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Sample records for genome informatics advances

  1. Advances in biotechnology and informatics to link variation in the genome to phenotypes in plants and animals.

    PubMed

    Appels, R; Barrero, R; Bellgard, M

    2013-03-01

    Advances in our understanding of genome structure provide consistent evidence for the existence of a core genome representing species classically defined by phenotype, as well as conditionally dispensable components of the genome that shows extensive variation between individuals of a given species. Generally, conservation of phenotypic features between species reflects conserved features of the genome; however, this is evidently not necessarily always the case as demonstrated by the analysis of the tunicate chordate Oikopleura dioica. In both plants and animals, the methylation activity of DNA and histones continues to present new variables for modifying (eventually) the phenotype of an organism and provides for structural variation that builds on the point mutations, rearrangements, indels, and amplification of retrotransposable elements traditionally considered. The translation of the advances in the structure/function analysis of the genome to industry is facilitated through the capture of research outputs in "toolboxes" that remain accessible in the public domain.

  2. 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''.

  3. 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.

  4. Interrogating the druggable genome with structural informatics.

    PubMed

    Hambly, Kevin; Danzer, Joseph; Muskal, Steven; Debe, Derek A

    2006-08-01

    Structural genomics projects are producing protein structure data at an unprecedented rate. In this paper, we present the Target Informatics Platform (TIP), a novel structural informatics approach for amplifying the rapidly expanding body of experimental protein structure information to enhance the discovery and optimization of small molecule protein modulators on a genomic scale. In TIP, existing experimental structure information is augmented using a homology modeling approach, and binding sites across multiple target families are compared using a clique detection algorithm. We report here a detailed analysis of the structural coverage for the set of druggable human targets, highlighting drug target families where the level of structural knowledge is currently quite high, as well as those areas where structural knowledge is sparse. Furthermore, we demonstrate the utility of TIP's intra- and inter-family binding site similarity analysis using a series of retrospective case studies. Our analysis underscores the utility of a structural informatics infrastructure for extracting drug discovery-relevant information from structural data, aiding researchers in the identification of lead discovery and optimization opportunities as well as potential "off-target" liabilities.

  5. Mouse Genome Informatics (MGI): Resources for Mining Mouse Genetic, Genomic, and Biological Data in Support of Primary and Translational Research.

    PubMed

    Eppig, Janan T; Smith, Cynthia L; Blake, Judith A; Ringwald, Martin; Kadin, James A; Richardson, Joel E; Bult, Carol J

    2017-01-01

    The Mouse Genome Informatics (MGI), resource ( www.informatics.jax.org ) has existed for over 25 years, and over this time its data content, informatics infrastructure, and user interfaces and tools have undergone dramatic changes (Eppig et al., Mamm Genome 26:272-284, 2015). Change has been driven by scientific methodological advances, rapid improvements in computational software, growth in computer hardware capacity, and the ongoing collaborative nature of the mouse genomics community in building resources and sharing data. Here we present an overview of the current data content of MGI, describe its general organization, and provide examples using simple and complex searches, and tools for mining and retrieving sets of data.

  6. Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology.

    PubMed

    Karp, Peter D; Latendresse, Mario; Paley, Suzanne M; Krummenacker, Markus; Ong, Quang D; Billington, Richard; Kothari, Anamika; Weaver, Daniel; Lee, Thomas; Subhraveti, Pallavi; Spaulding, Aaron; Fulcher, Carol; Keseler, Ingrid M; Caspi, Ron

    2016-09-01

    Pathway Tools is a bioinformatics software environment with a broad set of capabilities. The software provides genome-informatics tools such as a genome browser, sequence alignments, a genome-variant analyzer and comparative-genomics operations. It offers metabolic-informatics tools, such as metabolic reconstruction, quantitative metabolic modeling, prediction of reaction atom mappings and metabolic route search. Pathway Tools also provides regulatory-informatics tools, such as the ability to represent and visualize a wide range of regulatory interactions. This article outlines the advances in Pathway Tools in the past 5 years. Major additions include components for metabolic modeling, metabolic route search, computation of atom mappings and estimation of compound Gibbs free energies of formation; addition of editors for signaling pathways, for genome sequences and for cellular architecture; storage of gene essentiality data and phenotype data; display of multiple alignments, and of signaling and electron-transport pathways; and development of Python and web-services application programming interfaces. Scientists around the world have created more than 9800 Pathway/Genome Databases by using Pathway Tools, many of which are curated databases for important model organisms.

  7. Informatics for Unveiling Hidden Genome Signatures

    PubMed Central

    Abe, Takashi; Kanaya, Shigehiko; Kinouchi, Makoto; Ichiba, Yuta; Kozuki, Tokio; Ikemura, Toshimichi

    2003-01-01

    With the increasing amount of available genome sequences, novel tools are needed for comprehensive analysis of species-specific sequence characteristics for a wide variety of genomes. We used an unsupervised neural network algorithm, a self-organizing map (SOM), to analyze di-, tri-, and tetranucleotide frequencies in a wide variety of prokaryotic and eukaryotic genomes. The SOM, which can cluster complex data efficiently, was shown to be an excellent tool for analyzing global characteristics of genome sequences and for revealing key combinations of oligonucleotides representing individual genomes. From analysis of 1- and 10-kb genomic sequences derived from 65 bacteria (a total of 170 Mb) and from 6 eukaryotes (460 Mb), clear species-specific separations of major portions of the sequences were obtained with the di-, tri-, and tetranucleotide SOMs. The unsupervised algorithm could recognize, in most 10-kb sequences, the species-specific characteristics (key combinations of oligonucleotide frequencies) that are signature features of each genome. We were able to classify DNA sequences within one and between many species into subgroups that corresponded generally to biological categories. Because the classification power is very high, the SOM is an efficient and fundamental bioinformatic strategy for extracting a wide range of genomic information from a vast amount of sequences. [Supplemental material is available online at www.genome.org.] PMID:12671005

  8. 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

    2016-07-12

    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

  9. 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

    2016-08-01

    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.

  10. 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

  11. Disease model curation improvements at Mouse Genome Informatics

    PubMed Central

    Bello, Susan M.; Richardson, Joel E.; Davis, Allan P.; Wiegers, Thomas C.; Mattingly, Carolyn J.; Dolan, Mary E.; Smith, Cynthia L.; Blake, Judith A.; Eppig, Janan T.

    2012-01-01

    Optimal curation of human diseases requires an ontology or structured vocabulary that contains terms familiar to end users, is robust enough to support multiple levels of annotation granularity, is limited to disease terms and is stable enough to avoid extensive reannotation following updates. At Mouse Genome Informatics (MGI), we currently use disease terms from Online Mendelian Inheritance in Man (OMIM) to curate mouse models of human disease. While OMIM provides highly detailed disease records that are familiar to many in the medical community, it lacks structure to support multilevel annotation. To improve disease annotation at MGI, we evaluated the merged Medical Subject Headings (MeSH) and OMIM disease vocabulary created by the Comparative Toxicogenomics Database (CTD) project. Overlaying MeSH onto OMIM provides hierarchical access to broad disease terms, a feature missing from the OMIM. We created an extended version of the vocabulary to meet the genetic disease-specific curation needs at MGI. Here we describe our evaluation of the CTD application, the extensions made by MGI and discuss the strengths and weaknesses of this approach. Database URL: http://www.informatics.jax.org/ PMID:22434831

  12. 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.

  13. 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.

  14. 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

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

    ScienceCinema

    Pop, Mihai [University of Maryland

    2016-07-12

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

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

    ScienceCinema

    Quake, Steve [University of Stanford

    2016-07-12

    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.

  18. Biomedical informatics advancing the national health agenda: the AMIA 2015 year-in-review in clinical and consumer informatics.

    PubMed

    Roberts, Kirk; Boland, Mary Regina; Pruinelli, Lisiane; Dcruz, Jina; Berry, Andrew; Georgsson, Mattias; Hazen, Rebecca; Sarmiento, Raymond F; Backonja, Uba; Yu, Kun-Hsing; Jiang, Yun; Brennan, Patricia Flatley

    2017-04-01

    The field of biomedical informatics experienced a productive 2015 in terms of research. In order to highlight the accomplishments of that research, elicit trends, and identify shortcomings at a macro level, a 19-person team conducted an extensive review of the literature in clinical and consumer informatics. The result of this process included a year-in-review presentation at the American Medical Informatics Association Annual Symposium and a written report (see supplemental data). Key findings are detailed in the report and summarized here. This article organizes the clinical and consumer health informatics research from 2015 under 3 themes: the electronic health record (EHR), the learning health system (LHS), and consumer engagement. Key findings include the following: (1) There are significant advances in establishing policies for EHR feature implementation, but increased interoperability is necessary for these to gain traction. (2) Decision support systems improve practice behaviors, but evidence of their impact on clinical outcomes is still lacking. (3) Progress in natural language processing (NLP) suggests that we are approaching but have not yet achieved truly interactive NLP systems. (4) Prediction models are becoming more robust but remain hampered by the lack of interoperable clinical data records. (5) Consumers can and will use mobile applications for improved engagement, yet EHR integration remains elusive.

  19. Advanced Spacesuit Informatics Software Design for Power, Avionics and Software Version 2.0

    NASA Technical Reports Server (NTRS)

    Wright, Theodore W.

    2016-01-01

    A description of the software design for the 2016 edition of the Informatics computer assembly of the NASAs Advanced Extravehicular Mobility Unit (AEMU), also called the Advanced Spacesuit. The Informatics system is an optional part of the spacesuit assembly. It adds a graphical interface for displaying suit status, timelines, procedures, and warning information. It also provides an interface to the suit mounted camera for recording still images, video, and audio field notes.

  20. 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

  1. 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.

  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

    2016-07-12

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

    SciTech Connect

    Crow, John

    2012-06-01

    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.

  4. Annotation of plant gene function via combined genomics, metabolomics and informatics.

    PubMed

    Tohge, Takayuki; Fernie, Alisdair R

    2012-06-17

    Given the ever expanding number of model plant species for which complete genome sequences are available and the abundance of bio-resources such as knockout mutants, wild accessions and advanced breeding populations, there is a rising burden for gene functional annotation. In this protocol, annotation of plant gene function using combined co-expression gene analysis, metabolomics and informatics is provided (Figure 1). This approach is based on the theory of using target genes of known function to allow the identification of non-annotated genes likely to be involved in a certain metabolic process, with the identification of target compounds via metabolomics. Strategies are put forward for applying this information on populations generated by both forward and reverse genetics approaches in spite of none of these are effortless. By corollary this approach can also be used as an approach to characterise unknown peaks representing new or specific secondary metabolites in the limited tissues, plant species or stress treatment, which is currently the important trial to understanding plant metabolism.

  5. Competency Recommendations for Advancing Nursing Informatics in the Next Decade: International Survey Results.

    PubMed

    Ronquillo, Charlene; Topaz, Maxim; Pruinelli, Lisiane; Peltonen, Laura-Maria; Nibber, Raji

    2017-01-01

    The IMIA-NIstudents' and emerging professionals' working group conducted a large international survey in 2015 regarding research trends in nursing informatics. The survey was translated into half-a-dozen languages and distributed through 18 international research collaborators' professional connections. The survey focused on the perspectives of nurse informaticians. A total of 272 participants responded to an open ended question concerning recommendations to advance nursing informatics. Five key areas for action were identified through our thematic content analysis: education, research, practice, visibility and collaboration. This chapter discusses these results with implications for nursing competency development. We propose how components of various competency lists might support the key areas for action. We also identify room to further develop existing competency guidelines to support in-service education for practicing nurses, promote nursing informatics visibility, or improve and facilitate collaboration and integration with other professions.

  6. 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.

  7. Clinical microbiology informatics.

    PubMed

    Rhoads, Daniel D; Sintchenko, Vitali; Rauch, Carol A; Pantanowitz, Liron

    2014-10-01

    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.

  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. 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.

  10. 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

    2016-07-12

    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.

  11. Innovative designs for the smart ICU: Part 3: Advanced ICU informatics.

    PubMed

    Halpern, Neil A

    2014-04-01

    This third and final installment of this series on innovative designs for the smart ICU addresses the steps involved in conceptualizing, actualizing, using, and maintaining the advanced ICU informatics infrastructure and systems. The smart ICU comprehensively and electronically integrates the patient in the ICU with all aspects of care, displays data in a variety of formats, converts data to actionable information, uses data proactively to enhance patient safety, and monitors the ICU environment to facilitate patient care and ICU management. The keys to success in this complex informatics design process include an understanding of advanced informatics concepts, sophisticated planning, installation of a robust infrastructure capable of both connectivity and interoperability, and implementation of middleware solutions that provide value. Although new technologies commonly appear compelling, they are also complicated and challenging to incorporate within existing or evolving hospital informatics systems. Therefore, careful analysis, deliberate testing, and a phased approach to the implementation of innovative technologies are necessary to achieve the multilevel solutions of the smart ICU.

  12. 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/.

  13. 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

  14. Reflections on biomedical informatics: from cybernetics to genomic medicine and nanomedicine.

    PubMed

    Maojo, Victor; Kulikowski, Casimir A

    2006-01-01

    Expanding on our previous analysis of Biomedical Informatics (BMI), the present perspective ranges from cybernetics to nanomedicine, based on its scientific, historical, philosophical, theoretical, experimental, and technological aspects as they affect systems developments, simulation and modelling, education, and the impact on healthcare. We then suggest that BMI is still searching for strong basic scientific principles around which it can crystallize. As -omic biological knowledge increasingly impacts the future of medicine, ubiquitous computing and informatics become even more essential, not only for the technological infrastructure, but as a part of the scientific enterprise itself. The Virtual Physiological Human and investigations into nanomedicine will surely produce yet more unpredictable opportunities, leading to significant changes in biomedical research and practice. As a discipline involved in making such advances possible, BMI is likely to need to re-define itself and extend its research horizons to meet the new challenges.

  15. 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.

  16. Advances in yeast genome engineering.

    PubMed

    David, Florian; Siewers, Verena

    2015-02-01

    Genome engineering based on homologous recombination has been applied to yeast for many years. However, the growing importance of yeast as a cell factory in metabolic engineering and chassis in synthetic biology demands methods for fast and efficient introduction of multiple targeted changes such as gene knockouts and introduction of multistep metabolic pathways. In this review, we summarize recent improvements of existing genome engineering methods, the development of novel techniques, for example for advanced genome redesign and evolution, and the importance of endonucleases as genome engineering tools.

