some of the environment of turbo-charged energy characterized by areas that were directly addressed by the HITECH Act, such as quality data reporting, care management, and of course, core electronic health record (EHR) development. On the other hand, an interesting combination of factors--rapidly advancing technology, the expansion of the image archiving concept across different medical specialties, and the inclusion of diagnostic image-sharing as one element in the development of health information exchange (HIE) arrangements nationwide--is nonetheless pushing imaging informatics forward towards new innovations. The five articles below provide readers with different glimpses of the path ahead for imaging informatics. The first presents a look at the current policy and reimbursement landscape. Each of the four subsequent articles delve into different aspects of innovation, from a process developed at a public hospital to improve and speed up the diagnostic process for trauma patients, to a radiology-specific financial analytics solution in the group practice setting, to an advance in cardiology information systems, to a self-developed federated image viewing platform at one of the nation's largest integrated health systems. Each of those initiatives is very different; yet it is clear that a great deal of innovation is taking place across the US. healthcare system when it comes to imaging informatics. With a landscape filled with uncertainties and potential policy, reimbursement, and industry shifts in the offing, CIOs, CMIOs, and other healthcare IT leaders will need to think very

  5. Nursing informatics competences still challenging nurse educators.

    PubMed

    Rajalahti, Elina; Saranto, Kaija

    2012-01-01

    In recent years nursing documentation has been one of the most important development areas of nursing informatics (NI) in Finland. The purpose of this study is to describe the development of the nurse educators' competences in nursing documentation during a project called eNNI. The eNNI project (2008-2010) was a cooperative project by nurse educators and working life experts. The goal of the project was to implement the national documentation model and thereby improve operational processes at workplaces. The study includes pre- and post-test questioning of NI applications with a web-based questionnaire (n=136). The data were analyzed with distribution, cross-tabulations and average tests and descriptive statistic multivariate method. According to the results, the ICT skills of the nurse educators were good at the end of the project, and they had good information literacy competence. On the other hand, their advanced NI skills left room for improvement. PMID:22874332

  6. Biological information specialists for biological informatics

    PubMed Central

    Heidorn, P Bryan; Palmer, Carole L; Wright, Dan

    2007-01-01

    Data management and integration are complicated and ongoing problems that will require commitment of resources and expertise from the various biological science communities. Primary components of successful cross-scale integration are smooth information management and migration from one context to another. We call for a broadening of the definition of bioinformatics and bioinformatics training to span biological disciplines and biological scales. Training programs are needed that educate a new kind of informatics professional, Biological Information Specialists, to work in collaboration with various discipline-specific research personnel. Biological Information Specialists are an extension of the informationist movement that began within library and information science (LIS) over 30 years ago as a professional position to fill a gap in clinical medicine. These professionals will help advance science by improving access to scientific information and by freeing scientists who are not interested in data management to concentrate on their science. PMID:17295920

  7. The Role of Genomic Profiling in Advanced Breast Cancer: The Two Faces of Janus

    PubMed Central

    Eralp, Yesim

    2016-01-01

    Recent advances in genomic technology have led to considerable improvement in our understanding of the molecular basis that underpins breast cancer biology. Through the use of comprehensive whole genome genomic profiling by next-generation sequencing, an unprecedented bulk of data on driver mutations, key genomic rearrangements, and mechanisms on tumor evolution has been generated. These developments have marked the beginning of a new era in oncology called “personalized or precision medicine.” Elucidation of biologic mechanisms that underpin carcinogenetic potential and metastatic behavior has led to an inevitable explosion in the development of effective targeted agents, many of which have gained approval over the past decade. Despite energetic efforts and the enormous support gained within the oncology community, there are many obstacles in the clinical implementation of precision medicine. Other than the well-known biologic markers, such as ER and Her-2/neu, no proven predictive marker exists to determine the responsiveness to a certain biologic agent. One of the major issues in this regard is teasing driver mutations among the background noise within the bulk of coexisting passenger mutations. Improving bioinformatics tools through electronic models, enhanced by improved insight into pathway dependency may be the step forward to overcome this problem. Next, is the puzzle on spatial and temporal tumoral heterogeneity, which remains to be solved by ultra-deep sequencing and optimizing liquid biopsy techniques. Finally, there are multiple logistical and financial issues that have to be meticulously tackled in order to optimize the use of “precision medicine” in the real-life setting. PMID:27547031

  8. The Role of Genomic Profiling in Advanced Breast Cancer: The Two Faces of Janus.

    PubMed

    Eralp, Yesim

    2016-01-01

    Recent advances in genomic technology have led to considerable improvement in our understanding of the molecular basis that underpins breast cancer biology. Through the use of comprehensive whole genome genomic profiling by next-generation sequencing, an unprecedented bulk of data on driver mutations, key genomic rearrangements, and mechanisms on tumor evolution has been generated. These developments have marked the beginning of a new era in oncology called "personalized or precision medicine." Elucidation of biologic mechanisms that underpin carcinogenetic potential and metastatic behavior has led to an inevitable explosion in the development of effective targeted agents, many of which have gained approval over the past decade. Despite energetic efforts and the enormous support gained within the oncology community, there are many obstacles in the clinical implementation of precision medicine. Other than the well-known biologic markers, such as ER and Her-2/neu, no proven predictive marker exists to determine the responsiveness to a certain biologic agent. One of the major issues in this regard is teasing driver mutations among the background noise within the bulk of coexisting passenger mutations. Improving bioinformatics tools through electronic models, enhanced by improved insight into pathway dependency may be the step forward to overcome this problem. Next, is the puzzle on spatial and temporal tumoral heterogeneity, which remains to be solved by ultra-deep sequencing and optimizing liquid biopsy techniques. Finally, there are multiple logistical and financial issues that have to be meticulously tackled in order to optimize the use of "precision medicine" in the real-life setting. PMID:27547031

  9. Clinical health informatics education for a 21st Century World.

    PubMed

    Liaw, Siaw Teng; Gray, Kathleen

    2010-01-01

    This chapter gives an educational overview of: * health informatics competencies in medical, nursing and allied clinical health professions * health informatics learning cultures and just-in-time health informatics training in clinical work settings * major considerations in selecting or developing health informatics education and training programs for local implementation * using elearning effectively to meet the objectives of health informatics education. PMID:20407180

  10. MBAT: A scalable informatics system for unifying digital atlasing workflows

    PubMed Central

    2010-01-01

    Background Digital atlases provide a common semantic and spatial coordinate system that can be leveraged to compare, contrast, and correlate data from disparate sources. As the quality and amount of biological data continues to advance and grow, searching, referencing, and comparing this data with a researcher's own data is essential. However, the integration process is cumbersome and time-consuming due to misaligned data, implicitly defined associations, and incompatible data sources. This work addressing these challenges by providing a unified and adaptable environment to accelerate the workflow to gather, align, and analyze the data. Results The MouseBIRN Atlasing Toolkit (MBAT) project was developed as a cross-platform, free open-source application that unifies and accelerates the digital atlas workflow. A tiered, plug-in architecture was designed for the neuroinformatics and genomics goals of the project to provide a modular and extensible design. MBAT provides the ability to use a single query to search and retrieve data from multiple data sources, align image data using the user's preferred registration method, composite data from multiple sources in a common space, and link relevant informatics information to the current view of the data or atlas. The workspaces leverage tool plug-ins to extend and allow future extensions of the basic workspace functionality. A wide variety of tool plug-ins were developed that integrate pre-existing as well as newly created technology into each workspace. Novel atlasing features were also developed, such as supporting multiple label sets, dynamic selection and grouping of labels, and synchronized, context-driven display of ontological data. Conclusions MBAT empowers researchers to discover correlations among disparate data by providing a unified environment for bringing together distributed reference resources, a user's image data, and biological atlases into the same spatial or semantic context. Through its extensible

  11. The Biodiversity Informatics Potential Index

    PubMed Central

    2011-01-01

    Background Biodiversity informatics is a relatively new discipline extending computer science in the context of biodiversity data, and its development to date has not been uniform throughout the world. Digitizing effort and capacity building are costly, and ways should be found to prioritize them rationally. The proposed 'Biodiversity Informatics Potential (BIP) Index' seeks to fulfill such a prioritization role. We propose that the potential for biodiversity informatics be assessed through three concepts: (a) the intrinsic biodiversity potential (the biological richness or ecological diversity) of a country; (b) the capacity of the country to generate biodiversity data records; and (c) the availability of technical infrastructure in a country for managing and publishing such records. Methods Broadly, the techniques used to construct the BIP Index were rank correlation, multiple regression analysis, principal components analysis and optimization by linear programming. We built the BIP Index by finding a parsimonious set of country-level human, economic and environmental variables that best predicted the availability of primary biodiversity data accessible through the Global Biodiversity Information Facility (GBIF) network, and constructing an optimized model with these variables. The model was then applied to all countries for which sufficient data existed, to obtain a score for each country. Countries were ranked according to that score. Results Many of the current GBIF participants ranked highly in the BIP Index, although some of them seemed not to have realized their biodiversity informatics potential. The BIP Index attributed low ranking to most non-participant countries; however, a few of them scored highly, suggesting that these would be high-return new participants if encouraged to contribute towards the GBIF mission of free and open access to biodiversity data. Conclusions The BIP Index could potentially help in (a) identifying countries most likely to

  12. Nursing Informatics: Decades of Contribution to Health Informatics

    PubMed Central

    Mæland Knudsen, Lina Merete

    2013-01-01

    Objectives In this paper we present a contemporary understanding of "nursing informatics" and relate it to applications in three specific contexts, hospitals, community health, and home dwelling, to illustrate achievements that contribute to the overall schema of health informatics. Methods We identified literature through database searches in MEDLINE, EMBASE, CINAHL, and the Cochrane Library. Database searching was complemented by one author search and hand searches in six relevant journals. The literature review helped in conceptual clarification and elaborate on use that are supported by applications in different settings. Results Conceptual clarification of nursing data, information and knowledge has been expanded to include wisdom. Information systems and support for nursing practice benefits from conceptual clarification of nursing data, information, knowledge, and wisdom. We introduce three examples of information systems and point out core issues for information integration and practice development. Conclusions Exploring interplays of data, information, knowledge, and wisdom, nursing informatics takes a practice turn, accommodating to processes of application design and deployment for purposeful use by nurses in different settings. Collaborative efforts will be key to further achievements that support task shifting, mobility, and ubiquitous health care. PMID:23882413

  13. The Scope and Direction of Health Informatics

    NASA Technical Reports Server (NTRS)

    McGinnis, Patrick J.

    2001-01-01

    Health Informatics (HI) is a dynamic discipline based upon the medical sciences, information sciences, and cognitive sciences. Its domain is can broadly be defined as medical information management. The purpose of this paper is to provide an overview of this domain, discuss the current "state of the art" , and indicate the likely growth areas for health informatics. The sources of information utilized in this paper are selected publications from the literature of Health Informatics, HI 5300: Introduction to Health Informatics, which is a course from the Department of Health Informatics at the University of Texas Houston Health Sciences Center, and the author's personal experience in practicing telemedicine and implementing an electronic medical record at the NASA Johnson Space Center. The conclusion is that the direction of Health Informatics is in the direction of data management, transfer, and representation via electronic medical records and the Internet.

  14. Health informatics: managing information to deliver value.

    PubMed

    Ball, M J; Douglas, J V; Lillis, J

    2001-01-01

    Can informatics improve health? This paper answers yes, exploring its components, benefits, and effect on a wide variety of health-related activities. We first examine how information technology enables health informatics, supporting information management and knowledge creation through its four cornerstones. Success factors in using informatics are covered next, including human factors, the role of trained health informaticians, and the importance of matching informatics initiatives with business goals and establishing and measuring value. We demonstrate the potential effect of the Internet on health services through such e-health applications as enterprise-wide patient records, state-of-the-art call centers, and data repositories. For current evidence that informatics is already improving health, we turn to such topics as disease management, telehealth, patient safety, and decision support. As more organizations move informatics from theory into practice and realize its value, they will transform inefficient processes and improve care for all. PMID:11604752

  15. The scope and direction of health informatics

    NASA Technical Reports Server (NTRS)

    McGinnis, Patrick J.

    2002-01-01

    Health Informatics (HI) is a dynamic discipline based on the medical sciences, information sciences, and cognitive sciences. Its domain can broadly be defined as medical information management. The purpose of this paper is to provide an overview of this domain, discuss the current "state of the art," and indicate the likely growth areas for health informatics. The sources of information used in this paper are selected publications from the literature of Health Informatics, HI 5300: Introduction to Health Informatics, which is a course from the Department of Health Informatics at the University of Texas Houston Health Sciences Center, and the author's personal experience in practicing telemedicine and implementing an electronic medical record at the NASA-Johnson Space Center. The conclusion is that the direction of Health Informatics is in the direction of data management, transfer, and representation via electronic medical records and the Internet.

  16. A 400,000-year-old mitochondrial genome questions phylogenetic relationships amongst archaic hominins: using the latest advances in ancient genomics, the mitochondrial genome sequence of a 400,000-year-old hominin has been deciphered.

    PubMed

    Orlando, Ludovic

    2014-06-01

    By combining state-of-the-art approaches in ancient genomics, Meyer and co-workers have reconstructed the mitochondrial sequence of an archaic hominin that lived at Sierra de Atapuerca, Spain about 400,000 years ago. This achievement follows recent advances in molecular anthropology that delivered the genome sequence of younger archaic hominins, such as Neanderthals and Denisovans. Molecular phylogenetic reconstructions placed the Atapuercan as a sister group to Denisovans, although its morphology suggested closer affinities with Neanderthals. In addition to possibly challenging our interpretation of the fossil record, this study confirms that genomic information can be recovered from extremely damaged DNA molecules, even in the presence of significant levels of human contamination. Together with the recent characterization of a 700,000-year-old horse genome, this study opens the Middle Pleistocene to genomics, thereby extending the scope of ancient DNA to the last million years. PMID:24706482

  17. [Advances in congenital vertebral malformation caused by genomic copy number variation].

    PubMed

    Liu, Zhenlei; Wu, Nan; Wu, Zhihong; Zuo, Yuzhi; Qiu, Guixing

    2016-04-01

    Congenital vertebral malformation (CVM) is a congenital vertebral structural deformity caused by abnormal somitogenesis during embryonic development, of which the reason lies in gene mutation or abnormal regulation of the genes that coordinate somitogenesis during embryonic period. ICVAS had proposed a new classification algorithm for CVM, which facilitated exploration for its genetic etiology. Genomic Copy Number Variation (CNV) is a kind of DNA mutation, which is important for human evolution, phenotype polymorphism and diseases. Series of advances have been made on genetic causes of CVM, especially on CVM caused by CNV. CNVs of chromosome 16p11.2, 10q24.31, 17p11.2, 20p11, 22q11.2 and a few other regions are associated with CVM, indicating that gene dosage may play important roles in the development of the spinal cord. PMID:27029207

  18. Limited Genomic Heterogeneity of Circulating Melanoma Cells in Advanced Stage Patients

    PubMed Central

    Ruiz, Carmen; Li, Julia; Luttgen, Madelyn S.; Kolatkar, Anand; Kendall, Jude T.; Flores, Edna; Topp, Zheng; Samlowski, Wolfram E.; McClay, Ed; Bethel, Kelly; Ferrone, Soldano; Hicks, James; Kuhn, Peter

    2015-01-01

    Purpose Circulating melanoma cells (CMCs) constitute a potentially important representation of time-resolved tumor biology in patients. To date, genomic characterization of CMCs has been limited due to the lack of a robust methodology capable of identifying them in a format suitable for downstream characterization. Here, we have developed a methodology to detect intact CMCs that enables phenotypic, morphometric and genomic analysis at the single cell level. Experimental design Blood samples from 40 metastatic melanoma patients and 10 normal blood donors (NBD) were prospectively collected. A panel of 7 chondroitin sulfate proteoglycan 4 (CSPG4)-specific monoclonal antibodies (mAb) was used to immunocytochemically label CMCs. Detection was performed by automated digital fluorescence microscopy and multi-parametric computational analysis. Individual CMCs were captured by micromanipulation for whole genome amplification (WGA) and copy number variation (CNV) analysis. Results Based on CSPG4 expression and nuclear size, 1 to 250 CMCs were detected in 22 (55%) of 40 metastatic melanoma patients (0.5 to 371.5 CMCs/ml). Morphometric analysis revealed that CMCs have a broad spectrum of morphologies and sizes but exhibit a relatively homogeneous nuclear size that was on average 1.5-fold larger than that of surrounding PBMCs. CNV analysis of single CMCs identified deletions of CDKN2A and PTEN, and amplification(s) of TERT, BRAF, KRAS and MDM2. Furthermore, novel chromosomal amplifications in chr12, 17 and 19 were also found. Conclusions Our findings show that CSPG4 expressing CMCs can be found in the majority of advanced melanoma patients. High content analysis of this population may contribute to develop effective therapeutic strategies. PMID:25574741

  19. Limited genomic heterogeneity of circulating melanoma cells in advanced stage patients

    NASA Astrophysics Data System (ADS)

    Ruiz, Carmen; Li, Julia; Luttgen, Madelyn S.; Kolatkar, Anand; Kendall, Jude T.; Flores, Edna; Topp, Zheng; Samlowski, Wolfram E.; McClay, Edward; Bethel, Kelly; Ferrone, Soldano; Hicks, James; Kuhn, Peter

    2015-02-01

    Purpose. Circulating melanoma cells (CMCs) constitute a potentially important representation of time-resolved tumor biology in patients. To date, genomic characterization of CMCs has been limited due to the lack of a robust methodology capable of identifying them in a format suitable for downstream characterization. Here, we have developed a methodology to detect intact CMCs that enables phenotypic, morphometric and genomic analysis at the single cell level. Experimental design. Blood samples from 40 metastatic melanoma patients and 10 normal blood donors were prospectively collected. A panel of 7 chondroitin sulfate proteoglycan 4 (CSPG4)-specific monoclonal antibodies (mAbs) was used to immunocytochemically label CMCs. Detection was performed by automated digital fluorescence microscopy and multi-parametric computational analysis. Individual CMCs were captured by micromanipulation for whole genome amplification and copy number variation (CNV) analysis. Results. Based on CSPG4 expression and nuclear size, 1-250 CMCs were detected in 22 (55%) of 40 metastatic melanoma patients (0.5-371.5 CMCs ml-1). Morphometric analysis revealed that CMCs have a broad spectrum of morphologies and sizes but exhibit a relatively homogeneous nuclear size that was on average 1.5-fold larger than that of surrounding PBMCs. CNV analysis of single CMCs identified deletions of CDKN2A and PTEN, and amplification(s) of TERT, BRAF, KRAS and MDM2. Furthermore, novel chromosomal amplifications in chr12, 17 and 19 were also found. Conclusions. Our findings show that CSPG4 expressing CMCs can be found in the majority of advanced melanoma patients. High content analysis of this cell population may contribute to the design of effective personalized therapies in patients with melanoma.

  20. Cognitive hacking and intelligence and security informatics

    NASA Astrophysics Data System (ADS)

    Thompson, Paul

    2004-08-01

    This paper describes research on cognitive and semantic attacks on computer systems and their users. Several countermeasures against such attacks are described, including a description of a prototype News Verifier system. It is argued that because misinformation and deception play a much more significant role in intelligence and security informatics than in other informatics disciplines such as science, medicine, and the law, a new science of intelligence and security informatics must concern itself with semantic attacks and countermeasures.

  1. Medical imaging, PACS, and imaging informatics: retrospective.

    PubMed

    Huang, H K

    2014-01-01

    Historical reviews of PACS (picture archiving and communication system) and imaging informatics development from different points of view have been published in the past (Huang in Euro J Radiol 78:163-176, 2011; Lemke in Euro J Radiol 78:177-183, 2011; Inamura and Jong in Euro J Radiol 78:184-189, 2011). This retrospective attempts to look at the topic from a different angle by identifying certain basic medical imaging inventions in the 1960s and 1970s which had conceptually defined basic components of PACS guiding its course of development in the 1980s and 1990s, as well as subsequent imaging informatics research in the 2000s. In medical imaging, the emphasis was on the innovations at Georgetown University in Washington, DC, in the 1960s and 1970s. During the 1980s and 1990s, research and training support from US government agencies and public and private medical imaging manufacturers became available for training of young talents in biomedical physics and for developing the key components required for PACS development. In the 2000s, computer hardware and software as well as communication networks advanced by leaps and bounds, opening the door for medical imaging informatics to flourish. Because many key components required for the PACS operation were developed by the UCLA PACS Team and its collaborative partners in the 1980s, this presentation is centered on that aspect. During this period, substantial collaborative research efforts by many individual teams in the US and in Japan were highlighted. Credits are due particularly to the Pattern Recognition Laboratory at Georgetown University, and the computed radiography (CR) development at the Fuji Electric Corp. in collaboration with Stanford University in the 1970s; the Image Processing Laboratory at UCLA in the 1980s-1990s; as well as the early PACS development at the Hokkaido University, Sapporo, Japan, in the late 1970s, and film scanner and digital radiography developed by Konishiroku Photo Ind. Co. Ltd

  2. Engaging clinicians in health informatics projects.

    PubMed

    Caballero Muñoz, Erika; Hullin Lucay Cossio, Carola M

    2010-01-01

    This chapter gives an educational overview of: * The importance of the engagement of clinicians within a health informatics project * Strategies required for an effective involvement of clinicians throughout a change management process within a clinical context for the implementation of a health informatics project * The critical aspects for a successful implementation of a health informatics project that involves clinicians as end users * Key factors during the administration of changes during the implementation of an informatics project for an information system in clinical practice. PMID:20407162

  3. Perspectives from Nurse Managers on Informatics Competencies

    PubMed Central

    Cui, Dan; Zhu, Xuemei; Zhao, Qiuli; Xiao, Ningning; Shen, Xiaoying

    2014-01-01

    Background and Purpose. Nurse managers are in an excellent position for providing leadership and support within the institutions they serve and are often responsible for accessing information that is vital to the improvement of health facility processes and patients' outcomes. Therefore, competency in informatics is essential. The purposes of this study are to examine current informatics competency levels of nurse managers and to identify the variables that influence these competencies. Methods. A questionnaire designed to assess demographic information and nursing informatics competency was completed by 68 nurse managers. Multiple linear regression analysis was conducted to analyze the factors influencing informatics competency. Results. Descriptive analysis of the data revealed that informatics competency of these nurse managers was in the moderate range (77.65 ± 8.14). Multiple linear regression analysis indicated that level of education, nursing administration experience, and informatics education/training were significant factors affecting competency levels. Conclusion. The factors identified in this study can serve as a reference for nurse managers who were wishing to improve their informatics competency, hospital administrators seeking to provide appropriate training, and nursing educators who were making decisions about nursing informatics curricula. These findings suggest that efforts to enhance the informatics competency of nurse managers have marked potential benefits. PMID:24790565

  4. The cancer translational research informatics platform

    PubMed Central

    McConnell, Patrick; Dash, Rajesh C; Chilukuri, Ram; Pietrobon, Ricardo; Johnson, Kimberly; Annechiarico, Robert; Cuticchia, A Jamie

    2008-01-01

    Background Despite the pressing need for the creation of applications that facilitate the aggregation of clinical and molecular data, most current applications are proprietary and lack the necessary compliance with standards that would allow for cross-institutional data exchange. In line with its mission of accelerating research discoveries and improving patient outcomes by linking networks of researchers, physicians, and patients focused on cancer research, caBIG (cancer Biomedical Informatics Grid™) has sponsored the creation of the caTRIP (Cancer Translational Research Informatics Platform) tool, with the purpose of aggregating clinical and molecular data in a repository that is user-friendly, easily accessible, as well as compliant with regulatory requirements of privacy and security. Results caTRIP has been developed as an N-tier architecture, with three primary tiers: domain services, the distributed query engine, and the graphical user interface, primarily making use of the caGrid infrastructure to ensure compatibility with other tools currently developed by caBIG. The application interface was designed so that users can construct queries using either the Simple Interface via drop-down menus or the Advanced Interface for more sophisticated searching strategies to using drag-and-drop. Furthermore, the application addresses the security concerns of authentication, authorization, and delegation, as well as an automated honest broker service for deidentifying data. Conclusion Currently being deployed at Duke University and a few other centers, we expect that caTRIP will make a significant contribution to further the development of translational research through the facilitation of its data exchange and storage processes. PMID:19108734

  5. Transformation of health care through innovative use of information technology: challenges for health and medical informatics education.

    PubMed

    Haux, R; Swinkels, W; Ball, M; Knaup, P; Lun, K C

    1998-06-01

    Information storage and processing continues to become increasingly important for health care, and offers enormous potential to be realised in the delivery of health care. Therefore, it is imperative that all health care professionals should learn skills and gain knowledge in the field of health informatics, or medical informatics, respectively. Working Group 1, Health and Medical Informatics Education, of the International Medical Informatics Association (IMIA WG1) seeks to advance the knowledge of how these skills are taught in courses for the various health care professions around the world, and includes physicians, nurses, administrators, and specialists in medical informatics. IMIA WG1 held its 6th International Conference on Health and Medical Education in Newcastle, Australia, in August 1997. The theme of the conference was 'Transformation of Healthcare through Innovative Use of Information Technology'. This special issue of the International Journal of Medical Informatics on Health and Medical Informatics Education contains selected papers presented at the conference. In addition to the central topic, Educating Health Care Professionals in Medical Informatics the topics telematics, distance education and computer based training were also discussed at the conference. PMID:9726487

  6. Nanoinformatics: new challenges for biomedical informatics at the nano level.

    PubMed

    De La Iglesia, Diana; Chiesa, Stefano; Kern, Josipa; Maojo, Victor; Martin-Sanchez, Fernando; Potamias, George; Moustakis, Vassilis; Mitchell, Joyce A

    2009-01-01

    Over the last decades Nanotechnology has promised to advance science and technology in many areas. Within medicine, Nanomedicine promises to deliver new methods for diagnosis, prognosis and therapy. As the amount of available information is rapidly growing, new Biomedical Informatics approaches have to be developed to satisfy the increasing demand on data and knowledge management. In 2007, a new sub-discipline, already named "Nanoinformatics", was created with support from the US National Science Foundation. In Europe, a project named ACTION-Grid was launched in 2008 with support from the European Commission to analyze the challenges and agenda for developing Nanoinformatics as a discipline related to Nanotechnology, Biomedicine and Informatics. For MIE 2009, members of this consortium proposed a workshop to discuss the scientific and strategic issues associated with this topic. Nanoinformatics aims to create a bridge between Nanomedicine and Information Technology applying computational methods to manage the information created in the nanomedical domain. PMID:19745461

  7. Information technology challenges of biodiversity and ecosystems informatics

    USGS Publications Warehouse

    Schnase, J.L.; Cushing, J.; Frame, M.; Frondorf, A.; Landis, E.; Maier, D.; Silberschatz, A.

    2003-01-01

    Computer scientists, biologists, and natural resource managers recently met to examine the prospects for advancing computer science and information technology research by focusing on the complex and often-unique challenges found in the biodiversity and ecosystem domain. The workshop and its final report reveal that the biodiversity and ecosystem sciences are fundamentally information sciences and often address problems having distinctive attributes of scale and socio-technical complexity. The paper provides an overview of the emerging field of biodiversity and ecosystem informatics and demonstrates how the demands of biodiversity and ecosystem research can advance our understanding and use of information technologies.

  8. Basic medical science education must include medical informatics.

    PubMed

    Sarbadhikari, Suptendra Nath

    2004-10-01

    Medical Informatics is the science and art of processing medical information. In this age of "Information Explosion" choosing the useful one is rather difficult, and there lies the scope of electronic database management. However, still many outstanding personnel related to the healthcare sector take pride in being "computer illiterate". The onus of the best use lies on the end-user health care providers only. Another term tele-health encompasses all the e-health and telemedicine services. Computer aided or assisted learning (CAL) is a computer based tutorial method that uses the computer to pose questions, provide remedial information and chart a student through a course. Now the emphasis in medical education, is on problem based learning (PBL) and there CAL could be of utmost help if used judiciously. Basic Medical Education and Research lays the foundation for advancing and applying proper healthcare delivery systems. There is no doubt that deep knowledge of anatomy is mandatory for successful surgery. Also, comprehensive knowledge of physiology is essential for grasping the principles of pathology and pharmacology adequately, to avoid incorrect and inadequate practice of medicine. Similarly, medical informatics is not just a subject to be learnt and forgotten after the first professional MBBS examination. The final aim of every student should not only be to become a good user but also an expert for advancing medical knowledge base through medical informatics. In view of the fast changing world of medical informatics, it is of utmost necessity to formulate a flexible syllabus rather than a rigid one. PMID:15907048

  9. The Chief Clinical Informatics Officer (CCIO)

    PubMed Central

    Sengstack, Patricia; Thyvalikakath, Thankam Paul; Poikonen, John; Middleton, Blackford; Payne, Thomas; Lehmann, Christoph U

    2016-01-01

    Summary Introduction The emerging operational role of the “Chief Clinical Informatics Officer” (CCIO) remains heterogeneous with individuals deriving from a variety of clinical settings and backgrounds. The CCIO is defined in title, responsibility, and scope of practice by local organizations. The term encompasses the more commonly used Chief Medical Informatics Officer (CMIO) and Chief Nursing Informatics Officer (CNIO) as well as the rarely used Chief Pharmacy Informatics Officer (CPIO) and Chief Dental Informatics Officer (CDIO). Background The American Medical Informatics Association (AMIA) identified a need to better delineate the knowledge, education, skillsets, and operational scope of the CCIO in an attempt to address the challenges surrounding the professional development and the hiring processes of CCIOs. Discussion An AMIA task force developed knowledge, education, and operational skillset recommendations for CCIOs focusing on the common core aspect and describing individual differences based on Clinical Informatics focus. The task force concluded that while the role of the CCIO currently is diverse, a growing body of Clinical Informatics and increasing certification efforts are resulting in increased homogeneity. The task force advised that 1.) To achieve a predictable and desirable skillset, the CCIO must complete clearly defined and specified Clinical Informatics education and training. 2.) Future education and training must reflect the changing body of knowledge and must be guided by changing day-to-day informatics challenges. Conclusion A better defined and specified education and skillset for all CCIO positions will motivate the CCIO workforce and empower them to perform the job of a 21st century CCIO. Formally educated and trained CCIOs will provide a competitive advantage to their respective enterprise by fully utilizing the power of Informatics science. PMID:27081413

  10. Mobile healthcare informatics.

    PubMed

    Siau, Keng; Shen, Zixing

    2006-06-01

    Advances in wireless technology give pace to the rapid development of mobile applications. The coming mobile revolution will bring dramatic and fundamental changes to our daily life. It will influence the way we live, the way we do things, and the way we take care of our health. For the healthcare industry, mobile applications provide a new frontier in offering better care and services to patients, and a more flexible and mobile way of communicating with suppliers and patients. Mobile applications will provide important real time data for patients, physicians, insurers, and suppliers. In addition, it will revolutionalize the way information is managed in the healthcare industry and redefine the doctor - patient communication. This paper discusses different aspects of mobile healthcare. Specifically, it presents mobile applications in healthcare, and discusses possible challenges facing the development of mobile applications. Obstacles in developing mobile healthcare applications include mobile device limitations, wireless networking problems, infrastructure constraints, security concerns, and user distrust. Research issues in resolving or alleviating these problems are also discussed in the paper. PMID:16777784

  11. Measuring nursing informatics competencies of practicing nurses in Korea: Nursing Informatics Competencies Questionnaire.

    PubMed

    Chung, Seon Yoon; Staggers, Nancy

    2014-12-01

    Informatics competencies are a necessity for contemporary nurses. However, few researchers have investigated informatics competencies for practicing nurses. A full set of Informatics competencies, an instrument to measure these competencies, and potential influencing factors have yet to be identified for practicing nurses. The Nursing Informatics Competencies Questionnaire was designed, tested for psychometrics, and used to measure beginning and experienced levels of practice. A pilot study using 54 nurses ensured item comprehension and clarity. Internal consistency and face and content validity were established. A cross-sectional survey was then conducted on 230 nurses in Seoul, Korea, to determine construct validity, describe a complete set of informatics competencies, and explore possible influencing factors on existing informatics competencies. Principal components analysis, descriptive statistics, and multiple regression were used for data analysis. Principal components analysis gives support for the Nursing Informatics Competencies Questionnaire construct validity. Survey results indicate that involvement in a managerial position and self-directed informatics-related education may be more influential for improving informatics competencies, whereas general clinical experience and workplace settings are not. This study provides a foundation for understanding how informatics competencies might be integrated throughout nurses' work lives and how to develop appropriate strategies to support nurses in their informatics practice in clinical settings. PMID:25393832

  12. Perspective: Materials informatics and big data: Realization of the "fourth paradigm" of science in materials science

    NASA Astrophysics Data System (ADS)

    Agrawal, Ankit; Choudhary, Alok

    2016-05-01

    Our ability to collect "big data" has greatly surpassed our capability to analyze it, underscoring the emergence of the fourth paradigm of science, which is data-driven discovery. The need for data informatics is also emphasized by the Materials Genome Initiative (MGI), further boosting the emerging field of materials informatics. In this article, we look at how data-driven techniques are playing a big role in deciphering processing-structure-property-performance relationships in materials, with illustrative examples of both forward models (property prediction) and inverse models (materials discovery). Such analytics can significantly reduce time-to-insight and accelerate cost-effective materials discovery, which is the goal of MGI.

  13. The Impact of Medical Informatics on Librarianship.

    ERIC Educational Resources Information Center

    Dalrymple, Prudence W.

    The thesis of this paper is that the growth of the field of medical informatics, while seemingly a potential threat to medical librarianship, is in fact an opportunity for librarianship to both extend its reach and also to further define its unique characteristics in contrast to those of medical informatics. Furthermore, because medical…

  14. Medical Informatics in Academic Health Science Centers.

    ERIC Educational Resources Information Center

    Frisse, Mark E.

    1992-01-01

    An analysis of the state of medical informatics, the application of computer and information technology to biomedicine, looks at trends and concerns, including integration of traditionally distinct enterprises (clinical information systems, financial information, scholarly support activities, infrastructures); informatics career choice and…

  15. Medical Informatics: Market for IS/IT.

    ERIC Educational Resources Information Center

    Morris, Theodore Allan

    2002-01-01

    Uses co-occurrence analysis of INSPEC classification codes and thesaurus terms assigned to medical informatics (biomedical information) journal articles and proceedings papers to reveal a more complete perspective of how information science and information technology (IS/IT) authors view medical informatics. Discusses results of cluster analysis…

  16. The Teaching of Informatics for Business Students

    ERIC Educational Resources Information Center

    Sora, Sebastian A.

    2008-01-01

    Informatics is a branch of computer science that concerns itself, in actuality, with the use of information systems. The objective of this paper is to focus on the business curriculum for graduate students and their gaining proficiency in informatics so that they can understand the concept of information, the access of information, the use of…

  17. Informatics Education in Italian Secondary Schools

    ERIC Educational Resources Information Center

    Bellettini, Carlo; Lonati, Violetta; Malchiodi, Dario; Monga, Mattia; Morpurgo, Anna; Torelli, Mauro; Zecca, Luisa

    2014-01-01

    This article describes the state of informatics education in the Italian secondary schools, highlighting how the learning objectives set up by the Ministry of Education are difficult to meet, due to the fact that the subject is often taught by teachers not holding an informatics degree, the lack of suitable teaching material and the expectations…

  18. Teaching Some Informatics Concepts Using Formal System

    ERIC Educational Resources Information Center

    Yang, Sojung; Park, Seongbin

    2014-01-01

    There are many important issues in informatics and many agree that algorithms and programming are most important issues that need to be included in informatics education (Dagiene and Jevsikova, 2012). In this paper, we propose how some of these issues can be easily taught using the notion of a formal system which consists of axioms and inference…

  19. The Evolution of Bioinformatics in Toxicology: Advancing Toxicogenomics

    PubMed Central

    Afshari, Cynthia A.; Hamadeh, Hisham K.; Bushel, Pierre R.

