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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. 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.

  16. 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.

  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. 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.

  16. 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.

  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)

    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.

  7. 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.

  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. 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

  4. 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.

  5. 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

  6. 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

  7. 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.

  8. 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

  9. 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.

  10. 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.

  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 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

  17. 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

  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 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

  1. 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

  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. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  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. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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

  18. 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

  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. 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.

  9. 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

  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. 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

  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. 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

  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

    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 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

  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. 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

  10. 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

  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. 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…

  14. 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…

  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. 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

  8. 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

  9. 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

  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. 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

  4. 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

  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 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

  12. 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

  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. 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.

  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. 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

  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. 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

  4. 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

  5. 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

  6. 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

  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. 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.

  18. [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

  19. 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

  20. 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.

  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