  17. Advances in targeted genome editing.

    PubMed

    Perez-Pinera, Pablo; Ousterout, David G; Gersbach, Charles A

    2012-08-01

    New technologies have recently emerged that enable targeted editing of genomes in diverse systems. This includes precise manipulation of gene sequences in their natural chromosomal context and addition of transgenes to specific genomic loci. This progress has been facilitated by advances in engineering targeted nucleases with programmable, site-specific DNA-binding domains, including zinc finger proteins and transcription activator-like effectors (TALEs). Recent improvements have enhanced nuclease performance, accelerated nuclease assembly, and lowered the cost of genome editing. These advances are driving new approaches to many areas of biotechnology, including biopharmaceutical production, agriculture, creation of transgenic organisms and cell lines, and studies of genome structure, regulation, and function. Genome editing is also being investigated in preclinical and clinical gene therapies for many diseases.

  18. Manual Gene Ontology annotation workflow at the Mouse Genome Informatics Database.

    PubMed

    Drabkin, Harold J; Blake, Judith A

    2012-01-01

    The Mouse Genome Database, the Gene Expression Database and the Mouse Tumor Biology database are integrated components of the Mouse Genome Informatics (MGI) resource (http://www.informatics.jax.org). The MGI system presents both a consensus view and an experimental view of the knowledge concerning the genetics and genomics of the laboratory mouse. From genotype to phenotype, this information resource integrates information about genes, sequences, maps, expression analyses, alleles, strains and mutant phenotypes. Comparative mammalian data are also presented particularly in regards to the use of the mouse as a model for the investigation of molecular and genetic components of human diseases. These data are collected from literature curation as well as downloads of large datasets (SwissProt, LocusLink, etc.). MGI is one of the founding members of the Gene Ontology (GO) and uses the GO for functional annotation of genes. Here, we discuss the workflow associated with manual GO annotation at MGI, from literature collection to display of the annotations. Peer-reviewed literature is collected mostly from a set of journals available electronically. Selected articles are entered into a master bibliography and indexed to one of eight areas of interest such as 'GO' or 'homology' or 'phenotype'. Each article is then either indexed to a gene already contained in the database or funneled through a separate nomenclature database to add genes. The master bibliography and associated indexing provide information for various curator-reports such as 'papers selected for GO that refer to genes with NO GO annotation'. Once indexed, curators who have expertise in appropriate disciplines enter pertinent information. MGI makes use of several controlled vocabularies that ensure uniform data encoding, enable robust analysis and support the construction of complex queries. These vocabularies range from pick-lists to structured vocabularies such as the GO. All data associations are supported

  19. 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.

  20. 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.

  1. The phytophthora genome initiative database: informatics and analysis for distributed pathogenomic research.

    PubMed

    Waugh, M; Hraber, P; Weller, J; Wu, Y; Chen, G; Inman, J; Kiphart, D; Sobral, B

    2000-01-01

    The Phytophthora Genome Initiative (PGI) is a distributed collaboration to study the genome and evolution of a particularly destructive group of plant pathogenic oomycete, with the goal of understanding the mechanisms of infection and resistance. NCGR provides informatics support for the collaboration as well as a centralized data repository. In the pilot phase of the project, several investigators prepared Phytophthora infestans and Phytophthora sojae EST and Phytophthora sojae BAC libraries and sent them to another laboratory for sequencing. Data from sequencing reactions were transferred to NCGR for analysis and curation. An analysis pipeline transforms raw data by performing simple analyses (i.e., vector removal and similarity searching) that are stored and can be retrieved by investigators using a web browser. Here we describe the database and access tools, provide an overview of the data therein and outline future plans. This resource has provided a unique opportunity for the distributed, collaborative study of a genus from which relatively little sequence data are available. Results may lead to insight into how better to control these pathogens. The homepage of PGI can be accessed at http:www.ncgr.org/pgi, with database access through the database access hyperlink.

  2. Bioimage informatics for experimental biology.

    PubMed

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

    2009-01-01

    Over the past twenty years there have been great advances in light microscopy with the result that multidimensional imaging has driven a revolution in modern biology. The development of new approaches of data acquisition is reported frequently, and yet the significant data management and analysis challenges presented by these new complex datasets remain largely unsolved. As in 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 solutions.

  3. 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.

  4. An information technology emphasis in biomedical informatics education.

    PubMed

    Kane, Michael D; Brewer, Jeffrey L

    2007-02-01

    Unprecedented growth in the interdisciplinary domain of biomedical informatics reflects the recent advancements in genomic sequence availability, high-content biotechnology screening systems, as well as the expectations of computational biology to command a leading role in drug discovery and disease characterization. These forces have moved much of life sciences research almost completely into the computational domain. Importantly, educational training in biomedical informatics has been limited to students enrolled in the life sciences curricula, yet much of the skills needed to succeed in biomedical informatics involve or augment training in information technology curricula. This manuscript describes the methods and rationale for training students enrolled in information technology curricula in the field of biomedical informatics, which augments the existing information technology curriculum and provides training on specific subjects in Biomedical Informatics not emphasized in bioinformatics courses offered in life science programs, and does not require prerequisite courses in the life sciences.

  5. 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

  6. 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.

  7. 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.

  8. Advances on Genome Duplication Distances

    NASA Astrophysics Data System (ADS)

    Gagnon, Yves; Savard, Olivier Tremblay; Bertrand, Denis; El-Mabrouk, Nadia

    Given a phylogenetic tree involving Whole Genome Duplication events, we contribute to the problem of computing the rearrangement distance on a branch of a tree linking a duplication node d to a speciation node or a leaf s. In the case of a genome G at s containing exactly two copies of each gene, the genome halving problem is to find a perfectly duplicated genome D at d minimizing the rearrangement distance with G. We generalize the existing exact linear-time algorithm for genome halving to the case of a genome G with missing gene copies. In the case of a known ancestral duplicated genome D, we develop a greedy approach for computing the distance between G and D that is shown time-efficient and very accurate for both the rearrangement and DCJ distances.

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

    ScienceCinema

    Chain, Patrick [DOE JGI at LANL

    2016-07-12

    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.

  10. Crop genomics: advances and applications

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The completion of reference genome sequences for many important crops and the ability to perform high-throughput resequencing are providing opportunities for improving our understanding of the history of plant domestication and to accelerate crop improvement. Crop plant comparative genomics is being...

  11. 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...

  12. Biomedical informatics and translational medicine.

    PubMed

    Sarkar, Indra Neil

    2010-02-26

    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.

  13. Single Cell Genomics: Advances and Future Perspectives

    PubMed Central

    Macaulay, Iain C.; Voet, Thierry

    2014-01-01

    Advances in whole-genome and whole-transcriptome amplification have permitted the sequencing of the minute amounts of DNA and RNA present in a single cell, offering a window into the extent and nature of genomic and transcriptomic heterogeneity which occurs in both normal development and disease. Single-cell approaches stand poised to revolutionise our capacity to understand the scale of genomic, epigenomic, and transcriptomic diversity that occurs during the lifetime of an individual organism. Here, we review the major technological and biological breakthroughs achieved, describe the remaining challenges to overcome, and provide a glimpse into the promise of recent and future developments. PMID:24497842

  14. 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

  15. 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 ...

  16. 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.

  17. Translational Bioinformatics and Clinical Research (Biomedical) Informatics.

    PubMed

    Sirintrapun, S Joseph; Zehir, Ahmet; Syed, Aijazuddin; Gao, JianJiong; Schultz, Nikolaus; Cheng, Donavan T

    2016-03-01

    Translational bioinformatics and clinical research (biomedical) informatics are the primary domains related to informatics activities that support translational research. Translational bioinformatics focuses on computational techniques in genetics, molecular biology, and systems biology. Clinical research (biomedical) informatics involves the use of informatics in discovery and management of new knowledge relating to health and disease. This article details 3 projects that are hybrid applications of translational bioinformatics and clinical research (biomedical) informatics: The Cancer Genome Atlas, the cBioPortal for Cancer Genomics, and the Memorial Sloan Kettering Cancer Center clinical variants and results database, all designed to facilitate insights into cancer biology and clinical/therapeutic correlations.

  18. Translational Bioinformatics and Clinical Research (Biomedical) Informatics.

    PubMed

    Sirintrapun, S Joseph; Zehir, Ahmet; Syed, Aijazuddin; Gao, JianJiong; Schultz, Nikolaus; Cheng, Donavan T

    2015-06-01

    Translational bioinformatics and clinical research (biomedical) informatics are the primary domains related to informatics activities that support translational research. Translational bioinformatics focuses on computational techniques in genetics, molecular biology, and systems biology. Clinical research (biomedical) informatics involves the use of informatics in discovery and management of new knowledge relating to health and disease. This article details 3 projects that are hybrid applications of translational bioinformatics and clinical research (biomedical) informatics: The Cancer Genome Atlas, the cBioPortal for Cancer Genomics, and the Memorial Sloan Kettering Cancer Center clinical variants and results database, all designed to facilitate insights into cancer biology and clinical/therapeutic correlations.

  19. 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

  20. [Biomedical informatics].

    PubMed

    Capurro, Daniel; Soto, Mauricio; Vivent, Macarena; Lopetegui, Marcelo; Herskovic, Jorge R

    2011-12-01

    Biomedical Informatics is a new discipline that arose from the need to incorporate information technologies to the generation, storage, distribution and analysis of information in the domain of biomedical sciences. This discipline comprises basic biomedical informatics, and public health informatics. The development of the discipline in Chile has been modest and most projects have originated from the interest of individual people or institutions, without a systematic and coordinated national development. Considering the unique features of health care system of our country, research in the area of biomedical informatics is becoming an imperative.

  1. Informatics competencies for nurse practitioners.

    PubMed

    Curran, Christine R

    2003-08-01

    Informatics knowledge and skills are essential if clinicians are to master the large volume of information generated in healthcare today. Thus, it is vital that informatics competencies be defined for nursing and incorporated into both curricula and practice. Staggers, Gassert, and Curran have defined informatics competencies for four general levels of nursing practice. However, informatics competencies by role (eg, those specific for advanced practice nursing) have not been defined and validated. This article presents an initial proposed list of informatics competencies essential for nurse practitioner education and practice. To this list, derived from the work of Staggers et al., 1 has been added informatics competencies related to evidence-based practice. Two nurse informaticists and six nurse practitioners, who are program directors, were involved in the development of the proposed competencies. The next step will be to validate these competencies via research.

  2. Integrating Health Information Technology Safety into Nursing Informatics Competencies.

    PubMed

    Borycki, Elizabeth M; Cummings, Elizabeth; Kushniruk, Andre W; Saranto, Kaija

    2017-01-01

    Nursing informatics competencies are constantly changing in response to advances in the health information technology (HIT) industry and research emerging from the fields of nursing and health informatics. In this paper we build off the work of Staggers and colleagues in defining nursing informatics competencies at five levels: the beginning nurse, the experienced nurse, the nursing informatics specialist, the nursing informatics innovator and the nursing informatics researcher in the area of HIT safety. The work represents a significant contribution to the literature in the area of nursing informatics competency development as it extends nursing informatics competencies to include those focused on the area of technology-induced errors and HIT safety.

  3. Advances in Swine Biomedical Model Genomics

    PubMed Central

    Lunney, Joan K.

    2007-01-01

    This review 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 progression. The pig model allows for deliberately timed studies, imaging of internal vessels and organs using standard human technologies, and collection of repeated peripheral samples and, at kill, detailed mucosal tissues. The ability to use pigs from the same litter, or cloned or transgenic pigs, facilitates comparative analyses and genetic mapping. The availability of numerous well defined cell lines, representing a broad range of tissues, further facilitates testing of gene expression, drug susceptibility, etc. Thus the pig is an excellent biomedical model for humans. For genomic applications it is an asset that the pig genome has high sequence and chromosome structure homology with humans. With the swine genome sequence now well advanced there are improving genetic and proteomic tools for these comparative analyses. The review will discuss some of the genomic approaches used to probe these models. The review will highlight genomic studies of melanoma and of infectious disease resistance, discussing issues to consider in designing such studies. It will end with a short discussion of the potential for genomic approaches to develop new alternatives for control of the most economically important disease of pigs, porcine reproductive and respiratory syndrome (PRRS), and the potential for applying knowledge gained with this virus for human viral infectious disease studies. PMID:17384736

  4. 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

  5. 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…

  6. 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.

  7. 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

  8. Advances in health informatics education: educating students at the intersection of health care and information technology.

    PubMed

    Kushniruk, Andre; Borycki, Elizabeth; Armstrong, Brian; Kuo, Mu-Hsing

    2012-01-01

    The paper describes the authors' work in the area of health informatics (HI) education involving emerging health information technologies. A range of information technologies promise to modernize health care. Foremost among these are electronic health records (EHRs), which are expected to significantly improve and streamline health care practice. Major national and international efforts are currently underway to increase EHR adoption. However, there have been numerous issues affecting the widespread use of such information technology, ranging from a complex array of technical problems to social issues. This paper describes work in the integration of information technologies directly into the education and training of HI students at both the undergraduate and graduate level. This has included work in (a) the development of Web-based computer tools and platforms to allow students to have hands-on access to the latest technologies and (b) development of interdisciplinary educational models that can be used to guide integrating information technologies into HI education. The paper describes approaches that allow for remote hands-on access by HI students to a range of EHRs and related technology. To date, this work has been applied in HI education in a variety of ways. Several approaches for integration of this essential technology into HI education and training are discussed, along with future directions for the integration of EHR technology into improving and informing the education of future health and HI professionals.

  9. Facilitating the iterative design of informatics tools to advance the science of autism.

    PubMed

    Kaufman, David R; Cronin, Patrick; Rozenblit, Leon; Voccola, David; Horton, Amanda; Shine, Alisabeth; Johnson, Stephen B

    2011-01-01

    This paper describes a usability evaluation study of an innovative first generation system (Data Dig) designed to retrieve phenotypic data from the large SFARI data set of 2700 families each of which has one child affected with autism spectrum disorder. The usability methods included a cognitive walkthrough and usability testing. Although the subjects were able to learn to use the system, more than 50 usability problems of varying severity were noted. The problems with the greatest frequency resulted from users being unable to understand meanings of variables, filter categories correctly, use the Boolean filter, and correctly interpret the feedback provided by the system. Subjects had difficulty forming a mental model of the organizational system underlying the database. This precluded them from making informed navigation choices while formulating queries. Clinical research informatics is a new and immensely promising discipline. However in its nascent stage, it lacks a stable interaction paradigm to support a range of users on pertinent tasks. This presents great opportunity for researchers to further this science by harnessing the powers of user-centered iterative design.

  10. 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

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

    ScienceCinema

    Simpson, Jared [Wellcome Trust Sanger Institute

    2016-07-12

    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

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

    ScienceCinema

    Dehal, Paramvir [LBNL

    2016-07-12

    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.

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

    ScienceCinema

    Mavrommatis, Kostas [JGI

    2016-07-12

    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.