    2011-01-01

    As one reflects back through the past 50 years of scientific research, a significant accomplishment was the advance into the genomic era. Basic research scientists have uncovered the genetic code and the foundation of the most fundamental building blocks for the molecular activity that supports biological structure and function. Accompanying these structural and functional discoveries is the advance of techniques and technologies to probe molecular events, in time, across environmental and chemical exposures, within individuals, and across species. The field of toxicology has kept pace with advances in molecular study, and the past 50 years recognizes significant growth and explosive understanding of the impact of the compounds and environment to basic cellular and molecular machinery. The advancement of molecular techniques applied in a whole-genomic capacity to the study of toxicant effects, toxicogenomics, is no doubt a significant milestone for toxicological research. Toxicogenomics has also provided an avenue for advancing a joining of multidisciplinary sciences including engineering and informatics in traditional toxicological research. This review will cover the evolution of the field of toxicogenomics in the context of informatics integration its current promise, and limitations. PMID:21177775

  20. Five Periods in Development of Medical Informatics

    PubMed Central

    Masic, Izet

    2014-01-01

    Medical informatics, as scientific discipline, has to do with all aspects of understanding and promoting the effective organization, analysis, management, and use of information in health care. While the field of Medical informatics shares the general scope of these interests with some other health care specialities and disciplines, Medical (Health) informatics has developed its own areas of emphasis and approaches that have set it apart from other disciplines and specialities. For the last fifties of 20th century and some more years of 21st century, Medical informatics had the five time periods of characteristic development. In this paper author shortly described main scientific innovations and inventors who created development of Medical informatics. PMID:24648619

  1. What informatics is and isn't.

    PubMed

    Friedman, Charles P

    2013-01-01

    The term informatics is currently enveloped in chaos. One way to clarify the meaning of informatics is to identify the competencies associated with training in the field, but this approach can conceal the whole that the competencies atomistically describe. This work takes a different approach by offering three higher-level visions of what characterizes the field, viewing informatics as: (1) cross-training between basic informational sciences and an application domain, (2) the relentless pursuit of making people better at what they do, and (3) a field encompassing four related types of activities. Applying these perspectives to describe what informatics is, one can also conclude that informatics is not: tinkering with computers, analysis of large datasets per se, employment in circumscribed health IT workforce roles, the practice of health information management, or anything done using a computer. PMID:23059730

  2. Five periods in development of medical informatics.

    PubMed

    Masic, Izet

    2014-02-01

    Medical informatics, as scientific discipline, has to do with all aspects of understanding and promoting the effective organization, analysis, management, and use of information in health care. While the field of Medical informatics shares the general scope of these interests with some other health care specialities and disciplines, Medical (Health) informatics has developed its own areas of emphasis and approaches that have set it apart from other disciplines and specialities. For the last fifties of 20th century and some more years of 21st century, Medical informatics had the five time periods of characteristic development. In this paper author shortly described main scientific innovations and inventors who created development of Medical informatics. PMID:24648619

  3. Bringing nursing informatics into the undergraduate classroom.

    PubMed

    Vanderbeek, J; Ulrich, D; Jaworski, R; Werner, L; Hergert, D; Beery, T; Baas, L

    1994-01-01

    Nursing informatics is not formally addressed in most undergraduate nursing education programs. Nurses usually rely on their employer and/or device vendors to provide this education. Few nurses are able to capitalize on the potential of computer technology because they have not been sufficiently exposed to nursing informatics during their nursing education. Biomedical computer technology/informatics needs to be brought into the classroom, away from the pressures of the work environment. Informatics training needs to be incorporated into undergraduate nursing education through an integrated systems approach, combining elements of nursing, systems analysis, and engineering. In this article, a university-based state-of-the-art classroom and education plan using an integrated approach to educate nurses in nursing informatics is described. PMID:7954066

  4. Phytozome Comparative Plant Genomics Portal

    SciTech Connect

    Goodstein, David; Batra, Sajeev; Carlson, Joseph; Hayes, Richard; Phillips, Jeremy; Shu, Shengqiang; Schmutz, Jeremy; Rokhsar, Daniel

    2014-09-09

    The Dept. of Energy Joint Genome Institute is a genomics user facility supporting DOE mission science in the areas of Bioenergy, Carbon Cycling, and Biogeochemistry. The Plant Program at the JGI applies genomic, analytical, computational and informatics platforms and methods to: 1. Understand and accelerate the improvement (domestication) of bioenergy crops 2. Characterize and moderate plant response to climate change 3. Use comparative genomics to identify constrained elements and infer gene function 4. Build high quality genomic resource platforms of JGI Plant Flagship genomes for functional and experimental work 5. Expand functional genomic resources for Plant Flagship genomes

  5. Lessons learned from the application of whole-genome analysis to the treatment of patients with advanced cancers.

    PubMed

    Laskin, Janessa; Jones, Steven; Aparicio, Samuel; Chia, Stephen; Ch'ng, Carolyn; Deyell, Rebecca; Eirew, Peter; Fok, Alexandra; Gelmon, Karen; Ho, Cheryl; Huntsman, David; Jones, Martin; Kasaian, Katayoon; Karsan, Aly; Leelakumari, Sreeja; Li, Yvonne; Lim, Howard; Ma, Yussanne; Mar, Colin; Martin, Monty; Moore, Richard; Mungall, Andrew; Mungall, Karen; Pleasance, Erin; Rassekh, S Rod; Renouf, Daniel; Shen, Yaoqing; Schein, Jacqueline; Schrader, Kasmintan; Sun, Sophie; Tinker, Anna; Zhao, Eric; Yip, Stephen; Marra, Marco A

    2015-10-01

    Given the success of targeted agents in specific populations it is expected that some degree of molecular biomarker testing will become standard of care for many, if not all, cancers. To facilitate this, cancer centers worldwide are experimenting with targeted "panel" sequencing of selected mutations. Recent advances in genomic technology enable the generation of genome-scale data sets for individual patients. Recognizing the risk, inherent in panel sequencing, of failing to detect meaningful somatic alterations, we sought to establish processes to integrate data from whole-genome analysis (WGA) into routine cancer care. Between June 2012 and August 2014, 100 adult patients with incurable cancers consented to participate in the Personalized OncoGenomics (POG) study. Fresh tumor and blood samples were obtained and used for whole-genome and RNA sequencing. Computational approaches were used to identify candidate driver mutations, genes, and pathways. Diagnostic and drug information were then sought based on these candidate "drivers." Reports were generated and discussed weekly in a multidisciplinary team setting. Other multidisciplinary working groups were assembled to establish guidelines on the interpretation, communication, and integration of individual genomic findings into patient care. Of 78 patients for whom WGA was possible, results were considered actionable in 55 cases. In 23 of these 55 cases, the patients received treatments motivated by WGA. Our experience indicates that a multidisciplinary team of clinicians and scientists can implement a paradigm in which WGA is integrated into the care of late stage cancer patients to inform systemic therapy decisions. PMID:27148575

  6. Challenges, Solutions, and Quality Metrics of Personal Genome Assembly in Advancing Precision Medicine

    PubMed Central

    Xiao, Wenming; Wu, Leihong; Yavas, Gokhan; Simonyan, Vahan; Ning, Baitang; Hong, Huixiao

    2016-01-01

    Even though each of us shares more than 99% of the DNA sequences in our genome, there are millions of sequence codes or structure in small regions that differ between individuals, giving us different characteristics of appearance or responsiveness to medical treatments. Currently, genetic variants in diseased tissues, such as tumors, are uncovered by exploring the differences between the reference genome and the sequences detected in the diseased tissue. However, the public reference genome was derived with the DNA from multiple individuals. As a result of this, the reference genome is incomplete and may misrepresent the sequence variants of the general population. The more reliable solution is to compare sequences of diseased tissue with its own genome sequence derived from tissue in a normal state. As the price to sequence the human genome has dropped dramatically to around $1000, it shows a promising future of documenting the personal genome for every individual. However, de novo assembly of individual genomes at an affordable cost is still challenging. Thus, till now, only a few human genomes have been fully assembled. In this review, we introduce the history of human genome sequencing and the evolution of sequencing platforms, from Sanger sequencing to emerging “third generation sequencing” technologies. We present the currently available de novo assembly and post-assembly software packages for human genome assembly and their requirements for computational infrastructures. We recommend that a combined hybrid assembly with long and short reads would be a promising way to generate good quality human genome assemblies and specify parameters for the quality assessment of assembly outcomes. We provide a perspective view of the benefit of using personal genomes as references and suggestions for obtaining a quality personal genome. Finally, we discuss the usage of the personal genome in aiding vaccine design and development, monitoring host immune

  7. Challenges, Solutions, and Quality Metrics of Personal Genome Assembly in Advancing Precision Medicine.

    PubMed

    Xiao, Wenming; Wu, Leihong; Yavas, Gokhan; Simonyan, Vahan; Ning, Baitang; Hong, Huixiao

    2016-01-01

    Even though each of us shares more than 99% of the DNA sequences in our genome, there are millions of sequence codes or structure in small regions that differ between individuals, giving us different characteristics of appearance or responsiveness to medical treatments. Currently, genetic variants in diseased tissues, such as tumors, are uncovered by exploring the differences between the reference genome and the sequences detected in the diseased tissue. However, the public reference genome was derived with the DNA from multiple individuals. As a result of this, the reference genome is incomplete and may misrepresent the sequence variants of the general population. The more reliable solution is to compare sequences of diseased tissue with its own genome sequence derived from tissue in a normal state. As the price to sequence the human genome has dropped dramatically to around $1000, it shows a promising future of documenting the personal genome for every individual. However, de novo assembly of individual genomes at an affordable cost is still challenging. Thus, till now, only a few human genomes have been fully assembled. In this review, we introduce the history of human genome sequencing and the evolution of sequencing platforms, from Sanger sequencing to emerging "third generation sequencing" technologies. We present the currently available de novo assembly and post-assembly software packages for human genome assembly and their requirements for computational infrastructures. We recommend that a combined hybrid assembly with long and short reads would be a promising way to generate good quality human genome assemblies and specify parameters for the quality assessment of assembly outcomes. We provide a perspective view of the benefit of using personal genomes as references and suggestions for obtaining a quality personal genome. Finally, we discuss the usage of the personal genome in aiding vaccine design and development, monitoring host immune-response, tailoring

  8. Publication trends in the medical informatics literature: 20 years of "Medical Informatics" in MeSH

    PubMed Central

    2009-01-01

    Background The purpose of this study is to identify publication output, and research areas, as well as descriptively and quantitatively characterize the field of medical informatics through publication trend analysis over a twenty year period (1987–2006). Methods A bibliometric analysis of medical informatics citations indexed in Medline was performed using publication trends, journal frequency, impact factors, MeSH term frequencies and characteristics of citations. Results There were 77,023 medical informatics articles published during this 20 year period in 4,644 unique journals. The average annual article publication growth rate was 12%. The 50 identified medical informatics MeSH terms are rarely assigned together to the same document and are almost exclusively paired with a non-medical informatics MeSH term, suggesting a strong interdisciplinary trend. Trends in citations, journals, and MeSH categories of medical informatics output for the 20-year period are summarized. Average impact factor scores and weighted average impact factor scores increased over the 20-year period with two notable growth periods. Conclusion There is a steadily growing presence and increasing visibility of medical informatics literature over the years. Patterns in research output that seem to characterize the historic trends and current components of the field of medical informatics suggest it may be a maturing discipline, and highlight specific journals in which the medical informatics literature appears most frequently, including general medical journals as well as informatics-specific journals. PMID:19159472

  9. Advances in functional genomics for investigating salinity stress tolerance mechanisms in cereals.

    PubMed

    Shelden, Megan C; Roessner, Ute

    2013-01-01

    Abiotic stresses such as low water availability and high salinity are major causes of cereal crop yield losses and significantly impact on sustainability. Wheat and barley are two of the most important cereal crops (after maize and rice) and are grown in increasingly hostile environments with soil salinity and drought both expected to increase this century, reducing the availability of arable land. Barley and wheat are classified as glycophytes (salt-sensitive), yet they are more salt-tolerant than other cereal crops such as rice and so are good models for studying salt tolerance in cereals. The exploitation of genetic variation of phenotypic traits through plant breeding could significantly improve growth of cereals in salinity-affected regions, thus leading to improved crop yields. Genetic variation in phenotypic traits for abiotic stress tolerance have been identified in land races and wild germplasm but the molecular basis of these differences is often difficult to determine due to the complex genetic nature of these species. High-throughput functional genomics technologies, such as transcriptomics, metabolomics, proteomics, and ionomics are powerful tools for investigating the molecular responses of plants to abiotic stress. The advancement of these technologies has allowed for the identification and quantification of transcript/metabolites in specific cell types and/or tissues. Using these new technologies on plants will provide a powerful tool to uncovering genetic traits in more complex species such as wheat and barley and provide novel insights into the molecular mechanisms of salinity stress tolerance. PMID:23717314

  10. Recent patents and advances in genomic biomarker discovery for colorectal cancers.

    PubMed

    Quyun, Chen; Ye, Zhiyun; Lin, Sheng-Cai; Lin, Biaoyang

    2010-06-01

    Colorectal cancer (CRC) is the third most common cancer in the world. Early diagnosis of colorectal cancer is the key to reducing the death rate of CRC patients. Predicting the response to current therapeutic modalities of CRC will also have a great impact on patient care. This review summarizes recent advances and patents in biomarker discovery in CRC under five major categories; including genomic changes, expression changes, mutations, epigenetic changes and microRNAs. The interesting patents include: 1) a patent for a method to differentiate normal exfoliated cells from cancer cells based on whether they were subjected to apoptosis and DNA degradation; 2) A model (PM-33 multiple molecular marker model) based on expression changes of up-regulation of the MDM2, DUSP6, and NFl genes down-regulation of the RNF4, MMD and EIF2S3 genes, which achieved an 88% sensitivity, and an 82% specificity for CRC diagnosis; 3) gene mutations in PTEN, KRAS, PIK3CA for predicting the response to anti-EGFR therapies, a common drug used for CRC treatment; 4) patents on epigenetic changes of ITGA4, SEPT9, ALX4, TFAP2E FOXL2, SARM1, ID4 etc. and many key miRNAs. Finally, future directions in the fields were commented on or suggested, including the combination of multiple categories of biomarkers and pathway central or network-based biomarker panels. PMID:20426761

  11. Early experiences of accredited clinical informatics fellowships.

    PubMed

    Longhurst, Christopher A; Pageler, Natalie M; Palma, Jonathan P; Finnell, John T; Levy, Bruce P; Yackel, Thomas R; Mohan, Vishnu; Hersh, William R

    2016-07-01

    Since the launch of the clinical informatics subspecialty for physicians in 2013, over 1100 physicians have used the practice and education pathways to become board-certified in clinical informatics. Starting in 2018, only physicians who have completed a 2-year clinical informatics fellowship program accredited by the Accreditation Council on Graduate Medical Education will be eligible to take the board exam. The purpose of this viewpoint piece is to describe the collective experience of the first four programs accredited by the Accreditation Council on Graduate Medical Education and to share lessons learned in developing new fellowship programs in this novel medical subspecialty. PMID:27206458

  12. Medical Informatics in Croatia – a Historical Survey

    PubMed Central

    Dezelic, Gjuro; Kern, Josipa; Petrovecki, Mladen; Ilakovac, Vesna; Hercigonja-Szekeres, Mira

    2014-01-01

    A historical survey of medical informatics (MI) in Croatia is presented from the beginnings in the late sixties of the 20th century to the present time. Described are MI projects, applications in clinical medicine and public health, start and development of MI research and education, beginnings of international cooperation, establishment of the Croatian Society for MI and its membership to EFMI and IMIA. The current status of computerization of the Croatian healthcare system is sketched as well as the present graduate and postgraduate study MI curricula. The information contained in the paper shows that MI in Croatia developed and still develops along with its advancement elsewhere. PMID:24648620

  13. Health Informatics in the Classroom: An Empirical Study to Investigate Higher Education's Response to Healthcare Transformation

    ERIC Educational Resources Information Center

    Ashrafi, Noushin; Kuilboer, Jean-Pierre; Joshi, Chaitanya; Ran, Iris; Pande, Priyanka

    2014-01-01

    The explosive advances in information technology combined with the current climate for health care reform have intensified the need for skilled individuals who can develop, understand, and manage medical information systems in organizations. Health Informatics facilitates quality care at a reasonable cost by allowing access to the right data by…

  14. Development, Implementation, and Evaluation of Health Informatics Masters Program at KSAU-HS University, Saudi Arabia

    ERIC Educational Resources Information Center

    Majid, Altuwaijri

    2007-01-01

    The Saudi health sector has witnessed a significant progress in recent decades with some Saudi hospitals receiving international recognition. However, this progress has not been accompanied by the same advancement in the health informatics field whose applications have become a necessity for hospitals in order to achieve important objectives such…

  15. Consumer Informatics in Chronic Illness

    PubMed Central

    Tetzlaff, Linda

    1997-01-01

    Abstract Objective: To explore the informatic requirements in the home care of chronically ill patients. Design: A number of strategies were deployed to help evoke a picture of home care informatics needs: A detailed questionnaire evaluating informational needs and assessing programmable technologies was distributed to a clinic population of parents of children with cancer. Open ended questionnaires were distributed to medical staff and parents soliciting a list of questions asked of medical staff. Parent procedure training was observed to evaluate the training dialog, and parents were observed interacting with a prototype information and education computer offering. Results: Parents' concerns ranged from the details of managing day to day, to conceptual information about disease and treatment, to management of psychosocial problems. They sought information to solve problems and to provide emotional support, which may create conflicts of interest when the material is threatening. Whether they preferred to be informed by a doctor, nurse, or another parent depended on the nature of the information. Live interaction was preferred to video, which was preferred to text for all topics. Respondents used existing technologies in a straightforward way but were enthusiastic about the proposed use of computer technology to support home care. Multimedia solutions appear to complement user needs and preferences. Conclusion: Consumers appear positively disposed toward on-line solutions. On-line systems can offer breadth, depth and timeliness currently unattainable. Patients should be involved in the formation and development process in much the same way that users are involved in usercentered computer interface design. A generic framework for patient content is presented that could be applied across multiple disorders. PMID:9223035

  16. Bioimage Informatics in the context of Drosophila research.

    PubMed

    Jug, Florian; Pietzsch, Tobias; Preibisch, Stephan; Tomancak, Pavel

    2014-06-15

    Modern biological research relies heavily on microscopic imaging. The advanced genetic toolkit of Drosophila makes it possible to label molecular and cellular components with unprecedented level of specificity necessitating the application of the most sophisticated imaging technologies. Imaging in Drosophila spans all scales from single molecules to the entire populations of adult organisms, from electron microscopy to live imaging of developmental processes. As the imaging approaches become more complex and ambitious, there is an increasing need for quantitative, computer-mediated image processing and analysis to make sense of the imagery. Bioimage Informatics is an emerging research field that covers all aspects of biological image analysis from data handling, through processing, to quantitative measurements, analysis and data presentation. Some of the most advanced, large scale projects, combining cutting edge imaging with complex bioimage informatics pipelines, are realized in the Drosophila research community. In this review, we discuss the current research in biological image analysis specifically relevant to the type of systems level image datasets that are uniquely available for the Drosophila model system. We focus on how state-of-the-art computer vision algorithms are impacting the ability of Drosophila researchers to analyze biological systems in space and time. We pay particular attention to how these algorithmic advances from computer science are made usable to practicing biologists through open source platforms and how biologists can themselves participate in their further development. PMID:24732429

  17. Advances in targeted and immunobased therapies for colorectal cancer in the genomic era

    PubMed Central

    Seow, Heng Fong; Yip, Wai Kien; Fifis, Theodora

    2016-01-01

    Targeted therapies require information on specific defective signaling pathways or mutations. Advances in genomic technologies and cell biology have led to identification of new therapeutic targets associated with signal-transduction pathways. Survival times of patients with colorectal cancer (CRC) can be extended with combinations of conventional cytotoxic agents and targeted therapies. Targeting EGFR- and VEGFR-signaling systems has been the major focus for treatment of metastatic CRC. However, there are still limitations in their clinical application, and new and better drug combinations are needed. This review provides information on EGFR and VEGF inhibitors, new therapeutic agents in the pipeline targeting EGFR and VEGFR pathways, and those targeting other signal-transduction pathways, such as MET, IGF1R, MEK, PI3K, Wnt, Notch, Hedgehog, and death-receptor signaling pathways for treatment of metastatic CRC. Additionally, multitargeted approaches in combination therapies targeting negative-feedback loops, compensatory networks, and cross talk between pathways are highlighted. Then, immunobased strategies to enhance antitumor immunity using specific monoclonal antibodies, such as the immune-checkpoint inhibitors anti-CTLA4 and anti-PD1, as well as the challenges that need to be overcome for increased efficacy of targeted therapies, including drug resistance, predictive markers of response, tumor subtypes, and cancer stem cells, are covered. The review concludes with a brief insight into the applications of next-generation sequencing, expression profiling for tumor subtyping, and the exciting progress made in in silico predictive analysis in the development of a prescription strategy for cancer therapy. PMID:27099521

  18. Comparative effectiveness research and medical informatics.

    PubMed

    D'Avolio, Leonard W; Farwell, Wildon R; Fiore, Louis D

    2010-12-01

    As is the case for environmental, ecological, astronomical, and other sciences, medical practice and research finds itself in a tsunami of data. This data deluge, due primarily to the introduction of digitalization in routine medical care and medical research, affords the opportunity for improved patient care and scientific discovery. Medical informatics is the subdiscipline of medicine created to make greater use of information in order to improve healthcare. The 4 areas of medical informatics research (information access, structure, analysis, and interaction) are used as a framework to discuss the overlap in information needs of comparative effectiveness research and potential contributions of medical informatics. Examples of progress from the medical informatics literature and the Veterans Affairs Healthcare System are provided. PMID:21184865

  19. Moving toward a United States strategic plan in primary care informatics: a White Paper of the Primary Care Informatics Working Group, American Medical Informatics Association.

    PubMed

    Little, David R; Zapp, John A; Mullins, Henry C; Zuckerman, Alan E; Teasdale, Sheila; Johnson, Kevin B

    2003-01-01

    The Primary Care Informatics Working Group (PCIWG) of the American Medical Informatics Association (AMIA) has identified the absence of a national strategy for primary care informatics. Under PCIWG leadership, major national and international societies have come together to create the National Alliance for Primary Care Informatics (NAPCI), to promote a connection between the informatics community and the organisations that support primary care. The PCIWG clinical practice subcommittee has recognised the necessity of a global needs assessment, and proposed work in point-of-care technology, clinical vocabularies, and ambulatory electronic medical record development. Educational needs include a consensus statement on informatics competencies, recommendations for curriculum and teaching methods, and methodologies to evaluate their effectiveness. The research subcommittee seeks to define a primary care informatics research agenda, and to support and disseminate informatics research throughout the primary care community. The AMIA board of directors has enthusiastically endorsed the conceptual basis for this White Paper. PMID:14567875

  20. Evolution of Trends in European Medical Informatics

    PubMed Central

    I. Mihalas, George

    2014-01-01

    This presentation attempts to analyze the trends in Medical Informatics along half a century, in the European socio-political and technological development context. Based on the major characteristics which seem dominant in some periods, a staging is proposed, with a description of each period – the context, major ideas, views and events. A summary of major features of each period is also added. This paper has an original presentation of the evolution of major trends in medical informatics. PMID:24648618

  1. From classification to epilepsy ontology and informatics.

    PubMed

    Zhang, Guo-Qiang; Sahoo, Satya S; Lhatoo, Samden D

    2012-07-01

    The 2010 International League Against Epilepsy (ILAE) classification and terminology commission report proposed a much needed departure from previous classifications to incorporate advances in molecular biology, neuroimaging, and genetics. It proposed an interim classification and defined two key requirements that need to be satisfied. The first is the ability to classify epilepsy in dimensions according to a variety of purposes including clinical research, patient care, and drug discovery. The second is the ability of the classification system to evolve with new discoveries. Multidimensionality and flexibility are crucial to the success of any future classification. In addition, a successful classification system must play a central role in the rapidly growing field of epilepsy informatics. An epilepsy ontology, based on classification, will allow information systems to facilitate data-intensive studies and provide a proven route to meeting the two foregoing key requirements. Epilepsy ontology will be a structured terminology system that accommodates proposed and evolving ILAE classifications, the National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS) Common Data Elements, the International Classification of Diseases (ICD) systems and explicitly specifies all known relationships between epilepsy concepts in a proper framework. This will aid evidence-based epilepsy diagnosis, investigation, treatment and research for a diverse community of clinicians and researchers. Benefits range from systematization of electronic patient records to multimodal data repositories for research and training manuals for those involved in epilepsy care. Given the complexity, heterogeneity, and pace of research advances in the epilepsy domain, such an ontology must be collaboratively developed by key stakeholders in the epilepsy community and experts in knowledge engineering and computer science. PMID:22765502

  2. From Classification to Epilepsy Ontology and Informatics

    PubMed Central

    Zhang, Guo-Qiang; Sahoo, Satya S; Lhatoo, Samden D

    2012-01-01

    Summary The 2010 International League Against Epilepsy (ILAE) classification and terminology commission report proposed a much needed departure from previous classifications to incorporate advances in molecular biology, neuroimaging, and genetics. It proposed an interim classification and defined two key requirements that need to be satisfied. The first is the ability to classify epilepsy in dimensions according to a variety of purposes including clinical research, patient care, and drug discovery. The second is the ability of the classification system to evolve with new discoveries. Multi-dimensionality and flexibility are crucial to the success of any future classification. In addition, a successful classification system must play a central role in the rapidly growing field of epilepsy informatics. An epilepsy ontology, based on classification, will allow information systems to facilitate data-intensive studies and provide a proven route to meeting the two foregoing key requirements. Epilepsy ontology will be a structured terminology system that accommodates proposed and evolving ILAE classifications, the NIH/NINDS Common Data Elements, the ICD systems and explicitly specifies all known relationships between epilepsy concepts in a proper framework. This will aid evidence based epilepsy diagnosis, investigation, treatment and research for a diverse community of clinicians and researchers. Benefits range from systematization of electronic patient records to multi-modal data repositories for research and training manuals for those involved in epilepsy care. Given the complexity, heterogeneity and pace of research advances in the epilepsy domain, such an ontology must be collaboratively developed by key stakeholders in the epilepsy community and experts in knowledge engineering and computer science. PMID:22765502

  3. Heritability and Genome-wide Association Study To Assess Genetic Differences Between Advanced Age-Related Macular Degeneration Subtypes

    PubMed Central

    Sobrin, Lucia; Ripke, Stephan; Yu, Yi; Fagerness, Jesen; Bhangale, Tushar R.; Tan, Perciliz L.; Souied, Eric H.; Buitendijk, Gabriëlle H.S.; Merriam, Joanna E.; Richardson, Andrea J.; Raychaudhuri, Soumya; Reynolds, Robyn; Chin, Kimberly A.; Lee, Aaron Y.; Leveziel, Nicolas; Zack, Donald J.; Campochiaro, Peter; Smith, R. Theodore; Barile, Gaetano R.; Hogg, Ruth E.; Chakravarthy, Usha; Behrens, Timothy W.; Uitterlinden, André G.; van Duijn, Cornelia M.; Vingerling, Johannes R.; Brantley, Milam A.; Baird, Paul N.; Klaver, Caroline C.W.; Allikmets, Rando; Katsanis, Nicholas; Graham, Robert R.; Ioannidis, John P.A.; Daly, Mark J.; Seddon, Johanna M.

    2013-01-01

    Purpose To investigate whether the two subtypes of advanced age-related macular degeneration (AMD), choroidal neovascularization (CNV) and geographic atrophy (GA), segregate separately in families and to identify which genetic variants are associated with these two subtypes. Design Sibling correlation study and genome-wide association study (GWAS) Participants For the sibling correlation study, we included 209 sibling pairs with advanced AMD. For the GWAS, we included 2594 participants with advanced AMD subtypes and 4134 controls. Replication cohorts included 5383 advanced AMD participants and 15,240 controls. Methods Participants had AMD grade assigned based on fundus photography and/or examination. To determine heritability of advanced AMD subtypes, we performed a sibling correlation study. For the GWAS, we conducted genome-wide genotyping and imputed 6,036,699 single nucleotide polymorphism (SNPs). We then analyzed SNPs with a generalized linear model controlling for genotyping platform and genetic ancestry. The most significant associations were evaluated in independent cohorts. Main Outcome Measures Concordance of advanced AMD subtypes in sibling pairs and associations between SNPs with GA and CNV advanced AMD subtypes. Results The difference between the observed and expected proportion of siblings concordant for the same subtype of advanced AMD was different to a statistically significant degree (P=4.2 x 10−5) meaning that siblings of probands with CNV or GA are more likely to develop CNV or GA, respectively. In the analysis comparing participants with CNV to those with GA, we observed a statistically significant association at the ARMS2/HTRA1 locus [rs10490924, odds ratio (OR)=1.47, P=4.3 ×10−9] which was confirmed in the replication samples (OR=1.38, P=7.4 x 10−14 for combined discovery and replication analysis). Conclusions Whether a patient with AMD develops CNV vs. GA is determined in part by genetic variation. In this large GWAS meta-analysis and

  4. Integrating experiential learning into a double degree masters program in nursing and health informatics.

    PubMed

    Borycki, Elizabeth M; Frisch, Noreen; Kushniruk, Andre W; McIntyre, Marjorie; Hutchinson, David

    2012-01-01

    In Canada there are few nurses who have advanced practice competencies in nursing informatics. This is a significant issue for regional health authorities, governments and electronic health record vendors in Canada who are implementing electronic health records. Few Schools of Nursing provide formalized opportunities for nurses to develop informatics competencies. Many of these opportunities take the form of post-baccalaureate certificate programs or individual undergraduate or graduate level courses in nursing. The purpose of this paper will be to: (1) describe the health and human resource issues in this area in Canada, (2) provide a brief overview of the design and development of a new, innovative double degree program at the intersection of nursing and health informatics that interleaves cooperative learning, (3) describe the integration of cooperative learning into this new program, and (4) outline the lessons learned in integrating cooperative education into such a graduate program. PMID:24199044

  5. Health informatics and analytics - building a program to integrate business analytics across clinical and administrative disciplines.

    PubMed

    Tremblay, Monica Chiarini; Deckard, Gloria J; Klein, Richard

    2016-07-01

    Health care organizations must develop integrated health information systems to respond to the numerous government mandates driving the movement toward reimbursement models emphasizing value-based and accountable care. Success in this transition requires integrated data analytics, supported by the combination of health informatics, interoperability, business process design, and advanced decision support tools. This case study presents the development of a master's level cross- and multidisciplinary informatics program offered through a business school. The program provides students from diverse backgrounds with the knowledge, leadership, and practical application skills of health informatics, information systems, and data analytics that bridge the interests of clinical and nonclinical professionals. This case presents the actions taken and challenges encountered in navigating intra-university politics, specifying curriculum, recruiting the requisite interdisciplinary faculty, innovating the educational format, managing students with diverse educational and professional backgrounds, and balancing multiple accreditation agencies. PMID:27274022

  6. An analysis of published nursing informatics competencies.

    PubMed

    Carter-Templeton, Heather; Patterson, Ramona; Russell, Cynthia

    2009-01-01

    Nursing informatics competency lists can provide a clear picture of required skills, knowledge, and attitudes needed for today's nursing workforce in a high-tech environment. Many stakeholders such as employers and educators have a vested interest in defining nursing informatics competencies for nurses. The primary objective of this paper was to compare and contrast published nursing informatics competencies. A literature search was conducted using the terms "informatics competencies" and "nursing informatics competencies" via PubMeb and CINAHL for relevant articles. The search captured 37 articles; however, only six met the inclusion criteria set prior to the search. These six competency lists were reviewed for audience, sample size, design, categories used to classify competencies and operational examples of competencies. Findings revealed that there is variation among published informatics competencies in regard to content, presentation, and audience. A general list of competencies that can be utilized by nurses at all levels is needed. As a result nurses could operationalize and measure the skills, knowledge, and attitudes necessary to execute safe and effective nursing care in today's health care setting. PMID:19592901

  7. Using Informatics to Improve the Care of Patients Susceptible to Malignant Hyperthermia.

    PubMed

    Denholm, Bonnie G

    2016-04-01

    Perioperative nurses and nurse leaders should understand how to apply a nursing informatics framework and informatics concepts to strengthen data interpretation, transitions in care, and engagement with patients susceptible to malignant hyperthermia (MH) and their family members. Patient outcomes can be improved when informatics solutions facilitate identifying risks, clinical decision making in a crisis situation, retrieving priority information during transitions of care, and involving patients in planning care. Incorporating informatics solutions into existing quality improvement processes can help evaluate knowledge and preparedness related to managing care for a patient in an MH crisis. Informatics solutions can also help enhance interoperability by evaluating workflow related to transitions in care. Perioperative nurses and nurse leaders should advocate for diligence in submitting reports of MH-suspected events to databases. Improved data collection and data sharing enhance aggregated standardized data sets, which can advance research and increase the quality of evidence available with which to guide practice. PMID:27004500

  8. MIRASS: medical informatics research activity support system using information mashup network.

    PubMed

    Kiah, M L M; Zaidan, B B; Zaidan, A A; Nabi, Mohamed; Ibraheem, Rabiu

    2014-04-01

    The advancement of information technology has facilitated the automation and feasibility of online information sharing. The second generation of the World Wide Web (Web 2.0) enables the collaboration and sharing of online information through Web-serving applications. Data mashup, which is considered a Web 2.0 platform, plays an important role in information and communication technology applications. However, few ideas have been transformed into education and research domains, particularly in medical informatics. The creation of a friendly environment for medical informatics research requires the removal of certain obstacles in terms of search time, resource credibility, and search result accuracy. This paper considers three glitches that researchers encounter in medical informatics research; these glitches include the quality of papers obtained from scientific search engines (particularly, Web of Science and Science Direct), the quality of articles from the indices of these search engines, and the customizability and flexibility of these search engines. A customizable search engine for trusted resources of medical informatics was developed and implemented through data mashup. Results show that the proposed search engine improves the usability of scientific search engines for medical informatics. Pipe search engine was found to be more efficient than other engines. PMID:24700079

  9. An informatics agenda for public health: summarized recommendations from the 2011 AMIA PHI Conference

    PubMed Central

    Goodman, Kenneth W; Gotham, Ivan J; Holmes, John H; Lang, Lisa; Miner, Kathleen; Potenziani, David D; Richards, Janise; Turner, Anne M; Fu, Paul C

    2012-01-01

    The AMIA Public Health Informatics 2011 Conference brought together members of the public health and health informatics communities to revisit the national agenda developed at the AMIA Spring Congress in 2001, assess the progress that has been made in the past decade, and develop recommendations to further guide the field. Participants met in five discussion tracks: technical framework; research and evaluation; ethics; education, professional training, and workforce development; and sustainability. Participants identified 62 recommendations, which clustered into three key themes related to the need to (1) enhance communication and information sharing within the public health informatics community, (2) improve the consistency of public health informatics through common public health terminologies, rigorous evaluation methodologies, and competency-based training, and (3) promote effective coordination and leadership that will champion and drive the field forward. The agenda and recommendations from the meeting will be disseminated and discussed throughout the public health and informatics communities. Both communities stand to gain much by working together to use these recommendations to further advance the application of information technology to improve health. PMID:22395299

  10. Genomic Methods Take the Plunge: Recent Advances in High-Throughput Sequencing of Marine Mammals.

    PubMed

    Cammen, Kristina M; Andrews, Kimberly R; Carroll, Emma L; Foote, Andrew D; Humble, Emily; Khudyakov, Jane I; Louis, Marie; McGowen, Michael R; Olsen, Morten Tange; Van Cise, Amy M

    2016-11-01

    The dramatic increase in the application of genomic techniques to non-model organisms (NMOs) over the past decade has yielded numerous valuable contributions to evolutionary biology and ecology, many of which would not have been possible with traditional genetic markers. We review this recent progression with a particular focus on genomic studies of marine mammals, a group of taxa that represent key macroevolutionary transitions from terrestrial to marine environments and for which available genomic resources have recently undergone notable rapid growth. Genomic studies of NMOs utilize an expanding range of approaches, including whole genome sequencing, restriction site-associated DNA sequencing, array-based sequencing of single nucleotide polymorphisms and target sequence probes (e.g., exomes), and transcriptome sequencing. These approaches generate different types and quantities of data, and many can be applied with limited or no prior genomic resources, thus overcoming one traditional limitation of research on NMOs. Within marine mammals, such studies have thus far yielded significant contributions to the fields of phylogenomics and comparative genomics, as well as enabled investigations of fitness, demography, and population structure. Here we review the primary options for generating genomic data, introduce several emerging techniques, and discuss the suitability of each approach for different applications in the study of NMOs. PMID:27511190

  11. Recent advances in ecological genomics: from phenotypic plasticity to convergent and adaptive evolution and speciation.

    PubMed

    Landry, Christian R; Aubin-Horth, Nadia

    2014-01-01

    Biological diversity emerges from the interaction between genomes and their environment. Recent conceptual and technological developments allow dissecting these interactions over short and long time-scales. The 16 contributions to this book by leaders in the field cover major recent progresses in the field of Ecological Genomics. Altogether, they illustrate the interplay between the life-history and genomic architecture of organisms, how the interaction of the environment and the genome is shaping phenotypic variation through phenotypic plasticity, how the process of adaptation may be constrained and fueled by internal and external features of organisms and finally, how species formation is the result of intricate interactions between genomes and the ecological conditions. These contributions also show how fundamental questions in biology transcend the boundaries of kingdoms, species and environments and illustrate how integrative approaches are powerful means to answer the most important and challenging questions in ecology and evolution. PMID:24277292

  12. Cyanobacterial KnowledgeBase (CKB), a Compendium of Cyanobacterial Genomes and Proteomes

    PubMed Central

    Mohandass, Shylajanaciyar; Varadharaj, Sangeetha; Thilagar, Sivasudha; Abdul Kareem, Kaleel Ahamed; Dharmar, Prabaharan; Gopalakrishnan, Subramanian; Lakshmanan, Uma

    2015-01-01

    Cyanobacterial KnowledgeBase (CKB) is a free access database that contains the genomic and proteomic information of 74 fully sequenced cyanobacterial genomes belonging to seven orders. The database also contains tools for sequence analysis. The Species report and the gene report provide details about each species and gene (including sequence features and gene ontology annotations) respectively. The database also includes cyanoBLAST, an advanced tool that facilitates comparative analysis, among cyanobacterial genomes and genomes of E. coli (prokaryote) and Arabidopsis (eukaryote). The database is developed and maintained by the Sub-Distributed Informatics Centre (sponsored by the Department of Biotechnology, Govt. of India) of the National Facility for Marine Cyanobacteria, a facility dedicated to marine cyanobacterial research. CKB is freely available at http://nfmc.res.in/ckb/index.html. PMID:26305368

  13. Lessons learned from the application of whole-genome analysis to the treatment of patients with advanced cancers

    PubMed Central

    Laskin, Janessa; Jones, Steven; Aparicio, Samuel; Chia, Stephen; Ch'ng, Carolyn; Deyell, Rebecca; Eirew, Peter; Fok, Alexandra; Gelmon, Karen; Ho, Cheryl; Huntsman, David; Jones, Martin; Kasaian, Katayoon; Karsan, Aly; Leelakumari, Sreeja; Li, Yvonne; Lim, Howard; Ma, Yussanne; Mar, Colin; Martin, Monty; Moore, Richard; Mungall, Andrew; Mungall, Karen; Pleasance, Erin; Rassekh, S. Rod; Renouf, Daniel; Shen, Yaoqing; Schein, Jacqueline; Schrader, Kasmintan; Sun, Sophie; Tinker, Anna; Zhao, Eric; Yip, Stephen; Marra, Marco A.

    2015-01-01

    Given the success of targeted agents in specific populations it is expected that some degree of molecular biomarker testing will become standard of care for many, if not all, cancers. To facilitate this, cancer centers worldwide are experimenting with targeted “panel” sequencing of selected mutations. Recent advances in genomic technology enable the generation of genome-scale data sets for individual patients. Recognizing the risk, inherent in panel sequencing, of failing to detect meaningful somatic alterations, we sought to establish processes to integrate data from whole-genome analysis (WGA) into routine cancer care. Between June 2012 and August 2014, 100 adult patients with incurable cancers consented to participate in the Personalized OncoGenomics (POG) study. Fresh tumor and blood samples were obtained and used for whole-genome and RNA sequencing. Computational approaches were used to identify candidate driver mutations, genes, and pathways. Diagnostic and drug information were then sought based on these candidate “drivers.” Reports were generated and discussed weekly in a multidisciplinary team setting. Other multidisciplinary working groups were assembled to establish guidelines on the interpretation, communication, and integration of individual genomic findings into patient care. Of 78 patients for whom WGA was possible, results were considered actionable in 55 cases. In 23 of these 55 cases, the patients received treatments motivated by WGA. Our experience indicates that a multidisciplinary team of clinicians and scientists can implement a paradigm in which WGA is integrated into the care of late stage cancer patients to inform systemic therapy decisions. PMID:27148575

  14. GeneMed: An Informatics Hub for the Coordination of Next-Generation Sequencing Studies that Support Precision Oncology Clinical Trials

    PubMed Central

    Zhao, Yingdong; Polley, Eric C; Li, Ming-Chung; Lih, Chih-Jian; Palmisano, Alida; Sims, David J; Rubinstein, Lawrence V; Conley, Barbara A; Chen, Alice P; Williams, P Mickey; Kummar, Shivaani; Doroshow, James H; Simon, Richard M

    2015-01-01

    We have developed an informatics system, GeneMed, for the National Cancer Institute (NCI) molecular profiling-based assignment of cancer therapy (MPACT) clinical trial (NCT01827384) being conducted in the National Institutes of Health (NIH) Clinical Center. This trial is one of the first to use a randomized design to examine whether assigning treatment based on genomic tumor screening can improve the rate and duration of response in patients with advanced solid tumors. An analytically validated next-generation sequencing (NGS) assay is applied to DNA from patients’ tumors to identify mutations in a panel of genes that are thought likely to affect the utility of targeted therapies available for use in the clinical trial. The patients are randomized to a treatment selected to target a somatic mutation in the tumor or with a control treatment. The GeneMed system streamlines the workflow of the clinical trial and serves as a communications hub among the sequencing lab, the treatment selection team, and clinical personnel. It automates the annotation of the genomic variants identified by sequencing, predicts the functional impact of mutations, identifies the actionable mutations, and facilitates quality control by the molecular characterization lab in the review of variants. The GeneMed system collects baseline information about the patients from the clinic team to determine eligibility for the panel of drugs available. The system performs randomized treatment assignments under the oversight of a supervising treatment selection team and generates a patient report containing detected genomic alterations. NCI is planning to expand the MPACT trial to multiple cancer centers soon. In summary, the GeneMed system has been proven to be an efficient and successful informatics hub for coordinating the reliable application of NGS to precision medicine studies. PMID:25861217

  15. Discovery of Nigri/nox and Panto/pox site-specific recombinase systems facilitates advanced genome engineering.

    PubMed

    Karimova, Madina; Splith, Victoria; Karpinski, Janet; Pisabarro, M Teresa; Buchholz, Frank

    2016-01-01

    Precise genome engineering is instrumental for biomedical research and holds great promise for future therapeutic applications. Site-specific recombinases (SSRs) are valuable tools for genome engineering due to their exceptional ability to mediate precise excision, integration and inversion of genomic DNA in living systems. The ever-increasing complexity of genome manipulations and the desire to understand the DNA-binding specificity of these enzymes are driving efforts to identify novel SSR systems with unique properties. Here, we describe two novel tyrosine site-specific recombination systems designated Nigri/nox and Panto/pox. Nigri originates from Vibrio nigripulchritudo (plasmid VIBNI_pA) and recombines its target site nox with high efficiency and high target-site selectivity, without recombining target sites of the well established SSRs Cre, Dre, Vika and VCre. Panto, derived from Pantoea sp. aB, is less specific and in addition to its native target site, pox also recombines the target site for Dre recombinase, called rox. This relaxed specificity allowed the identification of residues that are involved in target site selectivity, thereby advancing our understanding of how SSRs recognize their respective DNA targets. PMID:27444945

  16. Cloning-free genome engineering in Sinorhizobium meliloti advances applications of Cre/loxP site-specific recombination.

    PubMed

    Döhlemann, Johannes; Brennecke, Meike; Becker, Anke

    2016-09-10

    The soil-dwelling α-proteobacterium Sinorhizobium meliloti serves as model for studies of symbiotic nitrogen fixation, a highly important process in sustainable agriculture. Here, we report advancements of the genetic toolbox accelerating genome editing in S. meliloti. The hsdMSR operon encodes a type-I restriction-modification (R-M) system. Transformation of S. meliloti is counteracted by the restriction endonuclease HsdR degrading DNA which lacks the appropriate methylation pattern. We provide a stable S. meliloti hsdR deletion mutant showing enhanced transformation with Escherichia coli-derived plasmid DNA and demonstrate that using an E. coli plasmid donor, expressing S. meliloti methyl transferase genes, is an alternative strategy of increasing the transformation efficiency of S. meliloti. Furthermore, we devise a novel cloning-free genome editing (CFGE) method for S. meliloti, Agrobacterium tumefaciens and Xanthomonas campestris, and demonstrate the applicability of this method for intricate applications of the Cre/lox recombination system in S. meliloti. An enhanced Cre/lox system, allowing for serial deletions of large genomic regions, was established. An assay of lox spacer mutants identified a set of lox sites mediating specific recombination. The availability of several non-promiscuous Cre recognition sites enables simultaneous specific Cre/lox recombination events. CFGE combined with Cre/lox recombination is put forward as powerful approach for targeted genome editing, involving serial steps of manipulation to expedite the genetic accessibility of S. meliloti as chassis. PMID:27393468

  17. Discovery of Nigri/nox and Panto/pox site-specific recombinase systems facilitates advanced genome engineering

    PubMed Central

    Karimova, Madina; Splith, Victoria; Karpinski, Janet; Pisabarro, M. Teresa; Buchholz, Frank

    2016-01-01

    Precise genome engineering is instrumental for biomedical research and holds great promise for future therapeutic applications. Site-specific recombinases (SSRs) are valuable tools for genome engineering due to their exceptional ability to mediate precise excision, integration and inversion of genomic DNA in living systems. The ever-increasing complexity of genome manipulations and the desire to understand the DNA-binding specificity of these enzymes are driving efforts to identify novel SSR systems with unique properties. Here, we describe two novel tyrosine site-specific recombination systems designated Nigri/nox and Panto/pox. Nigri originates from Vibrio nigripulchritudo (plasmid VIBNI_pA) and recombines its target site nox with high efficiency and high target-site selectivity, without recombining target sites of the well established SSRs Cre, Dre, Vika and VCre. Panto, derived from Pantoea sp. aB, is less specific and in addition to its native target site, pox also recombines the target site for Dre recombinase, called rox. This relaxed specificity allowed the identification of residues that are involved in target site selectivity, thereby advancing our understanding of how SSRs recognize their respective DNA targets. PMID:27444945

  18. MI-Lab - A Laboratory Environment for Medical Informatics Students.

    PubMed

    Brandt, Karsten; Löbe, Matthias; Schaaf, Michael; Jahn, Franziska; Winter, Alfred; Stäubert, Sebastian

    2016-01-01

    Medical research and health care highly depend on the use of information technology. There is a wide range of application systems (patient administration system, laboratory information system, communication server etc.) and heterogeneous data types (administrative data, clinical data, laboratory data, image data, genomic data etc.). Students and researchers do not often have the possibility to use productive application systems of e.g. hospitals or medical practices to gain practical experiences or examine new components and technologies. Therefore, the aim of this project is to develop a dedicated laboratory environment for patient health care and clinical research. Essential application systems were identified and a suitable architecture was designed for this purpose. It is accompanied by a teaching plan that considers learning modules for bachelor and master degrees in medical informatics. We implemented the laboratory environment called MI-Lab with multiple free and open source software components. All components are installed on virtual machines and/or Docker containers. This modular architecture creates a flexible system which can be deployed in various scenarios. The preliminary evaluation results suggests that laboratory environments like MI-Lab work well in teaching practical aspects of medical informatics and are widely accepted by students. PMID:27577339

  19. Public Health and Epidemiology Informatics: Recent Research and Trends in the United States

    PubMed Central

    Dixon, B. E.; Kharrazi, H.

    2015-01-01

    Summary Objectives To survey advances in public health and epidemiology informatics over the past three years. Methods We conducted a review of English-language research works conducted in the domain of public health informatics (PHI), and published in MEDLINE between January 2012 and December 2014, where information and communication technology (ICT) was a primary subject, or a main component of the study methodology. Selected articles were synthesized using a thematic analysis using the Essential Services of Public Health as a typology. Results Based on themes that emerged, we organized the advances into a model where applications that support the Essential Services are, in turn, supported by a socio-technical infrastructure that relies on government policies and ethical principles. That infrastructure, in turn, depends upon education and training of the public health workforce, development that creates novel or adapts existing infrastructure, and research that evaluates the success of the infrastructure. Finally, the persistence and growth of infrastructure depends on financial sustainability. Conclusions Public health informatics is a field that is growing in breadth, depth, and complexity. Several Essential Services have benefited from informatics, notably, “Monitor Health,” “Diagnose & Investigate,” and “Evaluate.” Yet many Essential Services still have not yet benefited from advances such as maturing electronic health record systems, interoperability amongst health information systems, analytics for population health management, use of social media among consumers, and educational certification in clinical informatics. There is much work to be done to further advance the science of PHI as well as its impact on public health practice. PMID:26293869

  20. X-Informatics: Practical Semantic Science

    NASA Astrophysics Data System (ADS)

    Borne, K. D.

    2009-12-01

    The discipline of data science is merging with multiple science disciplines to form new X-informatics research disciplines. They are almost too numerous to name, but they include geoinformatics, bioinformatics, cheminformatics, biodiversity informatics, ecoinformatics, materials informatics, and the emerging discipline of astroinformatics. Within any X-informatics discipline, the information granules are unique to that discipline -- e.g., gene sequences in bio, the sky object in astro, and the spatial object in geo (such as points, lines, and polygons in the vector model, and pixels in the raster model). Nevertheless the goals are similar: transparent data re-use across subdisciplines and within education settings, information and data integration and fusion, personalization of user interactions with the data collection, semantic search and retrieval, and knowledge discovery. The implementation of an X-informatics framework enables these semantic e-science research goals. We describe the concepts, challenges, and new developments associated with the new discipline of astroinformatics, and how geoinformatics provides valuable lessons learned and a model for practical semantic science within a traditional science discipline through the accretion of data science methodologies (such as formal metadata creation, data models, data mining, information retrieval, knowledge engineering, provenance, taxonomies, and ontologies). The emerging concept of data-as-a-service (DaaS) builds upon the concept of smart data (or data DNA) for intelligent data management, automated workflows, and intelligent processing. Smart data, defined through X-informatics, enables several practical semantic science use cases, including self-discovery, data intelligence, automatic recommendations, relevance analysis, dimension reduction, feature selection, constraint-based mining, interdisciplinary data re-use, knowledge-sharing, data use in education, and more. We describe these concepts within the

  1. Advances and perspectives on the use of CRISPR/Cas9 systems in plant genomics research.

    PubMed

    Liu, Degao; Hu, Rongbin; Palla, Kaitlin J; Tuskan, Gerald A; Yang, Xiaohan

    2016-04-01

    Genome editing with site-specific nucleases has become a powerful tool for functional characterization of plant genes and genetic improvement of agricultural crops. Among the various site-specific nuclease-based technologies available for genome editing, the clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9) systems have shown the greatest potential for rapid and efficient editing of genomes in plant species. This article reviews the current status of application of CRISPR/Cas9 to plant genomics research, with a focus on loss-of-function and gain-of-function analysis of individual genes in the context of perennial plants and the potential application of CRISPR/Cas9 to perturbation of gene expression, and identification and analysis of gene modules as part of an accelerated domestication and synthetic biology effort. PMID:26896588

  2. Advances in Aspergillus secondary metabolite research in the post-genomic era

    PubMed Central

    Sanchez, James F.; Somoza, Amber D.; Keller, Nancy P.

    2015-01-01

    This review studies the impact of whole genome sequencing on Aspergillus secondary metabolite research. There has been a proliferation of many new, intriguing discoveries since sequencing data became widely available. What is more, the genomes disclosed the surprising finding that there are many more secondary metabolite biosynthetic pathways than laboratory research had suggested. Activating these pathways has been met with some success, but many more dormant genes remain to be awakened. PMID:22228366

  3. Recent advances in developing molecular tools for targeted genome engineering of mammalian cells.

    PubMed

    Lim, Kwang-il

    2015-01-01

    Various biological molecules naturally existing in diversified species including fungi, bacteria, and bacteriophage have functionalities for DNA binding and processing. The biological molecules have been recently actively engineered for use in customized genome editing of mammalian cells as the molecule-encoding DNA sequence information and the underlying mechanisms how the molecules work are unveiled. Excitingly, multiple novel methods based on the newly constructed artificial molecular tools have enabled modifications of specific endogenous genetic elements in the genome context at efficiencies that are much higher than that of the conventional homologous recombination based methods. This minireview introduces the most recently spotlighted molecular genome engineering tools with their key features and ongoing modifications for better performance. Such ongoing efforts have mainly focused on the removal of the inherent DNA sequence recognition rigidity from the original molecular platforms, the addition of newly tailored targeting functions into the engineered molecules, and the enhancement of their targeting specificity. Effective targeted genome engineering of mammalian cells will enable not only sophisticated genetic studies in the context of the genome, but also widely-applicable universal therapeutics based on the pinpointing and correction of the disease-causing genetic elements within the genome in the near future. PMID:25104401

  4. The Electronic Medical Records and Genomics (eMERGE) Network: past, present, and future

    PubMed Central

    Gottesman, Omri; Kuivaniemi, Helena; Tromp, Gerard; Faucett, W. Andrew; Li, Rongling; Manolio, Teri A.; Sanderson, Saskia C.; Kannry, Joseph; Zinberg, Randi; Basford, Melissa A.; Brilliant, Murray; Carey, David J.; Chisholm, Rex L.; Chute, Christopher G.; Connolly, John J.; Crosslin, David; Denny, Joshua C.; Gallego, Carlos J.; Haines, Jonathan L.; Hakonarson, Hakon; Harley, John; Jarvik, Gail P.; Kohane, Isaac; Kullo, Iftikhar J.; Larson, Eric B.; McCarty, Catherine; Ritchie, Marylyn D.; Roden, Dan M.; Smith, Maureen E.; Böttinger, Erwin P.; Williams, Marc S.

    2013-01-01

    The Electronic Medical Records and Genomics Network is a National Human Genome Research Institute–funded consortium engaged in the development of methods and best practices for using the electronic medical record as a tool for genomic research. Now in its sixth year and second funding cycle, and comprising nine research groups and a coordinating center, the network has played a major role in validating the concept that clinical data derived from electronic medical records can be used successfully for genomic research. Current work is advancing knowledge in multiple disciplines at the intersection of genomics and health-care informatics, particularly for electronic phenotyping, genome-wide association studies, genomic medicine implementation, and the ethical and regulatory issues associated with genomics research and returning results to study participants. Here, we describe the evolution, accomplishments, opportunities, and challenges of the network from its inception as a five-group consortium focused on genotype–phenotype associations for genomic discovery to its current form as a nine-group consortium pivoting toward the implementation of genomic medicine. Genet Med 15 10, 761–771. PMID:23743551

  5. The Electronic Medical Records and Genomics (eMERGE) Network: past, present, and future.

    PubMed

    Gottesman, Omri; Kuivaniemi, Helena; Tromp, Gerard; Faucett, W Andrew; Li, Rongling; Manolio, Teri A; Sanderson, Saskia C; Kannry, Joseph; Zinberg, Randi; Basford, Melissa A; Brilliant, Murray; Carey, David J; Chisholm, Rex L; Chute, Christopher G; Connolly, John J; Crosslin, David; Denny, Joshua C; Gallego, Carlos J; Haines, Jonathan L; Hakonarson, Hakon; Harley, John; Jarvik, Gail P; Kohane, Isaac; Kullo, Iftikhar J; Larson, Eric B; McCarty, Catherine; Ritchie, Marylyn D; Roden, Dan M; Smith, Maureen E; Böttinger, Erwin P; Williams, Marc S

    2013-10-01

    The Electronic Medical Records and Genomics Network is a National Human Genome Research Institute-funded consortium engaged in the development of methods and best practices for using the electronic medical record as a tool for genomic research. Now in its sixth year and second funding cycle, and comprising nine research groups and a coordinating center, the network has played a major role in validating the concept that clinical data derived from electronic medical records can be used successfully for genomic research. Current work is advancing knowledge in multiple disciplines at the intersection of genomics and health-care informatics, particularly for electronic phenotyping, genome-wide association studies, genomic medicine implementation, and the ethical and regulatory issues associated with genomics research and returning results to study participants. Here, we describe the evolution, accomplishments, opportunities, and challenges of the network from its inception as a five-group consortium focused on genotype-phenotype associations for genomic discovery to its current form as a nine-group consortium pivoting toward the implementation of genomic medicine. PMID:23743551

  6. [Informatics in the Croatian health care system].

    PubMed

    Kern, Josipa; Strnad, Marija

    2005-01-01

    Informatization process of the Croatian health care system started relatively early. Computer processing of data of persons not covered by health insurance started in 1968 in Zagreb. Remetinec Health Center served as a model of computer data processing (CDP) in primary health care and Sveti Duh General Hospital in inpatient CDP, whereas hospital administration and health service were first introduced to Zagreb University Hospital Center and Sestre Milosrdnice University Hospital. At Varazdin Medical Center CDP for health care services started in 1970. Several registries of chronic diseases have been established: cancer, psychosis, alcoholism, and hospital registries as well as pilot registries of lung tuberculosis patients and diabetics. Health statistics reports on healthcare services, work accidents and sick-leaves as well as on hospital mortality started to be produced by CDP in 1977. Besides alphanumeric data, the modern information technology (IT) can give digital images and signals. Communication in health care system demands a standardized format of all information, especially for telemedicine. In 2000, Technical Committee for Standardization in Medical Informatics was founded in Croatia, in order to monitor the activities of the International Standardization Organization (ISO) and Comite Européen de Normalisation (CEN), and to implement their international standards in the Croatian standardization procedure. The HL7 Croatia has also been founded to monitor developments in the communication standard HL7. So far, the Republic of Croatia has a number of acts regulating informatization in general and consequently the informatization of the health care system (Act on Personal Data Confidentiality, Act on Digital Signature, Act of Standardization) enacted. The ethical aspect of data security and data protection has been covered by the Code of Ethics for medical informaticians. It has been established by the International Medical Informatics Association (IMIA

  7. Re-imagining the medical informatics curriculum.

    PubMed

    Frisse, M E

    1997-01-01

    Most physicians in academics, administration, and private practice are insufficiently trained to cope with the current challenges facing medicine. Although information technology, and medical informatics in particular, has been considered to be part of the solution to this problem, the philosophical underpinnings of informatics remain a source of much discussion. Too often, new technology is seen as a new way to do the same things, rather than as an opportunity for a radical reenvisioning of the processes and practices themselves. As a consequence, practitioners and educators fail to make the best uses of new technologies, and fail to offer medical students the comprehensive training in medical informatics that they will need as they move into the real worlds of practice and academics. In this paper, the author describes an imaginary informatics curriculum made up of six core courses: Introduction to Complexity, Decisions and Outcomes, Scarcity and Conflict, Teamwork and Organizations, Representing Knowledge and Action, and Groupware and Collaboration. He does not recommend that these hypothetical courses actually be implemented, but presents them in the hope that they may serve as a starting point for discussions of how informatics can be incorporated into the curriculum in a more substantive way. PMID:9008566

  8. Medical Informatics Education & Research in Greece

    PubMed Central

    Chouvarda, I.

    2015-01-01

    Summary Objectives This paper aims to present an overview of the medical informatics landscape in Greece, to describe the Greek ehealth background and to highlight the main education and research axes in medical informatics, along with activities, achievements and pitfalls. Methods With respect to research and education, formal and informal sources were investigated and information was collected and presented in a qualitative manner, including also quantitative indicators when possible. Results Greece has adopted and applied medical informatics education in various ways, including undergraduate courses in health sciences schools as well as multidisciplinary postgraduate courses. There is a continuous research effort, and large participation in EU-wide initiatives, in all the spectrum of medical informatics research, with notable scientific contributions, although technology maturation is not without barriers. Wide-scale deployment of eHealth is anticipated in the healthcare system in the near future. While ePrescription deployment has been an important step, ICT for integrated care and telehealth have a lot of room for further deployment. Conclusions Greece is a valuable contributor in the European medical informatics arena, and has the potential to offer more as long as the barriers of research and innovation fragmentation are addressed and alleviated. PMID:26123910

  9. The experience of informatics nurses in Taiwan.

    PubMed

    Liu, Chia-Hui; Lee, Ting-Ting; Mills, Mary Etta

    2015-01-01

    Despite recent progress in information technology, health care institutions are constantly confronted with the need to adapt to the resulting new processes of information management and use. Facilitating an effective technology implementation requires dedication from informatics nurses (INs) to bridge the gap between clinical care and technology. The purpose of this study was to explore the working experiences of INs, and alternatives to assist the growth and development of the specialty. This qualitative study recruited 8 participants, and data were collected in 2009 by use of interview guides related to work roles, responsibilities, competencies, and challenges. The emerged themes included (a) diversified roles and functions, (b) vague job description, (c) no decision-making authority, (d) indispensable management support, and (e) searching resources for work fulfillment. Findings indicate that for organizations where nursing informatics development is ongoing, the IN role should be clearly defined as a specialist with identified support resources and decision-making authority. Nursing informatics interest groups should further develop training and certification programs to validate the professional image of the role. Concepts of nursing informatics should be included seamlessly throughout the educational curricula and informatics competency-based courses designed to strengthen student's technology use and data management capabilities. PMID:25839956

  10. Advances in genome editing technology and its promising application in evolutionary and ecological studies

    PubMed Central

    2014-01-01

    Genetic modification has long provided an approach for “reverse genetics”, analyzing gene function and linking DNA sequence to phenotype. However, traditional genome editing technologies have not kept pace with the soaring progress of the genome sequencing era, as a result of their inefficiency, time-consuming and labor-intensive methods. Recently, invented genome modification technologies, such as ZFN (Zinc Finger Nuclease), TALEN (Transcription Activator-Like Effector Nuclease), and CRISPR/Cas9 nuclease (Clustered Regularly Interspaced Short Palindromic Repeats/Cas9 nuclease) can initiate genome editing easily, precisely and with no limitations by organism. These new tools have also offered intriguing possibilities for conducting functional large-scale experiments. In this review, we begin with a brief introduction of ZFN, TALEN, and CRISPR/Cas9 technologies, then generate an extensive prediction of effective TALEN and CRISPR/Cas9 target sites in the genomes of a broad range of taxonomic species. Based on the evidence, we highlight the potential and practicalities of TALEN and CRISPR/Cas9 editing in non-model organisms, and also compare the technologies and test interesting issues such as the functions of candidate domesticated, as well as candidate genes in life-environment interactions. When accompanied with a high-throughput sequencing platform, we forecast their potential revolutionary impacts on evolutionary and ecological research, which may offer an exciting prospect for connecting the gap between DNA sequence and phenotype in the near future. PMID:25414792

  11. Pathology imaging informatics for quantitative analysis of whole-slide images

    PubMed Central

    Kothari, Sonal; Phan, John H; Stokes, Todd H; Wang, May D

    2013-01-01

    Objectives With the objective of bringing clinical decision support systems to reality, this article reviews histopathological whole-slide imaging informatics methods, associated challenges, and future research opportunities. Target audience This review targets pathologists and informaticians who have a limited understanding of the key aspects of whole-slide image (WSI) analysis and/or a limited knowledge of state-of-the-art technologies and analysis methods. Scope First, we discuss the importance of imaging informatics in pathology and highlight the challenges posed by histopathological WSI. Next, we provide a thorough review of current methods for: quality control of histopathological images; feature extraction that captures image properties at the pixel, object, and semantic levels; predictive modeling that utilizes image features for diagnostic or prognostic applications; and data and information visualization that explores WSI for de novo discovery. In addition, we highlight future research directions and discuss the impact of large public repositories of histopathological data, such as the Cancer Genome Atlas, on the field of pathology informatics. Following the review, we present a case study to illustrate a clinical decision support system that begins with quality control and ends with predictive modeling for several cancer endpoints. Currently, state-of-the-art software tools only provide limited image processing capabilities instead of complete data analysis for clinical decision-making. We aim to inspire researchers to conduct more research in pathology imaging informatics so that clinical decision support can become a reality. PMID:23959844

  12. Recommendations of the International Medical Informatics Association (IMIA) on education in health and medical informatics.

    PubMed

    2000-08-01

    The International Medical Informatics Association (IMIA) agreed on international recommendations in health informatics/medical informatics education. These should help to establish courses, course tracks or even complete programs in this field, to further develop existing educational activities in the various nations and to support international initiatives concerning education in health and medical informatics (HMI), particularly international activities in educating HMI specialists and the sharing of courseware. The IMIA recommendations centre on educational needs for healthcare professionals to acquire knowledge and skills in information processing and information and communication technology. The educational needs are described as a three-dimensional framework. The dimensions are: 1) professionals in healthcare (physicians, nurses, HMI professionals, ...), 2) type of specialisation in health and medical informatics (IT users, HMI specialists) and 3) stage of career progression (bachelor, master, ...). Learning outcomes are defined in terms of knowledge and practical skills for healthcare professionals in their role (a) as IT user and (b) as HMI specialist. Recommendations are given for courses/course tracks in HMI as part of educational programs in medicine, nursing, healthcare management, dentistry, pharmacy, public health, health record administration, and informatics/computer science as well as for dedicated programs in HMI (with bachelor, master or doctor degree). To support education in HMI, IMIA offers to award a certificate for high quality HMI education and supports information exchange on programs and courses in HMI through a WWW server of its Working Group on Health and Medical Informatics Education (http:www.imia.org/wg1). PMID:10992757

  13. Clinical Informatics Board Certification: History, Current Status, and Predicted Impact on the Clinical Informatics Workforce

    PubMed Central

    Detmer, Don E.; Munger, Benson S.; Lehmann, Christoph U.

    2010-01-01

    Within health and health care, medical informatics and its subspecialties of biomedical, clinical, and public health informatics have emerged as a new discipline with increasing demands for its own work force. Knowledge and skills in medical informatics are widely acknowledged as crucial to future success in patient care, research relating to biomedicine, clinical care, and public health, as well as health policy design. The maturity of the domain and the demand on expertise necessitate standardized training and certification of professionals. The American Medical Informatics Association (AMIA) embarked on a major effort to create professional level education and certification for physicians of various professions and specialties in informatics. This article focuses on the AMIA effort in the professional structure of medical specialization, e.g., the American Board of Medical Specialties (ABMS) and the related Accreditation Council for Graduate Medical Education (ACGME). This report summarizes the current progress to create a recognized sub-certificate of competence in Clinical Informatics and discusses likely near term (three to five year) implications on training, certification, and work force with an emphasis on clinical applied informatics. PMID:23616825

  14. Advances in genomics, transcriptomics and proteomics of toxin-producing cyanobacteria.

    PubMed

    D'Agostino, Paul M; Woodhouse, Jason N; Makower, A Katharina; Yeung, Anna C Y; Ongley, Sarah E; Micallef, Melinda L; Moffitt, Michelle C; Neilan, Brett A

    2016-02-01

    A common misconception persists that the genomes of toxic and non-toxic cyanobacterial strains are largely conserved with the exception of the presence or absence of the genes responsible for toxin production. Implementation of -omics era technologies has challenged this paradigm, with comparative analyses providing increased insight into the differences between strains of the same species. The implementation of genomic, transcriptomic and proteomic approaches has revealed distinct profiles between toxin-producing and non-toxic strains. Further, metagenomics and metaproteomics highlight the genomic potential and functional state of toxic bloom events over time. In this review, we highlight how these technologies have shaped our understanding of the complex relationship between these molecules, their producers and the environment at large within which they persist. PMID:26663762

  15. Advances in CRISPR-Cas9 genome engineering: lessons learned from RNA interference

    PubMed Central

    Barrangou, Rodolphe; Birmingham, Amanda; Wiemann, Stefan; Beijersbergen, Roderick L.; Hornung, Veit; Smith, Anja van Brabant

    2015-01-01

    The discovery that the machinery of the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-Cas9 bacterial immune system can be re-purposed to easily create deletions, insertions and replacements in the mammalian genome has revolutionized the field of genome engineering and re-invigorated the field of gene therapy. Many parallels have been drawn between the newly discovered CRISPR-Cas9 system and the RNA interference (RNAi) pathway in terms of their utility for understanding and interrogating gene function in mammalian cells. Given this similarity, the CRISPR-Cas9 field stands to benefit immensely from lessons learned during the development of RNAi technology. We examine how the history of RNAi can inform today's challenges in CRISPR-Cas9 genome engineering such as efficiency, specificity, high-throughput screening and delivery for in vivo and therapeutic applications. PMID:25800748

  16. Health Informatics for Pediatric Disaster Preparedness Planning

    PubMed Central

    Burke, R.V.; Ryutov, T.; Neches, R.; Upperman, J.S.

    2010-01-01

    Objective 1. To conduct a review of the role of informatics in pediatric disaster preparedness using all medical databases. 2. To provide recommendations to improve pediatric disaster preparedness by the application of informatics. Methods A literature search was conducted using MEDLINE, CINHL and the Cochrane Library using the key words “children” AND “disaster preparedness and disaster” AND “informatics”. Results A total of 314 papers were initially produced by the search and eight that met the selection criteria were included in the review. Four themes emerged: tools for disaster preparedness, education, reunification and planning and response. Conclusion The literature pertaining to informatics and pediatric disaster preparedness is sparse and many gaps still persist. Current disaster preparedness tools focus on the general population and do not specifically address children. The most progress has been achieved in family reunification; however, the recommendations delineated are yet to be completed. PMID:23616840

  17. NASA Biomedical Informatics Capabilities and Needs

    NASA Technical Reports Server (NTRS)

    Johnson-Throop, Kathy A.

    2009-01-01

    To improve on-orbit clinical capabilities by developing and providing operational support for intelligent, robust, reliable, and secure, enterprise-wide and comprehensive health care and biomedical informatics systems with increasing levels of autonomy, for use on Earth, low Earth orbit & exploration class missions. Biomedical Informatics is an emerging discipline that has been defined as the study, invention, and implementation of structures and algorithms to improve communication, understanding and management of medical information. The end objective of biomedical informatics is the coalescing of data, knowledge, and the tools necessary to apply that data and knowledge in the decision-making process, at the time and place that a decision needs to be made.

  18. Software engineering education in medical informatics.

    PubMed

    Leven, F J

    1989-11-01

    Requirements and approaches of Software Engineering education in the field of Medical Informatics are described with respect to the impact of (1) experiences characterizing the "software misery", (2) status and tendencies in software methodology, and (3) educational status and needs in computer science education influenced by the controversy "theoretical versus practical education". Special attention is directed toward the growing importance of analysis, design methods, and techniques in the professional spectrum of Medical Informatics, the relevance of general principles of systems engineering in health care, the potential of non-procedural programming paradigms, and the intersection of Artificial Intelligence and education. Realizations of and experiences with programs in the field of Software Engineering are reported with respect to special requirements in Medical Informatics. PMID:2695780

  19. Core Content for the Subspecialty of Clinical Informatics

    PubMed Central

    Gardner, Reed M.; Overhage, J. Marc; Steen, Elaine B.; Munger, Benson S.; Holmes, John H.; Williamson, Jeffrey J.; Detmer, Don E.

    2009-01-01

    The Core Content for Clinical Informatics defines the boundaries of the discipline and informs the Program Requirements for Fellowship Education in Clinical Informatics. The Core Content includes four major categories: fundamentals, clinical decision making and care process improvement, health information systems, and leadership and management of change. The AMIA Board of Directors approved the Core Content for Clinical Informatics in November 2008. PMID:19074296

  20. Genome-Wide Association Studies and the Problem of Relatedness Among Advanced Intercross Lines and Other Highly Recombinant Populations

    PubMed Central

    Cheng, Riyan; Lim, Jackie E.; Samocha, Kaitlin E.; Sokoloff, Greta; Abney, Mark; Skol, Andrew D.; Palmer, Abraham A.

    2010-01-01

    Model organisms offer many advantages for the genetic analysis of complex traits. However, identification of specific genes is often hampered by a lack of recombination between the genomes of inbred progenitors. Recently, genome-wide association studies (GWAS) in humans have offered gene-level mapping resolution that is possible because of the large number of accumulated recombinations among unrelated human subjects. To obtain analogous improvements in mapping resolution in mice, we used a 34th generation advanced intercross line (AIL) derived from two inbred strains (SM/J and LG/J). We used simulations to show that familial relationships among subjects must be accounted for when analyzing these data; we then used a mixed model that included polygenic effects to address this problem in our own analysis. Using a combination of F2 and AIL mice derived from the same inbred progenitors, we identified genome-wide significant, subcentimorgan loci that were associated with methamphetamine sensitivity, (e.g., chromosome 18; LOD = 10.5) and non-drug-induced locomotor activity (e.g., chromosome 8; LOD = 18.9). The 2-LOD support interval for the former locus contains no known genes while the latter contains only one gene (Csmd1). This approach is broadly applicable in terms of phenotypes and model organisms and allows GWAS to be performed in multigenerational crosses between and among inbred strains where familial relatedness is often unavoidable. PMID:20439773

  1. Recent Developments in Using Advanced Sequencing Technologies for the Genomic Studies of Lignin and Cellulose Degrading Microorganisms.