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

    ScienceCinema

    Kyrpides, Nikos [DOE JGI

    2016-07-12

    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

  15. Open source bioimage informatics for cell biology.

    PubMed

    Swedlow, Jason R; Eliceiri, Kevin W

    2009-11-01

    Significant technical advances in imaging, molecular biology and genomics have fueled a revolution in cell biology, in that the molecular and structural processes of the cell are now visualized and measured routinely. Driving much of this recent development has been the advent of computational tools for the acquisition, visualization, analysis and dissemination of these datasets. These tools collectively make up a new subfield of computational biology called bioimage informatics, which is facilitated by open source approaches. We discuss why open source tools for image informatics in cell biology are needed, some of the key general attributes of what make an open source imaging application successful, and point to opportunities for further operability that should greatly accelerate future cell biology discovery.

  16. 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.

  17. 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

  18. 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…

  19. Advances in genomics for flatfish aquaculture.

    PubMed

    Cerdà, Joan; Manchado, Manuel

    2013-01-01

    Fish aquaculture is considered to be one of the most sustainable sources of protein for humans. Many different species are cultured worldwide, but among them, marine flatfishes comprise a group of teleosts of high commercial interest because of their highly prized white flesh. However, the aquaculture of these fishes is seriously hampered by the scarce knowledge on their biology. In recent years, various experimental 'omics' approaches have been applied to farmed flatfishes to increment the genomic resources available. These tools are beginning to identify genetic markers associated with traits of commercial interest, and to unravel the molecular basis of different physiological processes. This article summarizes recent advances in flatfish genomics research in Europe. We focus on the new generation sequencing technologies, which can produce a massive amount of DNA sequencing data, and discuss their potentials and applications for de novo genome sequencing and transcriptome analysis. The relevance of these methods in nutrigenomics and foodomics approaches for the production of healthy animals, as well as high quality and safety products for the consumer, is also briefly discussed.

  20. A Web Portal that Enables Collaborative Use of Advanced Medical Image Processing and Informatics Tools through the Biomedical Informatics Research Network (BIRN)

    PubMed Central

    Murphy, Shawn N.; Mendis, Michael E.; Grethe, Jeffrey S.; Gollub, Randy L.; Kennedy, David; Rosen, Bruce R.

    2006-01-01

    Launched in 2001, the Biomedical Informatics Research Network (BIRN; http://www.nbirn.net) is an NIH – NCRR initiative that enables researchers to collaborate in an environment for biomedical research and clinical information management, focused particularly upon medical imaging. Although it supports a vast array of programs to transform and calculate upon medical images, three fundamental problems emerged that inhibited collaborations. The first was that the complexity of the programs, and at times legal restrictions, combined to prohibit these programs from being accessible to all members of the teams and indeed the general researcher, although this was a fundamental mission of the BIRN. Second, the calculations that needed to be performed were very complex, and required many steps that often needed to be performed by different groups. Third, many of the analysis programs were not interoperable. These problems combined to created tremendous logistical problems. The solution was to create a portal-based workflow application that allowed the complex, collaborative tasks to take place and enabled new kinds of calculations that had not previously been practical. PMID:17238407

  1. Advances in the translational genomics of neuroblastoma

    PubMed Central

    Bosse, Kristopher R.; Maris, John M.

    2015-01-01

    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, which has catalyzed not only a more comprehensive understanding of neuroblastoma tumorigenesis, but has also revealed novel oncogenic vulnerabilities that are being leveraged therapeutically. Neuroblastoma is a model pediatric solid tumor in its use of recurrent genomic alterations, such as high-level MYCN 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 towards aberrantly regulated pathways in relapsed disease. This review will summarize the current state of knowledge of 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. Exploiting HPC Platforms for Metagenomics: Challenges and Opportunities (MICW - Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    ScienceCinema

    Canon, Shane [LBNL

    2016-07-12

    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.

  3. Advancing oral medicine through informatics and information technology: a proposed framework and strategy.

    PubMed

    Schleyer, T; Mattsson, U; Ní Ríordáin, R; Brailo, V; Glick, M; Zain, R B; Jontell, M

    2011-04-01

    The implementation of information technology in healthcare is a significant focus for many nations around the world. However, information technology support for clinical care, research and education in oral medicine is currently poorly developed. This situation hampers our ability to transform oral medicine into a 'learning healthcare discipline' in which the divide between clinical practice and research is diminished and, ultimately, eliminated. This paper reviews the needs of and requirements for information technology support of oral medicine and proposes an agenda designed to meet those needs. For oral medicine, this agenda includes analyzing and reviewing current clinical and documentation practices, working toward progressively standardizing clinical data, and helping define requirements for oral medicine systems. IT professionals can contribute by conducting baseline studies about the use of electronic systems, helping develop controlled vocabularies and ontologies, and designing, implementing, and evaluating novel systems centered on the needs of clinicians, researchers and educators. Successfully advancing IT support for oral medicine will require close coordination and collaboration among oral medicine professionals, information technology professionals, system vendors, and funding agencies. If current barriers and obstacles are overcome, practice and research in oral medicine stand ready to derive significant benefits from the application of information technology.

  4. 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;…

  5. 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.

  6. 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...

  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. 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

  9. 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.

  10. Advances in Arachis genomics for peanut improvement.

    PubMed

    Pandey, Manish K; Monyo, Emmanuel; Ozias-Akins, Peggy; Liang, Xuanquiang; Guimarães, Patricia; Nigam, Shyam N; Upadhyaya, Hari D; Janila, Pasupuleti; Zhang, Xinyou; Guo, Baozhu; Cook, Douglas R; Bertioli, David J; Michelmore, Richard; Varshney, Rajeev K

    2012-01-01

    Peanut genomics is very challenging due to its inherent problem of genetic architecture. Blockage of gene flow from diploid wild relatives to the tetraploid; cultivated peanut, recent polyploidization combined with self pollination, and the narrow genetic base of the primary genepool have resulted in low genetic diversity that has remained a major bottleneck for genetic improvement of peanut. Harnessing the rich source of wild relatives has been negligible due to differences in ploidy level as well as genetic drag and undesirable alleles for low yield. Lack of appropriate genomic resources has severely hampered molecular breeding activities, and this crop remains among the less-studied crops. The last five years, however, have witnessed accelerated development of genomic resources such as development of molecular markers, genetic and physical maps, generation of expressed sequenced tags (ESTs), development of mutant resources, and functional genomics platforms that facilitate the identification of QTLs and discovery of genes associated with tolerance/resistance to abiotic and biotic stresses and agronomic traits. Molecular breeding has been initiated for several traits for development of superior genotypes. The genome or at least gene space sequence is expected to be available in near future and this will further accelerate use of biotechnological approaches for peanut improvement.

  11. 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

  12. 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

  13. 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

  14. 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

  15. Advances in biotechnology and genomics of switchgrass.

    PubMed

    Nageswara-Rao, Madhugiri; Soneji, Jaya R; Kwit, Charles; Stewart, C Neal

    2013-05-12

    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.

  16. IPHIE: an International Partnership in Health Informatics Education.

    PubMed

    Jaspers, M W; Gardner, R M; Gatewood, L C; Haux, R; Leven, F J; Limburg, M; Ravesloot, J H; Schmidt, D; Wetter, T

    2000-01-01

    Medical informatics contributes significantly to high quality and efficient health care and medical research. The need for well educated professionals in the field of medical informatics therefore is now worldwide recognized. Students of medicine, computer science/informatics are educated in the field of medical informatics and dedicated curricula on medical informatics have emerged. To advance and further develop the beneficial role of medical informatics in the medical field, an international orientation of health and medical informatics students seems an indispensable part of their training. An international orientation and education of medical informatics students may help to accelerate the dissemination of acquired knowledge and skills in the field and the promotion of medical informatics research results on a more global level. Some years ago, the departments of medical informatics of the university of Heidelberg/university of applied sciences Heilbronn and the university of Amsterdam decided to co-operate in the field of medical informatics. Now, this co-operation has grown out to an International Partnership of Health Informatics Education (IPHIE) of 5 universities, i.e. the university of Heidelberg, the university of Heilbronn, the university of Minnesota, the university of Utah and the university of Amsterdam. This paper presents the rationale behind this international partnership, the state of the art of the co-operation and our future plans for expanding this international co-operation.

  17. 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

  18. A survey of informatics approaches to whole-exome and whole-genome clinical reporting in the electronic health record

    PubMed Central

    Tarczy-Hornoch, Peter; Amendola, Laura; Aronson, Samuel J.; Garraway, Levi; Gray, Stacy; Grundmeier, Robert W.; Hindorff, Lucia A.; Jarvik, Gail; Karavite, Dean; Lebo, Matthew; Plon, Sharon E.; Van Allen, Eliezer; Weck, Karen E.; White, Peter S.; Yang, Yaping

    2014-01-01

    Purpose Genome-scale clinical sequencing is being adopted more broadly in medical practice. The National Institutes of Health developed the Clinical Sequencing Exploratory Research (CSER) program to guide implementation and dissemination of best practices for the integration of sequencing into clinical care. This study describes and compares the state of the art of incorporating whole-exome and whole-genome sequencing results into the electronic health record, including approaches to decision support across the six current CSER sites. Methods The CSER Medical Record Working Group collaboratively developed and completed an in-depth survey to assess the communication of genome-scale data into the electronic health record. We summarized commonalities and divergent approaches. Results Despite common sequencing platform (Illumina) adoptions, there is a great diversity of approaches to annotation tools and workflow, as well as to report generation. At all sites, reports are human-readable structured documents available as passive decision support in the electronic health record. Active decision support is in early implementation at two sites. Conclusion The parallel efforts across CSER sites in the creation of systems for report generation and integration of reports into the electronic health record, as well as the lack of standardized approaches to interfacing with variant databases to create active clinical decision support, create opportunities for cross-site and vendor collaborations. PMID:24071794

  19. Nursing informatics, outcomes, and quality improvement.

    PubMed

    Charters, Kathleen G

    2003-08-01

    Nursing informatics actively supports nursing by providing standard language systems, databases, decision support, readily accessible research results, and technology assessments. Through normalized datasets spanning an entire enterprise or other large demographic, nursing informatics tools support improvement of healthcare by answering questions about patient outcomes and quality improvement on an enterprise scale, and by providing documentation for business process definition, business process engineering, and strategic planning. Nursing informatics tools provide a way for advanced practice nurses to examine their practice and the effect of their actions on patient outcomes. Analysis of patient outcomes may lead to initiatives for quality improvement. Supported by nursing informatics tools, successful advance practice nurses leverage their quality improvement initiatives against the enterprise strategic plan to gain leadership support and resources.

  20. 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

    2016-07-12

    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.

  1. 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

    2016-07-12

    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.

  2. 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

    2016-07-12

    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.

  3. Recent advances in targeted genome engineering in mammalian systems.

    PubMed

    Sun, Ning; Abil, Zhanar; Zhao, Huimin

    2012-09-01

    Targeted genome engineering enables researchers to disrupt, insert, or replace a genomic sequence precisely at a predetermined locus. One well-established technology to edit a mammalian genome is known as gene targeting, which is based on the homologous recombination (HR) mechanism. However, the low HR frequency in mammalian cells (except for mice) prevents its wide application. To address this limitation, a custom-designed nuclease is used to introduce a site-specific DNA double-strand break (DSB) on the chromosome and the subsequent repair of the DSB by the HR mechanism or the non-homologous end joining mechanism results in efficient targeted genome modifications. Engineered homing endonucleases (also called meganucleases), zinc finger nucleases, and transcription activator-like effector nucleases represent the three major classes of custom-designed nucleases that have been successfully applied in many different organisms for targeted genome engineering. This article reviews the recent developments of these genome engineering tools and highlights a few representative applications in mammalian systems. Recent advances in gene delivery strategies of these custom-designed nucleases are also briefly discussed.

  4. Recent advances in tomato functional genomics: utilization of VIGS.

    PubMed

    Sahu, Pranav Pankaj; Puranik, Swati; Khan, Moinuddin; Prasad, Manoj

    2012-10-01

    Tomato unquestionably occupies a significant position in world vegetable production owing to its world-wide consumption. The tomato genome sequencing efforts being recently concluded, it becomes more imperative to recognize important functional genes from this treasure of generated information for improving tomato yield. While much progress has been made in conventional tomato breeding, post-transcriptional gene silencing (PTGS) offers an alternative approach for advancement of tomato functional genomics. In particular, virus-induced gene silencing (VIGS) is increasingly being used as rapid, reliable, and lucrative screening strategy to elucidate gene function. In this review, we focus on the recent advancement made through exploiting the potential of this technique for manipulating different agronomically important traits in tomato by discussing several case studies.

  5. Advances in genome studies in plants and animals.

    PubMed

    Appels, R; Nystrom-Persson, J; Keeble-Gagnere, G

    2014-03-01

    The area of plant and animal genomics covers the entire suite of issues in biology because it aims to determine the structure and function of genetic material. Although specific issues define research advances at an organism level, it is evident that many of the fundamental features of genome structure and the translation of encoded information to function share common ground. The Plant and Animal Genome (PAG) conference held in San Diego (California), in January each year provides an overview across all organisms at the genome level, and often it is evident that investments in the human area provide leadership, applications, and discoveries for researchers studying other organisms. This mini-review utilizes the plenary lectures as a basis for summarizing the trends in the genome-level studies of organisms, and the lectures include presentations by Ewan Birney (EBI, UK), Eric Green (NIH, USA), John Butler (NIST, USA), Elaine Mardis (Washington, USA), Caroline Dean (John Innes Centre, UK), Trudy Mackay (NC State University, USA), Sue Wessler (UC Riverside, USA), and Patrick Wincker (Genoscope, France). The work reviewed is based on published papers. Where unpublished information is cited, permission to include the information in this manuscript was obtained from the presenters.

  6. 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.

  7. 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.

  8. Translational informatics: an industry perspective.

    PubMed

    Cantor, Michael N

    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.

  9. 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

  10. Office of Biological Informatics and Outreach geospatial technology activities

    USGS Publications Warehouse

    ,

    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.

  11. 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

  12. 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

    2016-07-12

    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)

    ScienceCinema

    Stepanauskas, Ramunas [Bigelow Laboratory

    2016-07-12

    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. 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

  15. Comprehensive Genomic Profiling of Advanced Penile Carcinoma Suggests a High Frequency of Clinically Relevant Genomic Alterations

    PubMed Central

    Pal, Sumanta K.; Wang, Kai; Palma, Norma A.; Sanford, Eric; Bailey, Mark; He, Jie; Elvin, Julia A.; Chmielecki, Juliann; Squillace, Rachel; Dow, Edward; Morosini, Deborah; Buell, Jamie; Yelensky, Roman; Lipson, Doron; Frampton, Garrett M.; Howley, Peter; Ross, Jeffrey S.; Stephens, Philip J.; Miller, Vincent A.