    PubMed

    Kameshwar, Ayyappa Kumar Sista; Qin, Wensheng

    2016-01-01

    Lignin is a complex polyphenyl aromatic compound which exists in tight associations with cellulose and hemicellulose to form plant primary and secondary cell wall. Lignocellulose is an abundant renewable biomaterial present on the earth. It has gained much attention in the scientific community in recent years because of its potential applications in bio-based industries. Microbial degradation of lignocellulose polymers was well studied in wood decaying fungi. Based on the plant materials they degrade these fungi were classified as white rot, brown rot and soft rot. However, some groups of bacteria belonging to the actinomycetes, α-proteobacteria and β-proteobacteria were also found to be efficient in degrading lignocellulosic biomass but not well understood unlike the fungi. In this review we focus on recent advancements deployed for finding and understanding the lignocellulose degradation by microorganisms. Conventional molecular methods like sequencing 16s rRNA and Inter Transcribed Spacer (ITS) regions were used for identification and classification of microbes. Recent progression in genomics mainly next generation sequencing technologies made the whole genome sequencing of microbes possible in a great ease. The whole genome sequence studies reveals high quality information about genes and canonical pathways involved in the lignin and other cell wall components degradation. PMID:26884714

  2. Recent Developments in Using Advanced Sequencing Technologies for the Genomic Studies of Lignin and Cellulose Degrading Microorganisms

    PubMed Central

    Kameshwar, Ayyappa kumar Sista; Qin, Wensheng

    2016-01-01

    Lignin is a complex polyphenyl aromatic compound which exists in tight associations with cellulose and hemicellulose to form plant primary and secondary cell wall. Lignocellulose is an abundant renewable biomaterial present on the earth. It has gained much attention in the scientific community in recent years because of its potential applications in bio-based industries. Microbial degradation of lignocellulose polymers was well studied in wood decaying fungi. Based on the plant materials they degrade these fungi were classified as white rot, brown rot and soft rot. However, some groups of bacteria belonging to the actinomycetes, α-proteobacteria and β-proteobacteria were also found to be efficient in degrading lignocellulosic biomass but not well understood unlike the fungi. In this review we focus on recent advancements deployed for finding and understanding the lignocellulose degradation by microorganisms. Conventional molecular methods like sequencing 16s rRNA and Inter Transcribed Spacer (ITS) regions were used for identification and classification of microbes. Recent progression in genomics mainly next generation sequencing technologies made the whole genome sequencing of microbes possible in a great ease. The whole genome sequence studies reveals high quality information about genes and canonical pathways involved in the lignin and other cell wall components degradation. PMID:26884714

  3. Advancing grass crop genomics with the new model plant Brachypodium distachyon

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The majority of domesticated grasses are cool season species that belong to one of the four tribes, including the Triticeae, Aveneae, Poeae, and Bromeae. Despite the many available genomic resources for rice, it is not a highly practical model system for cool season grasses because of its distant ev...

  4. Advances in genomic- and proteomic-based methods to study food-borne pathogens

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In recent years, a number of “omics” technologies, including genomics, proteomics, metabolomics, and others are being utilized to enhance the understanding of the complexities of pathogen behavior at the molecular level and for the development of improved pathogen detection and typing systems. Gene...

  5. Photovoltaics Informatics: Harnessing Energy Science via Data-Driven Approaches

    SciTech Connect

    Suh, C.; Munch, K.; Biagioni, D.; Glynn, S.; Scharf, J.; Contreras, M. A.; Perkins, J. D.; Nelson, B. P.; Jones, W. B.

    2011-01-01

    We discuss our current research focus on photovoltaic (PV) informatics, which is dedicated to functionality enhancement of solar materials through data management and data mining-aided, integrated computational materials engineering (ICME) for rapid screening and identification of multi-scale processing/structure/property/performance relationships. Our current PV informatics research ranges from transparent conducting oxides (TCO) to solar absorber materials. As a test bed, we report on examples of our current data management system for PV research and advanced data mining to improve the performance of solar cells such as CuIn{sub x}Ga{sub 1-x}Se{sub 2} (CIGS) aiming at low-cost and high-rate processes. For the PV data management, we show recent developments of a strategy for data modeling, collection and aggregation methods, and construction of data interfaces, which enable proper archiving and data handling for data mining. For scientific data mining, the value of high-dimensional visualizations and non-linear dimensionality reduction is demonstrated to quantitatively assess how process conditions or properties are interconnected in the context of the development of Al-doped ZnO (AZO) thin films as the TCO layers for CIGS devices. Such relationships between processing and property of TCOs lead to optimal process design toward enhanced performance of CIGS cells/devices.

  6. THE ROLE OF INFORMATICS IN PROMOTING PATIENT-CENTERED CARE

    PubMed Central

    Snyder, Claire F.; Wu, Albert W.; Miller, Robert S.; Jensen, Roxanne E.; Bantug, Elissa T.; Wolff, Antonio C.

    2011-01-01

    Patient-centered care is an important aspect of high-quality care. Health informatics, particularly advances in technology, has the potential to facilitate, or detract from, patient-centered cancer care. Informatics can provide a mechanism for patients to provide their clinician(s) with critical information, and to share information with family, friends, and other patients. This information may enable patients to exert greater control over their own care. Clinicians may use information systems (e.g., electronic medical records) to coordinate care and share information with other clinicians. Patients and clinicians may use communication tools and information resources to interact with one another in new ways. Caution in using new information resources is warranted to avoid reliance on biased or inappropriate data, and clinicians may need to direct patients to appropriate information resources. Perhaps the greatest challenge for both patients and providers is identifying information that is high-quality and which enhances (and does not impede) their interactions. PMID:21799327

  7. Things to come: postmodern digital knowledge management and medical informatics.

    PubMed Central

    Matheson, N W

    1995-01-01

    The overarching informatics grand challenge facing society is the creation of knowledge management systems that can acquire, conserve, organize, retrieve, display, and distribute what is known today in a manner that informs and educates, facilitates the discovery and creation of new knowledge, and contributes to the health and welfare of the planet. At one time the private, national, and university libraries of the world collectively constituted the memory of society's intellectual history. In the future, these new digital knowledge management systems will constitute human memory in its entirety. The current model of multiple local collections of duplicated resources will give way to specialized sole-source servers. In this new environment all scholarly scientific knowledge should be public domain knowledge: managed by scientists, organized for the advancement of knowledge, and readily available to all. Over the next decade, the challenge for the field of medical informatics and for the libraries that serve as the continuous memory for the biomedical sciences will be to come together to form a new organization that will lead to the development of postmodern digital knowledge management systems for medicine. These systems will form a portion of the evolving world brain of the 21st century. PMID:7743318

  8. Translating Genomic Advances to Physical Therapist Practice: A Closer Look at the Nature and Nurture of Common Diseases.

    PubMed

    Curtis, Catherine L; Goldberg, Allon; Kleim, Jeffrey A; Wolf, Steven L

    2016-04-01

    The Human Genome Project and the International HapMap Project have yielded new understanding of the influence of the human genome on health and disease, advancing health care in significant ways. In personalized medicine, genetic factors are used to identify disease risk and tailor preventive and therapeutic regimens. Insight into the genetic bases of cellular processes is revealing the causes of disease and effects of exercise. Many diseases known to have a major lifestyle contribution are highly influenced by common genetic variants. Genetic variants are associated with increased risk for common diseases such as cardiovascular disease and osteoarthritis. Exercise response also is influenced by genetic factors. Knowledge of genetic factors can help clinicians better understand interindividual differences in disease presentation, pain experience, and exercise response. Family health history is an important genetic tool and encourages clinicians to consider the wider client-family unit. Clinicians in this new era need to be prepared to guide patients and their families on a variety of genomics-related concerns, including genetic testing and other ethical, legal, or social issues. Thus, it is essential that clinicians reconsider the role of genetics in the preservation of wellness and risk for disease to identify ways to best optimize fitness, health, or recovery. Clinicians with knowledge of the influence of genetic variants on health and disease will be uniquely positioned to institute individualized lifestyle interventions, thereby fulfilling roles in prevention and wellness. This article describes how discoveries in genomics are rapidly evolving the understanding of health and disease by highlighting 2 conditions: cardiovascular disease and osteoarthritis. Genetic factors related to exercise effects also are considered. PMID:26637647

  9. Harnessing next-generation informatics for personalizing medicine: a report from AMIA's 2014 Health Policy Invitational Meeting.

    PubMed

    Wiley, Laura K; Tarczy-Hornoch, Peter; Denny, Joshua C; Freimuth, Robert R; Overby, Casey L; Shah, Nigam; Martin, Ross D; Sarkar, Indra Neil

    2016-03-01

    The American Medical Informatics Association convened the 2014 Health Policy Invitational Meeting to develop recommendations for updates to current policies and to establish an informatics research agenda for personalizing medicine. In particular, the meeting focused on discussing informatics challenges related to personalizing care through the integration of genomic or other high-volume biomolecular data with data from clinical systems to make health care more efficient and effective. This report summarizes the findings (n = 6) and recommendations (n = 15) from the policy meeting, which were clustered into 3 broad areas: (1) policies governing data access for research and personalization of care; (2) policy and research needs for evolving data interpretation and knowledge representation; and (3) policy and research needs to ensure data integrity and preservation. The meeting outcome underscored the need to address a number of important policy and technical considerations in order to realize the potential of personalized or precision medicine in actual clinical contexts. PMID:26911808

  10. The Informatics Opportunities at the Intersection of Patient Safety and Clinical Informatics

    PubMed Central

    Kilbridge, Peter M.; Classen, David C.

    2008-01-01

    Health care providers have a basic responsibility to protect patients from accidental harm. At the institutional level, creating safe health care organizations necessitates a systematic approach. Effective use of informatics to enhance safety requires the establishment and use of standards for concept definitions and for data exchange, development of acceptable models for knowledge representation, incentives for adoption of electronic health records, support for adverse event detection and reporting, and greater investment in research at the intersection of informatics and patient safety. Leading organizations have demonstrated that health care informatics approaches can improve safety. Nevertheless, significant obstacles today limit optimal application of health informatics to safety within most provider environments. The authors offer a series of recommendations for addressing these challenges. PMID:18436896

  11. Human Genome Project

    SciTech Connect

    Block, S.; Cornwall, J.; Dally, W.; Dyson, F.; Fortson, N.; Joyce, G.; Kimble, H. J.; Lewis, N.; Max, C.; Prince, T.; Schwitters, R.; Weinberger, P.; Woodin, W. H.

    1998-01-04

    The study reviews Department of Energy supported aspects of the United States Human Genome Project, the joint National Institutes of Health/Department of Energy program to characterize all human genetic material, to discover the set of human genes, and to render them accessible for further biological study. The study concentrates on issues of technology, quality assurance/control, and informatics relevant to current effort on the genome project and needs beyond it. Recommendations are presented on areas of the genome program that are of particular interest to and supported by the Department of Energy.

  12. Human Genome Program

    SciTech Connect

    Not Available

    1993-01-01

    The DOE Human Genome program has grown tremendously, as shown by the marked increase in the number of genome-funded projects since the last workshop held in 1991. The abstracts in this book describe the genome research of DOE-funded grantees and contractors and invited guests, and all projects are represented at the workshop by posters. The 3-day meeting includes plenary sessions on ethical, legal, and social issues pertaining to the availability of genetic data; sequencing techniques, informatics support; and chromosome and cDNA mapping and sequencing.

  13. An overview of the medical informatics curriculum in medical schools.

    PubMed Central

    Espino, J. U.; Levine, M. G.

    1998-01-01

    As medical schools incorporate medical informatics into their curriculum the problems of implementation arise. Because there are no standards regarding a medical informatics curriculum, medical schools are implementing the subjects in various ways. A survey was undertaken to amass an overview of the medical informatics curriculum nationally. Of the responding schools, most have aspects of medical informatics incorporated into current courses and utilize existing faculty. Literature searching, clinical decision-making, and Internet are the basic topics in the current curricula. The trend is for medical informatics to be incorporated throughout all four years of medical school. Barriers are the difficulties in faculty training, and slow implementation. PMID:9929263

  14. Medical informatics on the Internet: creating the sci.med. informatics newsgroup.

    PubMed

    Zakaria, A M; Sittig, D F

    1995-01-01

    A Usenet newsgroup, sci.med.informatics, has been created to serve as an international electronic forum for discussion of issues related to medical informatics. The creation process follows a set of administrative rules set out by the Usenet administration on the Internet and consists of five steps: 1) informal discussion, 2) request for formal discussion, 3) formal discussion, 4) voting, and 5) posting of results. The newsgroup can be accessed using any news reader via the Internet. PMID:7583645

  15. Genetics/genomics advances to influence care for patients with chronic disease.

    PubMed

    Beery, Theresa Alice; Smith, Carolyn R

    2011-01-01

    Rapid changes in the field of genetics/genomics are affecting the way we practice nursing. Staying current on this dynamic field is a challenge for all healthcare professionals. This article discusses genetics/genomics issues that are likely to have a strong influence on nurses who care for patients with chronic disease. Complex diseases involving the actions of genes and environment are the most common causes of morbidity and mortality. Pharmacogenetics/pharmacogenomics has the potential to alter the way we choose both medications and appropriate doses. Nutrigenomics promises to help us understand how diet affects gene expression and how genetic variants affect the way we use nutrients. Genetic testing can be purchased through the Internet and currently is being marketed directly to consumers. Each of these topics has present and future implications for all healthcare professionals, especially those caring for people with chronic disease. PMID:21473561

  16. Advances in Understanding Bacterial Pathogenesis Gained from Whole-Genome Sequencing and Phylogenetics.

    PubMed

    Klemm, Elizabeth; Dougan, Gordon

    2016-05-11

    The development of next-generation sequencing as a cost-effective technology has facilitated the analysis of bacterial population structure at a whole-genome level and at scale. From these data, phylogenic trees have been constructed that define population structures at a local, national, and global level, providing a framework for genetic analysis. Although still at an early stage, these approaches have yielded progress in several areas, including pathogen transmission mapping, the genetics of niche colonization and host adaptation, as well as gene-to-phenotype association studies. Antibiotic resistance has proven to be a major challenge in the early 21(st) century, and phylogenetic analyses have uncovered the dramatic effect that the use of antibiotics has had on shaping bacterial population structures. An update on insights into bacterial evolution from comparative genomics is provided in this review. PMID:27173928

  17. Genomics of elite sporting performance: what little we know and necessary advances.

    PubMed

    Pitsiladis, Yannis; Wang, Guan; Wolfarth, Bernd; Scott, Robert; Fuku, Noriyuki; Mikami, Eri; He, Zihong; Fiuza-Luces, Carmen; Eynon, Nir; Lucia, Alejandro

    2013-06-01

    Numerous reports of genetic associations with performance-related phenotypes have been published over the past three decades but there has been limited progress in discovering and characterising the genetic contribution to elite/world-class performance, mainly owing to few coordinated research efforts involving major funding initiatives/consortia and the use primarily of the candidate gene analysis approach. It is timely that exercise genomics research has moved into a new era utilising well-phenotyped, large cohorts and genome-wide technologies--approaches that have begun to elucidate the genetic basis of other complex traits/diseases. This review summarises the most recent and significant findings from sports genetics and explores future trends and possibilities. PMID:23632745

  18. Developing curriculum in nursing informatics in Europe.

    PubMed

    Mantas, J

    1998-06-01

    The NIGHTINGALE Project (NIGHTINGALE Project: HC1109 DGXIII Contract and Technical Annex, European Commission, December 1995) which started on the 1st of January, 1996, after the approval of the European Commission, has a 36 month duration. It is essential in planning and implementing a strategy in training the nursing profession in using and applying healthcare information systems. NIGHTINGALE contributes towards the appropriate use of the developed telematics infrastructure across Europe by educating and training nurses in a harmonious way across Europe in the upcoming field of nursing informatics. NIGHTINGALE develops courseware material based on the curriculum development process using multimedia technologies. Computer based training software packages in nursing informatics will be the basis of the training material and the corresponding courses. CD-ROM based training and reference material will also be provided in the courses whereas the traditional booklets, teaching material and textbooks can also play an adequate role in training. NIGHTINGALE will disseminate all information and courseware material freely to all interested parties through the publications of the proceedings of the conferences, through the establishment of the world wide web (WWW) server in nursing informatics for Europe (http://www.dn.uoa.gr/nightingale), which will become a depository of nursing information knowledge across Europe as well as a dissemination node of nursing informatics throughout the European members states for the benefit and welfare of the European citizen. PMID:9726502

  19. Medical informatics and telemedicine: A vision

    NASA Technical Reports Server (NTRS)

    Clemmer, Terry P.

    1991-01-01

    The goal of medical informatics is to improve care. This requires the commitment and harmonious collaboration between the computer scientists and clinicians and an integrated database. The vision described is how medical information systems are going to impact the way medical care is delivered in the future.

  20. Optimizing Clinical Research Participant Selection with Informatics

    PubMed Central

    Weng, Chunhua

    2015-01-01

    Clinical research participants are often not reflective of the real-world patients due to overly restrictive eligibility criteria. Meanwhile, unselected participants introduce confounding factors and reduce research efficiency. Biomedical Informatics, especially Big Data increasingly made available from electronic health records, offers promising aids to optimize research participant selection through data-driven transparency. PMID:26549161

  1. Geo-Engineering through Internet Informatics (GEMINI)

    SciTech Connect

    Doveton, John H.; Watney, W. Lynn

    2003-03-06

    The program, for development and methodologies, was a 3-year interdisciplinary effort to develop an interactive, integrated Internet Website named GEMINI (Geo-Engineering Modeling through Internet Informatics) that would build real-time geo-engineering reservoir models for the Internet using the latest technology in Web applications.

  2. Nursing informatics knowledge and competencies: a national survey of nursing education programs in the United States.

    PubMed

    McNeil, Barbara J; Elfrink, Victoria L; Pierce, Susan T; Beyea, Suzanne C; Bickford, Carol J; Averill, Carolyn

    2005-12-01

    An online survey of deans/directors of 266 baccalaureate and higher nursing programs in the U.S. was developed by informatics expert nurses. Participants (1) identified nursing informatics (NI) competencies and knowledge of undergraduate and/or graduate students in their nursing programs; (2) determined faculty preparedness to teach NI and to use informatics tools; and (3) provided perceptions of NI requirements of local practicing nurses. Frequency data and qualitative responses were analyzed. Approximately half of undergraduate nursing programs were teaching information literacy skills and required students to enter with word-processing and email skills. Least visible informatics content at all levels included the use of information system data standards, the Nursing Information and Data Set Evaluation Center criteria, the unified medical language system (UMLS), and the nurse's role in the life cycle of an information system. Almost 50% of respondents perceived faculty as "novice" and "advanced beginners" in teaching and using NI applications. Participants reported no future plans to offer NI training in their region. Findings have major implications for nurse faculty, staff developers, and program administrators who are planning continuing education opportunities and designing nursing curricula that prepare nurses for use of the electronic health record and 21st century professional practice. PMID:16046276

  3. Informatics Systems and Tools to Facilitate Patient-centered Care Coordination

    PubMed Central

    Kneale, L.

    2015-01-01

    Summary Introduction There is a growing international focus on patient-centered care. A model designed to facilitate this type of care in the primary care setting is the patient-centered medical home. This model of care strives to be patient-focused, comprehensive, team-based, coordinated, accessible, and focused on quality and safety of care. Objective The objective of this paper is to identify the current status and future trends of patient-centered care and the role of informatics systems and tools in facilitating this model of care. Methods In this paper we review recent scientific literature of the past four years to identify trends and state of current evidence when it comes to patient-centered care overall, and more specifically medical homes. Results There are several studies that indicate growth and development in seven informatics areas within patient-centered care, namely clinical decision support, registries, team care, care transitions, personal health records, telehealth, and measurement. In some cases we are still lacking large randomized clinical trials and the evidence base is not always solid, but findings strongly indicate the potential of informatics to support patient-centered care. Conclusion Current evidence indicates that advancements have been made in implementing and evaluating patient-centered care models. Technical, legal, and practical challenges still remain. Further examination of the impact of patient-centered informatics tools and systems on clinical outcomes is needed. PMID:26293847

  4. Current Status of Nursing Informatics Education in Korea

    PubMed Central

    Jeon, Eunjoo; Kim, Jeongeun; Lee, Ji-Hyun; Kim, Jungha; Jin, Meiling; Ahn, Shinae; Jun, Jooyeon; Song, Healim; On, Jeongah; Jung, Hyesil; Hong, Yeong Joo; Yim, Suran

    2016-01-01

    Objectives This study presents the current status of nursing informatics education, the content covered in nursing informatics courses, the faculty efficacy, and the barriers to and additional supports for teaching nursing informatics in Korea. Methods A set of questionnaires consisting of an 18-item questionnaire for nursing informatics education, a 6-item questionnaire for faculty efficacy, and 2 open-ended questions for barriers and additional supports were sent to 204 nursing schools via email and the postal service. Nursing schools offering nursing informatics were further asked to send their syllabuses. The subjects taught were analyzed using nursing informatics competency categories and other responses were tailed using descriptive statistics. Results A total of 72 schools (35.3%) responded to the survey, of which 38 reported that they offered nursing informatics courses in their undergraduate nursing programs. Nursing informatics courses at 11 schools were taught by a professor with a degree majoring in nursing informatics. Computer technology was the most frequently taught subject (27 schools), followed by information systems used for practice (25 schools). The faculty efficacy was 3.76 ± 0.86 (out of 5). The most frequently reported barrier to teaching nursing informatics (n = 9) was lack of awareness of the importance of nursing informatics. Training and educational opportunities was the most requested additional support. Conclusions Nursing informatics education has increased during the last decade in Korea. However, the proportions of faculty with degrees in nursing informatics and number of schools offering nursing informatics courses have not increased much. Thus, a greater focus is needed on training faculty and developing the courses. PMID:27200224

  5. IMIA Accreditation of Health Informatics Programs

    PubMed Central

    Mantas, John

    2013-01-01

    Objectives Health informatics programs usually are evaluated by national accreditation committees. Not always are the members of these committees well informed about the international level of (education in) health informatics. Therefore, when a program is accredited by a national accreditation committee, this does not always mean that the program is of an international level. The International Medical Informatics Association (IMIA) has expertise in the field of education. The IMIA Recommendations on Education in Biomedical and Health Informatics guide curricula development. The goal of this article is to show that IMIA can also play the role of accreditation agency and to present the IMIA accreditation protocol and experiences obtained with it. Methods The accreditation procedure used in the Netherlands and Belgium was taken as a template for the design of the IMIA accreditation protocol. In a trial period of one and a half year the protocol is tested out on six health informatics programs. Results An accreditation protocol was designed. For judging the curriculum of a program the IMIA Recommendations are used. The institution has to write a self-assessment report and a site visit committee visits the program and judges its quality, supported by the self-assessment report and discussions with all stakeholders of the program. Conclusions After having visited three programs it appears that the IMIA accreditation procedure works well. Only a few changes had to be introduced. Writing the self-assessment report already appears to be beneficial for the management of the program to obtain a better insight in the quality of their program. PMID:24175114

  6. Coalescing medical systems: a challenge for health informatics in a global world.

    PubMed

    Stranieri, Andrew; Vaughan, Stephen

    2010-01-01

    As globalisation advances, patients in many nations increasingly access diverse medical systems including Western medicine, Traditional Chinese Medicine, Homeopathy and Ayervedic medicine. The trend toward co-existence of medical systems presents challenges for health informatics including the need to develop standards that can encompass the diversity required, the need to develop software applications that effectively inter-operate across diverse systems and the need to support patients when evaluating competing systems. This article advances the notion that the challenges can most effectively be met with the development of informatics approaches that do not assume the superiority of one medical system over another. Argument visualization to support patient decision making in selecting an appropriate medical system is presented as an application that exemplifies this stance. PMID:21191169

  7. p-medicine: A Medical Informatics Platform for Integrated Large Scale Heterogeneous Patient Data

    PubMed Central

    Marés, J.; Shamardin, L.; Weiler, G.; Anguita, A.; Sfakianakis, S.; Neri, E.; Zasada, S.J.; Graf, N.; Coveney, P.V.

    2014-01-01

    Secure access to patient data is becoming of increasing importance, as medical informatics grows in significance, to both assist with population health studies, and patient specific medicine in support of treatment. However, assembling the many different types of data emanating from the clinic is in itself a difficulty, and doing so across national borders compounds the problem. In this paper we present our solution: an easy to use distributed informatics platform embedding a state of the art data warehouse incorporating a secure pseudonymisation system protecting access to personal healthcare data. Using this system, a whole range of patient derived data, from genomics to imaging to clinical records, can be assembled and linked, and then connected with analytics tools that help us to understand the data. Research performed in this environment will have immediate clinical impact for personalised patient healthcare. PMID:25954394

  8. Biodiversity informatics: managing and applying primary biodiversity data.

    PubMed Central

    Soberón, Jorge; Peterson, A Townsend

    2004-01-01

    Recently, advances in information technology and an increased willingness to share primary biodiversity data are enabling unprecedented access to it. By combining presences of species data with electronic cartography via a number of algorithms, estimating niches of species and their areas of distribution becomes feasible at resolutions one to three orders of magnitude higher than it was possible a few years ago. Some examples of the power of that technique are presented. For the method to work, limitations such as lack of high-quality taxonomic determination, precise georeferencing of the data and availability of high-quality and updated taxonomic treatments of the groups must be overcome. These are discussed, together with comments on the potential of these biodiversity informatics techniques not only for fundamental studies but also as a way for developing countries to apply state of the art bioinformatic methods and large quantities of data, in practical ways, to tackle issues of biodiversity management. PMID:15253354

  9. Informatics: essential infrastructure for quality assessment and improvement in nursing.

    PubMed Central

    Henry, S B

    1995-01-01

    In recent decades there have been major advances in the creation and implementation of information technologies and in the development of measures of health care quality. The premise of this article is that informatics provides essential infrastructure for quality assessment and improvement in nursing. In this context, the term quality assessment and improvement comprises both short-term processes such as continuous quality improvement (CQI) and long-term outcomes management. This premise is supported by 1) presentation of a historical perspective on quality assessment and improvement; 2) delineation of the types of data required for quality assessment and improvement; and 3) description of the current and potential uses of information technology in the acquisition, storage, transformation, and presentation of quality data, information, and knowledge. PMID:7614118

  10. Polyene macrolide biosynthesis in streptomycetes and related bacteria: recent advances from genome sequencing and experimental studies.

    PubMed

    Caffrey, Patrick; De Poire, Eimear; Sheehan, James; Sweeney, Paul

    2016-05-01

    The polyene macrolide group includes important antifungal drugs, to which resistance does not arise readily. Chemical and biological methods have been used in attempts to make polyene antibiotics with fewer toxic side effects. Genome sequencing of producer organisms is contributing to this endeavour, by providing access to new compounds and by enabling yield improvement for polyene analogues obtained by engineered biosynthesis. This recent work is also enhancing bioinformatic methods for deducing the structures of cryptic natural products from their biosynthetic enzymes. The stereostructure of candicidin D has recently been determined by NMR spectroscopy. Genes for the corresponding polyketide synthase have been uncovered in several different genomes. Analysis of this new information strengthens the view that protein sequence motifs can be used to predict double bond geometry in many polyketides.Chemical studies have shown that improved polyenes can be obtained by modifying the mycosamine sugar that is common to most of these compounds. Glycoengineered analogues might be produced by biosynthetic methods, but polyene glycosyltransferases show little tolerance for donors other than GDP-α-D-mycosamine. Genome sequencing has revealed extending glycosyltransferases that add a second sugar to the mycosamine of some polyenes. NppY of Pseudonocardia autotrophica uses UDP-N-acetyl-α-D-glucosamine as donor whereas PegA from Actinoplanes caeruleus uses GDP-α-D-mannose. These two enzymes show 51 % sequence identity and are also closely related to mycosaminyltransferases. These findings will assist attempts to construct glycosyltransferases that transfer alternative UDP- or (d)TDP-linked sugars to polyene macrolactones. PMID:27023916

  11. Pathology Informatics Essentials for Residents: A flexible informatics curriculum linked to Accreditation Council for Graduate Medical Education milestones

    PubMed Central

    Henricks, Walter H; Karcher, Donald S; Harrison, James H; Sinard, John H; Riben, Michael W; Boyer, Philip J; Plath, Sue; Thompson, Arlene; Pantanowitz, Liron

    2016-01-01

    Context: Recognition of the importance of informatics to the practice of pathology has surged. Training residents in pathology informatics have been a daunting task for most residency programs in the United States because faculty often lacks experience and training resources. Nevertheless, developing resident competence in informatics is essential for the future of pathology as a specialty. Objective: The objective of the study is to develop and deliver a pathology informatics curriculum and instructional framework that guides pathology residency programs in training residents in critical pathology informatics knowledge and skills and meets Accreditation Council for Graduate Medical Education Informatics Milestones. Design: The College of American Pathologists, Association of Pathology Chairs, and Association for Pathology Informatics formed a partnership and expert work group to identify critical pathology informatics training outcomes and to create a highly adaptable curriculum and instructional approach, supported by a multiyear change management strategy. Results: Pathology Informatics Essentials for Residents (PIER) is a rigorous approach for educating all pathology residents in important pathology informatics knowledge and skills. PIER includes an instructional resource guide and toolkit for incorporating informatics training into residency programs that vary in needs, size, settings, and resources. PIER is available at http://www.apcprods.org/PIER (accessed April 6, 2016). Conclusions: PIER is an important contribution to informatics training in pathology residency programs. PIER introduces pathology trainees to broadly useful informatics concepts and tools that are relevant to practice. PIER provides residency program directors with a means to implement a standardized informatics training curriculum, to adapt the approach to local program needs, and to evaluate resident performance and progress over time. PMID:27563486

  12. International Co-Teaching of Medical Informatics for Training-the-Trainers in Content and Distance Education

    ERIC Educational Resources Information Center

    Lewis, Kadriye O.; Sincan, Murat

    2009-01-01

    In this technologically advanced age, much emphasis is put on collaboration in education at many levels. As a result, faculty co-teaching (collaborative teaching) has grown dramatically. This paper introduces how two instructors from different countries (USA and Turkey), one experienced in online teaching and the other in medical informatics,…

  13. Type 2 diabetes, genomics, and nursing: necessary next steps to advance the science into improved, personalized care.

    PubMed

    Underwood, Patricia C

    2011-01-01

    Type 2 diabetes mellitus (T2DM) is an inherited, chronic disorder with long-term complications; including cardiovascular disease the leading cause of mortality in the United States. The prevalence of T2DM and its complications are on the rise in the United States, highlighting the need for improved individualized prevention and treatment strategies. Exciting advancements in the field of genomics has led to the recent discovery of numerous genetic markers for T2DM; completing a promising first step toward improved, individualized prevention and treatment strategies for T2DM. These genomic markers, identified using genome-wide association studies (GWAS), candidate gene, and rare variant methodology, identify new physiologic pathways underlying the development of T2DM. Much more work is needed to successfully translate the identification of genetic markers for T2DM into improved, individualized prevention and treatment strategies. As front line providers and leaders of prevention and treatment strategies for chronic disease, nurses, nurse practitioners, and nurse scientists must contribute to this translational effort. Thus, it is important for nurses at all levels to (a) be aware of the current science of genetics and T2DM and (b) participate in the translation of this genetic information into improved, personalized patient care. The aim of this review is to (a) provide an overview of the current state of the science of genetic markers and T2DM and (b) highlight essential next steps to successfully translate the identification of genetic markers for T2DM into improved prevention and treatment strategies; focusing particularly on the role of nursing in this process. PMID:22891509

  14. Approaches to advancing quantitative human health risk assessment of environmental chemicals in the post-genomic era

    SciTech Connect

    Chiu, Weihsueh A.; Euling, Susan Y.; Scott, Cheryl Siegel; Subramaniam, Ravi P.

    2013-09-15

    The contribution of genomics and associated technologies to human health risk assessment for environmental chemicals has focused largely on elucidating mechanisms of toxicity, as discussed in other articles in this issue. However, there is interest in moving beyond hazard characterization to making more direct impacts on quantitative risk assessment (QRA) — i.e., the determination of toxicity values for setting exposure standards and cleanup values. We propose that the evolution of QRA of environmental chemicals in the post-genomic era will involve three, somewhat overlapping phases in which different types of approaches begin to mature. The initial focus (in Phase I) has been and continues to be on “augmentation” of weight of evidence — using genomic and related technologies qualitatively to increase the confidence in and scientific basis of the results of QRA. Efforts aimed towards “integration” of these data with traditional animal-based approaches, in particular quantitative predictors, or surrogates, for the in vivo toxicity data to which they have been anchored are just beginning to be explored now (in Phase II). In parallel, there is a recognized need for “expansion” of the use of established biomarkers of susceptibility or risk of human diseases and disorders for QRA, particularly for addressing the issues of cumulative assessment and population risk. Ultimately (in Phase III), substantial further advances could be realized by the development of novel molecular and pathway-based biomarkers and statistical and in silico models that build on anticipated progress in understanding the pathways of human diseases and disorders. Such efforts would facilitate a gradual “reorientation” of QRA towards approaches that more directly link environmental exposures to human outcomes.

  15. Genomics of adaptation and speciation in cichlid fishes: recent advances and analyses in African and Neotropical lineages

    PubMed Central

    Fan, Shaohua; Elmer, Kathryn R.; Meyer, Axel

    2012-01-01

    Cichlid fishes are remarkably phenotypically diverse and species-rich. Therefore, they provide an exciting opportunity for the study of the genetics of adaptation and speciation by natural and sexual selection. Here, we review advances in the genomics and transcriptomics of cichlids, particularly regarding ecologically relevant differences in body shape, trophic apparatus, coloration and patterning, and sex determination. Research conducted so far has focused almost exclusively on African cichlids. To analyse genomic diversity and selection in a Neotropical radiation, we conducted a comparative transcriptomic analysis between sympatric, ecologically divergent crater-lake Midas cichlids (Lake Xiloá Amphilophus amarillo and Amphilophus sagittae). We pyrosequenced (Roche 454) expressed sequence tag (EST) libraries and generated more than 178 000 000 ESTs and identified nine ESTs under positive selection between these sister species (Ka/Ks > 1). None of these ESTs were found to be under selection in African cichlids. Of 11 candidate genes for ecomorphological differentiation in African cichlids, none showed signs of selection between A. amarillo and A. sagittae. Although more population-level studies are now needed to thoroughly document patterns of divergence during speciation of cichlids, available information so far suggests that adaptive phenotypic diversification in Neotropical and African cichlids may be evolving through non-parallel genetic bases. PMID:22201168

  16. Advanced Yellow Fever Virus Genome Detection in Point-of-Care Facilities and Reference Laboratories

    PubMed Central

    Patel, Pranav; Yillah, Jasmin; Weidmann, Manfred; Méndez, Jairo A.; Nakouné, Emmanuel Rivalyn; Niedrig, Matthias

    2012-01-01

    Reported methods for the detection of the yellow fever viral genome are beset by limitations in sensitivity, specificity, strain detection spectra, and suitability to laboratories with simple infrastructure in areas of endemicity. We describe the development of two different approaches affording sensitive and specific detection of the yellow fever genome: a real-time reverse transcription-quantitative PCR (RT-qPCR) and an isothermal protocol employing the same primer-probe set but based on helicase-dependent amplification technology (RT-tHDA). Both assays were evaluated using yellow fever cell culture supernatants as well as spiked and clinical samples. We demonstrate reliable detection by both assays of different strains of yellow fever virus with improved sensitivity and specificity. The RT-qPCR assay is a powerful tool for reference or diagnostic laboratories with real-time PCR capability, while the isothermal RT-tHDA assay represents a useful alternative to earlier amplification techniques for the molecular diagnosis of yellow fever by field or point-of-care laboratories. PMID:23052311

  17. MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences

    PubMed Central

    Luo, Chengwei; Rodriguez-R, Luis M.; Konstantinidis, Konstantinos T.

    2014-01-01

    Determining the taxonomic affiliation of sequences assembled from metagenomes remains a major bottleneck that affects research across the fields of environmental, clinical and evolutionary microbiology. Here, we introduce MyTaxa, a homology-based bioinformatics framework to classify metagenomic and genomic sequences with unprecedented accuracy. The distinguishing aspect of MyTaxa is that it employs all genes present in an unknown sequence as classifiers, weighting each gene based on its (predetermined) classifying power at a given taxonomic level and frequency of horizontal gene transfer. MyTaxa also implements a novel classification scheme based on the genome-aggregate average amino acid identity concept to determine the degree of novelty of sequences representing uncharacterized taxa, i.e. whether they represent novel species, genera or phyla. Application of MyTaxa on in silico generated (mock) and real metagenomes of varied read length (100–2000 bp) revealed that it correctly classified at least 5% more sequences than any other tool. The analysis also showed that ∼10% of the assembled sequences from human gut metagenomes represent novel species with no sequenced representatives, several of which were highly abundant in situ such as members of the Prevotella genus. Thus, MyTaxa can find several important applications in microbial identification and diversity studies. PMID:24589583

  18. Technical advances: genome-wide cDNA-AFLP analysis of the Arabidopsis transcriptome.

    PubMed

    Volkmuth, Wayne; Turk, Stefan; Shapiro, Amy; Fang, Yiwen; Kiegle, Ed; van Haaren, Mark; Donson, Jonathan

    2003-01-01

    cDNA-AFLP, a technology historically used to identify small numbers of differentially expressed genes, was adapted as a genome-wide transcript profiling method. mRNA levels were assayed in a diverse range of tissues from Arabidopsis thaliana plants grown under a variety of environmental conditions. The resulting cDNA-AFLP fragments were sequenced. By linking cDNA-AFLP fragments to their corresponding mRNAs via these sequences, a database was generated that contained quantitative expression information for up to two-thirds of gene loci in A. thaliana, ecotype Ws. Using this resource, the expression levels of genes, including those with high nucleotide sequence similarity, could be determined in a high-throughput manner merely by comparing cDNA-AFLP profiles with the database. The lengths of cDNA-AFLP fragments inferred from their electrophoretic mobilities correlated well with actual fragment lengths determined by sequencing. In addition, the concentrations of AFLP fragments from single cDNAs were highly correlated, illustrating the validity of cDNA-AFLP as a quantitative, genome-wide, transcript profiling method. cDNA-AFLP profiles were also qualitatively consistent with mRNA profiles obtained from parallel microarray analysis, and with data from previous studies. PMID:14506844

  19. Recent advances in globin research using genome-wide association studies and gene editing.

    PubMed

    Orkin, Stuart H

    2016-03-01

    A long-sought goal in the hemoglobin field has been an improved understanding of the mechanisms that regulate the switch from fetal (HbF) to adult (HbA) hemoglobin during development. With such knowledge, the hope is that strategies for directed reactivation of HbF in adults could be devised as an approach to therapy for the β-hemoglobinopathies thalassemia and sickle cell disease. Recent genome-wide association studies (GWAS) led to identification of three loci (BCL11A, HBS1L-MYB, and the β-globin cluster itself) in which natural genetic variation is correlated with different HbF levels in populations. Here, the central role of BCL11A in control of HbF is reviewed from the perspective of how findings may be translated to gene therapy in the not-too-distant future. This summary traces the evolution of recent studies from the initial recognition of BCL11A through GWAS to identification of critical sequences in an enhancer required for its erythroid-specific expression, thereby highlighting an Achilles heel for genome editing. PMID:26866328

  20. Recommendations of the International Medical Informatics Association (IMIA) on education in health and medical informatics.