    2016-01-01

    Background. Advanced penile squamous cell carcinoma (PSCC) is associated with poor survival due to the aggressiveness of the disease and lack of effective systemic therapies. Comprehensive genomic profiling (CGP) was performed to identify clinically relevant genomic alterations (CRGAs). Materials and Methods. DNA was extracted from 40 μm of formalin-fixed, paraffin-embedded sections in patients with advanced PSCC. CGP was performed on hybridization-captured, adaptor ligation-based libraries to a mean coverage depth of 692× for 3,769 exons of 236 cancer-related genes plus 47 introns from 19 genes frequently rearranged in cancer. CRGAs were defined as genomic alterations (GAs) linked to targeted therapies on the market or under evaluation in mechanism-driven clinical trials. Results. Twenty male patients with a median age of 60 years (range, 46–87 years) were assessed. Seventeen (85%) cases were stage IV and three cases (15%) were stage III. CGP revealed 109 GAs (5.45 per tumor), 44 of which were CRGAs (2.2 per tumor). At least one CRGA was detected in 19 (95%) cases, and the most common CRGAs were CDKN2A point mutations and homozygous deletion (40%), NOTCH1 point mutations and rearrangements (25%), PIK3CA point mutations and amplification (25%), EGFR amplification (20%), CCND1 amplification (20%), BRCA2 insertions/deletions (10%), RICTOR amplifications (10%), and FBXW7 point mutations (10%). Conclusion. CGP identified CRGAs in patients with advanced PSCC, including EGFR amplification and PIK3CA alterations, which can lead to the rational administration of targeted therapy and subsequent benefit for these patients. Implications for Practice: Few treatment options exist for patients with advanced penile squamous cell carcinoma (PSCC). Outcomes are dismal with platinum-based chemotherapy, with median survival estimated at 1 year or less across multiple series. Biological studies of patients with PSCC to date have principally focused on human papillomavirus status

  16. 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.

  17. Advances in Pig Genomics and Functional Gene Discovery

    PubMed Central

    2003-01-01

    Advances in pig gene identification, mapping and functional analysis have continued to make rapid progress. The porcine genetic linkage map now has nearly 3000 loci, including several hundred genes, and is likely to expand considerably in the next few years, with many more genes and amplified fragment length polymorphism (AFLP) markers being added to the map. The physical genetic map is also growing rapidly and has over 3000 genes and markers. Several recent quantitative trait loci (QTL) scans and candidate gene analyses have identified important chromosomal regions and individual genes associated with traits of economic interest. The commercial pig industry is actively using this information and traditional performance information to improve pig production by marker-assisted selection (MAS). Research to study the co-expression of thousands of genes is now advancing and methods to combine these approaches to aid in gene discovery are under way. The pig's role in xenotransplantation and biomedical research makes the study of its genome important for the study of human disease. This review will briefly describe advances made, directions for future research and the implications for both the pig industry and human health. PMID:18629119

  18. 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.

  19. Convergence of advances in genomics, team science, and repositories as drivers of progress in psychiatric genomics.

    PubMed

    Lehner, Thomas; Senthil, Geetha; Addington, Anjené M

    2015-01-01

    After many years of unfilled promise, psychiatric genetics has seen an unprecedented number of successes in recent years. We hypothesize that the field has reached an inflection point through a confluence of four key developments: advances in genomics; the orientation of the scientific community around large collaborative team science projects; the development of sample and data repositories; and a policy framework for sharing and accessing these resources. We discuss these domains and their effect on scientific progress and provide a perspective on why we think this is only the beginning of a new era in scientific discovery.

  20. Investigating Informatics Activity, Control, and Training Needs in Large, Medium, and Small Health Departments

    PubMed Central

    Arnold, Ryan; Yang, Biru

    2016-01-01

    Introduction: A recent National Association of City & County Health Officials survey shed light on informatics workforce development needs. Local health departments (LHDs) of various jurisdictional sizes and control over informatics may differ on training needs and activity. Understanding the precise nature of this variation will allow stakeholders to appropriately develop workforce development tools to advance the field. Objective: To understand the informatics training needs for LHDs of different jurisdictional sizes. Methods: Survey responses were analyzed by comparing training needs and LHD population size. Results: Larger health departments consistently reported having greater informatics-related capacity and informatics-related training needs. Quantitative data analysis was identified as a primary need for large LHDs. In addition, LHDs that report higher control of informatics/information technology were able to engage in more informatics activities. Conclusion: Smaller LHDs need additional resources to improve informatics-related capacity and engagement with the field. PMID:27684621

  1. 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

  2. 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.

  3. Advances in Exercise, Fitness, and Performance Genomics in 2012

    PubMed Central

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

    2013-01-01

    A small number of excellent papers on exercise genomics issues have been 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 (BMI) 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. 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 ENCODE project. PMID:23470294

  4. 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

  5. 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.

  6. 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

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

    ScienceCinema

    Rokhsar, Daniel

    2016-07-12

    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.

  8. 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.

  9. What is biomedical informatics?

    PubMed

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

    2010-02-01

    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.

  10. Lost and found in behavioral informatics.

    PubMed

    Haendel, Melissa A; Chesler, Elissa J

    2012-01-01

    From early anatomical lesion studies to the molecular and cellular methods of today, a wealth of technologies have provided increasingly sophisticated strategies for identifying and characterizing the biological basis of behaviors. Bioinformatics is a growing discipline that has emerged from the practical needs of modern biology, and the history of systematics and ontology in data integration and scientific knowledge construction. This revolution in biology has resulted in a capability to couple the rich molecular, anatomical, and psychological assays with advances in data dissemination and integration. However, behavioral science poses unique challenges for biology and medicine, and many unique resources have been developed to take advantage of the strategies and technologies of an informatics approach. The collective developments of this diverse and interdisciplinary field span the fundamentals of database development and data integration, ontology development, text mining, genetics, genomics, high-throughput analytics, image analysis and archiving, and numerous others. For the behavioral sciences, this provides a fundamental shift in our ability to associate and dissociate behavioral processes and relate biological and behavioral entities, thereby pinpointing the biological basis of behavior.

  11. What Is Primary Care Informatics?

    PubMed Central

    de Lusignan, Simon

    2003-01-01

    Primary care informatics is an emerging academic discipline that remains undefined. The unique nature of primary care necessitates the development of its own informatics discipline. A definition of primary care informatics is proposed, which encompasses the distinctive nature of primary care. The core concepts and theory that should underpin it are described. Primary care informatics is defined as a science and as a subset of health informatics. The proposed definition is intended to focus the development of a generalizable core theory for this informatics subspecialty. PMID:12668690

  12. 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

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

    PubMed

    Cherry, J Michael

    2015-12-02

    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.

  14. 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

  15. 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…

  16. Quantum Approach to Informatics

    NASA Astrophysics Data System (ADS)

    Stenholm, Stig; Suominen, Kalle-Antti

    2005-08-01

    An essential overview of quantum information Information, whether inscribed as a mark on a stone tablet or encoded as a magnetic domain on a hard drive, must be stored in a physical object and thus made subject to the laws of physics. Traditionally, information processing such as computation occurred in a framework governed by laws of classical physics. However, information can also be stored and processed using the states of matter described by non-classical quantum theory. Understanding this quantum information, a fundamentally different type of information, has been a major project of physicists and information theorists in recent years, and recent experimental research has started to yield promising results. Quantum Approach to Informatics fills the need for a concise introduction to this burgeoning new field, offering an intuitive approach for readers in both the physics and information science communities, as well as in related fields. Only a basic background in quantum theory is required, and the text keeps the focus on bringing this theory to bear on contemporary informatics. Instead of proofs and other highly formal structures, detailed examples present the material, making this a uniquely accessible introduction to quantum informatics. Topics covered include: * An introduction to quantum information and the qubit * Concepts and methods of quantum theory important for informatics * The application of information concepts to quantum physics * Quantum information processing and computing * Quantum gates * Error correction using quantum-based methods * Physical realizations of quantum computing circuits A helpful and economical resource for understanding this exciting new application of quantum theory to informatics, Quantum Approach to Informatics provides students and researchers in physics and information science, as well as other interested readers with some scientific background, with an essential overview of the field.

  17. 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

  18. How advances in genomics are changing patient care.

    PubMed

    Bancroft, Elizabeth K

    2013-12-01

    The completion of the Human Genome Project has led to a greater understanding of the role of genetics/genomics in the development of all common diseases, which is leading to the routine integration of genetics and genomics into all aspects of health care. This change in practice presents new challenges for health care professionals. This article provides an overview of how genetics/genomics has the potential to improve health care within many different clinical scenarios, and highlights the key issues for nurses working in a variety of settings.

  19. 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

  20. Mouse genome database 2016.

    PubMed

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

    2016-01-04

    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.

  1. RAS - Target Identification - Informatics

    Cancer.gov

    The RAS Informatics lab group develops tools to track and analyze “big data” from the RAS Initiative, as well as analyzes data from external projects. By integrating internal and external data, this group helps improve understanding of RAS-driven cancers.

  2. 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,…

  3. Recent advances in genome-based polyketide discovery.

    PubMed

    Helfrich, Eric J N; Reiter, Silke; Piel, Jörn

    2014-10-01

    Polyketides are extraordinarily diverse secondary metabolites of great pharmacological value and with interesting ecological functions. The post-genomics era has led to fundamental changes in natural product research by inverting the workflow of secondary metabolite discovery. As opposed to traditional bioactivity-guided screenings, genome mining is an in silico method to screen and analyze sequenced genomes for natural product biosynthetic gene clusters. Since genes for known compounds can be recognized at the early computational stage, genome mining presents an opportunity for dereplication. This review highlights recent progress in bioinformatics, pathway engineering and chemical analytics to extract the biosynthetic secrets hidden in the genome of both well-known natural product sources as well as previously neglected bacteria.

  4. 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.

  5. Overview on the Role of Advance Genomics in Conservation Biology of Endangered Species.

    PubMed

    Khan, Suliman; Nabi, Ghulam; Ullah, Muhammad Wajid; Yousaf, Muhammad; Manan, Sehrish; Siddique, Rabeea; Hou, Hongwei

    2016-01-01

    In the recent era, due to tremendous advancement in industrialization, pollution and other anthropogenic activities have created a serious scenario for biota survival. It has been reported that present biota is entering a "sixth" mass extinction, because of chronic exposure to anthropogenic activities. Various ex situ and in situ measures have been adopted for conservation of threatened and endangered plants and animal species; however, these have been limited due to various discrepancies associated with them. Current advancement in molecular technologies, especially, genomics, is playing a very crucial role in biodiversity conservation. Advance genomics helps in identifying the segments of genome responsible for adaptation. It can also improve our understanding about microevolution through a better understanding of selection, mutation, assertive matting, and recombination. Advance genomics helps in identifying genes that are essential for fitness and ultimately for developing modern and fast monitoring tools for endangered biodiversity. This review article focuses on the applications of advanced genomics mainly demographic, adaptive genetic variations, inbreeding, hybridization and introgression, and disease susceptibilities, in the conservation of threatened biota. In short, it provides the fundamentals for novice readers and advancement in genomics for the experts working for the conservation of endangered plant and animal species.

  6. Overview on the Role of Advance Genomics in Conservation Biology of Endangered Species

    PubMed Central

    Khan, Suliman; Nabi, Ghulam; Ullah, Muhammad Wajid; Yousaf, Muhammad; Manan, Sehrish; Siddique, Rabeea

    2016-01-01

    In the recent era, due to tremendous advancement in industrialization, pollution and other anthropogenic activities have created a serious scenario for biota survival. It has been reported that present biota is entering a “sixth” mass extinction, because of chronic exposure to anthropogenic activities. Various ex situ and in situ measures have been adopted for conservation of threatened and endangered plants and animal species; however, these have been limited due to various discrepancies associated with them. Current advancement in molecular technologies, especially, genomics, is playing a very crucial role in biodiversity conservation. Advance genomics helps in identifying the segments of genome responsible for adaptation. It can also improve our understanding about microevolution through a better understanding of selection, mutation, assertive matting, and recombination. Advance genomics helps in identifying genes that are essential for fitness and ultimately for developing modern and fast monitoring tools for endangered biodiversity. This review article focuses on the applications of advanced genomics mainly demographic, adaptive genetic variations, inbreeding, hybridization and introgression, and disease susceptibilities, in the conservation of threatened biota. In short, it provides the fundamentals for novice readers and advancement in genomics for the experts working for the conservation of endangered plant and animal species. PMID:28025636

  7. 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.

  8. [Advances of genome and secondary metabolism in Streptomyces].

    PubMed

    Wu, Xue-Chang; Miao, Ke-Pai; Qian, Kai-Xian

    2005-11-01

    Streptomycetes are Gram-positive, soil-inhabiting bacteria of Actinomycetales. These organisms exhibit complex life cycle and secondary metabolic pathways, and produce many economically important secondary metabolites. This review presented recent progress in Streptomycetes chromosome structure,genomics and the research of secondary metabolic pathway in Streptomyces. As more genomic sequences become available, it wiil be greatly facilitated to elucidate metabolic and regulatory networks and gain the over-production of desired metabolites or create the novel production of commercially important compounds.

  9. 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.

  10. 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

  11. Parallel computing in genomic research: advances and applications.

    PubMed

    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.

  12. Biomedical informatics: changing what physicians need to know and how they learn.

    PubMed

    Stead, William W; Searle, John R; Fessler, Henry E; Smith, Jack W; Shortliffe, Edward H

    2011-04-01

    The explosive growth of biomedical complexity calls for a shift in the paradigm of medical decision making-from a focus on the power of an individual brain to the collective power of systems of brains. This shift alters professional roles and requires biomedical informatics and information technology (IT) infrastructure. The authors illustrate this future role of medical informatics with a vignette and summarize the evolving understanding of both beneficial and deleterious effects of informatics-rich environments on learning, clinical care, and research. The authors also provide a framework of core informatics competencies for health professionals of the future and conclude with broad steps for faculty development. They recommend that medical schools advance on four fronts to prepare their faculty to teach in a biomedical informatics-rich world: (1) create academic units in biomedical informatics; (2) adapt the IT infrastructure of academic health centers (AHCs) into testing laboratories; (3) introduce medical educators to biomedical informatics sufficiently for them to model its use; and (4) retrain AHC faculty to lead the transformation to health care based on a new systems approach enabled by biomedical informatics. The authors propose that embracing this collective and informatics-enhanced future of medicine will provide opportunities to advance education, patient care, and biomedical science.

  13. Advances in silkworm studies accelerated by the genome sequencing of Bombyx mori.

    PubMed

    Xia, Qingyou; Li, Sheng; Feng, Qili

    2014-01-01

    Significant progress has been achieved in silkworm (Bombyx mori) research since the last review on this insect was published in this journal in 2005. In this article, we review the new and exciting progress and discoveries that have been made in B. mori during the past 10 years, which include the construction of a fine genome sequence and a genetic variation map, the evolution of genomes, the advent of functional genomics, the genetic basis of silk production, metamorphic development, immune response, and the advances in genetic manipulation. These advances, which were accelerated by the genome sequencing project, have promoted B. mori as a model organism not only for lepidopterans but also for general biology.