    PubMed

    2004-01-01

    The International Medical Informatics Association (IMIA) agreed on international recommendations in health informatics / medical informatics education. These should help to establish courses, course tracks or even complete programs in this field, to further develop existing educational activities in the various nations and to support international initiatives concerning education in health and medical informatics (HMI), particularly international activities in educating HMI specialists and the sharing of courseware. The IMIA recommendations centre on educational needs for health care professionals to acquire knowledge and skills in information processing and information and communication technology. The educational needs are described as a three-dimensional framework. The dimensions are: 1) professionals in health care (physicians, nurses, HMI professionals, ...), 2) type of specialisation in health and medical informatics (IT users, HMI specialists) and 3) stage of career progression (bachelor, master, ...). Learning outcomes are defined in terms of knowledge and practical skills for health care professionals in their role (a) as IT user and (b) as HMI specialist. Recommendations are given for courses/course tracks in HMI as part of educational programs in medicine, nursing, health care management, dentistry, pharmacy, public health, health record administration, and informatics/computer science as well as for dedicated programs in HMI (with bachelor, master or doctor degree). To support education in HMI, IMIA offers to award a certificate for high quality HMI education and supports information exchange on programs and courses in HMI through a WWW server of its Working Group on Health and Medical Informatics Education (http://www.imia.org/wg1). PMID:15718686

  1. Implementation of the CDC translational informatics platform - from genetic variants to the national Swedish Rheumatology Quality Register

    PubMed Central

    2013-01-01

    Background Sequencing of the human genome and the subsequent analyses have produced immense volumes of data. The technological advances have opened new windows into genomics beyond the DNA sequence. In parallel, clinical practice generate large amounts of data. This represents an underused data source that has much greater potential in translational research than is currently realized. This research aims at implementing a translational medicine informatics platform to integrate clinical data (disease diagnosis, diseases activity and treatment) of Rheumatoid Arthritis (RA) patients from Karolinska University Hospital and their research database (biobanks, genotype variants and serology) at the Center for Molecular Medicine, Karolinska Institutet. Methods Requirements engineering methods were utilized to identify user requirements. Unified Modeling Language and data modeling methods were used to model the universe of discourse and data sources. Oracle11g were used as the database management system, and the clinical development center (CDC) was used as the application interface. Patient data were anonymized, and we employed authorization and security methods to protect the system. Results We developed a user requirement matrix, which provided a framework for evaluating three translation informatics systems. The implementation of the CDC successfully integrated biological research database (15172 DNA, serum and synovial samples, 1436 cell samples and 65 SNPs per patient) and clinical database (5652 clinical visit) for the cohort of 379 patients presents three profiles. Basic functionalities provided by the translational medicine platform are research data management, development of bioinformatics workflow and analysis, sub-cohort selection, and re-use of clinical data in research settings. Finally, the system allowed researchers to extract subsets of attributes from cohorts according to specific biological, clinical, or statistical features. Conclusions Research and

  2. Emerging Genomic Tools for Legume Breeding: Current Status and Future Prospects.

    PubMed

    Pandey, Manish K; Roorkiwal, Manish; Singh, Vikas K; Ramalingam, Abirami; Kudapa, Himabindu; Thudi, Mahendar; Chitikineni, Anu; Rathore, Abhishek; Varshney, Rajeev K

    2016-01-01

    Legumes play a vital role in ensuring global nutritional food security and improving soil quality through nitrogen fixation. Accelerated higher genetic gains is required to meet the demand of ever increasing global population. In recent years, speedy developments have been witnessed in legume genomics due to advancements in next-generation sequencing (NGS) and high-throughput genotyping technologies. Reference genome sequences for many legume crops have been reported in the last 5 years. The availability of the draft genome sequences and re-sequencing of elite genotypes for several important legume crops have made it possible to identify structural variations at large scale. Availability of large-scale genomic resources and low-cost and high-throughput genotyping technologies are enhancing the efficiency and resolution of genetic mapping and marker-trait association studies. Most importantly, deployment of molecular breeding approaches has resulted in development of improved lines in some legume crops such as chickpea and groundnut. In order to support genomics-driven crop improvement at a fast pace, the deployment of breeder-friendly genomics and decision support tools seems appear to be critical in breeding programs in developing countries. This review provides an overview of emerging genomics and informatics tools/approaches that will be the key driving force for accelerating genomics-assisted breeding and ultimately ensuring nutritional and food security in developing countries. PMID:27199998

  3. Emerging Genomic Tools for Legume Breeding: Current Status and Future Prospects

    PubMed Central

    Pandey, Manish K.; Roorkiwal, Manish; Singh, Vikas K.; Ramalingam, Abirami; Kudapa, Himabindu; Thudi, Mahendar; Chitikineni, Anu; Rathore, Abhishek; Varshney, Rajeev K.

    2016-01-01

    Legumes play a vital role in ensuring global nutritional food security and improving soil quality through nitrogen fixation. Accelerated higher genetic gains is required to meet the demand of ever increasing global population. In recent years, speedy developments have been witnessed in legume genomics due to advancements in next-generation sequencing (NGS) and high-throughput genotyping technologies. Reference genome sequences for many legume crops have been reported in the last 5 years. The availability of the draft genome sequences and re-sequencing of elite genotypes for several important legume crops have made it possible to identify structural variations at large scale. Availability of large-scale genomic resources and low-cost and high-throughput genotyping technologies are enhancing the efficiency and resolution of genetic mapping and marker-trait association studies. Most importantly, deployment of molecular breeding approaches has resulted in development of improved lines in some legume crops such as chickpea and groundnut. In order to support genomics-driven crop improvement at a fast pace, the deployment of breeder-friendly genomics and decision support tools seems appear to be critical in breeding programs in developing countries. This review provides an overview of emerging genomics and informatics tools/approaches that will be the key driving force for accelerating genomics-assisted breeding and ultimately ensuring nutritional and food security in developing countries. PMID:27199998

  4. Managing information well: Toward an ontology-driven informatics platform for data sharing and secondary use in epilepsy self-management research centers.

    PubMed

    Sahoo, Satya S; Zhang, Guo-Qiang; Bamps, Yvan; Fraser, Robert; Stoll, Shelley; Lhatoo, Samden D; Tatsuoka, Curtis; Sams, Johnny; Welter, Elisabeth; Sajatovic, Martha

    2016-09-01

    Epilepsy is a chronic neurological condition that requires active self-management to reduce personal and population burden. The Managing Epilepsy Well Network, funded by the US Centers for Disease Control and Prevention, conducts research on epilepsy self-management. There is an urgent need to develop an integrated informatics platform to maximize the secondary use of existing Managing Epilepsy Well Network data. We have implemented multiple steps to develop an informatics platform, including: (a) a survey of existing outcome data, (b) identification of common data elements, and (c) an integrated database using an epilepsy domain ontology to reconcile data heterogeneity. The informatics platform enables assessment of epilepsy self-management samples by site and in aggregate to support data interpretations for clinical care and ongoing epilepsy self-management research. The Managing Epilepsy Well informatics platform is expected to help advance epilepsy self-management, improve health outcomes, and has potential application in other thematic research networks. PMID:25769938

  5. The Present and Future of Biomarkers in Prostate Cancer: Proteomics, Genomics, and Immunology Advancements

    PubMed Central

    Gaudreau, Pierre-Olivier; Stagg, John; Soulières, Denis; Saad, Fred

    2016-01-01

    Prostate cancer (PC) is the second most common form of cancer in men worldwide. Biomarkers have emerged as essential tools for treatment and assessment since the variability of disease behavior, the cost and diversity of treatments, and the related impairment of quality of life have given rise to a need for a personalized approach. High-throughput technology platforms in proteomics and genomics have accelerated the development of biomarkers. Furthermore, recent successes of several new agents in PC, including immunotherapy, have stimulated the search for predictors of response and resistance and have improved the understanding of the biological mechanisms at work. This review provides an overview of currently established biomarkers in PC, as well as a selection of the most promising biomarkers within these particular fields of development. PMID:27168728

  6. The Present and Future of Biomarkers in Prostate Cancer: Proteomics, Genomics, and Immunology Advancements.

    PubMed

    Gaudreau, Pierre-Olivier; Stagg, John; Soulières, Denis; Saad, Fred

    2016-01-01

    Prostate cancer (PC) is the second most common form of cancer in men worldwide. Biomarkers have emerged as essential tools for treatment and assessment since the variability of disease behavior, the cost and diversity of treatments, and the related impairment of quality of life have given rise to a need for a personalized approach. High-throughput technology platforms in proteomics and genomics have accelerated the development of biomarkers. Furthermore, recent successes of several new agents in PC, including immunotherapy, have stimulated the search for predictors of response and resistance and have improved the understanding of the biological mechanisms at work. This review provides an overview of currently established biomarkers in PC, as well as a selection of the most promising biomarkers within these particular fields of development. PMID:27168728

  7. Genomics of elite sporting performance: what little we know and necessary advances.

    PubMed

    Wang, Guan; Padmanabhan, Sandosh; Wolfarth, Bernd; Fuku, Noriyuki; Lucia, Alejandro; Ahmetov, Ildus I; Cieszczyk, Pawel; Collins, Malcolm; Eynon, Nir; Klissouras, Vassilis; Williams, Alun; Pitsiladis, Yannis

    2013-01-01

    Numerous reports of genetic associations with performance- and injury-related phenotypes have been published over the past three decades; these studies have employed primarily the candidate gene approach to identify genes that associate with elite performance or with variation in performance-and/or injury-related traits. Although generally with small effect sizes and heavily prone to type I statistic error, the number of candidate genetic variants that can potentially explain elite athletic status, injury predisposition, or indeed response to training will be much higher than that examined by numerous biotechnology companies. Priority should therefore be given to applying whole genome technology to sufficiently large study cohorts of world-class athletes with adequately measured phenotypes where it is possible to increase statistical power. Some of the elite athlete cohorts described in the literature might suffice, and collectively, these cohorts could be used for replication purposes. Genome-wide association studies are ongoing in some of these cohorts (i.e., Genathlete, Russian, Spanish, Japanese, United States, and Jamaican cohorts), and preliminary findings include the identification of one single nucleotide polymorphism (SNP; among more than a million SNPs analyzed) that associates with sprint performance in Japanese, American (i.e., African American), and Jamaican cohorts with a combined effect size of ~2.6 (P-value <5×10(-7)) and good concordance with endurance performance between select cohorts. Further replications of these signals in independent cohorts will be required, and any replicated SNPs will be taken forward for fine-mapping/targeted resequencing and functional studies to uncover the underlying biological mechanisms. Only after this lengthy and costly process will the true potential of genetic testing in sport be determined. PMID:24262098

  8. Power, resolution and bias: recent advances in insect phylogeny driven by the genomic revolution.

    PubMed

    Yeates, David K; Meusemann, Karen; Trautwein, Michelle; Wiegmann, Brian; Zwick, Andreas

    2016-02-01

    Our understanding on the phylogenetic relationships of insects has been revolutionised in the last decade by the proliferation of next generation sequencing technologies (NGS). NGS has allowed insect systematists to assemble very large molecular datasets that include both model and non-model organisms. Such datasets often include a large proportion of the total number of protein coding sequences available for phylogenetic comparison. We review some early entomological phylogenomic studies that employ a range of different data sampling protocols and analyses strategies, illustrating a fundamental renaissance in our understanding of insect evolution all driven by the genomic revolution. The analysis of phylogenomic datasets is challenging because of their size and complexity, and it is obvious that the increasing size alone does not ensure that phylogenetic signal overcomes systematic biases in the data. Biases can be due to various factors such as the method of data generation and assembly, or intrinsic biological feature of the data per se, such as similarities due to saturation or compositional heterogeneity. Such biases often cause violations in the underlying assumptions of phylogenetic models. We review some of the bioinformatics tools available and being developed to detect and minimise systematic biases in phylogenomic datasets. Phylogenomic-scale data coupled with sophisticated analyses will revolutionise our understanding of insect functional genomics. This will illuminate the relationship between the vast range of insect phenotypic diversity and underlying genetic diversity. In combination with rapidly developing methods to estimate divergence times, these analyses will also provide a compelling view of the rates and patterns of lineagenesis (birth of lineages) over the half billion years of insect evolution. PMID:27436549

  9. Supporting the Saudi e-health initiative: the Master of Health Informatics programme at KSAU-HS.

    PubMed

    Altuwaijri, M M

    2010-01-01

    The health sector in Saudi Arabia has made significant progress in recent decades with some hospitals receiving international recognition. However, this has not been accompanied by advancements in the field of health informatics, which are necessary for hospitals to achieve certain objectives such as enhancing the quality of health care and reducing the time and cost of health care delivery. In this paper we describe the status of e-health in Saudi Arabia, along with some of the national e-health initiatives such the establishment of a new Master of Health Informatics degree programme and the Saudi Association for Health Informatics. A proposal for an e-health plan in Saudi Arabia is also discussed. PMID:20214169

  10. The imaging 3.0 informatics scorecard.

    PubMed

    Kohli, Marc; Dreyer, Keith J; Geis, J Raymond

    2015-04-01

    Imaging 3.0 is a radiology community initiative to empower radiologists to create and demonstrate value for their patients, referring physicians, and health systems. In image-guided health care, radiologists contribute to the entire health care process, well before and after the actual examination, and out to the point at which they guide clinical decisions and affect patient outcome. Because imaging is so pervasive, radiologists who adopt Imaging 3.0 concepts in their practice can help their health care systems provide consistently high-quality care at reduced cost. By doing this, radiologists become more valuable in the new health care setting. The authors describe how informatics is critical to embracing Imaging 3.0 and present a scorecard that can be used to gauge a radiology group's informatics resources and capabilities. PMID:25842018

  11. Medical informatics and health care organizations.

    PubMed

    Holden, F M

    1991-01-01

    A dialogue between upper management and operational elements over an organization's informatics policies and procedures could take place in an environment in which both parties could succeed. Excellent patient care practices can exist in organizational settings where upper management is not concerned with the specifics of the medical care process. But as the medical care process itself becomes costly, complex, and part of the purview of upper management, solutions to ambiguous informatics policies and practices need to be found. As the discussion of cost determination suggests, a comprehensive "top-down" solution may not be feasible. Allowing patient care expertise to drive the design and implementation of clinical computing modules without unduly restrictive specifications from above is probably the best way to proceed. But if the organization needs to know the specifics of a treatment episode, then the informatics definitions specific to treatment episodes need to be unambiguous and consistently applied. As the discussion of Social Security numbers suggests, communication of information across various parts of the organization not only requires unambiguous data structure definitions, but also suggests that the communication process not be dependent on the content of the messages. Both ideas--consistent data structure definitions for essential data and open system communication architectures--are current in the medical informatician's vocabulary. The same ideas are relevant to the management and operation of large and diffuse health care enterprises. The lessons we are learning about informatics policy and practice controls in clinical computing need to be applied to the enterprise as a whole. PMID:1921663

  12. The Renewed Promise of Medical Informatics.

    PubMed

    van Bemmel, J H; McCray, A T

    2016-01-01

    The promise of the field of Medical Informatics has been great and its impact has been significant. In 1999, the Yearbook editors of the International Medical Informatics Association (IMIA) - also the authors of the present paper - sought to assess this impact by selecting a number of seminal papers in the field, and asking experts to comment on these articles. In particular, it was requested whether and how the expectations, represented by these papers, had been fulfilled since their publication several decades earlier. Each expert was also invited to comment on what might be expected in the future. In the present paper, these areas are briefly reviewed again. Where did these early papers have an impact and where were they not as successful as originally expected? It should be noted that the extraordinary developments in computer technology observed in the last two decades could not have been foreseen by these early researchers. In closing, some of the possibilities and limitations of research in medical informatics are outlined in the context of a framework that considers six levels of computer applications in medicine and health care. For each level, some predictions are made for the future, concluded with thoughts on fruitful areas for ongoing research in the field. PMID:27199195

  13. Loop-linker PCR: an advanced PCR technique for genome walking.

    PubMed

    Trinh, Quoclinh; Shi, Hui; Xu, Wentao; Hao, Junran; Luo, Yunbo; Huang, Kunlun

    2012-10-01

    In this article, we developed a novel PCR method, termed loop-linker PCR, to isolate flanking sequences in transgenic crops. The novelty of this approach is its use of a stem-loop structure to design a loop-linker adapter. The adapter is designed to form a nick site when ligated with restricted DNA. This modification not only can prevent the self-ligation of adapters but also promotes the elongation of the 3' end of the loop-linker adapter to generate a stem-loop structure in the ligation products. Moreover, the suppressive effect of the stem-loop structure decreases nonspecific amplification and increases the success rate of the approach; all extension products will suppress exponential amplification except from the ligation product that contains the specific primer binding site. Using this method, 442, 1830, 107, and 512 bp left border flanking sequences were obtained from the transgenic maizes LY038, DAS-59122-7, Event 3272, and the transgenic soybean MON89788, respectively. The experimental results demonstrated that loop-linker PCR is an efficient, reliable, and cost-effective method for identifying flanking sequences in transgenic crops and could be applied for other genome walking applications. PMID:23008115

  14. Advancing Pharmacogenomics Education in the Core PharmD Curriculum through Student Personal Genomic Testing

    PubMed Central

    Adams, Solomon M.; Anderson, Kacey B.; Coons, James C.; Smith, Randall B.; Meyer, Susan M.; Parker, Lisa S.

    2016-01-01

    Objective. To develop, implement, and evaluate “Test2Learn” a program to enhance pharmacogenomics education through the use of personal genomic testing (PGT) and real genetic data. Design. One hundred twenty-two second-year doctor of pharmacy (PharmD) students in a required course were offered PGT as part of a larger program approach to teach pharmacogenomics within a robust ethical framework. The program added novel learning objectives, lecture materials, analysis tools, and exercises using individual-level and population-level genetic data. Outcomes were assessed with objective measures and pre/post survey instruments. Assessment. One hundred students (82%) underwent PGT. Knowledge significantly improved on multiple assessments. Genotyped students reported a greater increase in confidence in understanding test results by the end of the course. Similarly, undergoing PGT improved student’s self-perceived ability to empathize with patients compared to those not genotyped. Most students (71%) reported feeling PGT was an important part of the course, and 60% reported they had a better understanding of pharmacogenomics specifically because of the opportunity. Conclusion. Implementation of PGT in the core pharmacy curriculum was feasible, well-received, and enhanced student learning of pharmacogenomics. PMID:26941429

  15. Advancing Pharmacogenomics Education in the Core PharmD Curriculum through Student Personal Genomic Testing.

    PubMed

    Adams, Solomon M; Anderson, Kacey B; Coons, James C; Smith, Randall B; Meyer, Susan M; Parker, Lisa S; Empey, Philip E

    2016-02-25

    Objective. To develop, implement, and evaluate "Test2Learn" a program to enhance pharmacogenomics education through the use of personal genomic testing (PGT) and real genetic data. Design. One hundred twenty-two second-year doctor of pharmacy (PharmD) students in a required course were offered PGT as part of a larger program approach to teach pharmacogenomics within a robust ethical framework. The program added novel learning objectives, lecture materials, analysis tools, and exercises using individual-level and population-level genetic data. Outcomes were assessed with objective measures and pre/post survey instruments. Assessment. One hundred students (82%) underwent PGT. Knowledge significantly improved on multiple assessments. Genotyped students reported a greater increase in confidence in understanding test results by the end of the course. Similarly, undergoing PGT improved student's self-perceived ability to empathize with patients compared to those not genotyped. Most students (71%) reported feeling PGT was an important part of the course, and 60% reported they had a better understanding of pharmacogenomics specifically because of the opportunity. Conclusion. Implementation of PGT in the core pharmacy curriculum was feasible, well-received, and enhanced student learning of pharmacogenomics. PMID:26941429

  16. Recent Advances in Discovery, Biosynthesis and Genome Mining of Medicinally Relevant Polycyclic Tetramate Macrolactams.

    PubMed

    Zhang, Guangtao; Zhang, Wenjun; Saha, Subhasish; Zhang, Changsheng

    2016-01-01

    Polycyclic tetramate macrolactams (PTMs), a widely distributed class of structurally complex natural products exhibiting diverse biological activities, share a tetramate-containing macrocyclic lactam ring fused to a subset of carbocyclic rings. More than 30 naturally occurring PTM members have been reported. Representative members include ikarugamycin, HSAF, and alteramides. The emerging significance of PTMs in medicinal applications has raised attentions on their biosynthetic studies. These studies have unveiled the unexpected conservation of compact PTM biosynthetic loci in phylogenetically diverse bacteria and elucidated mechanisms for key steps in PTM biosynthesis. PTMs were demonstrated to be derived from the common origin of a hybrid polyketide synthase (PKS)/nonribosomal peptide synthetase (NRPS) pathway, in which the PKS portion was iteratively used to generate two separate polyketide chains. A common tetramate-containing polyene intermediate was proposed to be the final product of all PTM PKS/NRPS assembly lines. Subsequently, a set of oxidoreductases acted in a not yet clearly understood way to dictate the manner of cyclizations to yield different polycycle ring systems in PTMs. The only well studied example was the formation of the inner fivemembered ring in ikarugamycin, which was catalyzed by an alcohol dehydrogenase via a [1 + 6] Michael addition. Nonetheless, these studies have illustrated the extraordinary simplicity of nature's art in the biosynthesis of PTMs with complex structures and paved the way to further expand the structural diversity of the family of medicinally relevant PTMs by genome mining and combinatorial biosynthesis. PMID:26456464

  17. Crossing the Chasm: Information Technology to Biomedical Informatics

    PubMed Central

    Fahy, Brenda G.; Balke, C. William; Umberger, Gloria H.; Talbert, Jeffery; Canales, Denise Niles; Steltenkamp, Carol L.; Conigliaro, Joseph

    2011-01-01

    Accelerating the translation of new scientific discoveries to improve human health and disease management is the overall goal of a series of initiatives integrated in the National Institutes of Health (NIH) “Roadmap for Medical Research.” The Clinical and Translational Research Award (CTSA) program is, arguably, the most visible component of the NIH Roadmap providing resources to institutions to transform their clinical and translational research enterprises along the goals of the Roadmap. The CTSA program emphasizes biomedical informatics as a critical component for the accomplishment of the NIH’s translational objectives. To be optimally effective, emerging biomedical informatics programs must link with the information technology (IT) platforms of the enterprise clinical operations within academic health centers. This report details one academic health center’s transdisciplinary initiative to create an integrated academic discipline of biomedical informatics through the development of its infrastructure for clinical and translational science infrastructure and response to the CTSA mechanism. This approach required a detailed informatics strategy to accomplish these goals. This transdisciplinary initiative was the impetus for creation of a specialized biomedical informatics core, the Center for Biomedical Informatics (CBI). Development of the CBI codified the need to incorporate medical informatics including quality and safety informatics and enterprise clinical information systems within the CBI. This paper describes the steps taken to develop the biomedical informatics infrastructure, its integration with clinical systems at one academic health center, successes achieved, and barriers encountered during these efforts. PMID:21383632

  18. Knowledge, Skills, and Resources for Pharmacy Informatics Education

    PubMed Central

    Fox, Brent I.; Flynn, Allen J.; Fortier, Christopher R.; Clauson, Kevin A.

    2011-01-01

    Pharmacy has an established history of technology use to support business processes. Pharmacy informatics education within doctor of pharmacy programs, however, is inconsistent, despite its inclusion as a requirement in the 2007 Accreditation Council for Pharmacy Education Standards and Guidelines. This manuscript describes pharmacy informatics knowledge and skills that all graduating pharmacy students should possess, conceptualized within the framework of the medication use process. Additionally, we suggest core source materials and specific learning activities to support pharmacy informatics education. We conclude with a brief discussion of emerging changes in the practice model. These changes are facilitated by pharmacy informatics and will inevitably become commonplace in our graduates’ practice environment. PMID:21829267

  19. (Bio)Medical Informatics in the Next Decade

    PubMed Central

    Rindfleisch, Thomas C.

    1998-01-01

    Even though medical informatics is most often viewed from the perspective of its host disciplines in clinical and biologic medicine, it has an identity and agenda of its own. This paper is an attempt to promote discussion about the long-term role and agenda for medical informatics as a discipline into the next decade. The discussion has two main lines of argument, one about the “engineering” goals of informatics and the other about the “basic research” goals. These are, of course, influenced by ongoing developments in computing, communications, and software infrastructures, but informatics is now mature enough that many of its goals transcend these changes. PMID:9760389

  20. Continuous quality improvement and medical informatics: the convergent synergy.

    PubMed

    Werth, G R; Connelly, D P

    1992-01-01

    Continuous quality improvement (CQI) and medical informatics specialists need to converge their efforts to create synergy for improving health care. Health care CQI needs medical informatics' expertise and technology to build the information systems needed to manage health care organizations according to quality improvement principles. Medical informatics needs CQI's philosophy and methods to build health care information systems that can evolve to meet the changing needs of clinicians and other stakeholders. This paper explores the philosophical basis for convergence of CQI and medical informatics efforts, and then examines a clinical computer workstation development project that is applying a combined approach. PMID:1482948

  1. An Optimized Informatics Pipeline for Mass Spectrometry-Based Peptidomics

    NASA Astrophysics Data System (ADS)

    Wu, Chaochao; Monroe, Matthew E.; Xu, Zhe; Slysz, Gordon W.; Payne, Samuel H.; Rodland, Karin D.; Liu, Tao; Smith, Richard D.

    2015-12-01

    The comprehensive MS analysis of the peptidome, the intracellular and intercellular products of protein degradation, has the potential to provide novel insights on endogenous proteolytic processing and its utility in disease diagnosis and prognosis. Along with the advances in MS instrumentation and related platforms, a plethora of proteomics data analysis tools have been applied for direct use in peptidomics; however, an evaluation of the currently available informatics pipelines for peptidomics data analysis has yet to be reported. In this study, we began by evaluating the results of several popular MS/MS database search engines, including MS-GF+, SEQUEST, and MS-Align+, for peptidomics data analysis, followed by identification and label-free quantification using the well-established accurate mass and time (AMT) tag and newly developed informed quantification (IQ) approaches, both based on direct LC-MS analysis. Our results demonstrated that MS-GF+ outperformed both SEQUEST and MS-Align+ in identifying peptidome peptides. Using a database established from MS-GF+ peptide identifications, both the AMT tag and IQ approaches provided significantly deeper peptidome coverage and less missing data for each individual data set than the MS/MS methods, while achieving robust label-free quantification. Besides having an excellent correlation with the AMT tag quantification results, IQ also provided slightly higher peptidome coverage. Taken together, we propose an optimized informatics pipeline combining MS-GF+ for initial database searching with IQ (or AMT tag) approaches for identification and label-free quantification for high-throughput, comprehensive, and quantitative peptidomics analysis.

  2. An Optimized Informatics Pipeline for Mass Spectrometry-Based Peptidomics

    SciTech Connect

    Wu, Chaochao; Monroe, Matthew E.; Xu, Zhe; Slysz, Gordon W.; Payne, Samuel H.; Rodland, Karin D.; Liu, Tao; Smith, Richard D.

    2015-12-26

    Comprehensive MS analysis of peptidome, the intracellular and intercellular products of protein degradation, has the potential to provide novel insights on endogenous proteolytic processing and their utility in disease diagnosis and prognosis. Along with the advances in MS instrumentation, a plethora of proteomics data analysis tools have been applied for direct use in peptidomics; however an evaluation of the currently available informatics pipelines for peptidomics data analysis has yet to be reported. In this study, we set off by evaluating the results of several popular MS/MS database search engines including MS-GF+, SEQUEST and MS-Align+ for peptidomics data analysis, followed by identification and label-free quantification using the well-established accurate mass and time (AMT) tag and newly developed informed quantification (IQ) approaches, both based on direct LC-MS analysis. Our result demonstrated that MS-GF+ outperformed both SEQUEST and MS-Align+ in identifying peptidome peptides. Using a database established from the MS-GF+ peptide identifications, both the AMT tag and IQ approaches provided significantly deeper peptidome coverage and less missing value for each individual data set than the MS/MS methods, while achieving robust label-free quantification. Besides having an excellent correlation with the AMT tag quantification results, IQ also provided slightly higher peptidome coverage than AMT. Taken together, we propose an optimal informatics pipeline combining MS-GF+ for initial database searching with IQ (or AMT) for identification and label-free quantification for high-throughput, comprehensive and quantitative peptidomics analysis.

  3. Epigenetic regulation of mitochondrial function in neurodegenerative disease: New insights from advances in genomic technologies.

    PubMed

    Devall, Matthew; Roubroeks, Janou; Mill, Jonathan; Weedon, Michael; Lunnon, Katie

    2016-06-20

    The field of mitochondrial epigenetics has received increased attention in recent years and changes in mitochondrial DNA (mtDNA) methylation has been implicated in a number of diseases, including neurodegenerative diseases such as amyotrophic lateral sclerosis. However, current publications have been limited by the use of global or targeted methods of measuring DNA methylation. In this review, we discuss current findings in mitochondrial epigenetics as well as its potential role as a regulator of mitochondria within the brain. Finally, we summarize the current technologies best suited to capturing mtDNA methylation, and how a move towards whole epigenome sequencing of mtDNA may help to advance our current understanding of the field. PMID:26876477

  4. [Genomic Tests: From Basic Research to Clinical Practice].

    PubMed

    Nakatani, Kaname; Mochiki, Ikuyo

    2015-03-01

    Advanced genomic analytical technologies are developing and challenging the current framework of clinical laboratory testing. However, most genomic tests have been devised as laboratory-developed tests (LDTs) without sufficient validation of their analytical validity. Quality assurance (QA) of tests is mandatory for routine clinical practice. External quality management systems such as ISO add QA. Other than QAs of pre-analysis, analytical procedures, reports, and laboratory personnel should be regularly assessed using appropriate best practices and guidelines for analytical validity. Moreover, ethical, legal, and social issues concerning genomic information should be resolved in genomic tests. Taken together, clinicians and health care policymakers must consider the accuracy with which a test identifies a patient's clinical status and the risks and benefits resulting from test use. Genomic tests in current use vary in terms of their accuracy and potential to improve health outcomes. Recently, high-throughput analysis using next-generation sequencing and microarrays is being developed and introduced into clinical practice. As analysis of these data sets is a huge challenge, it requires novel analytical processes that include data quality assessment, comprehensive analysis, interpretation of the results, and presenting the results to users. Especially, human resources are required to develop genome informatics to interpret large amounts of data. Another issue is to regulate Direct To Consumers (DTC) genetic tests by medical institutions as a salutary health service. Although advanced genomic analytical technologies present some issues, they are useful and powerful tools in clinical practice. Thus, they will be properly introduced into clinical practices in a step by step manner. PMID:26524861

  5. Quantum Bio-Informatics II From Quantum Information to Bio-Informatics

    NASA Astrophysics Data System (ADS)

    Accardi, L.; Freudenberg, Wolfgang; Ohya, Masanori

    2009-02-01

    The problem of quantum-like representation in economy cognitive science, and genetics / L. Accardi, A. Khrennikov and M. Ohya -- Chaotic behavior observed in linea dynamics / M. Asano, T. Yamamoto and Y. Togawa -- Complete m-level quantum teleportation based on Kossakowski-Ohya scheme / M. Asano, M. Ohya and Y. Tanaka -- Towards quantum cybernetics: optimal feedback control in quantum bio informatics / V. P. Belavkin -- Quantum entanglement and circulant states / D. Chruściński -- The compound Fock space and its application in brain models / K. -H. Fichtner and W. Freudenberg -- Characterisation of beam splitters / L. Fichtner and M. Gäbler -- Application of entropic chaos degree to a combined quantum baker's map / K. Inoue, M. Ohya and I. V. Volovich -- On quantum algorithm for multiple alignment of amino acid sequences / S. Iriyama and M. Ohya --Quantum-like models for decision making in psychology and cognitive science / A. Khrennikov -- On completely positive non-Markovian evolution of a d-level system / A. Kossakowski and R. Rebolledo -- Measures of entanglement - a Hilbert space approach / W. A. Majewski -- Some characterizations of PPT states and their relation / T. Matsuoka -- On the dynamics of entanglement and characterization ofentangling properties of quantum evolutions / M. Michalski -- Perspective from micro-macro duality - towards non-perturbative renormalization scheme / I. Ojima -- A simple symmetric algorithm using a likeness with Introns behavior in RNA sequences / M. Regoli -- Some aspects of quadratic generalized white noise functionals / Si Si and T. Hida -- Analysis of several social mobility data using measure of departure from symmetry / K. Tahata ... [et al.] -- Time in physics and life science / I. V. Volovich -- Note on entropies in quantum processes / N. Watanabe -- Basics of molecular simulation and its application to biomolecules / T. Ando and I. Yamato -- Theory of proton-induced superionic conduction in hydrogen-bonded systems

  6. Evidence-based Health Informatics and the Scientific Development of the Field.

    PubMed

    Wyatt, Jeremy C

    2016-01-01

    We define and discuss the nature of Evidence-based Health Informatics (EBHI), the kind of evidence health informatics researchers must generate to make EBHI a reality, and how we should grade such evidence. We propose adding principle-based evaluation studies to the list of common evaluation study types, and outline how to carry out such studies to generate evidence that will prove useful for establishing EBHI. The main purpose of a principle-based evaluation study is to test the impact on system acceptability, usage or effectiveness of a generalizable system design principle, so we also explore when during the system design process such principles are needed, and which disciplines are most promising as sources of design principles. We conclude with some challenges for EBHI, a list of the benefits of adopting this approach, and a test to ensure that we are advancing in the direction of science, as opposed to pseudoscience. PMID:27198088

  7. Imaging-based observational databases for clinical problem solving: the role of informatics

    PubMed Central

    Bui, Alex A T; Hsu, William; Arnold, Corey; El-Saden, Suzie; Aberle, Denise R; Taira, Ricky K

    2013-01-01

    Imaging has become a prevalent tool in the diagnosis and treatment of many diseases, providing a unique in vivo, multi-scale view of anatomic and physiologic processes. With the increased use of imaging and its progressive technical advances, the role of imaging informatics is now evolving—from one of managing images, to one of integrating the full scope of clinical information needed to contextualize and link observations across phenotypic and genotypic scales. Several challenges exist for imaging informatics, including the need for methods to transform clinical imaging studies and associated data into structured information that can be organized and analyzed. We examine some of these challenges in establishing imaging-based observational databases that can support the creation of comprehensive disease models. The development of these databases and ensuing models can aid in medical decision making and knowledge discovery and ultimately, transform the use of imaging to support individually-tailored patient care. PMID:23775172

  8. Better informed in clinical practice - a brief overview of dental informatics.

    PubMed

    Reynolds, P A; Harper, J; Dunne, S

    2008-03-22

    Uptake of dental informatics has been hampered by technical and user issues. Innovative systems have been developed, but usability issues have affected many. Advances in technology and artificial intelligence are now producing clinically useful systems, although issues still remain with adapting computer interfaces to the dental practice working environment. A dental electronic health record has become a priority in many countries, including the UK. However, experience shows that any dental electronic health record (EHR) system cannot be subordinate to, or a subset of, a medical record. Such a future dental EHR is likely to incorporate integrated care pathways. Future best dental practice will increasingly depend on computer-based support tools, although disagreement remains about the effectiveness of current support tools. Over the longer term, future dental informatics tools will incorporate dynamic, online evidence-based medicine (EBM) tools, and promise more adaptive, patient-focused and efficient dental care with educational advantages in training. PMID:18356882

  9. Informatics for RNA Sequencing: A Web Resource for Analysis on the Cloud.

    PubMed

    Griffith, Malachi; Walker, Jason R; Spies, Nicholas C; Ainscough, Benjamin J; Griffith, Obi L

    2015-08-01

    Massively parallel RNA sequencing (RNA-seq) has rapidly become the assay of choice for interrogating RNA transcript abundance and diversity. This article provides a detailed introduction to fundamental RNA-seq molecular biology and informatics concepts. We make available open-access RNA-seq tutorials that cover cloud computing, tool installation, relevant file formats, reference genomes, transcriptome annotations, quality-control strategies, expression, differential expression, and alternative splicing analysis methods. These tutorials and additional training resources are accompanied by complete analysis pipelines and test datasets made available without encumbrance at www.rnaseq.wiki. PMID:26248053

  10. Informatics for RNA Sequencing: A Web Resource for Analysis on the Cloud

    PubMed Central

    Griffith, Malachi; Walker, Jason R.; Spies, Nicholas C.; Ainscough, Benjamin J.; Griffith, Obi L.