  14. 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.

  15. A primer on precision medicine informatics.

    PubMed

    Sboner, Andrea; Elemento, Olivier

    2016-01-01

    In this review, we describe key components of a computational infrastructure for a precision medicine program that is based on clinical-grade genomic sequencing. Specific aspects covered in this review include software components and hardware infrastructure, reporting, integration into Electronic Health Records for routine clinical use and regulatory aspects. We emphasize informatics components related to reproducibility and reliability in genomic testing, regulatory compliance, traceability and documentation of processes, integration into clinical workflows, privacy requirements, prioritization and interpretation of results to report based on clinical needs, rapidly evolving knowledge base of genomic alterations and clinical treatments and return of results in a timely and predictable fashion. We also seek to differentiate between the use of precision medicine in germline and cancer.

  16. Technological Ecosystems in Health Informatics: A Brief Review Article

    PubMed Central

    WU, Zhongmei; ZHANG, Xiuxiu; CHEN, Ying; ZHANG, Yan

    2016-01-01

    Background: The existing models of information technology in health sciences have full scope of betterment and extension. The high demand pressures, public expectations, advanced platforms all collectively contribute towards hospital environment, which has to be kept in kind while designing of advanced technological ecosystem for information technology. Moreover, for the smooth conduct and operation of information system advanced management avenues are also essential in hospitals. It is the top priority of every hospital to deal with the essential needs of care for patients within the available resources of human and financial outputs. In these situations of high demand, the technological ecosystems in health informatics come in to play and prove its importance and role. The present review article would enlighten all these aspects of these ecosystems in hospital management and health care informatics. Methods: We searched the electronic database of MEDLINE, EMBASE, and PubMed for clinical controlled trials, pre-clinical studies reporting utilizaiono of ecosysyem advances in health information technology. Results: The primary outcome of eligible studies included confirmation of importance and role of advances ecosystems in health informatics. It was observed that technological ecosystems are the backbone of health informatics. Conclusion: Advancements in technological ecosystems are essential for proper functioning of health information system in clinical setting. PMID:27957459

  17. 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.

  18. 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…

  19. Advances in mRNA Silencing and Transgene Expression: a Gateway to Functional Genomics in Schistosomes

    PubMed Central

    Tchoubrieva, Elissaveta B.; Kalinna, Bernd H.

    2013-01-01

    The completion of the WHO Schistosoma Genome Project in 2008, although not fully annotated, provides a golden opportunity to actively pursue fundamental research on the parasites genome. This analysis will aid identification of targets for drugs, vaccines and markers for diagnostic tools as well as for studying the biological basis of drug resistance, infectivity and pathology. For the validation of drug and vaccine targets, the genomic sequence data is only of use if functional analyses can be conducted (in the parasite itself). Until recently, gene manipulation approaches had not been seriously addressed. This situation is now changing and rapid advances have been made in gene silencing and transgenesis of schistosomes. PMID:21415884

  20. Informatics applied to cytology.

    PubMed

    Pantanowitz, Liron; Hornish, Maryanne; Goulart, Robert A

    2008-12-29

    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.

  1. 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

  2. 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.

  3. Advances in Induced Pluripotent Stem Cells, Genomics, Biomarkers, and Antiplatelet Therapy

    PubMed Central

    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.

    2014-01-01

    The Journal provides the clinician and scientist with the latest advances in discovery research, emerging technologies, pre-clinical research design and testing, and clinical trials. We highlight advances in areas of induced pluripotent stem cells, genomics, biomarkers, multi-modality 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

  4. Evaluation of biomedical informatics innovations and their impact on public health.

    PubMed

    Sarkar, I N

    2012-01-01

    This issue of Methods of Information in Medicine contains four feature articles that are focused on the theme of evaluation. Evaluation approaches are increasingly essential in the assessment of determining the potential impact of contemporary informatics innovations. The featured articles offer practical perspectives to determining the impact of advancements. Internationally, there are significant advances being made across biomedical informatics and its related sub-disciplines. As with any scientific discipline, it is important for practitioners to be able to relate the potential importance of findings. To this end, it is especially important for biomedical informaticians to convey, in a quantifiable and comparable form, the significance of the informatics findings -not only to peers but also to those across the biomedical research spectrum. As such, the feature articles in this issue describe the evaluation of core infrastructure and fundamental informatics innovations as well as evaluation of informatics-based resources that are a core aspect of public health initiatives.

  5. Research Strategies for Biomedical and Health Informatics

    PubMed Central

    Kulikowski, Casimir A.; Bakken, Suzanne; de Lusignan, Simon; Kimura, Michio; Koch, Sabine; Mantas, John; Maojo, Victor; Marschollek, Michael; Martin-Sanchez, Fernando; Moen, Anne; Park, Hyeoun-Ae; Sarkar, Indra Neil; Leong, Tze Yun; McCray, Alexa T.

    2017-01-01

    Summary Background Medical informatics, or biomedical and health informatics (BMHI), has become an established scientific discipline. In all such disciplines there is a certain inertia to persist in focusing on well-established research areas and to hold on to well-known research methodologies rather than adopting new ones, which may be more appropriate. Objectives To search for answers to the following questions: What are research fields in informatics, which are not being currently adequately addressed, and which methodological approaches might be insufficiently used? Do we know about reasons? What could be consequences of change for research and for education? Methods Outstanding informatics scientists were invited to three panel sessions on this topic in leading international conferences (MIE 2015, Medinfo 2015, HEC 2016) in order to get their answers to these questions. Results A variety of themes emerged in the set of answers provided by the panellists. Some panellists took the theoretical foundations of the field for granted, while several questioned whether the field was actually grounded in a strong theoretical foundation. Panellists proposed a range of suggestions for new or improved approaches, methodologies, and techniques to enhance the BMHI research agenda. Conclusions The field of BMHI is on the one hand maturing as an academic community and intellectual endeavour. On the other hand vendor-supplied solutions may be too readily and uncritically accepted in health care practice. There is a high chance that BMHI will continue to flourish as an important discipline; its innovative interventions might then reach the original objectives of advancing science and improving health care outcomes.

  6. 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.

  7. Advancing Eucalyptus genomics: identification and sequencing of lignin biosynthesis genes from deep-coverage BAC libraries

    PubMed Central

    2011-01-01

    Background Eucalyptus species are among the most planted hardwoods in the world because of their rapid growth, adaptability and valuable wood properties. The development and integration of genomic resources into breeding practice will be increasingly important in the decades to come. Bacterial artificial chromosome (BAC) libraries are key genomic tools that enable positional cloning of important traits, synteny evaluation, and the development of genome framework physical maps for genetic linkage and genome sequencing. Results We describe the construction and characterization of two deep-coverage BAC libraries EG_Ba and EG_Bb obtained from nuclear DNA fragments of E. grandis (clone BRASUZ1) digested with HindIII and BstYI, respectively. Genome coverages of 17 and 15 haploid genome equivalents were estimated for EG_Ba and EG_Bb, respectively. Both libraries contained large inserts, with average sizes ranging from 135 Kb (Eg_Bb) to 157 Kb (Eg_Ba), very low extra-nuclear genome contamination providing a probability of finding a single copy gene ≥ 99.99%. Libraries were screened for the presence of several genes of interest via hybridizations to high-density BAC filters followed by PCR validation. Five selected BAC clones were sequenced and assembled using the Roche GS FLX technology providing the whole sequence of the E. grandis chloroplast genome, and complete genomic sequences of important lignin biosynthesis genes. Conclusions The two E. grandis BAC libraries described in this study represent an important milestone for the advancement of Eucalyptus genomics and forest tree research. These BAC resources have a highly redundant genome coverage (> 15×), contain large average inserts and have a very low percentage of clones with organellar DNA or empty vectors. These publicly available BAC libraries are thus suitable for a broad range of applications in genetic and genomic research in Eucalyptus and possibly in related species of Myrtaceae, including genome

  8. Opening plenary speaker: Human genomics, precision medicine, and advancing human health.

    PubMed

    Green, Eric D

    2016-08-01

    Starting with the launch of the Human Genome Project in 1990, the past quarter-century has brought spectacular achievements in genomics that dramatically empower the study of human biology and disease. The human genomics enterprise is now in the midst of an important transition, as the growing foundation of genomic knowledge is being used by researchers and clinicians to tackle increasingly complex problems in biomedicine. Of particular prominence is the use of revolutionary new DNA sequencing technologies for generating prodigious amounts of DNA sequence data to elucidate the complexities of genome structure, function, and evolution, as well as to unravel the genomic bases of rare and common diseases. Together, these developments are ushering in the era of genomic medicine. Augmenting the advances in human genomics have been innovations in technologies for measuring environmental and lifestyle information, electronic health records, and data science; together, these provide opportunities of unprecedented scale and scope for investigating the underpinnings of health and disease. To capitalize on these opportunities, U.S. President Barack Obama recently announced a major new research endeavor - the U.S. Precision Medicine Initiative. This bold effort will be framed around several key aims, which include accelerating the use of genomically informed approaches to cancer care, making important policy and regulatory changes, and establishing a large research cohort of >1 million volunteers to facilitate precision medicine research. The latter will include making the partnership with all participants a centerpiece feature in the cohort's design and development. The Precision Medicine Initiative represents a broad-based research program that will allow new approaches for individualized medical care to be rigorously tested, so as to establish a new evidence base for advancing clinical practice and, eventually, human health.

  9. 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

  10. Development of Advanced Technologies for Complete Genomic and Proteomic Characterization of Quantized Human Tumor Cells

    DTIC Science & Technology

    2015-09-01

    populations were successfully established from the corresponding parental cell lines (Figure 2). To generate quantized cell populations a single ...individual cells from the SN291 parental culture. Each dot represents a single cell. Color gradient indicates enrichment score for either published CD133... parental lines and quantized cell types (Specific Aim 5). We believe this program has significantly advanced genomic, proteomic and single -cell

  11. Trends in publication of nursing informatics research.

    PubMed

    Kim, Hyeoneui; Ohno-Machado, Lucila; Oh, Janet; Jiang, Xiaoqian

    2014-01-01

    We analyzed 741 journal articles on nursing informatics published in 7 biomedical/nursing informatics journals and 6 nursing journals from 2005 to 2013 to begin to understand publication trends in nursing informatics research and identify gaps. We assigned a research theme to each article using AMIA 2014 theme categories and normalized the citation counts using time from publication. Overall, nursing informatics research covered a broad spectrum of research topics in biomedical informatics and publication topics seem to be well aligned with the high priority research agenda identified by the nursing informatics community. The research themes with highest volume of publication were Clinical Workflow and Human Factors, Consumer Informatics and Personal Health Records, and Clinical Informatics, for which an increasing trend in publication was noted. Articles on Informatics Education and Workforce Development; Data Mining, NLP, Information Extraction; and Clinical Informatics showed steady and high volume of citations.

  12. Trends in Publication of Nursing Informatics Research

    PubMed Central

    Kim, Hyeoneui; Ohno-Machado, Lucila; Oh, Janet; Jiang, Xiaoqian

    2014-01-01

    We analyzed 741 journal articles on nursing informatics published in 7 biomedical/nursing informatics journals and 6 nursing journals from 2005 to 2013 to begin to understand publication trends in nursing informatics research and identify gaps. We assigned a research theme to each article using AMIA 2014 theme categories and normalized the citation counts using time from publication. Overall, nursing informatics research covered a broad spectrum of research topics in biomedical informatics and publication topics seem to be well aligned with the high priority research agenda identified by the nursing informatics community. The research themes with highest volume of publication were Clinical Workflow and Human Factors, Consumer Informatics and Personal Health Records, and Clinical Informatics, for which an increasing trend in publication was noted. Articles on Informatics Education and Workforce Development; Data Mining, NLP, Information Extraction; and Clinical Informatics showed steady and high volume of citations. PMID:25954387

  13. Epigenetics, chromatin and genome organization: recent advances from the ENCODE project.

    PubMed

    Siggens, L; Ekwall, K

    2014-09-01

    The organization of the genome into functional units, such as enhancers and active or repressed promoters, is associated with distinct patterns of DNA and histone modifications. The Encyclopedia of DNA Elements (ENCODE) project has advanced our understanding of the principles of genome, epigenome and chromatin organization, identifying hundreds of thousands of potential regulatory regions and transcription factor binding sites. Part of the ENCODE consortium, GENCODE, has annotated the human genome with novel transcripts including new noncoding RNAs and pseudogenes, highlighting transcriptional complexity. Many disease variants identified in genome-wide association studies are located within putative enhancer regions defined by the ENCODE project. Understanding the principles of chromatin and epigenome organization will help to identify new disease mechanisms, biomarkers and drug targets, particularly as ongoing epigenome mapping projects generate data for primary human cell types that play important roles in disease.

  14. 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.

  15. 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.

  16. 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

  17. Advancing Genetic Testing for Deafness with Genomic Technology

    PubMed Central

    Shearer, A. Eliot; Black-Ziegelbein, E. Ann; Hildebrand, Michael S.; Eppsteiner, Robert W.; Ravi, Harini; Joshi, Swati; Guiffre, Angelica C.; Sloan, Christina M.; Happe, Scott; Howard, Susanna D.; Novak, Barbara; DeLuca, Adam P.; Taylor, Kyle R.; Scheetz, Todd E.; Braun, Terry A.; Casavant, Thomas L.; Kimberling, William J.; LeProust, Emily M.; Smith, Richard J.H.

    2013-01-01

    Background Non-syndromic hearing loss (NSHL) is the most common sensory impairment in humans. Until recently its extreme genetic heterogeneity precluded comprehensive genetic testing. Using a platform that couples targeted genomic enrichment (TGE) and massively parallel sequencing (MPS) to sequence all exons of all genes implicated in NSHL, we test 100 persons with presumed genetic NSHL and in so doing establish sequencing requirements for maximum sensitivity and define MPS quality score metrics that obviate Sanger validation of variants. Methods We examined DNA from 100 sequentially collected probands with presumed genetic NSHL without exclusions due to inheritance, previous genetic testing, or type of hearing loss. We performed TGE using post-capture multiplexing in variable pool sizes followed by Illumina sequencing. We developed a local Galaxy installation on a high performance-computing cluster for bioinformatics analysis. Results To obtain maximum variant sensitivity with this platform 3.2–6.3 million total mapped sequencing reads per sample are required. Quality score analysis showed that Sanger validation is not required for 95% of variants. Our overall diagnostic rate was 42% but varied by clinical features from 0% for persons with asymmetric hearing loss to 56% for persons with bilateral autosomal recessive NSHL. Conclusions These findings will direct the use of TGE and MPS strategies for genetic diagnosis for NSHL. Our diagnostic rate highlights the need for further research on genetic deafness focused on novel gene identification and an improved understanding of the role of non-exonic mutations. The unsolved families we have identified provide a valuable resource to address these areas. PMID:23804846

  18. 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.