    2015-01-01

    Massively parallel RNA sequencing (RNA-seq) has rapidly become the assay of choice for interrogating RNA transcript abundance and diversity. This article provides a detailed introduction to fundamental RNA-seq molecular biology and informatics concepts. We make available open-access RNA-seq tutorials that cover cloud computing, tool installation, relevant file formats, reference genomes, transcriptome annotations, quality-control strategies, expression, differential expression, and alternative splicing analysis methods. These tutorials and additional training resources are accompanied by complete analysis pipelines and test datasets made available without encumbrance at www.rnaseq.wiki. PMID:26248053

  11. Creating a pipeline of talent for informatics: STEM initiative for high school students in computer science, biology, and biomedical informatics.

    PubMed

    Dutta-Moscato, Joyeeta; Gopalakrishnan, Vanathi; Lotze, Michael T; Becich, Michael J

    2014-01-01

    This editorial provides insights into how informatics can attract highly trained students by involving them in science, technology, engineering, and math (STEM) training at the high school level and continuing to provide mentorship and research opportunities through the formative years of their education. Our central premise is that the trajectory necessary to be expert in the emergent fields in front of them requires acceleration at an early time point. Both pathology (and biomedical) informatics are new disciplines which would benefit from involvement by students at an early stage of their education. In 2009, Michael T Lotze MD, Kirsten Livesey (then a medical student, now a medical resident at University of Pittsburgh Medical Center (UPMC)), Richard Hersheberger, PhD (Currently, Dean at Roswell Park), and Megan Seippel, MS (the administrator) launched the University of Pittsburgh Cancer Institute (UPCI) Summer Academy to bring high school students for an 8 week summer academy focused on Cancer Biology. Initially, pathology and biomedical informatics were involved only in the classroom component of the UPCI Summer Academy. In 2011, due to popular interest, an informatics track called Computer Science, Biology and Biomedical Informatics (CoSBBI) was launched. CoSBBI currently acts as a feeder program for the undergraduate degree program in bioinformatics at the University of Pittsburgh, which is a joint degree offered by the Departments of Biology and Computer Science. We believe training in bioinformatics is the best foundation for students interested in future careers in pathology informatics or biomedical informatics. We describe our approach to the recruitment, training and research mentoring of high school students to create a pipeline of exceptionally well-trained applicants for both the disciplines of pathology informatics and biomedical informatics. We emphasize here how mentoring of high school students in pathology informatics and biomedical informatics

  12. Creating a pipeline of talent for informatics: STEM initiative for high school students in computer science, biology, and biomedical informatics

    PubMed Central

    Dutta-Moscato, Joyeeta; Gopalakrishnan, Vanathi; Lotze, Michael T.; Becich, Michael J.

    2014-01-01

    This editorial provides insights into how informatics can attract highly trained students by involving them in science, technology, engineering, and math (STEM) training at the high school level and continuing to provide mentorship and research opportunities through the formative years of their education. Our central premise is that the trajectory necessary to be expert in the emergent fields in front of them requires acceleration at an early time point. Both pathology (and biomedical) informatics are new disciplines which would benefit from involvement by students at an early stage of their education. In 2009, Michael T Lotze MD, Kirsten Livesey (then a medical student, now a medical resident at University of Pittsburgh Medical Center (UPMC)), Richard Hersheberger, PhD (Currently, Dean at Roswell Park), and Megan Seippel, MS (the administrator) launched the University of Pittsburgh Cancer Institute (UPCI) Summer Academy to bring high school students for an 8 week summer academy focused on Cancer Biology. Initially, pathology and biomedical informatics were involved only in the classroom component of the UPCI Summer Academy. In 2011, due to popular interest, an informatics track called Computer Science, Biology and Biomedical Informatics (CoSBBI) was launched. CoSBBI currently acts as a feeder program for the undergraduate degree program in bioinformatics at the University of Pittsburgh, which is a joint degree offered by the Departments of Biology and Computer Science. We believe training in bioinformatics is the best foundation for students interested in future careers in pathology informatics or biomedical informatics. We describe our approach to the recruitment, training and research mentoring of high school students to create a pipeline of exceptionally well-trained applicants for both the disciplines of pathology informatics and biomedical informatics. We emphasize here how mentoring of high school students in pathology informatics and biomedical informatics

  13. Characteristics of Information Systems and Business Informatics Study Programs

    ERIC Educational Resources Information Center

    Helfert, Markus

    2011-01-01

    Over the last decade there is an intensive discussion within the Information Systems (IS) and Informatics community about the characteristics and identity of the discipline. Simultaneously with the discussion, there is an ongoing debate on essential skills and capabilities of IS and Business Informatics graduates as well as the profile of IS…

  14. Perspectives on Information Science and Health Informatics Education.

    ERIC Educational Resources Information Center

    Lunin, Lois F., Ed.; Ball, Marion J., Ed.

    1989-01-01

    This theoretical discussion of what information science can contribute to the health professions addresses questions of definition and describes application and knowledge models for the emerging profession of informatics. A review of existing programs includes curriculum models and provides details on informatics programs emphasizing information…

  15. A hypergraphic model of medical informatics: curriculum development guide.

    PubMed Central

    Chi, X.; Pavilcek, K.

    1999-01-01

    Medical informatics, as a descriptive, scientific study, must be mathematically or theoretically described. Is it important to define a model for medical informatics? The answer is worth pursuing. The medical informatics profession stands to benefit three-fold: first, by clarifying the vagueness of the definition of medical informatics, secondly, by identifying the scope and content for educational programs, and, thirdly, by defining career opportunities for its graduates. Existing medical informatics curricula are not comparable. Consequently, the knowledge and skills of graduates from these programs are difficult to assess. The challenge is to promote academics that develops graduates for prospective employers to fulfill the criteria of the health care industry and, simultaneously, compete with computer science programs that produce information technology graduates. In order to meet this challenge, medical informatics programs must have unique curricula that distinguishes its graduates. The solution is to educate students in a comparable manner across the domain of medical informatics. This paper discusses a theoretical model for medical informatics. Images Figure PMID:10566316

  16. The Recurrence Relations in Teaching Students of Informatics

    ERIC Educational Resources Information Center

    Bakoev, Valentin P.

    2010-01-01

    The topic "Recurrence relations" and its place in teaching students of Informatics is discussed in this paper. We represent many arguments about the importance, the necessity and the benefit of studying this subject by Informatics students. They are based on investigation of some fundamental books and textbooks on Discrete Mathematics,…

  17. Clinical Informatics Board Specialty Certification for Physicians: A Global View.

    PubMed

    Gundlapalli, Adi V; Gundlapalli, Aditya V; Greaves, William W; Kesler, Denece; Murray, Peter; Safran, Charles; Lehmann, Christoph U

    2015-01-01

    Clinical informatics workforce development is a high priority for medicine. Professional board certification for physicians is an important tool to demonstrating excellence. The recent recognition of clinical informatics as a subspecialty board in the U.S. has generated interest and excitement among the U.S. informatics community. To determine the extent of similar programs in countries around the world, we performed literature searches with relevant keywords and internet searches of websites of informatics societies around the world for mentions or descriptions of certifications and reviewed publicly available sources. The U.S. certification was prominent in the recent published literature. Germany and Belgium have long-standing certifications with South Korea and Sri Lanka considering similar programs. This is the first global view of clinical informatics board certification for physicians. Training and certification for non-physician informatics professionals in allied areas are widespread. Official recognition and certification for physicians and all informatics professionals represents a key component of capacity building and a means of addressing the shortage of a skilled informatics workforce. Wider adoption of certification programs may further attracting talent and accelerate growth of the field. PMID:26262101

  18. High throughput instruments, methods, and informatics for systems biology.

    SciTech Connect

    Sinclair, Michael B.; Cowie, Jim R.; Van Benthem, Mark Hilary; Wylie, Brian Neil; Davidson, George S.; Haaland, David Michael; Timlin, Jerilyn Ann; Aragon, Anthony D.; Keenan, Michael Robert; Boyack, Kevin W.; Thomas, Edward Victor; Werner-Washburne, Margaret C.; Mosquera-Caro, Monica P.; Martinez, M. Juanita; Martin, Shawn Bryan; Willman, Cheryl L.

    2003-12-01

    High throughput instruments and analysis techniques are required in order to make good use of the genomic sequences that have recently become available for many species, including humans. These instruments and methods must work with tens of thousands of genes simultaneously, and must be able to identify the small subsets of those genes that are implicated in the observed phenotypes, or, for instance, in responses to therapies. Microarrays represent one such high throughput method, which continue to find increasingly broad application. This project has improved microarray technology in several important areas. First, we developed the hyperspectral scanner, which has discovered and diagnosed numerous flaws in techniques broadly employed by microarray researchers. Second, we used a series of statistically designed experiments to identify and correct errors in our microarray data to dramatically improve the accuracy, precision, and repeatability of the microarray gene expression data. Third, our research developed new informatics techniques to identify genes with significantly different expression levels. Finally, natural language processing techniques were applied to improve our ability to make use of online literature annotating the important genes. In combination, this research has improved the reliability and precision of laboratory methods and instruments, while also enabling substantially faster analysis and discovery.

  19. Building a collaborative global health informatics website.

    PubMed

    Chan, Connie; Khan, Sharib; Nwankwo, Victor; Senathirajah, Yalini; Kukafka, Rita

    2008-01-01

    Information technology is playing an increasing role in managing the challenges of global public health issues. The emergence of Web 2.0 technologies provides a tremendous avenue to foster connections among diverse health professionals engaged in the development and implementation of informatics-based solutions for global health. Our website, www.globalhealthinformatics.org, leverages an open source platform that employs Web 2.0 functionalities to create such a global community with the objective of fostering collaboration and knowledge sharing. PMID:18999008

  20. Next generation neonatal health informatics with Artemis.

    PubMed

    McGregor, Carolyn; Catley, Christina; James, Andrew; Padbury, James

    2011-01-01

    This paper describes the deployment of a platform to enable processing of currently uncharted high frequency, high fidelity, synchronous data from medical devices. Such a platform would support the next generation of informatics solutions for neonatal intensive care. We present Artemis, a platform for real-time enactment of clinical knowledge as it relates to multidimensional data analysis and clinical research. Through specific deployment examples at two different neonatal intensive care units, we demonstrate that Artemis supports: 1) instantiation of clinical rules; 2) multidimensional analysis; 3) distribution of services for critical care via cloud computing; and 4) accomplishing 1 through 3 using current technology without a negative impact on patient care. PMID:21893725

  1. Development of a medical informatics data warehouse.

    PubMed

    Wu, Cai

    2006-01-01

    This project built a medical informatics data warehouse (MedInfo DDW) in an Oracle database to analyze medical information which has been collected through Baylor Family Medicine Clinic (FCM) Logician application. The MedInfo DDW used Star Schema with dimensional model, FCM database as operational data store (ODS); the data from on-line transaction processing (OLTP) were extracted and transferred to a knowledge based data warehouse through SQLLoad, and the patient information was analyzed by using on-line analytic processing (OLAP) in Crystal Report. PMID:17238767

  2. Developing a common reference model for the health informatics discipline.

    PubMed

    Hovenga, Evelyn; Grain, Heather

    2013-01-01

    This study reports on an examination of the IT industry's Skills Framework for the Information Age (SFIA) to determine if such a process and/or the use of this tool is suitable to be applied to the health informatics discipline. During this process, four sets of known and agreed-upon Health Informatics skill and knowledge domain statements and competencies were mapped to SFIA. The results showed that all high level SFIA skills apply to the health informatics discipline but that these need to be contextualized to suit the health industry and additional health industry specific skills and knowledge domains need to be included to truly reflect the necessary health informatics skill set from which competency statements can be developed. Adoption of an accord similar to the Seoul Accord process could be very beneficial in promoting a global understanding of the health informatics discipline. PMID:23920528

  3. Health Informatics via Machine Learning for the Clinical Management of Patients

    PubMed Central

    Niehaus, K. E.; Charlton, P.; Colopy, G. W.

    2015-01-01

    Summary Objectives To review how health informatics systems based on machine learning methods have impacted the clinical management of patients, by affecting clinical practice. Methods We reviewed literature from 2010-2015 from databases such as Pubmed, IEEE xplore, and INSPEC, in which methods based on machine learning are likely to be reported. We bring together a broad body of literature, aiming to identify those leading examples of health informatics that have advanced the methodology of machine learning. While individual methods may have further examples that might be added, we have chosen some of the most representative, informative exemplars in each case. Results Our survey highlights that, while much research is taking place in this high-profile field, examples of those that affect the clinical management of patients are seldom found. We show that substantial progress is being made in terms of methodology, often by data scientists working in close collaboration with clinical groups. Conclusions Health informatics systems based on machine learning are in their infancy and the translation of such systems into clinical management has yet to be performed at scale. PMID:26293849

  4. The World Informatics Scene: ICSU, International Unions and Associations, Professional Society Activities

    NASA Astrophysics Data System (ADS)

    Fox, P.; Barton, C.

    2009-04-01

    Now that the Electronic Geophysical Year (2007-2008) has concluded, a substantial number of new coordination efforts under the heading of informatics have emerged. These efforts range from divisions/ sections in societies such as the Geological Society of America, the American Geophysical Union and the European Geosciences Union devoted to all aspects of informatics. In each case there has been a strong community response at their regular meetings. These society efforts are closer to the working scientists, technologists and data producers, and managers. At the same time, in a recognition for the need of a sustained activity such as eGY, the International Union of Geodesy and Geophysics (IUGG) has formed a Union Commission for Data and Information and the Committee on Data for Science and Technology (CODATA) approved a Task Group on eGY Earth and Space Science Data Interoperability. The International Council of Science's (ICSU) Strategic Committee on Information and Data (SCID) implementation report was approved by the ICSU general assembly in October 2008. ICSU's priority area assessment strategy for ICSU to play a leadership role in the coordination of data and information efforts world-wide. This report is being implemented and influences entities such as CODATA, and forms a new World Data System. This presentation will give details on the abovementioned activities and indicate an emerging synergy for Informatics across many discipline and the advancement of science and societal goals.

  5. Consortium for Oral Health-Related Informatics: Improving Dental Research, Education, and Treatment

    PubMed Central

    Stark, Paul C.; Kalenderian, Elsbeth; White, Joel M.; Walji, Muhammad F.; Stewart, Denice C.L.; Kimmes, Nicole; Meng, Thomas R.; Willis, George P.; DeVries, Ted; Chapman, Robert J.

    2011-01-01

    Advances in informatics, particularly the implementation of electronic health records (EHR), in dentistry have facilitated the exchange of information. The majority of dental schools in North America use the same EHR system, providing an unprecedented opportunity to integrate these data into a repository that can be used for oral health education and research. In 2007, fourteen dental schools formed the Consortium for Oral Health-Related Informatics (COHRI). Since its inception, COHRI has established structural and operational processes, governance and bylaws, and a number of work groups organized in two divisions: one focused on research (data standardization, integration, and analysis), and one focused on education (performance evaluations, virtual standardized patients, and objective structured clinical examinations). To date, COHRI (which now includes twenty dental schools) has been successful in developing a data repository, pilot-testing data integration, and sharing EHR enhancements among the group. This consortium has collaborated on standardizing medical and dental histories, developing diagnostic terminology, and promoting the utilization of informatics in dental education. The consortium is in the process of assembling the largest oral health database ever created. This will be an invaluable resource for research and provide a foundation for evidence-based dentistry for years to come. PMID:20930236

  6. Food Safety Informatics: A Public Health Imperative

    PubMed Central

    Tucker, Cynthia A.; Larkin, Stephanie N.; Akers, Timothy A.

    2011-01-01

    To date, little has been written about the implementation of utilizing food safety informatics as a technological tool to protect consumers, in real-time, against foodborne illnesses. Food safety outbreaks have become a major public health problem, causing an estimated 48 million illnesses, 128,000 hospitalizations, and 3,000 deaths in the U.S. each year. Yet, government inspectors/regulators that monitor foodservice operations struggle with how to collect, organize, and analyze data; implement, monitor, and enforce safe food systems. Currently, standardized technologies have not been implemented to efficiently establish “near-in-time” or “just-in-time” electronic awareness to enhance early detection of public health threats regarding food safety. To address the potential impact of collection, organization and analyses of data in a foodservice operation, a wireless food safety informatics (FSI) tool was pilot tested at a university student foodservice center. The technological platform in this test collected data every six minutes over a 24 hour period, across two primary domains: time and temperatures within freezers, walk-in refrigerators and dry storage areas. The results of this pilot study briefly illustrated how technology can assist in food safety surveillance and monitoring by efficiently detecting food safety abnormalities related to time and temperatures so that efficient and proper response in “real time” can be addressed to prevent potential foodborne illnesses. PMID:23569605

  7. Translational Research from an Informatics Perspective

    NASA Technical Reports Server (NTRS)

    Bernstam, Elmer; Meric-Bernstam, Funda; Johnson-Throop, Kathy A.; Turley, James P.; Smith, Jack W.

    2007-01-01

    Clinical and translational research (CTR) is an essential part of a sustainable global health system. Informatics is now recognized as an important en-abler of CTR and informaticians are increasingly called upon to help CTR efforts. The US National Institutes of Health mandated biomedical informatics activity as part of its new national CTR grant initiative, the Clinical and Translational Science Award (CTSA). Traditionally, translational re-search was defined as the translation of laboratory discoveries to patient care (bench to bedside). We argue, however, that there are many other kinds of translational research. Indeed, translational re-search requires the translation of knowledge dis-covered in one domain to another domain and is therefore an information-based activity. In this panel, we will expand upon this view of translational research and present three different examples of translation to illustrate the point: 1) bench to bedside, 2) Earth to space and 3) academia to community. We will conclude with a discussion of our local translational research efforts that draw on each of the three examples.

  8. Food safety informatics: a public health imperative.

    PubMed

    Tucker, Cynthia A; Larkin, Stephanie N; Akers, Timothy A

    2011-01-01

    To date, little has been written about the implementation of utilizing food safety informatics as a technological tool to protect consumers, in real-time, against foodborne illnesses. Food safety outbreaks have become a major public health problem, causing an estimated 48 million illnesses, 128,000 hospitalizations, and 3,000 deaths in the U.S. each year. Yet, government inspectors/regulators that monitor foodservice operations struggle with how to collect, organize, and analyze data; implement, monitor, and enforce safe food systems. Currently, standardized technologies have not been implemented to efficiently establish "near-in-time" or "just-in-time" electronic awareness to enhance early detection of public health threats regarding food safety. To address the potential impact of collection, organization and analyses of data in a foodservice operation, a wireless food safety informatics (FSI) tool was pilot tested at a university student foodservice center. The technological platform in this test collected data every six minutes over a 24 hour period, across two primary domains: time and temperatures within freezers, walk-in refrigerators and dry storage areas. The results of this pilot study briefly illustrated how technology can assist in food safety surveillance and monitoring by efficiently detecting food safety abnormalities related to time and temperatures so that efficient and proper response in "real time" can be addressed to prevent potential foodborne illnesses. PMID:23569605

  9. The new informatics of national healthcare reform.

    PubMed

    Manderscheid, R W; Henderson, M J

    1994-01-01

    The President's Health Security Act has succeeded in attracting America's attention. Several of its initiatives have been well-publicized and hotly debated in Congress. The act also includes a number of implications for healthcare informatics, and devotes an entire chapter to this subject, although this area has not received as much publicity. Every behavioral healthcare provider's information system would be significantly affected by enactment of the Health Security Act. Selected forms and data elements for the management and delivery of behavioral healthcare services would need to be standardized. Organizations of behavioral healthcare providers, managed care companies and purchasers would increasingly share selected patient and subscriber information in aggregated form, for a variety of purposes. As a result, tougher laws to protect patient data privacy will likely be forthcoming. The following article gives an overview of the informatics needs of the soon-to-be reformed American healthcare system, into which behavioral healthcare will be integrated. As part of the larger system, behavioral healthcare services and information systems will need to comply with the same guidelines and requirements, outlined below, as other healthcare providers. Preparation to meet the information demands of the evolving healthcare system will require adaptation of existing computerized information systems, utilization of new technology, consultation with the system's major shareholders and attention to continuous quality improvement processes. PMID:10142491

  10. An Academic-Business Partnership for Advancing Clinical Informatics.

    ERIC Educational Resources Information Center

    Connors, Helen R.; Weaver, Charlotte; Warren, Judith; Miller, Karen L.

    2002-01-01

    A partnership between a university school of nursing and a health care information technology supplier resulted in the Simulated E-hEalth Delivery System (SEEDS). This program enables nursing students to learn clinical skills in a state-of-the-art environment using a live-production, clinical information system designed for care delivery. (JOW)

  11. NCI Workshop Report: Clinical and Computational Requirements for Correlating Imaging Phenotypes with Genomics Signatures.

    PubMed

    Colen, Rivka; Foster, Ian; Gatenby, Robert; Giger, Mary Ellen; Gillies, Robert; Gutman, David; Heller, Matthew; Jain, Rajan; Madabhushi, Anant; Madhavan, Subha; Napel, Sandy; Rao, Arvind; Saltz, Joel; Tatum, James; Verhaak, Roeland; Whitman, Gary

    2014-10-01

    The National Cancer Institute (NCI) Cancer Imaging Program organized two related workshops on June 26-27, 2013, entitled "Correlating Imaging Phenotypes with Genomics Signatures Research" and "Scalable Computational Resources as Required for Imaging-Genomics Decision Support Systems." The first workshop focused on clinical and scientific requirements, exploring our knowledge of phenotypic characteristics of cancer biological properties to determine whether the field is sufficiently advanced to correlate with imaging phenotypes that underpin genomics and clinical outcomes, and exploring new scientific methods to extract phenotypic features from medical images and relate them to genomics analyses. The second workshop focused on computational methods that explore informatics and computational requirements to extract phenotypic features from medical images and relate them to genomics analyses and improve the accessibility and speed of dissemination of existing NIH resources. These workshops linked clinical and scientific requirements of currently known phenotypic and genotypic cancer biology characteristics with imaging phenotypes that underpin genomics and clinical outcomes. The group generated a set of recommendations to NCI leadership and the research community that encourage and support development of the emerging radiogenomics research field to address short-and longer-term goals in cancer research. PMID:25389451

  12. NCI Workshop Report: Clinical and Computational Requirements for Correlating Imaging Phenotypes with Genomics Signatures

    PubMed Central

    Colen, Rivka; Foster, Ian; Gatenby, Robert; Giger, Mary Ellen; Gillies, Robert; Gutman, David; Heller, Matthew; Jain, Rajan; Madabhushi, Anant; Madhavan, Subha; Napel, Sandy; Rao, Arvind; Saltz, Joel; Tatum, James; Verhaak, Roeland; Whitman, Gary

    2014-01-01

    The National Cancer Institute (NCI) Cancer Imaging Program organized two related workshops on June 26–27, 2013, entitled “Correlating Imaging Phenotypes with Genomics Signatures Research” and “Scalable Computational Resources as Required for Imaging-Genomics Decision Support Systems.” The first workshop focused on clinical and scientific requirements, exploring our knowledge of phenotypic characteristics of cancer biological properties to determine whether the field is sufficiently advanced to correlate with imaging phenotypes that underpin genomics and clinical outcomes, and exploring new scientific methods to extract phenotypic features from medical images and relate them to genomics analyses. The second workshop focused on computational methods that explore informatics and computational requirements to extract phenotypic features from medical images and relate them to genomics analyses and improve the accessibility and speed of dissemination of existing NIH resources. These workshops linked clinical and scientific requirements of currently known phenotypic and genotypic cancer biology characteristics with imaging phenotypes that underpin genomics and clinical outcomes. The group generated a set of recommendations to NCI leadership and the research community that encourage and support development of the emerging radiogenomics research field to address short-and longer-term goals in cancer research. PMID:25389451

  13. Empowered Consumers and the Health Care Team: A Dynamic Model of Health Informatics.

    PubMed

    Mancuso, Peggy J; Myneni, Sahiti

    2016-01-01

    This article presents a dynamic new model of health informatics. Within the model, the focus of health informatics changes from the provider to the consumer and incorporates the dynamic relationship of technological change to health care. Bioinformatics is the scientific discipline that is translated into care through the practice of health informatics. The loci of health informatics practices are the consumer (consumer informatics), the patient (clinical informatics), and the community (public health informatics). The continuum from individual to community interacts with and contributes to health care technology, which is represented as a constantly changing progressive wave. PMID:26836991

  14. The history of pathology informatics: A global perspective.

    PubMed

    Park, Seung; Parwani, Anil V; Aller, Raymond D; Banach, Lech; Becich, Michael J; Borkenfeld, Stephan; Carter, Alexis B; Friedman, Bruce A; Rojo, Marcial Garcia; Georgiou, Andrew; Kayser, Gian; Kayser, Klaus; Legg, Michael; Naugler, Christopher; Sawai, Takashi; Weiner, Hal; Winsten, Dennis; Pantanowitz, Liron

    2013-01-01

    Pathology informatics has evolved to varying levels around the world. The history of pathology informatics in different countries is a tale with many dimensions. At first glance, it is the familiar story of individuals solving problems that arise in their clinical practice to enhance efficiency, better manage (e.g., digitize) laboratory information, as well as exploit emerging information technologies. Under the surface, however, lie powerful resource, regulatory, and societal forces that helped shape our discipline into what it is today. In this monograph, for the first time in the history of our discipline, we collectively perform a global review of the field of pathology informatics. In doing so, we illustrate how general far-reaching trends such as the advent of computers, the Internet and digital imaging have affected pathology informatics in the world at large. Major drivers in the field included the need for pathologists to comply with national standards for health information technology and telepathology applications to meet the scarcity of pathology services and trained people in certain countries. Following trials by a multitude of investigators, not all of them successful, it is apparent that innovation alone did not assure the success of many informatics tools and solutions. Common, ongoing barriers to the widespread adoption of informatics devices include poor information technology infrastructure in undeveloped areas, the cost of technology, and regulatory issues. This review offers a deeper understanding of how pathology informatics historically developed and provides insights into what the promising future might hold. PMID:23869286

  15. The history of pathology informatics: A global perspective

    PubMed Central

    Park, Seung; Parwani, Anil V.; Aller, Raymond D.; Banach, Lech; Becich, Michael J.; Borkenfeld, Stephan; Carter, Alexis B.; Friedman, Bruce A.; Rojo, Marcial Garcia; Georgiou, Andrew; Kayser, Gian; Kayser, Klaus; Legg, Michael; Naugler, Christopher; Sawai, Takashi; Weiner, Hal; Winsten, Dennis; Pantanowitz, Liron

    2013-01-01

    Pathology informatics has evolved to varying levels around the world. The history of pathology informatics in different countries is a tale with many dimensions. At first glance, it is the familiar story of individuals solving problems that arise in their clinical practice to enhance efficiency, better manage (e.g., digitize) laboratory information, as well as exploit emerging information technologies. Under the surface, however, lie powerful resource, regulatory, and societal forces that helped shape our discipline into what it is today. In this monograph, for the first time in the history of our discipline, we collectively perform a global review of the field of pathology informatics. In doing so, we illustrate how general far-reaching trends such as the advent of computers, the Internet and digital imaging have affected pathology informatics in the world at large. Major drivers in the field included the need for pathologists to comply with national standards for health information technology and telepathology applications to meet the scarcity of pathology services and trained people in certain countries. Following trials by a multitude of investigators, not all of them successful, it is apparent that innovation alone did not assure the success of many informatics tools and solutions. Common, ongoing barriers to the widespread adoption of informatics devices include poor information technology infrastructure in undeveloped areas, the cost of technology, and regulatory issues. This review offers a deeper understanding of how pathology informatics historically developed and provides insights into what the promising future might hold. PMID:23869286

  16. WE-E-12A-01: Medical Physics 1.0 to 2.0: MRI, Displays, Informatics

    SciTech Connect

    Pickens, D; Flynn, M; Peck, D

    2014-06-15

    , effective implementation of that oversight has been challenging due to the number and extend of medical displays in use at a facility. The advent of color display and mobile displays has added additional challenges to the task of the medical physicist. This informatics display lecture first addresses the current display guidelines (the 1.0 paradigm) and further outlines the initiatives and prospects for color and mobile displays (the 2.0 paradigm). Informatics Management 1.0 to 2.0: Imaging informatics is part of every radiology practice today. Imaging informatics covers everything from the ordering of a study, through the data acquisition and processing, display and archiving, reporting of findings and the billing for the services performed. The standardization of the processes used to manage the information and methodologies to integrate these standards is being developed and advanced continuously. These developments are done in an open forum and imaging organizations and professionals all have a part in the process. In the Informatics Management presentation, the flow of information and the integration of the standards used in the processes will be reviewed. The role of radiologists and physicists in the process will be discussed. Current methods (the 1.0 paradigm) and evolving methods (the 2.0 paradigm) for validation of informatics systems function will also be discussed. Learning Objectives: Identify requirements for improving quality assurance and compliance tools for advanced and hybrid MRI systems. Identify the need for new quality assurance metrics and testing procedures for advanced systems. Identify new hardware systems and new procedures needed to evaluate MRI systems. Understand the components of current medical physics expectation for medical displays. Understand the role and prospect fo medical physics for color and mobile display devices. Understand different areas of imaging informatics and the methodology for developing informatics standards. Understand

  17. Clinical fellowship training in pathology informatics: A program description

    PubMed Central

    Gilbertson, John R.; McClintock, David S.; Lee, Roy E.; Onozato, Maristela; Kuo, Frank C.; Beckwith, Bruce A.; Yagi, Yukako; Dighe, Anand S.; Gudewicz, Tom M.; Le, Long P.; Wilbur, David C.; Kim, Ji Yeon; Brodsky, Victor B.; Black-Schaffer, Stephen

    2012-01-01

    Background: In 2007, our healthcare system established a clinical fellowship program in pathology informatics. In 2011, the program benchmarked its structure and operations against a 2009 white paper “Program requirements for fellowship education in the subspecialty of clinical informatics”, endorsed by the Board of the American Medical Informatics Association (AMIA) that described a proposal for a general clinical informatics fellowship program. Methods: A group of program faculty members and fellows compared each of the proposed requirements in the white paper with the fellowship program's written charter and operations. The majority of white paper proposals aligned closely with the rules and activities in our program and comparison was straightforward. In some proposals, however, differences in terminology, approach, and philosophy made comparison less direct, and in those cases, the thinking of the group was recorded. After the initial evaluation, the remainder of the faculty reviewed the results and any disagreements were resolved. Results: The most important finding of the study was how closely the white paper proposals for a general clinical informatics fellowship program aligned with the reality of our existing pathology informatics fellowship. The program charter and operations of the program were judged to be concordant with the great majority of specific white paper proposals. However, there were some areas of discrepancy and the reasons for the discrepancies are discussed in the manuscript. Conclusions: After the comparison, we conclude that the existing pathology informatics fellowship could easily meet all substantive proposals put forth in the 2009 clinical informatics program requirements white paper. There was also agreement on a number of philosophical issues, such as the advantages of multiple fellows, the need for core knowledge and skill sets, and the need to maintain clinical skills during informatics training. However, there were other

  18. Consumer health informatics: a consensus description and commentary from American Medical Informatics Association members.

    PubMed Central

    Houston, T. K.; Chang, B. L.; Brown, S.; Kukafka, R.

    2001-01-01

    BACKGROUND: Although interest in Consumer Health Informatics (CHI) has increased, a consensus definition of CHI does not yet exist. PURPOSE: To conduct a hypothesis-generating survey of AMIA members regarding definition and research agenda for CHI. METHODS: We solicited participation among AMIA members in an Internet-based survey focusing on issues related to a definition of CHI. RESULTS: One hundred thirty-five AMIA members responded. Participants indicated a broad spectrum of topics important to CHI including "self-help for disease management" and "patient access to their own medical records." CHI research was felt to rely heavily on public health methods such as epidemiology and outcomes research, a paradigm shift from traditional medical informatics. Responses indicated a perceived lack of funding and need for further research in CHI. CONCLUSIONS: A working definition should emphasize the multidisciplinary nature of CHI, include consumer input into CHI design, and focus on public health approaches to evaluation. PMID:11825193

  19. Exposome informatics: considerations for the design of future biomedical research information systems

    PubMed Central

    Martin Sanchez, Fernando; Gray, Kathleen; Bellazzi, Riccardo; Lopez-Campos, Guillermo

    2014-01-01

    The environment's contribution to health has been conceptualized as the exposome. Biomedical research interest in environmental exposures as a determinant of physiopathological processes is rising as such data increasingly become available. The panoply of miniaturized sensing devices now accessible and affordable for individuals to use to monitor a widening range of parameters opens up a new world of research data. Biomedical informatics (BMI) must provide a coherent framework for dealing with multi-scale population data including the phenome, the genome, the exposome, and their interconnections. The combination of these more continuous, comprehensive, and personalized data sources requires new research and development approaches to data management, analysis, and visualization. This article analyzes the implications of a new paradigm for the discipline of BMI, one that recognizes genome, phenome, and exposome data and their intricate interactions as the basis for biomedical research now and for clinical care in the near future. PMID:24186958

  20. Report on the Conference on Transposition and Genome Engineering 2015 (TGE 2015): advancing cutting-edge genomics technology in the ancient city of Nara.

    PubMed

    Woltjen, Knut; Yamamoto, Takashi; Kokubu, Chikara; Takeda, Junji

    2016-05-01

    From November 17 to 20 in 2015, the Conference on Transposition and Genome Engineering 2015 (TGE 2015) was held at Nara Kasugano International Forum-IRAKA-in Nara, Japan, located at the center of Nara Park. All of the presentations were carried out at Nohgaku hall in Nara Kasugano International Forum-IRAKA. Participation totaled 148 persons (30 international, 118 domestic), who were able to engage in lively scientific discussions over the 4-day period. The guest speaker list consisted of many top-notch international researchers, an achievement for which the conference received praise from the attendees. There were 36 oral presentations including the keynote lecture (22 presentations from guest speakers, complemented with 14 selected from abstract submissions). Additionally, there were 46 poster presentations. The conference uniquely combined research mainly from two different genomics approaches: (i) transposon technology allowing random genomic integration followed by gene discovery-related phenotypes and (ii) genome editing technology with designer nuclease allowing precise modification of a gene-of-interest. PMID:27028186

  1. Genomics and Bioinformatics in Undergraduate Curricula: Contexts for Hybrid Laboratory/Lecture Courses for Entering and Advanced Science Students

    ERIC Educational Resources Information Center

    Temple, Louise; Cresawn, Steven G.; Monroe, Jonathan D.

    2010-01-01

    Emerging interest in genomics in the scientific community prompted biologists at James Madison University to create two courses at different levels to modernize the biology curriculum. The courses are hybrids of classroom and laboratory experiences. An upper level class uses raw sequence of a genome (plasmid or virus) as the subject on which to…

  2. Gap Analysis of Biomedical Informatics Graduate Education Competencies

    PubMed Central

    Ritko, Anna L.; Odlum, Michelle

    2013-01-01

    Graduate training in biomedical informatics (BMI) is evolving rapidly. BMI graduate programs differ in informatics domain, delivery method, degrees granted, as well as breadth and depth of curricular competencies. Using the current American Medical Informatics Association (AMIA) definition of BMI core competencies as a framework, we identified and labeled course offerings within graduate programs. From our qualitative analysis, gaps between defined competencies and curricula emerged. Topics missing from existing graduate curricula include community health, translational and clinical research, knowledge representation, data mining, communication and evidence-based practice. PMID:24551403

  3. The Role of Informatics in Health Care Reform

    PubMed Central

    Liu, Yueyi I.

    2012-01-01

    Improving healthcare quality while simultaneously reducing cost has become a high priority of healthcare reform. Informatics is crucial in tackling this challenge. The American Recovery and Reinvestment Act of 2009 mandates adaptation and “meaningful use (MU)” of health information technology. In this review, we will highlight several areas in which informatics can make significant contributions, with a focus on radiology. We also discuss informatics related to the increasing imperatives of state and local regulations (such as radiation dose tracking) and quality initiatives. PMID:22771052

  4. About the beginnings of medical informatics in europe.

    PubMed

    Roger France, Francis

    2014-02-01

    The term "Informatics" was created in 1962 from two words, information and automatic, and covers all techniques, information concepts and applications of computers. Among them, medicine is the field where we will describe some factors of development in Europe since the late sixties. It took some time for obtaining the acceptance of this new terminology worldwide, but today medical informatics is a well defined discipline which had a tremendous development last decades. This paper tries to recall the context and events from the beginning of medical informatics in Europe. PMID:24648614

  5. Bioimage informatics: a new area of engineering biology

    PubMed Central

    Peng, Hanchuan

    2008-01-01

    In recent years, the deluge of complicated molecular and cellular microscopic images creates compelling challenges for the image computing community. There has been an increasing focus on developing novel image processing, data mining, database and visualization techniques to extract, compare, search and manage the biological knowledge in these data-intensive problems. This emerging new area of bioinformatics can be called ‘bioimage informatics’. This article reviews the advances of this field from several aspects, including applications, key techniques, available tools and resources. Application examples such as high-throughput/high-content phenotyping and atlas building for model organisms demonstrate the importance of bioimage informatics. The essential techniques to the success of these applications, such as bioimage feature identification, segmentation and tracking, registration, annotation, mining, image data management and visualization, are further summarized, along with a brief overview of the available bioimage databases, analysis tools and other resources. Contact: pengh@janelia.hhmi.org Supplementary information: Supplementary data are available at Bioinformatics online. PMID:18603566

  6. [Looking for evidence-based medical informatics].