  19. 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.

  20. 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.

  1. 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

  2. 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

  3. An advanced reference genome of Trifolium subterraneum L. reveals genes related to agronomic performance.

    PubMed

    Kaur, Parwinder; Bayer, Philipp E; Milec, Zbyněk; Vrána, Jan; Yuan, Yuxuan; Appels, Rudi; Edwards, David; Batley, Jacqueline; Nichols, Phillip; Erskine, William; Doležel, Jaroslav

    2017-01-23

    Subterranean clover is an important annual forage legume, whose diploidy and inbreeding nature make it an ideal model for genomic analysis in Trifolium. We reported a draft genome assembly of the subterranean clover TSUd_r1.1. Here we evaluate genome mapping on nanochannel arrays and generation of a transcriptome atlas across tissues to advance the assembly and gene annotation. Using a BioNano-based assembly spanning 512 Mb (93% genome coverage), we validated the draft assembly, anchored unplaced contigs and resolved misassemblies. Multiple contigs (264) from the draft assembly coalesced into 97 super-scaffolds (43% of genome). Sequences longer than >1 Mb increased from 40 to 189 Mb giving 1.4-fold increase in N50 with total genome in pseudomolecules improved from 73 to 80%. The advanced assembly was re-annotated using transcriptome atlas data to contain 31,272 protein-coding genes capturing >96% of the gene content. Functional characterisation and GO enrichment confirmed gene expression for response to water deprivation, flavonoid biosynthesis, and embryo development ending in seed dormancy, reflecting adaptation to the harsh Mediterranean environment. Comparative analyses across Papilionoideae identified 24,893 Trifolium-specific and 6,325 subterranean-clover-specific genes that could be mined further for traits such as geocarpy and grazing tolerance. Eight key traits, including persistence, improved livestock health by isoflavonoid production in addition to important agro-morphological traits, were fine-mapped on the high density SNP linkage map anchored to the assembly. This new genomic information is crucial to identify loci governing traits allowing marker-assisted breeding, comparative mapping and identification of tissue-specific gene promoters for biotechnological improvement of forage legumes. This article is protected by copyright. All rights reserved.

  4. 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

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

    PubMed

    Denholm, Bonnie G

    2016-04-01

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

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

    PubMed

    Delmont, Tom O; Eren, A Murat

    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.

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

    PubMed Central

    Delmont, Tom O.

    2016-01-01

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

  8. Medical Informatics and the Science of Cognition

    PubMed Central

    Patel, Vimla L.; Kaufman, David R.

    1998-01-01

    Recent developments in medical informatics research have afforded possibilities for great advances in health care delivery. These exciting opportunities also present formidable challenges to the implementation and integration of technologies in the workplace. As in most domains, there is a gulf between technologic artifacts and end users. Since medical practice is a human endeavor, there is a need for bridging disciplines to enable clinicians to benefit from rapid technologic advances. This in turn necessitates a broadening of disciplinary boundaries to consider cognitive and social factors pertaining to the design and use of technology. The authors argue for a place of prominence for cognitive science. Cognitive science provides a framework for the analysis and modeling of complex human performance and has considerable applicability to a range of issues in informatics. Its methods have been employed to illuminate different facets of design and implementation. This approach has also yielded insights into the mechanisms and processes involved in collaborative design. Cognitive scientific methods and theories are illustrated in the context of two examples that examine human-computer interaction in medical contexts and computer-mediated collaborative processes. The framework outlined in this paper can be used to refine the process of iterative design, end-user training, and productive practice. PMID:9824797

  9. Hands-on Workshops as An Effective Means of Learning Advanced Technologies Including Genomics, Proteomics and Bioinformatics

    PubMed Central

    Reisdorph, Nichole; Stearman, Robert; Kechris, Katerina; Phang, Tzu Lip; Reisdorph, Richard; Prenni, Jessica; Erle, David J.; Coldren, Christopher; Schey, Kevin; Nesvizhskii, Alexey; Geraci, Mark

    2013-01-01

    Genomics and proteomics have emerged as key technologies in biomedical research, resulting in a surge of interest in training by investigators keen to incorporate these technologies into their research. At least two types of training can be envisioned in order to produce meaningful results, quality publications and successful grant applications: (1) immediate short-term training workshops and (2) long-term graduate education or visiting scientist programs. We aimed to fill the former need by providing a comprehensive hands-on training course in genomics, proteomics and informatics in a coherent, experimentally-based framework. This was accomplished through a National Heart, Lung, and Blood Institute (NHLBI)-sponsored 10-day Genomics and Proteomics Hands-on Workshop held at National Jewish Health (NJH) and the University of Colorado School of Medicine (UCD). The course content included comprehensive lectures and laboratories in mass spectrometry and genomics technologies, extensive hands-on experience with instrumentation and software, video demonstrations, optional workshops, online sessions, invited keynote speakers, and local and national guest faculty. Here we describe the detailed curriculum and present the results of short- and long-term evaluations from course attendees. Our educational program consistently received positive reviews from participants and had a substantial impact on grant writing and review, manuscript submissions and publications. PMID:24316330

  10. Hands-on workshops as an effective means of learning advanced technologies including genomics, proteomics and bioinformatics.

    PubMed

    Reisdorph, Nichole; Stearman, Robert; Kechris, Katerina; Phang, Tzu Lip; Reisdorph, Richard; Prenni, Jessica; Erle, David J; Coldren, Christopher; Schey, Kevin; Nesvizhskii, Alexey; Geraci, Mark

    2013-12-01

    Genomics and proteomics have emerged as key technologies in biomedical research, resulting in a surge of interest in training by investigators keen to incorporate these technologies into their research. At least two types of training can be envisioned in order to produce meaningful results, quality publications and successful grant applications: (1) immediate short-term training workshops and (2) long-term graduate education or visiting scientist programs. We aimed to fill the former need by providing a comprehensive hands-on training course in genomics, proteomics and informatics in a coherent, experimentally-based framework. This was accomplished through a National Heart, Lung, and Blood Institute (NHLBI)-sponsored 10-day Genomics and Proteomics Hands-on Workshop held at National Jewish Health (NJH) and the University of Colorado School of Medicine (UCD). The course content included comprehensive lectures and laboratories in mass spectrometry and genomics technologies, extensive hands-on experience with instrumentation and software, video demonstrations, optional workshops, online sessions, invited keynote speakers, and local and national guest faculty. Here we describe the detailed curriculum and present the results of short- and long-term evaluations from course attendees. Our educational program consistently received positive reviews from participants and had a substantial impact on grant writing and review, manuscript submissions and publications.

  11. ACGT: advancing clinico-genomic trials on cancer - four years of experience.

    PubMed

    Martin, Luis; Anguita, Alberto; Graf, Norbert; Tsiknakis, Manolis; Brochhausen, Mathias; Rüping, Stefan; Bucur, Anca; Sfakianakis, Stelios; Sengstag, Thierry; Buffa, Francesca; Stenzhorn, Holger

    2011-01-01

    The challenges regarding seamless integration of distributed, heterogeneous and multilevel data arising in the context of contemporary, post-genomic clinical trials cannot be effectively addressed with current methodologies. An urgent need exists to access data in a uniform manner, to share information among different clinical and research centers, and to store data in secure repositories assuring the privacy of patients. Advancing Clinico-Genomic Trials (ACGT) was a European Commission funded Integrated Project that aimed at providing tools and methods to enhance the efficiency of clinical trials in the -omics era. The project, now completed after four years of work, involved the development of both a set of methodological approaches as well as tools and services and its testing in the context of real-world clinico-genomic scenarios. This paper describes the main experiences using the ACGT platform and its tools within one such scenario and highlights the very promising results obtained.

  12. Improving human forensics through advances in genetics, genomics and molecular biology.

    PubMed

    Kayser, Manfred; de Knijff, Peter

    2011-03-01

    Forensic DNA profiling currently allows the identification of persons already known to investigating authorities. Recent advances have produced new types of genetic markers with the potential to overcome some important limitations of current DNA profiling methods. Moreover, other developments are enabling completely new kinds of forensically relevant information to be extracted from biological samples. These include new molecular approaches for finding individuals previously unknown to investigators, and new molecular methods to support links between forensic sample donors and criminal acts. Such advances in genetics, genomics and molecular biology are likely to improve human forensic case work in the near future.

  13. Advances in biotechnology and linking outputs to variation in complex traits: Plant and Animal Genome meeting January 2012.

    PubMed

    Appels, R; Barrero, R; Bellgard, M

    2012-03-01

    The Plant and Animal Genome (PAG, held annually) meeting in January 2012 provided insights into the advances in plant, animal, and microbe genome studies particularly as they impact on our understanding of complex biological systems. The diverse areas of biology covered included the advances in technologies, variation in complex traits, genome change in evolution, and targeting phenotypic changes, across the broad spectrum of life forms. This overview aims to summarize the major advances in research areas presented in the plenary lectures and does not attempt to summarize the diverse research activities covered throughout the PAG in workshops, posters, presentations, and displays by suppliers of cutting-edge technologies.

  14. Recent advances in genome editing and creation of genetically modified pigs.

    PubMed

    Butler, James R; Ladowski, Joseph M; Martens, Gregory R; Tector, Matthew; Tector, A Joseph

    2015-11-01

    The field of xenotransplantation is benefiting greatly from recent advances in genetic engineering. The efficiency and pace with which new model animals are being created has dramatically sped progress towards clinical relevance. Endonuclease-driven genome editing now allows for the efficient generation of targeted genetic alterations. Herein we review the available methods of genetic engineering that have been successfully employed to create genetically modified pigs.

  15. 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.

  16. 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.

  17. Returning genome sequences to research participants: Policy and practice

    PubMed Central

    2017-01-01

    Despite advances in genomic science stimulating an explosion of literature around returning health-related findings, the possibility of returning entire genome sequences to individual research participants has not been widely considered. Through direct involvement in large-scale translational genomics studies, we have identified a number of logistical challenges that would need to be overcome prior to returning individual genome sequence data, including verifying that the data belong to the requestor and providing appropriate informatics support. In addition, we identify a number of ethico-legal issues that require careful consideration, including returning data to family members, mitigating against unintended consequences, and ensuring appropriate governance. Finally, recognising that there is an opportunity cost to addressing these issues, we make some specific pragmatic suggestions for studies that are considering whether to share individual genomic datasets with individual study participants. If data are shared, research should be undertaken into the personal, familial and societal impact of receiving individual genome sequence data. PMID:28317033

  18. 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.

  19. 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...

  20. Informatics and Nursing in a Post-Nursing Informatics World: Future Directions for Nurses in an Automated, Artificially Intelligent, Social-Networked Healthcare Environment.

    PubMed

    Booth, Richard G

    2016-01-01

    The increased adoption and use of technology within healthcare and society has influenced the nursing informatics specialty in a multitude of fashions. Namely, the nursing informatics specialty currently faces a range of important decisions related to its knowledge base, established values and future directions - all of which are in need of development and future-proofing. In light of the increased use of automation, artificial intelligence and big data in healthcare, the specialty must also reconceptualize the roles of both nurses and informaticians to ensure that the nursing profession is ready to operate within future digitalized healthcare ecosystems. To explore these goals, the author of this manuscript outlines an examination of technological advancements currently taking place within healthcare, and also proposes implications for the nursing role and the nursing informatics specialty. Finally, recommendations and insights towards how the roles of nurses and informaticians might evolve or be shaped in the growing post-nursing informatics era are presented.

  1. Uses of informatics to solve real world problems in veterinary medicine.

    PubMed

    Santamaria, Suzanne L; Zimmerman, Kurt L

    2011-01-01

    Veterinary informatics is the science of structuring, analyzing, and leveraging information in an effort to advance animal health, disease surveillance, research, education, and business practices. Reference and terminology standards are core components of the informatics infrastructure. This paper focuses on three current activities that use reference standards in veterinary informatics: (1) the construction of a messaging standard in a national animal health laboratory network, (2) the creation of breed and species terminology lists for livestock disease surveillance, and (3) the development of a standardized diagnoses list for small animal practices. These and other endeavors will benefit from research conducted to identify innovative and superior tools, methods, and techniques. The authors believe there are many areas requiring study and special focus in order to advance veterinary informatics, and this paper highlights some of the needs and challenges surrounding these areas.

  2. 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.

  3. 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

  4. 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.

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

    PubMed

    Gunawardena, Sharmini; Karunaweera, Nadira D

    2015-05-01

    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.

  6. 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

  7. 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...

  8. 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.

  9. 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…

  10. Deep Learning for Health Informatics.

    PubMed

    Ravi, Daniele; Wong, Charence; Deligianni, Fani; Berthelot, Melissa; Andreu-Perez, Javier; Lo, Benny; Yang, Guang-Zhong

    2017-01-01

    With a massive influx of multimodality data, the role of data analytics in health informatics has grown rapidly in the last decade. This has also prompted increasing interests in the generation of analytical, data driven models based on machine learning in health informatics. Deep learning, a technique with its foundation in artificial neural networks, is emerging in recent years as a powerful tool for machine learning, promising to reshape the future of artificial intelligence. Rapid improvements in computational power, fast data storage, and parallelization have also contributed to the rapid uptake of the technology in addition to its predictive power and ability to generate automatically optimized high-level features and semantic interpretation from the input data. This article presents a comprehensive up-to-date review of research employing deep learning in health informatics, providing a critical analysis of the relative merit, and potential pitfalls of the technique as well as its future outlook. The paper mainly focuses on key applications of deep learning in the fields of translational bioinformatics, medical imaging, pervasive sensing, medical informatics, and public health.

  11. 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.

  12. Advanced Processing for Biomedical Informatics (APBI)

    DTIC Science & Technology

    2009-10-01

    to the CBCP Tissue /Blood protocol. (Signed consent on file) – Complete Questionnaire and Path Checklist on file. – Tissue /Blood samples available...White Post-menopausal 386 Malignant NOS Female White Post-menopausal We also performed gene expression study on breast tissues available from...the above 92 subjects. 84 of them have breast tissues , with different types of diagnosis as shown below. To enable meaningful analysis, we only

  13. 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

  14. 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.

  15. Performance support concepts for Web-based informatics instruction.

    PubMed Central

    Goodwin, L.

    1997-01-01

    Duke University first offered World Wide Web (WWW) based courses in Nursing Informatics in January of 1997. The first class enrolled 18 nurses who were completing either a Post-Master's Certificate Program or were near completion of their Master's degree. Courses were designed around principles of advanced nursing practice, performance support, mastery learning, and virtual learning communities. Extensive learning assessment included traditional papers, real-world application projects, and a variety of pre and post-test measurements. PMID:9357715

  16. Bioimage informatics for understanding spatiotemporal dynamics of cellular processes.

    PubMed

    Yang, Ge

    2013-01-01

    The inner environment of the cell is highly dynamic and heterogeneous yet exquisitely organized. Successful completion of cellular processes within this environment depends on the right molecules or molecular complexes to function at the right place at the right time. Understanding spatiotemporal behaviors of cellular processes is therefore essential to understanding their molecular mechanisms at the systems level. These behaviors are usually visualized and recorded using imaging techniques. However, to infer from them systems-level molecular mechanisms, computational analysis and understanding of recorded image data is crucial, not only for acquiring quantitative behavior measurements but also for comprehending complex interactions among the molecules or molecular complexes involved. The technology of computational analysis and understanding of biological images is often referred to simply as bioimage informatics. This article introduces fundamentals of bioimage informatics for understanding spatiotemporal dynamics of cellular processes and reviews recent advances on this topic. Basic bioimage informatics concepts and techniques for characterizing spatiotemporal cell dynamics are introduced first. Studies on specific cellular processes such as cell migration and signal transduction are then used as examples to analyze and summarize recent advances, with the focus on transforming quantitative measurements of spatiotemporal cellular behaviors into knowledge of underlying molecular mechanisms. Despite the advances made, substantial technological challenges remain, especially in representation of spatiotemporal cellular behaviors and inference of systems-level molecular mechanisms. These challenges are briefly discussed. Overall, understanding spatiotemporal cell dynamics will provide critical insights into how specific cellular processes as well as the entire inner cellular environment are dynamically organized and regulated.

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

    PubMed

    Olsson, Ida; Bjerling, Pernilla

    2011-02-01

    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.

  18. Genomic Prediction of Seed Quality Traits Using Advanced Barley Breeding Lines

    PubMed Central

    Nielsen, Nanna Hellum; Jahoor, Ahmed; Jensen, Jens Due; Orabi, Jihad; Cericola, Fabio; Edriss, Vahid; Jensen, Just

    2016-01-01

    Genomic selection was recently introduced in plant breeding. The objective of this study was to develop genomic prediction for important seed quality parameters in spring barley. The aim was to predict breeding values without expensive phenotyping of large sets of lines. A total number of 309 advanced spring barley lines tested at two locations each with three replicates were phenotyped and each line was genotyped by Illumina iSelect 9Kbarley chip. The population originated from two different breeding sets, which were phenotyped in two different years. Phenotypic measurements considered were: seed size, protein content, protein yield, test weight and ergosterol content. A leave-one-out cross-validation strategy revealed high prediction accuracies ranging between 0.40 and 0.83. Prediction across breeding sets resulted in reduced accuracies compared to the leave-one-out strategy. Furthermore, predicting across full and half-sib-families resulted in reduced prediction accuracies. Additionally, predictions were performed using reduced marker sets and reduced training population sets. In conclusion, using less than 200 lines in the training set can result in low prediction accuracy, and the accuracy will then be highly dependent on the family structure of the selected training set. However, the results also indicate that relatively small training sets (200 lines) are sufficient for genomic prediction in commercial barley breeding. In addition, our results indicate a minimum marker set of 1,000 to decrease the risk of low prediction accuracy for some traits or some families. PMID:27783639

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

    PubMed

    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

    2015-08-11

    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.

  20. Molecular tools for functional genomics in filamentous fungi: recent advances and new strategies.

    PubMed

    Jiang, Dewei; Zhu, Wei; Wang, Yunchuan; Sun, Chang; Zhang, Ke-Qin; Yang, Jinkui

    2013-12-01

    Advances in genetic transformation techniques have made important contributions to molecular genetics. Various molecular tools and strategies have been developed for functional genomic analysis of filamentous fungi since the first DNA transformation was successfully achieved in Neurospora crassa in 1973. Increasing amounts of genomic data regarding filamentous fungi are continuously reported and large-scale functional studies have become common in a wide range of fungal species. In this review, various molecular tools used in filamentous fungi are compared and discussed, including methods for genetic transformation (e.g., protoplast transformation, electroporation, and microinjection), the construction of random mutant libraries (e.g., restriction enzyme mediated integration, transposon arrayed gene knockout, and Agrobacterium tumefaciens mediated transformation), and the analysis of gene function (e.g., RNA interference and transcription activator-like effector nucleases). We also focused on practical strategies that could enhance the efficiency of genetic manipulation in filamentous fungi, such as choosing a proper screening system and marker genes, assembling target-cassettes or vectors effectively, and transforming into strains that are deficient in the nonhomologous end joining pathway. In summary, we present an up-to-date review on the different molecular tools and latest strategies that have been successfully used in functional genomics in filamentous fungi.

  1. Clinical Implementation of Integrated Genomic Profiling in Patients with Advanced Cancers.

    PubMed

    Borad, Mitesh J; Egan, Jan B; Condjella, Rachel M; Liang, Winnie S; Fonseca, Rafael; Ritacca, Nicole R; McCullough, Ann E; Barrett, Michael T; Hunt, Katherine S; Champion, Mia D; Patel, Maitray D; Young, Scott W; Silva, Alvin C; Ho, Thai H; Halfdanarson, Thorvardur R; McWilliams, Robert R; Lazaridis, Konstantinos N; Ramanathan, Ramesh K; Baker, Angela; Aldrich, Jessica; Kurdoglu, Ahmet; Izatt, Tyler; Christoforides, Alexis; Cherni, Irene; Nasser, Sara; Reiman, Rebecca; Cuyugan, Lori; McDonald, Jacquelyn; Adkins, Jonathan; Mastrian, Stephen D; Valdez, Riccardo; Jaroszewski, Dawn E; Von Hoff, Daniel D; Craig, David W; Stewart, A Keith; Carpten, John D; Bryce, Alan H

    2016-12-01

    DNA focused panel sequencing has been rapidly adopted to assess therapeutic targets in advanced/refractory cancer. Integrated Genomic Profiling (IGP) utilising DNA/RNA with tumour/normal comparisons in a Clinical Laboratory Improvement Amendments (CLIA) compliant setting enables a single assay to provide: therapeutic target prioritisation, novel target discovery/application and comprehensive germline assessment. A prospective study in 35 advanced/refractory cancer patients was conducted using CLIA-compliant IGP. Feasibility was assessed by estimating time to results (TTR), prioritising/assigning putative therapeutic targets, assessing drug access, ascertaining germline alterations, and assessing patient preferences/perspectives on data use/reporting. Therapeutic targets were identified using biointelligence/pathway analyses and interpreted by a Genomic Tumour Board. Seventy-five percent of cases harboured 1-3 therapeutically targetable mutations/case (median 79 mutations of potential functional significance/case). Median time to CLIA-validated results was 116 days with CLIA-validation of targets achieved in 21/22 patients. IGP directed treatment was instituted in 13 patients utilising on/off label FDA approved drugs (n = 9), clinical trials (n = 3) and single patient IND (n = 1). Preliminary clinical efficacy was noted in five patients (two partial response, three stable disease). Although barriers to broader application exist, including the need for wider availability of therapies, IGP in a CLIA-framework is feasible and valuable in selection/prioritisation of anti-cancer therapeutic targets.

  2. 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.

  3. An innovative capstone health care informatics clinical residency: Interprofessional team collaboration.

    PubMed

    Custis, Laura M; Hawkins, Shelley Y; Thomason, Tanna R

    2017-03-01

    Integrated information systems and wireless technology have been increasingly incorporated into health care organizations with the premise that information technology will promote safe, high-quality, cost-effective patient care. With the advancement of technology, the level of expertise necessary to assume health care information technology roles has escalated. The purpose of this article is to describe a clinical residency project whereby students in a graduate degree health care informatics program successfully fulfilled program competencies through a faculty-lead research project focused on the use of home telehealth with a group of heart failure patients. Through the use of Donabedian's framework of structure, process, and outcomes, the health care informatics students completed essential learning activities deemed essential for transition into the role of an informatics specialist. Health care informatics educational leaders are encouraged to adapt this template of applied learning into their practices.

  4. 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

  5. Plant Aquaporins: Genome-Wide Identification, Transcriptomics, Proteomics, and Advanced Analytical Tools

    PubMed Central

    Deshmukh, Rupesh K.; Sonah, Humira; Bélanger, Richard R.

    2016-01-01

    Aquaporins (AQPs) are channel-forming integral membrane proteins that facilitate the movement of water and many other small molecules. Compared to animals, plants contain a much higher number of AQPs in their genome. Homology-based identification of AQPs in sequenced species is feasible because of the high level of conservation of protein sequences across plant species. Genome-wide characterization of AQPs has highlighted several important aspects such as distribution, genetic organization, evolution and conserved features governing solute specificity. From a functional point of view, the understanding of AQP transport system has expanded rapidly with the help of transcriptomics and proteomics data. The efficient analysis of enormous amounts of data generated through omic scale studies has been facilitated through computational advancements. Prediction of protein tertiary structures, pore architecture, cavities, phosphorylation sites, heterodimerization, and co-expression networks has become more sophisticated and accurate with increasing computational tools and pipelines. However, the effectiveness of computational approaches is based on the understanding of physiological and biochemical properties, transport kinetics, solute specificity, molecular interactions, sequence variations, phylogeny and evolution of aquaporins. For this purpose, tools like Xenopus oocyte assays, yeast expression systems, artificial proteoliposomes, and lipid membranes have been efficiently exploited to study the many facets that influence solute transport by AQPs. In the present review, we discuss genome-wide identification of AQPs in plants in relation with recent advancements in analytical tools, and their availability and technological challenges as they apply to AQPs. An exhaustive review of omics resources available for AQP research is also provided in order to optimize their efficient utilization. Finally, a detailed catalog of computational tools and analytical pipelines is

  6. 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

  7. 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.

  8. 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.

  9. 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.

  10. Informatics competencies for healthcare professionals: the Technology Informatics Guiding Education Reform (TIGER) Initiative model.

    PubMed

    Hebda, Toni L; Calderone, Terri L

    2012-01-01

    A growing awareness exists that informatics competencies are essential skills for healthcare professionals today, yet the development of these competencies lags behind the need. The Technology Informatics Guiding Education Reform (TIGER) Initiative represents a comprehensive, interdisciplinary effort that is well suited to the integration of informatics into education, practice, administration, and research environments. This article briefly discusses the background and significance of the TIGER Initiative and why it may be used as a model to instill informatics among the healthcare professionals globally.

  11. 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.

  12. 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

  13. Foundational biomedical informatics research in the clinical and translational science era: a call to action.

    PubMed

    Payne, Philip R O; Embi, Peter J; Niland, Joyce

    2010-01-01

    Advances in clinical and translational science, along with related national-scale policy and funding mechanisms, have provided significant opportunities for the advancement of applied clinical research informatics (CRI) and translational bioinformatics (TBI). Such efforts are primarily oriented to application and infrastructure development and are critical to the conduct of clinical and translational research. However, they often come at the expense of the foundational CRI and TBI research needed to grow these important biomedical informatics subdisciplines and ensure future innovations. In light of this challenge, it is critical that a number of steps be taken, including the conduct of targeted advocacy campaigns, the development of community-accepted research agendas, and the continued creation of forums for collaboration and knowledge exchange. Such efforts are needed to ensure that the biomedical informatics community is able to advance CRI and TBI science in the context of the modern clinical and translational science era.

  14. The emerging role of educational informatics.

    PubMed

    Weiner, Elizabeth E; Trangenstein, Patricia A

    2009-01-01

    Initial growth in the field of nursing informatics has centered primarily on the clinical setting. Much has been written about the systems developed and evaluated and possible new roles that one can play in the clinical environment. The educational arena has not fared as well. Early attention has been focused on the integration of educational technology or on competency-based skills in informatics according to program levels of students. This paper will focus on the emerging role of educational informatics. Examples will provide nurses with a better understanding of the roles played by the educational informaticist in crafting the science of nursing informatics to produce better nursing education outcomes.

  15. 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

  16. Bioimage informatics: a new area of engineering biology.

    PubMed

    Peng, Hanchuan

    2008-09-01

    In recent years, the deluge of complicated molecular and cellular microscopic images creates compelling challenges for the image computing community. There has been an increasing focus on developing novel image processing, data mining, database and visualization techniques to extract, compare, search and manage the biological knowledge in these data-intensive problems. This emerging new area of bioinformatics can be called 'bioimage informatics'. This article reviews the advances of this field from several aspects, including applications, key techniques, available tools and resources. Application examples such as high-throughput/high-content phenotyping and atlas building for model organisms demonstrate the importance of bioimage informatics. The essential techniques to the success of these applications, such as bioimage feature identification, segmentation and tracking, registration, annotation, mining, image data management and visualization, are further summarized, along with a brief overview of the available bioimage databases, analysis tools and other resources.

  17. 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.

  18. Glutamine Synthetase in Legumes: Recent Advances in Enzyme Structure and Functional Genomics

    PubMed Central

    Betti, Marco; García-Calderón, Margarita; Pérez-Delgado, Carmen M.; Credali, Alfredo; Estivill, Guillermo; Galván, Francisco; Vega, José M.; Márquez, Antonio J.

    2012-01-01

    Glutamine synthetase (GS) is the key enzyme involved in the assimilation of ammonia derived either from nitrate reduction, N2 fixation, photorespiration or asparagine breakdown. A small gene family is encoding for different cytosolic (GS1) or plastidic (GS2) isoforms in legumes. We summarize here the recent advances carried out concerning the quaternary structure of GS, as well as the functional relationship existing between GS2 and processes such as nodulation, photorespiration and water stress, in this latter case by means of proline production. Functional genomic analysis using GS2-minus mutant reveals the key role of GS2 in the metabolic control of the plants and, more particularly, in carbon metabolism. PMID:22942686

  19. [Septic shock in ICU: advanced therapeutics, immunoparalysis and genomics. State of the art].

    PubMed

    Arriagada S, Daniela; Donoso F, Alejandro; Cruces R, Pablo; Díaz R, Franco

    2014-08-01

    New and important concepts have emerged for the advanced management of the child with septic shock in the recent decades. Attending physicians in the Pediatric intensive care unit must be fully aware of them to improve patient care in the critical care unit. It should be considered the use of immune therapy only in selected groups of patients. Continuous renal replacement therapies are well tolerated and their early use prevents deleterious fluid overload. Removal of inflammatory mediators by using high volume hemofiltration may play a role in hyperdynamic septic patients. The use of plasmapheresis is recommended in patients with thrombocytopenia-associated multiple organ failure. Extracorporeal support use should be considered in those with refractory septic shock despite goals directed therapy. The immunoparalysis has been associated with nosocomial infections and late mortality. The information from genetic markers may allow early intervention and preventive genomics-based medicine.