    PubMed

    Coiera, Enrico

    2016-03-01

    e-Health is experiencing a difficult time. On the one side, the forecast is for a bright digital health future created by precision medicine and smart devices. On the other hand, most large scale e-health projects struggle to make a difference and are often controversial. Both futures fail because they are not evidence-based. Medical informatics should follow the example of evidence-based medicine, i.e. conduct rigorous research that gives us evidence to solve real world problems, synthesise that evidence and then apply it strictly. We already have the tools for creating a different universe. What we need is evidence, will, a culture of learning, and hard work. PMID:27030221

  7. An Informatics-based Chronic Disease Practice

    PubMed Central

    Nordyke, Robert A.; Kulikowski, Casimir A.

    1998-01-01

    The authors present the case study of a 35-year informatics-based single subspecialty practice for the management of patients with chronic thyroid disease. This extensive experience provides a paradigm for the organization of longitudinal medical information by integrating individual patient care with clinical research and education. The kernel of the process is a set of worksheets easily completed by the physician during the patient encounter. It is a structured medical record that has been computerized since 1972, enabling analysis of different groups of patients to answer questions about chronic conditions and the effects of therapeutic interventions. The recording process and resulting studies severe as an important vehicle for medical education about the nuances of clinical practice. The authors suggest ways in which computerized medical records can become an integral part of medical practice, rather than a luxury or novelty. PMID:9452988

  8. Eco-informatics and natural resource management

    USGS Publications Warehouse

    Cushing, J.B.; Wilson, T.; Borning, A.; Delcambre, L.; Bowker, G.; Frame, M.; Schnase, J.; Sonntag, W.; Fulop, J.; Hert, C.; Hovy, E.; Jones, J.; Landis, E.; Schweik, C.; Brandt, L.; Gregg, V.; Spengler, S.

    2006-01-01

    This project highlight reports on the 2004 workshop [1], as well as follow-up activities in 2005 and 2006, regarding how informatics tools can help manage natural resources and decide policy. The workshop was sponsored jointly by sponsored by the NSF, NBII, NASA, and EPA, and attended by practitioners from government and non-government agencies, and university researchers from the computer, social, and ecological sciences. The workshop presented the significant information technology (IT) problems that resource managers face when integrating ecological or environmental information to make decisions. These IT problems fall into five categories: data presentation, data gaps, tools, indicators, and policy making and implementation. To alleviate such problems, we recommend informatics research in four IT areas, as defined in this abstract and our final report: modeling and simulation, data quality, information integration and ontologies, and social and human aspects. Additionally, we recommend that funding agencies provide infrastructure and some changes in funding habits to assure cycles of innovation in the domain were addressed. Follow-on activities to the workshop subsequent to dg.o 2005 included: an invited talk presenting workshop results at DILS 2005, publication of the workshop final report by the NBII [1], and a poster at the NBII All Hands Meeting (Oct. 2005). We also expect a special issue of the JIIS to appear in 2006 that addresses some of these questions. As we go to press, no solicitation by funding agencies has as yet been published, but various NASA and NBII, and NSF cyber-infrastructure and DG research efforts now underway address the above issues.

  9. Developing a Capstone Course within a Health Informatics Program

    PubMed Central

    Hackbarth, Gary; Cata, Teuta; Cole, Laura

    2012-01-01

    This article discusses the ongoing development of a health informatics capstone program in a Midwest university from the hiring of a program coordinator to the development of a capstone course, through initial student results. University health informatics programs require a strong academic program to be successful but also require a spirited program coordinator to manage resources and organize an effective capstone course. This is particularly true of health informatics master's programs that support health industry career fields, whereby employers can locate and work with a pool of qualified applicants. The analysis of students’ logs confirms that students’ areas of focus and concern are consistent with course objectives and company work requirements during the work-study portion of the student capstone project. The article further discusses lessons learned and future improvements to be made in the health informatics capstone course. PMID:22783150

  10. An Interdisciplinary Online Course in Health Care Informatics

    PubMed Central

    Smith, Scott R.

    2007-01-01

    Objectives To design an interdisciplinary course in health care informatics that enables students to: (1) understand how to incorporate technology into the provision of safe, effective and evidence-based health care; (2) make decisions about the value and ethical application of specific technologies; and (3) appreciate the perspectives and roles of patients and providers when using technology in care. Design An online, interdisciplinary elective course using a distributive learning model was created. Standard courseware was used to manage teaching and to facilitate student/instructor interactions. Interactive, multimedia lectures were developed using Internet communication software. Assessment Upon completion of the course, students demonstrated competency in identifying, analyzing, and applying informatics appropriately in diverse health settings. Conclusion Online education using multimedia software technology is effective in teaching students about health informatics and providing an innovative opportunity for interdisciplinary learning. In light of the growing need for efficient health care informatics training, additional study of this methodology is warranted. PMID:17619643

  11. Climate Informatics: Accelerating Discovering in Climate Science with Machine Learning

    NASA Technical Reports Server (NTRS)

    Monteleoni, Claire; Schmidt, Gavin A.; McQuade, Scott

    2014-01-01

    The goal of climate informatics, an emerging discipline, is to inspire collaboration between climate scientists and data scientists, in order to develop tools to analyze complex and ever-growing amounts of observed and simulated climate data, and thereby bridge the gap between data and understanding. Here, recent climate informatics work is presented, along with details of some of the field's remaining challenges. Given the impact of climate change, understanding the climate system is an international priority. The goal of climate informatics is to inspire collaboration between climate scientists and data scientists, in order to develop tools to analyze complex and ever-growing amounts of observed and simulated climate data, and thereby bridge the gap between data and understanding. Here, recent climate informatics work is presented, along with details of some of the remaining challenges.

  12. Excellence in Computational Biology and Informatics — EDRN Public Portal

    Cancer.gov

    9th Early Detection Research Network (EDRN) Scientific Workshop. Excellence in Computational Biology and Informatics: Sponsored by the EDRN Data Sharing Subcommittee Moderator: Daniel Crichton, M.S., NASA Jet Propulsion Laboratory

  13. A Short History of Medical Informatics in Bosnia and Herzegovina

    PubMed Central

    Masic, Izet

    2014-01-01

    The health informatics profession in Bosnia and Herzegovina has relatively long history. Thirty five years from the introduction of the first automatic manipulation of data, thirty years from the establishment of Society for Medical Informatics BiH, twenty years from the establishment of the Scientific journal “Acta Informatica Medica (Acta Inform Med”, indexed in PubMed, PubMed Central Scopus, Embase, etc.), twenty years on from the establishment of the first Cathedra for Medical Informatics on Biomedical Faculties in Bosnia and Herzegovina, ten years on from the introduction of the method of “Distance learning” in medical curriculum. The author of this article is eager to mark the importance of the above mentioned Anniversaries in the development of Health informatics in Bosnia and Herzegovina and have attempted, very briefly, to present the most significant events and persons with essential roles throughout this period. PMID:24648621

  14. Developing a capstone course within a health informatics program.

    PubMed

    Hackbarth, Gary; Cata, Teuta; Cole, Laura

    2012-01-01

    This article discusses the ongoing development of a health informatics capstone program in a Midwest university from the hiring of a program coordinator to the development of a capstone course, through initial student results. University health informatics programs require a strong academic program to be successful but also require a spirited program coordinator to manage resources and organize an effective capstone course. This is particularly true of health informatics master's programs that support health industry career fields, whereby employers can locate and work with a pool of qualified applicants. The analysis of students' logs confirms that students' areas of focus and concern are consistent with course objectives and company work requirements during the work-study portion of the student capstone project. The article further discusses lessons learned and future improvements to be made in the health informatics capstone course. PMID:22783150

  15. New study program: Interdisciplinary Postgraduate Specialist Study in Medical Informatics.

    PubMed

    Hercigonja-Szekeres, Mira; Simić, Diana; Božikov, Jadranka; Vondra, Petra

    2014-01-01

    Paper presents an overview of the EU funded Project of Curriculum Development for Interdisciplinary Postgraduate Specialist Study in Medical Informatics named MEDINFO to be introduced in Croatia. The target group for the program is formed by professionals in any of the areas of medicine, IT professionals working on applications of IT for health and researchers and teachers in medical informatics. In addition to Croatian students, the program will also provide opportunity for enrolling students from a wider region of Southeast Europe. Project partners are two faculties of the University of Zagreb - Faculty of Organization and Informatics from Varaždin and School of Medicine, Andrija Štampar School of Public Health from Zagreb with the Croatian Society for Medical Informatics, Croatian Chamber of Economy, and Ericsson Nikola Tesla Company as associates. PMID:24743088

  16. SWOT Analysis on Medical Informatics and Development Strategies

    ERIC Educational Resources Information Center

    Ma, Xiaoyan; Han, Zhongdong; Ma, Hua

    2015-01-01

    This article aims at clarifying the strategic significance of developing medical informatics, conducting SWOT analysis on this discipline and hence establishing the strategic objectives and focal points for its development.

  17. Representation of medical informatics in the wikipedia and its perspectives.

    PubMed

    Altmann, Udo

    2005-01-01

    A wiki is a technique for collaborative development of documents on the web. The Wikipedia is a comprehensive free online encyclopaedia based on this technique which has gained increasing popularity and quality. This paper's work explored the representation of Medical Informatics in the Wikipedia by a search of specific and less specific terms used in Medical Informatics and shows the potential uses of wikis and the Wikipedia for the specialty. Test entries into the Wikipedia showed that the practical use of the so-called WikiMedia software is convenient. Yet Medical Informatics is not represented sufficiently since a number of important topics is missing. The Medical Informatics communities should consider a more systematic use of these techniques for disseminating knowledge about the specialty for the public as well as for internal and educational purposes. PMID:16160349

  18. [Basic data in informatics illustrated by their application in surgery].

    PubMed

    Lambotte, L

    1986-01-01

    As an introduction to a study day devoted to informatic in surgery, some basis knowledges are summarized: architecture and function of computers, programmation language, data bases. They are illustrated by various applications made in the "Cliniques St Luc" te Brussel namely patient monitoring, artificial pancreas, office system and operating room management system. The future use of local area network is proposed in order to achieve medical department independence and the needed cooperation between all users of medical and hospital informatic. PMID:3788377

  19. Materials informatics: a journey towards material design and synthesis.

    PubMed

    Takahashi, Keisuke; Tanaka, Yuzuru

    2016-06-28

    Materials informatics has been gaining popularity with the rapid development of computational materials science. However, collaborations between information science and materials science have not yet reached the success. There are several issues which need to be overcome in order to establish the field of materials informatics. Construction of material big data, implementation of machine learning, and platform design for materials discovery are discussed with potential solutions. PMID:27292550

  20. TU-F-BRD-01: Biomedical Informatics for Medical Physicists

    SciTech Connect

    Phillips, M; Kalet, I; McNutt, T; Smith, W

    2014-06-15

    Biomedical informatics encompasses a very large domain of knowledge and applications. This broad and loosely defined field can make it difficult to navigate. Physicists often are called upon to provide informatics services and/or to take part in projects involving principles of the field. The purpose of the presentations in this symposium is to help medical physicists gain some knowledge about the breadth of the field and how, in the current clinical and research environment, they can participate and contribute. Three talks have been designed to give an overview from the perspective of physicists and to provide a more in-depth discussion in two areas. One of the primary purposes, and the main subject of the first talk, is to help physicists achieve a perspective about the range of the topics and concepts that fall under the heading of 'informatics'. The approach is to de-mystify topics and jargon and to help physicists find resources in the field should they need them. The other talks explore two areas of biomedical informatics in more depth. The goal is to highlight two domains of intense current interest--databases and models--in enough depth into current approaches so that an adequate background for independent inquiry is achieved. These two areas will serve as good examples of how physicists, using informatics principles, can contribute to oncology practice and research. Learning Objectives: To understand how the principles of biomedical informatics are used by medical physicists. To put the relevant informatics concepts in perspective with regard to biomedicine in general. To use clinical database design as an example of biomedical informatics. To provide a solid background into the problems and issues of the design and use of data and databases in radiation oncology. To use modeling in the service of decision support systems as an example of modeling methods and data use. To provide a background into how uncertainty in our data and knowledge can be

  1. Enabling functional genomics with genome engineering

    PubMed Central

    Hilton, Isaac B.; Gersbach, Charles A.

    2015-01-01

    Advances in genome engineering technologies have made the precise control over genome sequence and regulation possible across a variety of disciplines. These tools can expand our understanding of fundamental biological processes and create new opportunities for therapeutic designs. The rapid evolution of these methods has also catalyzed a new era of genomics that includes multiple approaches to functionally characterize and manipulate the regulation of genomic information. Here, we review the recent advances of the most widely adopted genome engineering platforms and their application to functional genomics. This includes engineered zinc finger proteins, TALEs/TALENs, and the CRISPR/Cas9 system as nucleases for genome editing, transcription factors for epigenome editing, and other emerging applications. We also present current and potential future applications of these tools, as well as their current limitations and areas for future advances. PMID:26430154

  2. Diverse convergent evidence in the genetic analysis of complex disease: coordinating omic, informatic, and experimental evidence to better identify and validate risk factors.

    PubMed

    Ciesielski, Timothy H; Pendergrass, Sarah A; White, Marquitta J; Kodaman, Nuri; Sobota, Rafal S; Huang, Minjun; Bartlett, Jacquelaine; Li, Jing; Pan, Qinxin; Gui, Jiang; Selleck, Scott B; Amos, Christopher I; Ritchie, Marylyn D; Moore, Jason H; Williams, Scott M

    2014-01-01

    In omic research, such as genome wide association studies, researchers seek to repeat their results in other datasets to reduce false positive findings and thus provide evidence for the existence of true associations. Unfortunately this standard validation approach cannot completely eliminate false positive conclusions, and it can also mask many true associations that might otherwise advance our understanding of pathology. These issues beg the question: How can we increase the amount of knowledge gained from high throughput genetic data? To address this challenge, we present an approach that complements standard statistical validation methods by drawing attention to both potential false negative and false positive conclusions, as well as providing broad information for directing future research. The Diverse Convergent Evidence approach (DiCE) we propose integrates information from multiple sources (omics, informatics, and laboratory experiments) to estimate the strength of the available corroborating evidence supporting a given association. This process is designed to yield an evidence metric that has utility when etiologic heterogeneity, variable risk factor frequencies, and a variety of observational data imperfections might lead to false conclusions. We provide proof of principle examples in which DiCE identified strong evidence for associations that have established biological importance, when standard validation methods alone did not provide support. If used as an adjunct to standard validation methods this approach can leverage multiple distinct data types to improve genetic risk factor discovery/validation, promote effective science communication, and guide future research directions. PMID:25071867

  3. Targeted multiplex next-generation sequencing: advances in techniques of mitochondrial and nuclear DNA sequencing for population genomics.

    PubMed

    Hancock-Hanser, Brittany L; Frey, Amy; Leslie, Matthew S; Dutton, Peter H; Archer, Frederick I; Morin, Phillip A

    2013-03-01

    Next-generation sequencing (NGS) is emerging as an efficient and cost-effective tool in population genomic analyses of nonmodel organisms, allowing simultaneous resequencing of many regions of multi-genomic DNA from multiplexed samples. Here, we detail our synthesis of protocols for targeted resequencing of mitochondrial and nuclear loci by generating indexed genomic libraries for multiplexing up to 100 individuals in a single sequencing pool, and then enriching the pooled library using custom DNA capture arrays. Our use of DNA sequence from one species to capture and enrich the sequencing libraries of another species (i.e. cross-species DNA capture) indicates that efficient enrichment occurs when sequences are up to about 12% divergent, allowing us to take advantage of genomic information in one species to sequence orthologous regions in related species. In addition to a complete mitochondrial genome on each array, we have included between 43 and 118 nuclear loci for low-coverage sequencing of between 18 kb and 87 kb of DNA sequence per individual for single nucleotide polymorphisms discovery from 50 to 100 individuals in a single sequencing lane. Using this method, we have generated a total of over 500 whole mitochondrial genomes from seven cetacean species and green sea turtles. The greater variation detected in mitogenomes relative to short mtDNA sequences is helping to resolve genetic structure ranging from geographic to species-level differences. These NGS and analysis techniques have allowed for simultaneous population genomic studies of mtDNA and nDNA with greater genomic coverage and phylogeographic resolution than has previously been possible in marine mammals and turtles. PMID:23351075

  4. Health informatics and the delivery of care to older people.

    PubMed

    Koch, Sabine; Hägglund, Maria

    2009-07-20

    In the light of an aging society, effective delivery of healthcare will be more dependent on different technological solutions supporting the decentralization of healthcare, higher patient involvement and increased societal demands. The aim of this article is therefore, to describe the role of health informatics in the care of elderly people and to give an overview of the state of the art in this field. Based on a review of the existing scientific literature, 29 review articles from the last 15 years and 119 original articles from the last 5 years were selected and further analysed. Results show that review articles cover the fields of information technology in the home environment, integrated health information systems, public health systems, consumer health informatics and non-technology oriented topics such as nutrition, physical behaviour, medication and the aging process in general. Articles presenting original data can be divided into 5 major clusters: information systems and decision support, consumer health informatics, emerging technologies, home telehealth, and informatics methods. Results show that health informatics in elderly care is an expanding field of interest but we still do lack knowledge about the elderly person's needs of technology and how it should best be designed. Surprisingly, few studies cover gender differences related to technology use. Further cross-disciplinary research is needed that relates informatics and technology to different stages of the aging process and that evaluates the effects of technical solutions. PMID:19487092

  5. Professional development of health informatics in Northern Ireland.

    PubMed

    McCullagh, Paul; McAllister, Gerry; Hanna, Paul; Finlay, Dewar; Comac, Paul

    2011-01-01

    This paper addresses the assessment and verification of health informatics professional competencies. Postgraduate provision in Health Informatics was targeted at informatics professionals working full-time in the National Health Service, in Northern Ireland, United Kingdom. Many informatics health service positions do not require a formal informatics background, and as we strive for professionalism, a recognized qualification provides important underpinning. The course, delivered from a computing perspective, builds upon work-based achievement and provides insight into emerging technologies associated with the 'connected health' paradigm. The curriculum was designed with collaboration from the Northern Ireland Health and Social Care ICT Training Group. Material was delivered by blended learning using a virtual learning environment and face-to-face sessions. Professional accreditation was of high importance. The aim was to provide concurrent qualifications: a postgraduate certificate, awarded by the University of Ulster and a professional certificate validated and accredited by a professional body comprising experienced health informatics professionals. Providing both qualifications puts significant demands upon part-time students, and a balance must be achieved for successful completion. PMID:21893745

  6. Preparing student nurses, faculty and clinicians for 21st century informatics practice: findings from a national survey of nursing education programs in the United States.

    PubMed

    McNeil, Barbara J; Elfrink, Victoria L; Pierce, Susan T

    2004-01-01

    Because healthcare delivery increasingly mandates data-driven decision-making, it is imperative that informatics knowledge and skills are integrated into nursing education curricula for all future nurse clinicians and educators. A national online survey of deans/directors of 266 baccalaureate and higher nursing education programs in the U.S. identified perceived informatics competencies and knowledge of under-graduate and graduate nursing students; determined the preparedness of nurse faculty to teach and use informatics tools; and elicited perceptions of informatics requirements of local practicing nurses. Frequency data and qualitative responses were analyzed. Approximately half of the programs reported requiring word processing and email skills upon entry into the nursing major. The use of standardized languages and the nurse's role in the life cycle of an information system were the least visible informatics content at all levels. Half of program faculty, rated as "novice" or "advanced beginners", are teaching information literacy skills. Findings have major implications for nurse educators, staff developers, and program administrators who are planning faculty/staff development opportunities and designing nursing education curricula that prepare nurses for professional practice. PMID:15360943

  7. Functional genomic and advanced genetic studies reveal novel insights into the metabolism, regulation, and biology of Haloferax volcanii.

    PubMed

    Soppa, Jörg

    2011-01-01

    The genome sequence of Haloferax volcanii is available and several comparative genomic in silico studies were performed that yielded novel insight for example into protein export, RNA modifications, small non-coding RNAs, and ubiquitin-like Small Archaeal Modifier Proteins. The full range of functional genomic methods has been established and results from transcriptomic, proteomic and metabolomic studies are discussed. Notably, Hfx. volcanii is together with Halobacterium salinarum the only prokaryotic species for which a translatome analysis has been performed. The results revealed that the fraction of translationally-regulated genes in haloarchaea is as high as in eukaryotes. A highly efficient genetic system has been established that enables the application of libraries as well as the parallel generation of genomic deletion mutants. Facile mutant generation is complemented by the possibility to culture Hfx. volcanii in microtiter plates, allowing the phenotyping of mutant collections. Genetic approaches are currently used to study diverse biological questions-from replication to posttranslational modification-and selected results are discussed. Taken together, the wealth of functional genomic and genetic tools make Hfx. volcanii a bona fide archaeal model species, which has enabled the generation of important results in recent years and will most likely generate further breakthroughs in the future. PMID:22190865

  8. Use of Modern Chemical Protein Synthesis and Advanced Fluorescent Assay Techniques to Experimentally Validate the Functional Annotation of Microbial Genomes

    SciTech Connect

    Kent, Stephen

    2012-07-20

    The objective of this research program was to prototype methods for the chemical synthesis of predicted protein molecules in annotated microbial genomes. High throughput chemical methods were to be used to make large numbers of predicted proteins and protein domains, based on microbial genome sequences. Microscale chemical synthesis methods for the parallel preparation of peptide-thioester building blocks were developed; these peptide segments are used for the parallel chemical synthesis of proteins and protein domains. Ultimately, it is envisaged that these synthetic molecules would be ‘printed’ in spatially addressable arrays. The unique ability of total synthesis to precision label protein molecules with dyes and with chemical or biochemical ‘tags’ can be used to facilitate novel assay technologies adapted from state-of-the art single molecule fluorescence detection techniques. In the future, in conjunction with modern laboratory automation this integrated set of techniques will enable high throughput experimental validation of the functional annotation of microbial genomes.

  9. Genomic Profiling of Advanced-Stage Oral Cancers Reveals Chromosome 11q Alterations as Markers of Poor Clinical Outcome

    PubMed Central

    Ambatipudi, Srikant; Gerstung, Moritz; Gowda, Ravindra; Pai, Prathamesh; Borges, Anita M.; Schäffer, Alejandro A.; Beerenwinkel, Niko; Mahimkar, Manoj B.

    2011-01-01

    Identifying oral cancer lesions associated with high risk of relapse and predicting clinical outcome remain challenging questions in clinical practice. Genomic alterations may add prognostic information and indicate biological aggressiveness thereby emphasizing the need for genome-wide profiling of oral cancers. High-resolution array comparative genomic hybridization was performed to delineate the genomic alterations in clinically annotated primary gingivo-buccal complex and tongue cancers (n = 60). The specific genomic alterations so identified were evaluated for their potential clinical relevance. Copy-number changes were observed on chromosomal arms with most frequent gains on 3q (60%), 5p (50%), 7p (50%), 8q (73%), 11q13 (47%), 14q11.2 (47%), and 19p13.3 (58%) and losses on 3p14.2 (55%) and 8p (83%). Univariate statistical analysis with correction for multiple testing revealed chromosomal gain of region 11q22.1–q22.2 and losses of 17p13.3 and 11q23–q25 to be associated with loco-regional recurrence (P = 0.004, P = 0.003, and P = 0.0003) and shorter survival (P = 0.009, P = 0.003, and P 0.0001) respectively. The gain of 11q22 and loss of 11q23-q25 were validated by interphase fluorescent in situ hybridization (I-FISH). This study identifies a tractable number of genomic alterations with few underlying genes that may potentially be utilized as biological markers for prognosis and treatment decisions in oral cancers. PMID:21386901

  10. Bioinformatics Methods and Tools to Advance Clinical Care

    PubMed Central

    Lecroq, T.

    2015-01-01

    Summary Objectives To summarize excellent current research in the field of Bioinformatics and Translational Informatics with application in the health domain and clinical care. Method We provide a synopsis of the articles selected for the IMIA Yearbook 2015, from which we attempt to derive a synthetic overview of current and future activities in the field. As last year, a first step of selection was performed by querying MEDLINE with a list of MeSH descriptors completed by a list of terms adapted to the section. Each section editor has evaluated separately the set of 1,594 articles and the evaluation results were merged for retaining 15 articles for peer-review. Results The selection and evaluation process of this Yearbook’s section on Bioinformatics and Translational Informatics yielded four excellent articles regarding data management and genome medicine that are mainly tool-based papers. In the first article, the authors present PPISURV a tool for uncovering the role of specific genes in cancer survival outcome. The second article describes the classifier PredictSNP which combines six performing tools for predicting disease-related mutations. In the third article, by presenting a high-coverage map of the human proteome using high resolution mass spectrometry, the authors highlight the need for using mass spectrometry to complement genome annotation. The fourth article is also related to patient survival and decision support. The authors present datamining methods of large-scale datasets of past transplants. The objective is to identify chances of survival. Conclusions The current research activities still attest the continuous convergence of Bioinformatics and Medical Informatics, with a focus this year on dedicated tools and methods to advance clinical care. Indeed, there is a need for powerful tools for managing and interpreting complex, large-scale genomic and biological datasets, but also a need for user-friendly tools developed for the clinicians in their

  11. From Bed to Bench: Bridging from Informatics Practice to Theory

    PubMed Central

    Lehmann, C.U.

    2014-01-01

    Summary Background In 2009, Applied Clinical Informatics (ACI) – focused on applications in clinical informatics – was launched as a companion journal to Methods of Information in Medicine (MIM). Both journals are official journals of the International Medical Informatics Association. Objectives To explore which congruencies and interdependencies exist in publications from theory to practice and from practice to theory and to determine existing gaps. Major topics discussed in ACI and MIM were analyzed. We explored if the intention of publishing companion journals to provide an information bridge from informatics theory to informatics practice and vice versa could be supported by this model. In this manuscript we will report on congruencies and interdependences from practice to theory and on major topics in MIM. Methods Retrospective, prolective observational study on recent publications of ACI and MIM. All publications of the years 2012 and 2013 were indexed and analyzed. Results Hundred and ninety-six publications were analyzed (ACI 87, MIM 109). In MIM publications, modelling aspects as well as methodological and evaluation approaches for the analysis of data, information, and knowledge in biomedicine and health care were frequently raised – and often discussed from an interdisciplinary point of view. Important themes were ambient-assisted living, anatomic spatial relations, biomedical informatics as scientific discipline, boosting, coding, computerized physician order entry, data analysis, grid and cloud computing, health care systems and services, health-enabling technologies, health information search, health information systems, imaging, knowledge-based decision support, patient records, signal analysis, and web science. Congruencies between journals could be found in themes, but with a different focus on content. Interdependencies from practice to theory, found in these publications, were only limited. Conclusions Bridging from informatics theory to

  12. Informatics critical to public health surveillance

    NASA Astrophysics Data System (ADS)

    Mirhaji, Parsa; Zhang, Jiajie; Smith, Jack W.; Madjid, Mohammad; Casscells, Samuel W.; Lillibridge, Scott R.

    2003-09-01

    Public health surveillance is the ongoing, systematic collection, analysis, interpretation, and dissemination of data regarding a health-related event for use in public health action to reduce morbidity and mortality and to improve health by effective response management and coordination. As new pressures for early detection of disease outbreaks have arisen, particularly for outbreaks of possible bioterrorism (BT) origin, and as electronic health data have become increasingly available, so has the demand for public health situation awareness systems. Although these systems are valuable for early warning of public health emergencies, there remains the cost of developing and managing such large and complex systems and of investigating inevitable false alarms. Whether these systems are dependable and cost effective enough and can demonstrate a significant and indispensable role in detection or prevention of mass casualty events of BT origin remains to be proven. This article will focus on the complexities of design, analysis, implementation and evaluation of public health surveillance and situation awareness systems and, in some cases, will discuss the key technologies being studied in Center for Biosecurity Informatics Research at University of Texas, Health Science Center at Houston.

  13. Recommendations of the International Medical Informatics Association (IMIA) on Education in Biomedical and Health Informatics. First Revision.

    PubMed

    Mantas, John; Ammenwerth, Elske; Demiris, George; Hasman, Arie; Haux, Reinhold; Hersh, William; Hovenga, Evelyn; Lun, K C; Marin, Heimar; Martin-Sanchez, Fernando; Wright, Graham

    2010-01-01

    Objective: The International Medical Informatics Association (IMIA) agreed on revising the existing international recommendations in health informatics/medical informatics education. These should help to establish courses, course tracks or even complete programs in this field, to further develop existing educational activities in the various nations and to support international initiatives concerning education in biomedical and health informatics (BMHI), particularly international activities in educating BMHI specialists and the sharing of courseware. Method: An IMIA task force, nominated in 2006, worked on updating the recommendations' first version. These updates have been broadly discussed and refined by members of IMIA's National Member Societies, IMIA's Academic Institutional Members and by members of IMIA's Working Group on Health and Medical Informatics Education. Results and Conclusions: The IMIA recommendations center on educational needs for health care professionals to acquire knowledge and skills in information processing and information and communication technology. The educational needs are described as a three-dimensional framework. The dimensions are: 1) professionals in health care (e.g. physicians, nurses, BMHI professionals), 2) type of specialization in BMHI (IT users, BMHI specialists), and 3) stage of career progression (bachelor, master, doctorate). Learning outcomes are defined in terms of knowledge and practical skills for health care professionals in their role a) as IT user and b) as BMHI specialist. Recommendations are given for courses/course tracks in BMHI as part of educational programs in medicine, nursing, health care management, dentistry, pharmacy, public health, health record administration, and informatics/computer science as well as for dedicated programs in BMHI (with bachelor, master or doctor degree). To support education in BMHI, IMIA offers to award a certificate for high-quality BMHI education. It supports information

  14. The World Informatics Scene: ICSU, International Unions and Associations, Professional Society Activities

    NASA Astrophysics Data System (ADS)

    Fox, Peter

    In the lead up to, and during, the Electronic Geophysical Year (2007-2008), a substantial number of new coordinated efforts under the heading of informatics (defined as: ) have emerged. These efforts range from the formation of divisions/ sections in societies such as the Geological Society of America, the American Geophysical Union and the European Geosciences Union devoted to all aspects of informatics and have seen strong community response at their regular meetings. These society efforts are closer to the working scientists, technologists and data producers, and managers. At the same time, in a recognition for the need of a sustained activity such as eGY, two ad-hoc committees produced proposals for a) the formation of a Union Commission for Data and Information within the International Union of Geodesy and Geophysics (IUGG) and b) the Committee on Data for Science and Technology (CODATA) approved a Working Group on XX, with the intent that it will become a Task Group after the 2008 CODATA general assembly. The International Council of Science's (ICSU) Strategic Committee on Information and Data (SCID) will deliver its report on implementation ICSU's priority area assessment strategy for ICSU to play a leadership role in the coordination of data and information efforts world-wide. This report will influence entities such as CODATA, the World Data Centres, the Federation of Astrophysical and Geophysical Data Services (FAGS) and, most likely, all ICSU Unions. This presentation will give details on the abovementioned activities and indicate an emerging synergy for Informatics across many discipline and the advancement of science and societal goals. The presentation will also include suggestions for the COSPAR community to engage in on-going activities.

  15. Clinical informatics: a workforce priority for 21st century healthcare.

    PubMed

    Smith, Susan E; Drake, Lesley E; Harris, Julie-Gai B; Watson, Kay; Pohlner, Peter G

    2011-05-01

    This paper identifies the contribution of health and clinical informatics in the support of healthcare in the 21st century. Although little is known about the health and clinical informatics workforce, there is widespread recognition that the health informatics workforce will require significant expansion to support national eHealth work agendas. Workforce issues including discipline definition and self-identification, formal professionalisation, weaknesses in training and education, multidisciplinarity and interprofessional tensions, career structure, managerial support, and financial allocation play a critical role in facilitating or hindering the development of a workforce that is capable of realising the benefits to be gained from eHealth in general and clinical informatics in particular. As well as the national coordination of higher level policies, local support of training and allocation of sufficient position hours in appropriately defined roles by executive and clinical managers is essential to develop the health and clinical informatics workforce and achieve the anticipated results from evolving eHealth initiatives. PMID:21612722

  16. Informatics in the care of patients: ten notable challenges.

    PubMed Central

    Altman, R B

    1997-01-01

    What is medical informatics, and why should practicing physicians care about it? Medical informatics is the study of the concepts and conceptual relationships within biomedical information and how they can be harnessed for practical applications. In the past decade, the field has exploded as health professionals recognize the importance of strategic information management and the inadequacies of traditional tools for information storage, retrieval, and analysis. At the same time that medical informatics has established a presence within many academic and industrial research facilities, its goals and methods have become less clear to practicing physicians. In this article, I outline 10 challenges in medical informatics that provide a framework for understanding developments in the field. These challenges have been divided into those relating to infrastructure, specific performance, and evaluation. The primary goals of medical informatics, as for any other branch of biomedical research, are to improve the overall health of patients by combining basic scientific and engineering insights with the useful application of these insights to important problems. PMID:9109328

  17. Orthology for comparative genomics in the mouse genome database.

    PubMed

    Dolan, Mary E; Baldarelli, Richard M; Bello, Susan M; Ni, Li; McAndrews, Monica S; Bult, Carol J; Kadin, James A; Richardson, Joel E; Ringwald, Martin; Eppig, Janan T; Blake, Judith A

    2015-08-01

    The mouse genome database (MGD) is the model organism database component of the mouse genome informatics system at The Jackson Laboratory. MGD is the international data resource for the laboratory mouse and facilitates the use of mice in the study of human health and disease. Since its beginnings, MGD has included comparative genomics data with a particular focus on human-mouse orthology, an essential component of the use of mouse as a model organism. Over the past 25 years, novel algorithms and addition of orthologs from other model organisms have enriched comparative genomics in MGD data, extending the use of orthology data to support the laboratory mouse as a model of human biology. Here, we describe current comparative data in MGD and review the history and refinement of orthology representation in this resource. PMID:26223881

  18. Genome-wide association study of advanced age-related macular degeneration identifies a role of the hepatic lipase gene (LIPC)

    PubMed Central

    Neale, Benjamin M.; Fagerness, Jesen; Reynolds, Robyn; Sobrin, Lucia; Parker, Margaret; Raychaudhuri, Soumya; Tan, Perciliz L.; Oh, Edwin C.; Merriam, Joanna E.; Souied, Eric; Bernstein, Paul S.; Li, Binxing; Frederick, Jeanne M.; Zhang, Kang; Brantley, Milam A.; Lee, Aaron Y.; Zack, Donald J.; Campochiaro, Betsy; Campochiaro, Peter; Ripke, Stephan; Smith, R. Theodore; Barile, Gaetano R.; Katsanis, Nicholas; Allikmets, Rando; Daly, Mark J.; Seddon, Johanna M.

    2010-01-01

    Advanced age-related macular degeneration (AMD) is the leading cause of late onset blindness. We present results of a genome-wide association study of 979 advanced AMD cases and 1,709 controls using the Affymetrix 6.0 platform with replication in seven additional cohorts (totaling 5,789 unrelated cases and 4,234 unrelated controls). We also present a comprehensive analysis of copy-number variations and polymorphisms for AMD. Our discovery data implicated the association between AMD and a variant in the hepatic lipase gene (LIPC) in the high-density lipoprotein cholesterol (HDL) pathway (discovery P = 4.53e-05 for rs493258). Our LIPC association was strongest for a functional promoter variant, rs10468017, (P = 1.34e-08), that influences LIPC expression and serum HDL levels with a protective effect of the minor T allele (HDL increasing) for advanced wet and dry AMD. The association we found with LIPC was corroborated by the Michigan/Penn/Mayo genome-wide association study; the locus near the tissue inhibitor of metalloproteinase 3 was corroborated by our replication cohort for rs9621532 with P = 3.71e-09. We observed weaker associations with other HDL loci (ABCA1, P = 9.73e-04; cholesterylester transfer protein, P = 1.41e-03; FADS1-3, P = 2.69e-02). Based on a lack of consistent association between HDL increasing alleles and AMD risk, the LIPC association may not be the result of an effect on HDL levels, but it could represent a pleiotropic effect of the same functional component. Results implicate different biologic pathways than previously reported and provide new avenues for prevention and treatment of AMD. PMID:20385826

  19. Evolution of dental informatics as a major research tool in oral pathology

    PubMed Central

    Singaraju, Sasidhar; Prasad, H; Singaraju, Medhini

    2012-01-01

    Bioinformatics is a relatively new field of science that incorporates the principles of biology and computer science. It is mainly concerned with collecting, storing, and retrieving data from large databases. Ever since the successful completion of the Human Genome Project, there has been an exponential growth in the volumes of biological data that is being generated worldwide. The evolution of bioinformatics has made it possible to access these databases and apply the information for better research. One discipline that has been benefitted from the advent of bioinformatics is oral pathology. Oral pathology is a branch of dentistry which deals with the diseases of the head and neck region. Remarkable progress has been made in the diagnosis and treatment of diseases with the aid of bioinformatics. This article attempts to review the evolution and progress of dental informatics as a specialty and its applications in oral pathology. PMID:22434944

  20. Graphical neuroimaging informatics: application to Alzheimer's disease.

    PubMed

    Van Horn, John Darrell; Bowman, Ian; Joshi, Shantanu H; Greer, Vaughan

    2014-06-01

    The Informatics Visualization for Neuroimaging (INVIZIAN) framework allows one to graphically display image and meta-data information from sizeable collections of neuroimaging data as a whole using a dynamic and compelling user interface. Users can fluidly interact with an entire collection of cortical surfaces using only their mouse. In addition, users can cluster and group brains according in multiple ways for subsequent comparison using graphical data mining tools. In this article, we illustrate the utility of INVIZIAN for simultaneous exploration and mining a large collection of extracted cortical surface data arising in clinical neuroimaging studies of patients with Alzheimer's Disease, mild cognitive impairment, as well as healthy control subjects. Alzheimer's Disease is particularly interesting due to the wide-spread effects on cortical architecture and alterations of volume in specific brain areas associated with memory. We demonstrate INVIZIAN's ability to render multiple brain surfaces from multiple diagnostic groups of subjects, showcase the interactivity of the system, and showcase how INVIZIAN can be employed to generate hypotheses about the collection of data which would be suitable for direct access to the underlying raw data and subsequent formal statistical analysis. Specifically, we use INVIZIAN show how cortical thickness and hippocampal volume differences between group are evident even in the absence of more formal hypothesis testing. In the context of neurological diseases linked to brain aging such as AD, INVIZIAN provides a unique means for considering the entirety of whole brain datasets, look for interesting relationships among them, and thereby derive new ideas for further research and study. PMID:24203652

  1. Current Advances in the Identification and Characterization of Putative Drug and Vaccine Targets in the Bacterial Genomes.

    PubMed

    Shahbaaz, Mohd; Bisetty, Krishna; Ahmad, Faizan; Hassan, Md Imtaiyaz

    2016-01-01

    The development in sequencing technologies over the past few decades have increased the pace of decoding genetic and functional information present in the genomes of pathogenic microorganisms. The knowledge obtained through sequencing projects facilitated the identification of genes that codes for virulence factors. A major portion of genomes of pathogenic of bacteria contains genes which are classified as "hypothetical or uncharacterized". Due to unavailability of precise information about the functionality of these genes, the pathogenic mechanisms utilized by varieties of microorganisms are not fully understood. This respective class of proteins draws a significant interest of pharmaceutical research as they have potential to provide new clues regarding the development of novel therapeutics particularly against the multidrug resistant strains of bacteria. The in silico identification of putative drug and vaccine targets in the set of uncharacterized proteins through comparative and subtractive genome analyses facilitates the increase usability and efficiency of the present drugs. The functional annotation of these characterized target proteins can uncover varieties of biochemical pathways important for the survival and pathogenesis of bacteria. This review focuses on the current protocols available for identification and functional annotations of these uncharacterized potential therapeutic targets. PMID:26303422

  2. 5th International ACC Symposium: Classification of Adrenocortical Cancers from Pathology to Integrated Genomics: Real Advances or Lost in Translation?

    PubMed

    de Krijger, Ronald E; Bertherat, Jérôme

    2016-02-01

    For the clinician, despite its rarity, adrenocortical cancer is a heterogeneous tumor both in term of steroid excess and tumor evolution. For patient management, it is crucial to have an accurate vision of this heterogeneity, in order to use a correct tumor classification. Pathology is the best way to classify operated adrenocortical tumors: to recognize their adrenocortical nature and to differentiate benign from malignant tumors. Among malignant tumors pathology also aims at prognosis assessment. Although progress has being made for prognosis assessment, there is still a need for improvement. Recent studies have established the value of Ki67 for adrenocortical cancer (ACC) prognostication, aiming also at standardization to reduce variability. The use of genomics to study adrenocortical tumors gives a very new insight in their pathogenesis and molecular classification. Genomics studies of ACC give now a clear description of the mRNA (transcriptome) and miRNA expression profile, as well as chromosomal and methylation alterations. Exome sequencing also established firmly the list of the main ACC driver genes. Interestingly, genomics study of ACC also revealed subtypes of malignant tumors with different pattern of molecular alterations, associated with different outcome. This leads to a new vision of adrenocortical tumors classification based on molecular analysis. Interestingly, these molecular classifications meet also the results of pathological analysis. This opens new perspectives on the development and use of various molecular tools to classify, along with pathological analysis, ACC, and guides patient management at the area of precision medicine. PMID:26676358

  3. A blow to the fly - Lucilia cuprina draft genome and transcriptome to support advances in biology and biotechnology.

    PubMed

    Anstead, Clare A; Batterham, Philip; Korhonen, Pasi K; Young, Neil D; Hall, Ross S; Bowles, Vernon M; Richards, Stephen; Scott, Maxwell J; Gasser, Robin B

    2016-01-01

    The blow fly, Lucilia cuprina (Wiedemann, 1830) is a parasitic insect of major global economic importance. Maggots of this fly parasitize the skin of animal hosts, feed on excretions and tissues, and cause severe disease (flystrike or myiasis). Although there has been considerable research on L. cuprina over the years, little is understood about the molecular biology, biochemistry and genetics of this parasitic fly, as well as its relationship with its hosts and the disease that it causes. This situation might change with the recent report of the draft genome and transcriptome of this blow fly, which has given new and global insights into its biology, interactions with the host animal and aspects of insecticide resistance at the molecular level. This genomic resource will likely enable many fundamental and applied research areas in the future. The present article gives a background on L. cuprina and myiasis, a brief account of past and current treatment, prevention and control approaches, and provides a perspective on the impact that the L. cuprina genome should have on future research of this and related parasitic flies, and the design of new and improved interventions for myiasis. PMID:26944522

  4. An author co-citation analysis of medical informatics*

    PubMed Central

    Andrews, James E.

    2003-01-01

    Objective: This study presents the results of an author co-citation analysis of the interdisciplinary field of medical informatics. Methods: An author co-citation analysis was conducted for the years 1994 to 1998, using the fifty most-cited American College of Medical Informatics fellows as an author population. Co-citation data were calculated for every author pair, and multivariate analyses were performed to ultimately show the relationships among all authors. A multidimensional map was created, wherein each author is represented as a point, and the proximity of these points reflects the relationships of authors as perceived by multiple citers. Results and Conclusion: The results from this analysis provide one perspective of the field of medical informatics and are used to suggest future research directions to address issues related to better understanding of communication and social networks in the field to inform better provision of information services. PMID:12568157

  5. Programmatic Role of Education Libraries in Informatics to Support Preservice Teacher Preparation Programs

    ERIC Educational Resources Information Center

    Farmer, Lesley S. J.

    2010-01-01

    Background/Context: The management, processing, and transformation of information constitute central tasks in education. Education informatics intersects the theories and practices of both informatics and education. In particular, informatics aids in the systematic incorporation of technology as educational stakeholders represent, process, and…

  6. Enhancing "Mathematics for Informatics" and its Correlation with Student Pass Rates

    ERIC Educational Resources Information Center

    Divjak, B.; Erjavec, Z.

    2008-01-01

    In this article, changes in "Mathematics for Informatics" at the Faculty of Organisation and Informatics in the University of Zagreb are described, and correlated with students pass rates. Students at the Faculty work in an interdisciplinary field, studying Informatics within a business context. The main reason for introducing the changes in the…

  7. Complete Genomic Sequence and Mass Spectrometric Analysis of Highly Diverse, Atypical Bacillus thuringiensis phage 0305φ8-36

    PubMed Central

    Thomas, Julie A.; Hardies, Stephen C.; Rolando, Mandy; Hayes, Shirley J.; Lieman, Karen; Carroll, Christopher A.; Weintraub, Susan T.; Serwer, Philip

    2007-01-01

    To investigate the apparent genomic complexity of long-genome bacteriophages, we have sequenced the 218,948-bp genome (6479 bp terminal repeat), and identified the virion proteins (55), of Bacillus thuringiensis bacteriophage 0305φ8-36. Phage 0305φ8-36 is an atypical myovirus with three large curly tail fibers. An accurate mode of DNA pyrosequencing was used to sequence the genome and mass spectrometry was used to accomplish the comprehensive virion protein survey. Advanced informatic techniques were used to identify classical morphogenesis genes. The 0305φ8-36 genes were highly diverged; 19% of 247 closely spaced genes have similarity to proteins with known functions. Genes for virion-associated, apparently fibrous proteins in a new class were found, in addition to strong candidates for the curly fiber genes. Phage 0305φ8-36 has twice the virion protein coding sequence of T4. Based on its genomic isolation, 0305φ8-36 is a resource for future studies of vertical gene transmission. PMID:17673272

  8. Ensembl comparative genomics resources

    PubMed Central

    Muffato, Matthieu; Beal, Kathryn; Fitzgerald, Stephen; Gordon, Leo; Pignatelli, Miguel; Vilella, Albert J.; Searle, Stephen M. J.; Amode, Ridwan; Brent, Simon; Spooner, William; Kulesha, Eugene; Yates, Andrew; Flicek, Paul

    2016-01-01

    Evolution provides the unifying framework with which to understand biology. The coherent investigation of genic and genomic data often requires comparative genomics analyses based on whole-genome alignments, sets of homologous genes and other relevant datasets in order to evaluate and answer evolutionary-related questions. However, the complexity and computational requirements of producing such data are substantial: this has led to only a small number of reference resources that are used for most comparative analyses. The Ensembl comparative genomics resources are one such reference set that facilitates comprehensive and reproducible analysis of chordate genome data. Ensembl computes pairwise and multiple whole-genome alignments from which large-scale synteny, per-base conservation scores and constrained elements are obtained. Gene alignments are used to define Ensembl Protein Families, GeneTrees and homologies for both protein-coding and non-coding RNA genes. These resources are updated frequently and have a consistent informatics infrastructure and data presentation across all supported species. Specialized web-based visualizations are also available including synteny displays, collapsible gene tree plots, a gene family locator and different alignment views. The Ensembl comparative genomics infrastructure is extensively reused for the analysis of non-vertebrate species by other projects including Ensembl Genomes and Gramene and much of the information here is relevant to these projects. The consistency of the annotation across species and the focus on vertebrates makes Ensembl an ideal system to perform and support vertebrate comparative genomic analyses. We use robust software and pipelines to produce reference comparative data and make it freely available. Database URL: http://www.ensembl.org. PMID:26896847

  9. Ensembl comparative genomics resources.

    PubMed

    Herrero, Javier; Muffato, Matthieu; Beal, Kathryn; Fitzgerald, Stephen; Gordon, Leo; Pignatelli, Miguel; Vilella, Albert J; Searle, Stephen M J; Amode, Ridwan; Brent, Simon; Spooner, William; Kulesha, Eugene; Yates, Andrew; Flicek, Paul

    2016-01-01

    Evolution provides the unifying framework with which to understand biology. The coherent investigation of genic and genomic data often requires comparative genomics analyses based on whole-genome alignments, sets of homologous genes and other relevant datasets in order to evaluate and answer evolutionary-related questions. However, the complexity and computational requirements of producing such data are substantial: this has led to only a small number of reference resources that are used for most comparative analyses. The Ensembl comparative genomics resources are one such reference set that facilitates comprehensive and reproducible analysis of chordate genome data. Ensembl computes pairwise and multiple whole-genome alignments from which large-scale synteny, per-base conservation scores and constrained elements are obtained. Gene alignments are used to define Ensembl Protein Families, GeneTrees and homologies for both protein-coding and non-coding RNA genes. These resources are updated frequently and have a consistent informatics infrastructure and data presentation across all supported species. Specialized web-based visualizations are also available including synteny displays, collapsible gene tree plots, a gene family locator and different alignment views. The Ensembl comparative genomics infrastructure is extensively reused for the analysis of non-vertebrate species by other projects including Ensembl Genomes and Gramene and much of the information here is relevant to these projects. The consistency of the annotation across species and the focus on vertebrates makes Ensembl an ideal system to perform and support vertebrate comparative genomic analyses. We use robust software and pipelines to produce reference comparative data and make it freely available. Database URL: http://www.ensembl.org. PMID:26896847

  10. A Primer on Aspects of Cognition for Medical Informatics

    PubMed Central

    Patel, Vimla L.; Arocha, José F.; Kaufman, David R.

    2001-01-01

    As a multidisciplinary field, medical informatics draws on a range of disciplines, such as computer science, information science, and the social and cognitive sciences. The cognitive sciences can provide important insights into the nature of the processes involved in human– computer interaction and help improve the design of medical information systems by providing insight into the roles that knowledge, memory, and strategies play in a variety of cognitive activities. In this paper, the authors survey literature on aspects of medical cognition and provide a set of claims that they consider to be important in medical informatics. PMID:11418539

  11. Role of Informatics in Patient Safety and Quality Assurance.

    PubMed

    Nakhleh, Raouf E

    2015-06-01

    Quality assurance encompasses monitoring daily processes for accurate, timely, and complete reports in surgical pathology. Quality assurance also includes implementation of policies and procedures that prevent or detect errors in a timely manner. This article presents uses of informatics in quality assurance. Three main foci are critical to the general improvement of diagnostic surgical pathology. First is the application of informatics to specimen identification with lean methods for real-time statistical control of specimen receipt and processing. Second is the development of case reviews before sign-out. Third is the development of information technology in communication of results to assure treatment in a timely manner. PMID:26065802

  12. A core curriculum for clinical fellowship training in pathology informatics

    PubMed Central

    McClintock, David S.; Levy, Bruce P.; Lane, William J.; Lee, Roy E.; Baron, Jason M.; Klepeis, Veronica E.; Onozato, Maristela L.; Kim, JiYeon; Dighe, Anand S.; Beckwith, Bruce A.; Kuo, Frank; Black-Schaffer, Stephen; Gilbertson, John R.

    2012-01-01

    Background: In 2007, our healthcare system established a clinical fellowship program in Pathology Informatics. In 2010 a core didactic course was implemented to supplement the fellowship research and operational rotations. In 2011, the course was enhanced by a formal, structured core curriculum and reading list. We present and discuss our rationale and development process for the Core Curriculum and the role it plays in our Pathology Informatics Fellowship Training Program. Materials and Methods: The Core Curriculum for Pathology Informatics was developed, and is maintained, through the combined efforts of our Pathology Informatics Fellows and Faculty. The curriculum was created with a three-tiered structure, consisting of divisions, topics, and subtopics. Primary (required) and suggested readings were selected for each subtopic in the curriculum and incorporated into a curated reading list, which is reviewed and maintained on a regular basis. Results: Our Core Curriculum is composed of four major divisions, 22 topics, and 92 subtopics that cover the wide breadth of Pathology Informatics. The four major divisions include: (1) Information Fundamentals, (2) Information Systems, (3) Workflow and Process, and (4) Governance and Management. A detailed, comprehensive reading list for the curriculum is presented in the Appendix to the manuscript and contains 570 total readings (current as of March 2012). Discussion: The adoption of a formal, core curriculum in a Pathology Informatics fellowship has significant impacts on both fellowship training and the general field of Pathology Informatics itself. For a fellowship, a core curriculum defines a basic, common scope of knowledge that the fellowship expects all of its graduates will know, while at the same time enhancing and broadening the traditional fellowship experience of research and operational rotations. For the field of Pathology Informatics itself, a core curriculum defines to the outside world, including

  13. Healthcare Informatics Schemata: A Paradigm Shift over Time.

    PubMed

    Erdley, W Scott

    2016-01-01

    The schemata "A paradigm shift over time©" (Sackett & Erdley, 2006) a graphic model, visualizes development and progression of informatics in health over time. The model portrays information technology trends, from computers as resource through computational ubiquity, and the shift to social networking and e-Health. The discrepancy between "real" and "proposed" suggests gaps involving issues such as value, interoperability and ontology requiring attention, development and ultimately adoption, hinging on a universal standards framework. The workshop objective is to review previous and current models of healthcare informatics to springboard revisions of the schemata for current and future use. PMID:27332341

  14. Theoretical Foundations for Evidence-Based Health Informatics: Why? How?

    PubMed

    Scott, Philip J; Georgiou, Andrew; Hyppönen, Hannele; Craven, Catherine K; Rigby, Michael; Brender McNair, Jytte

    2016-01-01

    A scientific approach to health informatics requires sound theoretical foundations. Health informatics implementation would be more effective if evidence-based and guided by theories about what is likely to work in what circumstances. We report on a Medinfo 2015 workshop on this topic jointly organized by the EFMI Working Group on Assessment of Health Information Systems and the IMIA Working Group on Technology Assessment and Quality Development. We discuss the findings of the workshop and propose an approach to consolidate empirical knowledge into testable middle-range theories. PMID:27577457

  15. An international health and nursing informatics module for distance education.

    PubMed

    Goossen, W; Timmons, S; Mol, M

    1998-06-01

    This paper describes why a module about health and nursing informatics is a necessary component for nursing education. Several developments in society and health care force health providers to manage the large amount of health data adequately. A module about health and nursing informatics was developed in international cooperation by three schools of nursing from Germany, The Netherlands and the UK. The content and learning activities of the realized example module for distance learning are described. Future plans include making this course material available in different languages on the World Wide Web. PMID:9726501

  16. Geo-spatial Informatics in International Public Health Nursing Education.

    PubMed

    Kerr, Madeleine J; Honey, Michelle L L; Krzyzanowski, Brittany

    2016-01-01

    This poster describes results of an undergraduate nursing informatics experience. Students applied geo-spatial methods to community assessments in two urban regions of New Zealand and the United States. Students used the Omaha System standardized language to code their observations during a brief community assessment activity and entered their data into a mapping program developed in Esri ArcGIS Online, a geographic information system. Results will be displayed in tables and maps to allow comparison among the communities. The next generation of nurses can employ geo-spatial informatics methods to contribute to innovative community assessment, planning and policy development. PMID:27332443

  17. About the Beginnings of Medical Informatics in Europe

    PubMed Central

    Roger France, Francis

    2014-01-01

    The term “Informatics” was created in 1962 from two words, information and automatic, and covers all techniques, information concepts and applications of computers. Among them, medicine is the field where we will describe some factors of development in Europe since the late sixties. It took some time for obtaining the acceptance of this new terminology worldwide, but today medical informatics is a well defined discipline which had a tremendous development last decades. This paper tries to recall the context and events from the beginning of medical informatics in Europe. PMID:24648614

  18. Behavioral Informatics and Computational Modeling in Support of Proactive Health Management and Care.

    PubMed

    Pavel, Misha; Jimison, Holly B; Korhonen, Ilkka; Gordon, Christine M; Saranummi, Niilo

    2015-12-01

    Health-related behaviors are among the most significant determinants of health and quality of life. Improving health behavior is an effective way to enhance health outcomes and mitigate the escalating challenges arising from an increasingly aging population and the proliferation of chronic diseases. Although it has been difficult to obtain lasting improvements in health behaviors on a wide scale, advances at the intersection of technology and behavioral science may provide the tools to address this challenge. In this paper, we describe a vision and an approach to improve health behavior interventions using the tools of behavioral informatics, an emerging transdisciplinary research domain based on system-theoretic principles in combination with behavioral science and information technology. The field of behavioral informatics has the potential to optimize interventions through monitoring, assessing, and modeling behavior in support of providing tailored and timely interventions. We describe the components of a closed-loop system for health interventions. These components range from fine grain sensor characterizations to individual-based models of behavior change. We provide an example of a research health coaching platform that incorporates a closed-loop intervention based on these multiscale models. Using this early prototype, we illustrate how the optimized and personalized methodology and technology can support self-management and remote care. We note that despite the existing examples of research projects and our platform, significant future research is required to convert this vision to full-scale implementations. PMID:26441408

  19. Behavioral Informatics and Computational Modeling in Support of Proactive Health Management and Care

    PubMed Central

    Jimison, Holly B.; Korhonen, Ilkka; Gordon, Christine M.; Saranummi, Niilo

    2016-01-01

    Health-related behaviors are among the most significant determinants of health and quality of life. Improving health behavior is an effective way to enhance health outcomes and mitigate the escalating challenges arising from an increasingly aging population and the proliferation of chronic diseases. Although it has been difficult to obtain lasting improvements in health behaviors on a wide scale, advances at the intersection of technology and behavioral science may provide the tools to address this challenge. In this paper, we describe a vision and an approach to improve health behavior interventions using the tools of behavioral informatics, an emerging transdisciplinary research domain based on system-theoretic principles in combination with behavioral science and information technology. The field of behavioral informatics has the potential to optimize interventions through monitoring, assessing, and modeling behavior in support of providing tailored and timely interventions. We describe the components of a closed-loop system for health interventions. These components range from fine grain sensor characterizations to individual-based models of behavior change. We provide an example of a research health coaching platform that incorporates a closed-loop intervention based on these multiscale models. Using this early prototype, we illustrate how the optimized and personalized methodology and technology can support self-management and remote care. We note that despite the existing examples of research projects and our platform, significant future research is required to convert this vision to full-scale implementations. PMID:26441408

  20. Design, implementation and operation of a multimodality research imaging informatics repository

    PubMed Central

    2015-01-01

    Background Biomedical imaging research increasingly involves acquiring, managing and processing large amounts of distributed imaging data. Integrated systems that combine data, meta-data and workflows are crucial for realising the opportunities presented by advances in imaging facilities. Methods This paper describes the design, implementation and operation of a multi-modality research imaging data management system that manages imaging data obtained from biomedical imaging scanners operated at Monash Biomedical Imaging (MBI), Monash University in Melbourne, Australia. In addition to Digital Imaging and Communications in Medicine (DICOM) images, raw data and non-DICOM biomedical data can be archived and distributed by the system. Imaging data are annotated with meta-data according to a study-centric data model and, therefore, scientific users can find, download and process data easily. Results The research imaging data management system ensures long-term usability, integrity inter-operability and integration of large imaging data. Research users can securely browse and download stored images and data, and upload processed data via subject-oriented informatics frameworks including the Distributed and Reflective Informatics System (DaRIS), and the Extensible Neuroimaging Archive Toolkit (XNAT). PMID:25870760

  1. Considering something 'ELSE': ethical, legal and socio-economic factors in medical imaging and medical informatics.

    PubMed

    Duquenoy, Penny; George, Carlisle; Solomonides, Anthony

    2008-12-01

    The focus on the use of existing and new technologies to facilitate advances in medical imaging and medical informatics (MIMI) is often directed to the technical capabilities and possibilities that these technologies bring. The technologies, though, in acting as a mediating agent alter the dynamics and context of information delivery in subtle ways. While these changes bring benefits in more efficient information transfer and offer the potential of better healthcare, they also disrupt traditional processes and practices which have been formulated for a different setting. The governance processes that underpin core ethical principles, such as patient confidentiality and informed consent, may no longer be appropriate in a new technological context. Therefore, in addition to discussing new methodologies, techniques and applications, there is need for a discussion of ethical, legal and socio-economic (ELSE) issues surrounding the use and application of technologies in MIMI. Consideration of these issues is especially important for the area of medical informatics which after all exists to support patients, healthcare practitioners and inform science. This paper brings to light some important ethical, legal and socio-economic issues related to MIMI with the aim of furthering an interdisciplinary approach to the increasing use of Information and Communication Technologies (ICT) in healthcare. PMID:18649968

  2. Meeting the challenges--the role of medical informatics in an ageing society.

    PubMed

    Koch, Sabine

    2006-01-01

    The objective of this paper is to identify trends and new technological developments that appear due to an ageing society and to relate them to current research in the field of medical informatics. A survey of the current literature reveals that recent technological advances have been made in the fields of "telecare and home-monitoring", "smart homes and robotics" and "health information systems and knowledge management". Innovative technologies such as wearable devices, bio- and environmental sensors and mobile, humanoid robots do already exist and ambient assistant living environments are being created for an ageing society. However, those technologies have to be adapted to older people's self-care processes and coping strategies, and to support new ways of healthcare delivery. Medical informatics can support this process by providing the necessary information infrastructure, contribute to standardisation, interoperability and security issues and provide modelling and simulation techniques for educational purposes. Research fields of increasing importance with regard to an ageing society are, moreover, the fields of knowledge management, ubiquitous computing and human-computer interaction. PMID:17108500

  3. A Bioimage Informatics Based Reconstruction of Breast Tumor Microvasculature with Computational Blood Flow Predictions

    PubMed Central

    Stamatelos, Spyros K.; Kim, Eugene; Pathak, Arvind P.; Popel, Aleksander S.

    2014-01-01

    Induction of tumor angiogenesis is among the hallmarks of cancer and a driver of metastatic cascade initiation. Recent advances in high-resolution imaging enable highly detailed three-dimensional geometrical representation of the whole-tumor microvascular architecture. This enormous increase in complexity of image-based data necessitates the application of informatics methods for the analysis, mining and reconstruction of these spatial graph data structures. We present a novel methodology that combines ex-vivo high-resolution micro-computed tomography imaging data with a bioimage informatics algorithm to track and reconstruct the whole-tumor vasculature of a human breast cancer model. The reconstructed tumor vascular network is used as an input of a computational model that estimates blood flow in each segment of the tumor microvascular network. This formulation involves a well-established biophysical model and an optimization algorithm that ensures mass balance and detailed monitoring of all the vessels that feed and drain blood from the tumor microvascular network. Perfusion maps for the whole-tumor microvascular network are computed. Morphological and hemodynamic indices from different regions are compared to infer their role in overall tumor perfusion. PMID:24342178

  4. The United States National Center for Interprofessional Practice and Education: Integrating an informatics approach to interprofessional work.

    PubMed

    Brandt, Barbara F; Cerra, Frank B; Delaney, Connie White

    2015-01-01

    The National Center for Interprofessional Practice and Education, a United States public-private partnership, was formed to provide national leadership, scholarship, evidence, and coordination to advance interprofessional education (IPE) and practice. Many external drivers led to the creation of the partnership that culminated in the National Center: patient safety initiatives, the need for care coordination and transitions efforts, quality improvement imperatives, calls for teamwork and workforce optimization, newly defined national core competencies for interprofessional collaborative practice, practice redesign, escalating health care costs, and state and federal policies. The National Center principals who have served in a variety of senior leadership roles--a clinician, educationalist, and informaticist--recognized the opportunity to leverage the potential that informatics could bring not only to the center but also to the field of IPECP. An informatics approach focuses on collaborative processes and works to address information processing, communications, and data collection. To do so, the National Center created multiple platforms: informatics education, a resource exchange, communication strategy, incubator network, national data repository, and learning system. PMID:26652632

  5. Center for Cancer Genomics | Office of Cancer Genomics

    Cancer.gov

    The Center for Cancer Genomics (CCG) was established to unify the National Cancer Institute's activities in cancer genomics, with the goal of advancing genomics research and translating findings into the clinic to improve the precise diagnosis and treatment of cancers. In addition to promoting genomic sequencing approach

  6. Human Genome Program Report. Part 2, 1996 Research Abstracts

    DOE R&D Accomplishments Database

    1997-11-01

    This report contains Part 2 of a two-part report to reflect research and progress in the US Department of Energy Human Genome Program from 1994 through 1996, with specified updates made just before publication. Part 2 consists of 1996 research abstracts. Attention is focused on the following: sequencing; mapping; informatics; ethical, legal, and social issues; infrastructure; and small business innovation research.

  7. DOE Human Genome Program contractor-grantee workshop

    SciTech Connect

    1996-01-01

    This volume contains the proceedings for the DOE Human Genome Program`s Contractor-Grantee Workshop V held in Sante Fe, New Mexico January 28, February 1, 1996. Presentations were divided into sessions entitled Sequencing; Mapping; Informatics; Ethical, Legal, and Social Issues; and Infrastructure. Reports of individual projects described herein are separately indexed and abstracted for the database.

  8. Human genome program report. Part 2, 1996 research abstracts

    SciTech Connect

    1997-11-01

    This report contains Part 2 of a two-part report to reflect research and progress in the US Department of Energy Human Genome Program from 1994 through 1996, with specified updates made just before publication. Part 2 consists of 1996 research abstracts. Attention is focused on the following: sequencing; mapping; informatics; ethical, legal, and social issues; infrastructure; and small business innovation research.

  9. Proteomics. Making sense of genomic information for drug discovery.

    PubMed

    Whitelegge, J P; le Coutre, J

    2001-01-01

    As an increasing number of available genomes triggers a gold rush in modern biology, the scientific challenge shifts towards understanding the total of the encoded information, most notably the proteins, their structures, functions and interactions. Currently this work is in its early stages but the near future will bring a merger of biology, engineering and informatics with a far broader impact on society than pure genomics has had so far. The challenge of characterizing the structures and functions of all proteins in a given cell demands technological advances beyond the classical methodologies of protein biochemistry. Mass spectrometry techniques for high-throughput protein identification, including peptide mass fingerprinting, sequence tagging and mass spectrometry on full-length proteins are providing the driving force behind proteomics endeavors. New technologies are needed to move high-resolution protein structure determination to an industrial scale. Nonetheless, improvements in techniques for the separation of intrinsic membrane proteins are enabling proteomics efforts towards identifying drug targets within this important class of biomolecules. Beyond the acquisition of data on sequences, structures and interactions, however, the major work in drug discovery remains: the screening of large candidate compound libraries combined with clever medicinal chemistry that guarantees selective action and defined delivery of the drug. PMID:12173311

  10. Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling

    PubMed Central

    Medina, Ignacio; Carbonell, José; Pulido, Luis; Madeira, Sara C.; Goetz, Stefan; Conesa, Ana; Tárraga, Joaquín; Pascual-Montano, Alberto; Nogales-Cadenas, Ruben; Santoyo, Javier; García, Francisco; Marbà, Martina; Montaner, David; Dopazo, Joaquín

    2010-01-01

    Babelomics is a response to the growing necessity of integrating and analyzing different types of genomic data in an environment that allows an easy functional interpretation of the results. Babelomics includes a complete suite of methods for the analysis of gene expression data that include normalization (covering most commercial platforms), pre-processing, differential gene expression (case-controls, multiclass, survival or continuous values), predictors, clustering; large-scale genotyping assays (case controls and TDTs, and allows population stratification analysis and correction). All these genomic data analysis facilities are integrated and connected to multiple options for the functional interpretation of the experiments. Different methods of functional enrichment or gene set enrichment can be used to understand the functional basis of the experiment analyzed. Many sources of biological information, which include functional (GO, KEGG, Biocarta, Reactome, etc.), regulatory (Transfac, Jaspar, ORegAnno, miRNAs, etc.), text-mining or protein–protein interaction modules can be used for this purpose. Finally a tool for the de novo functional annotation of sequences has been included in the system. This provides support for the functional analysis of non-model species. Mirrors of Babelomics or command line execution of their individual components are now possible. Babelomics is available at http://www.babelomics.org. PMID:20478823

  11. Metropolis revisited: the evolving role of librarians in informatics education for the health professions

    PubMed Central

    King, Samuel B.; Lapidus, Mariana

    2015-01-01

    Objective: The authors' goal was to assess changes in the role of librarians in informatics education from 2004 to 2013. This is a follow-up to “Metropolis Redux: The Unique Importance of Library Skills in Informatics,” a 2004 survey of informatics programs. Methods: An electronic survey was conducted in January 2013 and sent to librarians via the MEDLIB-L email discussion list, the library section of the American Association of Colleges of Pharmacy, the Medical Informatics Section of the Medical Library Association, the Information Technology Interest Group of the Association of College and Research Libraries/New England Region, and various library directors across the country. Results: Librarians from fifty-five institutions responded to the survey. Of these respondents, thirty-four included librarians in nonlibrary aspects of informatics training. Fifteen institutions have librarians participating in leadership positions in their informatics programs. Compared to the earlier survey, the role of librarians has evolved. Conclusions: Librarians possess skills that enable them to participate in informatics programs beyond a narrow library focus. Librarians currently perform significant leadership roles in informatics education. There are opportunities for librarian interdisciplinary collaboration in informatics programs. Implications: Informatics is much more than the study of technology. The information skills that librarians bring to the table enrich and broaden the study of informatics in addition to adding value to the library profession itself. PMID:25552939

  12. Informatics competencies essential to decision making in nursing management.

    PubMed

    Jensen, Rodrigo; Guedes, Erika de Souza; Leite, Maria Madalena Januário

    2016-02-01

    OBJECTIVE To identify informatics abilities essential to decision making in nursing management. METHOD Survey study with specialist nurses in health informatics and management. An electronic questionnaire was built based on the competencies Information Literacy (five categories; 40 abilities) and Information Management (nine categories; 69 abilities) of the TIGER - Technology Informatics Guiding Education Reform - initiative, with the guiding question: Which informatics abilities are essential to decision making in management? Answers were sorted in a Likert scale, ranging from 1 to 5. Rasch analysis was conducted with the software WINSTEPS ®. Results were presented in logits, with cutoff value zero. RESULTS Thirty-two specialists participated, coming from all regions of Brazil. In the information literacy competency, 18 abilities were considered essential and in Information Management, 38; these were sorted according to their degree of essentiality. CONCLUSION It is believed that the incorporation of these abilities in teaching can support the education of nurse managers and contribute to evidence-based practice, incorporation of information and communication technologies in health and information management. PMID:27007428

  13. Score Calculation in Informatics Contests Using Multiple Criteria Decision Methods

    ERIC Educational Resources Information Center

    Skupiene, Jurate

    2011-01-01

    The Lithuanian Informatics Olympiad is a problem solving contest for high school students. The work of each contestant is evaluated in terms of several criteria, where each criterion is measured according to its own scale (but the same scale for each contestant). Several jury members are involved in the evaluation. This paper analyses the problem…

  14. Improving the Evaluation Model for the Lithuanian Informatics Olympiads

    ERIC Educational Resources Information Center

    Skupiene, Jurate

    2010-01-01

    The Lithuanian Informatics Olympiads (LitIO) is a problem solving programming contest for students in secondary education. The work of the student to be evaluated is an algorithm designed by the student and implemented as a working program. The current evaluation process involves both automated (for correctness and performance of programs with the…

  15. Pre-School Teachers' Informatics and Information Literacy

    ERIC Educational Resources Information Center

    Tatkovic, Nevenka; Ruzic, Maja; Pecaric, Dilda

    2006-01-01

    The life and activities of every man in the period of transition from the second into the third millennium have been marked by epochal changes which appear as the consequence of scientific and technological revolution dominated by highly developed information and communication technology. Informatics and information education based on information…

  16. Informatics Futures in Dental Education and Research: Quality Assurance.

    ERIC Educational Resources Information Center

    Crall, James J.

    1991-01-01

    The paper addresses the potential of informatics to patient care quality assurance curricula, focusing on (1) terminology and developments related to quality of care evaluations; (2) criticisms of traditional approaches; (3) limitations of existing data sources for quality assurance in dentistry; and (4) quality assurance considerations in…

  17. Informatics and Telematics in Health. Present and Potential Uses.

    ERIC Educational Resources Information Center

    World Health Organization, Geneva (Switzerland).

    This report focuses on technical issues associated with informatics--a term covering all aspects of the development and operations of information systems, the supporting computer methodology and technology, and the supporting telecommunications links. The first of six chapters discusses the purpose of the report together with basic assumptions…

  18. A Review of Medical Education and Medical Informatics.

    ERIC Educational Resources Information Center

    Haynes, R. Brian; And Others

    1989-01-01

    Information technology may help physicians to manage information more effectively through more accessible clinical indexes, databases of diagnostic test characteristics, computerized audits of clinical activities, on-line access to medical literature, etc. Medical informatics, a new discipline dedicated to the solution of information problems in…

  19. A solo hospital librarian's experience in clinical informatics.

    PubMed

    Miles, Alisha

    2015-01-01

    This column reviews some of a solo librarian's experiences that led to involvement with the hospital Clinical Informatics Team. This included work on the electronic health record (EHR), computerized physician order entry (CPOE) system, development of order sets, and participation in the Physician Technology Committee. PMID:25927515

  20. An Abridged History of Medical Informatics Education in Europe

    PubMed Central

    Hasman, Arie; Mantas, John; Zarubina, Tatyana

    2014-01-01

    This contribution presents the development of medical informatics education in Europe. It does not discuss all developments that took place. Rather it discerns several themes that indicate the progress in the field, starting from the initiation phase to the final quality control phase. PMID:24648617