  20. Bovine babesiosis in the 21st century: advances in biology and functional genomics.

    PubMed

    Gohil, Sejal; Herrmann, Susann; Günther, Svenja; Cooke, Brian M

    2013-02-01

    Bovine babesiosis caused by the protozoan parasite, Babesia bovis, remains a significant cause of avoidable economic losses to the livestock industry in many countries throughout the world. The molecular mechanisms underlying the pathophysiology of severe disease in susceptible cattle are not well understood and the tools available to study the biology of the parasite, including technologies for genetic manipulation, have only recently been developed. Recent availability of multiple parasite genomes and bioinformatic tools, in combination with the development of new biological reagents, will facilitate our better understanding of the parasite. This will ultimately assist in the identification of novel targets for the development of new therapeutics and vaccines. Here we describe some recent advances in Babesia research and highlight some important challenges for the future.

  1. Advances in understanding cis regulation of the plant gene with an emphasis on comparative genomics.

    PubMed

    Burgess, Diane G; Xu, Jie; Freeling, Michael

    2015-10-01

    The plant gene model remains largely an extrapolation from animals, with the cis functional unit, the gene, cast as a dynamic looping structure. Molecular genetics with model plants continues to make advances; highlighted here are quantitative-occupancy results from the Arabidopsis thaliana (Arabidopsis) Phytochrome-Interacting bHLH transcription Factors (PIF) quartet. Compared to this complex snapshot, results from chromatin occupancy and other Encyclopedia of DNA Elements (ENCODE)-like approaches increase our transcription factor-motif cognate library, but regulation cannot by itself be inferred from binding. Complementary published Arabidopsis conserved noncoding sequence lists are compared, evaluated, merged, and released. Comparative genomic approaches have identified a cis modifier of a gene's expression-hypothetically, a transposon-based 'rheostat'-that works in all cells, times and places.

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

    PubMed

    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

    2015-01-09

    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.

  3. 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

  4. 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.

  5. Detection of genetic alterations in advanced prostate cancer by comparative genomic hybridization.

    PubMed

    Kasahara, Kotaro; Taguchi, Takahiro; Yamasaki, Ichiro; Kamada, Masayuki; Yuri, Kazunari; Shuin, Taro

    2002-08-01

    In this study, we examined nine cases of advanced Japanese prostate cancer by comparative genomic hybridization (CGH) to detect chromosomal imbalances across the entire genome and to identify several new regions likely to contain genes important to the development and progression of this disease. These cases had been previously examined for numerical chromosomal aberrations by fluorescence in situ hybridization (FISH). By CGH, the following regions were found to be over-represented (gains), with fluorescence ratio values higher than the threshold: 4p, 6p, 8q, 11q, 12q, 15q, 16p, 17q, 20, and 21 (>4 cases); underrepresentation (losses) involved: 1q, 4q, 5q, 6q, 13q, 14q, and 22 (>4 cases). The shortest regions of overlap (SRO) of gains were noted at 8q24.1 through q24.3, 12q23, and 17q23 through q24 (>5 cases). The SRO of losses were seen at 5q14 through q21, 6q16.1 through q21, 13q21.3 through q22, and 14q21 (>5 cases). Notably, the gain of chromosomes 8 and 12 by CGH was in agreement with the FISH data, suggesting that the gain of chromosomes 8 and 12 may play an important role in prostate carcinogenesis. The genes on the SRO regions were also discussed in relation to oncogenes and bone metastases.

  6. Recurrent and pathological gene fusions in breast cancer: current advances in genomic discovery and clinical implications.

    PubMed

    Veeraraghavan, Jamunarani; Ma, Jiacheng; Hu, Yiheng; Wang, Xiao-Song

    2016-07-01

    Gene fusions have long been considered principally as the oncogenic events of hematologic malignancies, but have recently gained wide attention in solid tumors due to several milestone discoveries and the advancement of deep sequencing technologies. With the progress in deep sequencing studies of breast cancer transcriptomes and genomes, the discovery of recurrent and pathological gene fusions in breast cancer is on the focus. Recently, driven by new deep sequencing studies, several recurrent or pathological gene fusions have been identified in breast cancer, including ESR1-CCDC170, SEC16A-NOTCH1, SEC22B-NOTCH2, and ESR1-YAP1 etc. More important, most of these gene fusions are preferentially identified in the more aggressive breast cancers, such as luminal B, basal-like, or endocrine-resistant breast cancer, suggesting recurrent gene fusions as additional key driver events in these tumors other than the known drivers such as the estrogen receptor. In this paper, we have comprehensively summarized the newly identified recurrent or pathological gene fusion events in breast cancer, reviewed the contributions of new genomic and deep sequencing technologies to new fusion discovery and the integrative bioinformatics tools to analyze these data, highlighted the biological relevance and clinical implications of these fusion discoveries, and discussed future directions of gene fusion research in breast cancer.

  7. Genomics and the Human Genome Project: implications for psychiatry.

    PubMed

    Kelsoe, John R

    2004-11-01

    In the past decade the Human Genome Project has made extraordinary strides in understanding of fundamental human genetics. The complete human genetic sequence has been determined, and the chromosomal location of almost all human genes identified. Presently, a large international consortium, the HapMap Project, is working to identify a large portion of genetic variation in different human populations and the structure and relationship of these variants to each other. The Human Genome Project has approached human genetics on a scale not previously seen in biology. This has been made possible by dramatic advances in high throughput technology and bio-informatics. Tools such as gene chips and micro-arrays have spawned an entirely new strategy to examine the function and expression of genes in a massively parallel fashion. Together these tools have dramatically advanced our knowledge about the human genome. They promise powerful new approaches to complex genetic traits such as psychiatric illness. The goals and progress of the Human Genome Project and the technology involved are reviewed. The implications of this science for psychiatric genetics are discussed.

  8. 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

  9. 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.

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

    PubMed

    Chung, Seon Yoon; Staggers, Nancy

    2014-12-01

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

  11. Informatics Education in Italian Secondary Schools

    ERIC Educational Resources Information Center

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

    2014-01-01

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

  12. Medical Informatics: Market for IS/IT.

    ERIC Educational Resources Information Center

    Morris, Theodore Allan

    2002-01-01

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

  13. Teaching Some Informatics Concepts Using Formal System

    ERIC Educational Resources Information Center

    Yang, Sojung; Park, Seongbin

    2014-01-01

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

  14. The Teaching of Informatics for Business Students

    ERIC Educational Resources Information Center

    Sora, Sebastian A.

    2008-01-01

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

  15. Medical Informatics in Academic Health Science Centers.

    ERIC Educational Resources Information Center

    Frisse, Mark E.

    1992-01-01

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

  16. Clinical informatics in critical care.

    PubMed

    Martich, G Daniel; Waldmann, Carl S; Imhoff, Michael

    2004-01-01

    Health care information systems have the potential to enable better care of patients in much the same manner as the widespread use of the automobile and telephone did in the early 20th century. The car and phone were rapidly accepted and embraced throughout the world when these breakthroughs occurred. However, the automation of health care with use of computerized information systems has not been as widely accepted and implemented as computer technology use in all other sectors of the global economy. In this article, the authors examine the need, risks, and rewards of clinical informatics in health care as well as its specific relationship to critical care medicine.

  17. Five Periods in Development of Medical Informatics

    PubMed Central

    Masic, Izet

    2014-01-01

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

  18. Medical informatics between technology, philosophy and science.

    PubMed

    Masic, Izet

    2004-01-01

    Medical (health) informatics occupies the central place in all the segments of modern medicine in the past thirty years--in practical work, education and scientific research. In all that, computers have taken over the most important role and are used intensively for the development of the health information systems. Following activities develop within the area of health informatics: health-documentation, health-statistics, health-informatics and biomedical scientific and professional information. The medical informatics as the separate medical discipline very quickly gets developed, both in Bosnia and Herzegovina. In our country, the medical informatics is a separate subject for the last ten years, regarding to the Medical curriculum at the biomedical faculties in Bosnia and Herzegovina is in accordance with the project of the education related to Bologna declaration and the project EURO MEDICINA.

  19. The European community and its standardization efforts in medical informatics

    NASA Astrophysics Data System (ADS)

    Mattheus, Rudy A.

    1992-07-01

    A summary of the CEN TC 251/4 ''Medical Imaging and Multi-Media'' activities will be given. CEN is the European standardization institute, TC 251 deals with medical informatics. Standardization is a condition for the wide scale use of health care and medical informatics and for the creation of a common market. In the last two years, three important categories-- namely, the Commission of the European Communities with their programs and the mandates, the medical informaticians through their European professional federation, and the national normalization institutes through the European committee--have shown to be aware of this problem and have taken actions. As a result, a number of AIM (Advanced Informatics in Medicine), CEC sponsored projects, the CEC mandates to CEN and EWOS, the EFMI working group on standardization, the technical committee of CEN, and the working groups and project teams of CEN and EWOS are working on the subject. On overview of the CEN TC 251/4 ''Medical Imaging and Multi-Media'' activities will be given, including their relation to other work.

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

    PubMed Central

    2009-01-01

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

  1. Cancer whole-genome sequencing: present and future.

    PubMed

    Nakagawa, H; Wardell, C P; Furuta, M; Taniguchi, H; Fujimoto, A

    2015-12-03

    Recent explosive advances in next-generation sequencing technology and computational approaches to massive data enable us to analyze a number of cancer genome profiles by whole-genome sequencing (WGS). To explore cancer genomic alterations and their diversity comprehensively, global and local cancer genome-sequencing projects, including ICGC and TCGA, have been analyzing many types of cancer genomes mainly by exome sequencing. However, there is limited information on somatic mutations in non-coding regions including untranslated regions, introns, regulatory elements and non-coding RNAs, and rearrangements, sometimes producing fusion genes, and pathogen detection in cancer genomes remain widely unexplored. WGS approaches can detect these unexplored mutations, as well as coding mutations and somatic copy number alterations, and help us to better understand the whole landscape of cancer genomes and elucidate functions of these unexplored genomic regions. Analysis of cancer genomes using the present WGS platforms is still primitive and there are substantial improvements to be made in sequencing technologies, informatics and computer resources. Taking account of the extreme diversity of cancer genomes and phenotype, it is also required to analyze much more WGS data and integrate these with multi-omics data, functional data and clinical-pathological data in a large number of sample sets to interpret them more fully and efficiently.

  2. An Approach for All in Pharmacy Informatics Education.

    PubMed

    Fox, Brent I; Flynn, Allen; Clauson, Kevin A; Seaton, Terry L; Breeden, Elizabeth

    2017-03-25

    Computerization is transforming health care. All clinicians are users of health information technology (HIT). Understanding fundamental principles of informatics, the field focused on information needs and uses, is essential if HIT is going to support improved patient outcomes. Informatics education for clinicians is a national priority. Additionally, some informatics experts are needed to bring about innovations in HIT. A common approach to pharmacy informatics education has been slow to develop. Meanwhile, accreditation standards for informatics in pharmacy education continue to evolve. A gap remains in the implementation of informatics education for all pharmacy students and it is unclear what expert informatics training should cover. In this article, we propose the first of two complementary approaches to informatics education in pharmacy: to incorporate fundamental informatics education into pharmacy curricula for all students. The second approach, to train those students interested in becoming informatics experts to design, develop, implement, and evaluate HIT, will be presented in a subsequent issue of the Journal.

  3. An Approach for All in Pharmacy Informatics Education

    PubMed Central

    Flynn, Allen; Clauson, Kevin A.; Seaton, Terry L.; Breeden, Elizabeth

    2017-01-01

    Computerization is transforming health care. All clinicians are users of health information technology (HIT). Understanding fundamental principles of informatics, the field focused on information needs and uses, is essential if HIT is going to support improved patient outcomes. Informatics education for clinicians is a national priority. Additionally, some informatics experts are needed to bring about innovations in HIT. A common approach to pharmacy informatics education has been slow to develop. Meanwhile, accreditation standards for informatics in pharmacy education continue to evolve. A gap remains in the implementation of informatics education for all pharmacy students and it is unclear what expert informatics training should cover. In this article, we propose the first of two complementary approaches to informatics education in pharmacy: to incorporate fundamental informatics education into pharmacy curricula for all students. The second approach, to train those students interested in becoming informatics experts to design, develop, implement, and evaluate HIT, will be presented in a subsequent issue of the Journal. PMID:28381898

  4. Multiscale integration of -omic, imaging, and clinical data in biomedical informatics.

    PubMed

    Phan, John H; Quo, Chang F; Cheng, Chihwen; Wang, May Dongmei

    2012-01-01

    This paper reviews challenges and opportunities in multiscale data integration for biomedical informatics. Biomedical data can come from different biological origins, data acquisition technologies, and clinical applications. Integrating such data across multiple scales (e.g., molecular, cellular/tissue, and patient) can lead to more informed decisions for personalized, predictive, and preventive medicine. However, data heterogeneity, community standards in data acquisition, and computational complexity are big challenges for such decision making. This review describes genomic and proteomic (i.e., molecular), histopathological imaging (i.e., cellular/tissue), and clinical (i.e., patient) data; it includes case studies for single-scale (e.g., combining genomic or histopathological image data), multiscale (e.g., combining histopathological image and clinical data), and multiscale and multiplatform (e.g., the Human Protein Atlas and The Cancer Genome Atlas) data integration. Numerous opportunities exist in biomedical informatics research focusing on integration of multiscale and multiplatform data.

  5. Genome-wide association for fear conditioning in an advanced intercross mouse line.

    PubMed

    Parker, Clarissa C; Sokoloff, Greta; Cheng, Riyan; Palmer, Abraham A

    2012-05-01

    Fear conditioning (FC) may provide a useful model for some components of post-traumatic stress disorder (PTSD). We used a C57BL/6J × DBA/2J F(2) intercross (n = 620) and a C57BL/6J × DBA/2J F(8) advanced intercross line (n = 567) to fine-map quantitative trait loci (QTL) associated with FC. We conducted an integrated genome-wide association analysis in QTLRel and identified five highly significant QTL affecting freezing to context as well as four highly significant QTL associated with freezing to cue. The average percent decrease in QTL width between the F(2) and the integrated analysis was 59.2%. Next, we exploited bioinformatic sequence and expression data to identify candidate genes based on the existence of non-synonymous coding polymorphisms and/or expression QTLs. We identified numerous candidate genes that have been previously implicated in either fear learning in animal models (Bcl2, Btg2, Dbi, Gabr1b, Lypd1, Pam and Rgs14) or PTSD in humans (Gabra2, Oprm1 and Trkb); other identified genes may represent novel findings. The integration of F(2) and AIL data maintains the advantages of studying FC in model organisms while significantly improving resolution over previous approaches.

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

    PubMed Central

    Shelden, Megan C.; Roessner, Ute

    2013-01-01

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

  7. [New Classification for Advanced Colorectal Cancer Using CancerPlex®Genomic Tests].

    PubMed

    Kameyama, Hitoshi; Shimada, Yoshifumi; Ichikawa, Hiroshi; Nagahashi, Masayuki; Sakata, Jun; Kobayashi, Takashi; Nogami, Hitoshi; Maruyama, Satoshi; Takii, Yasumasa; Okuda, Shujiro; Ling, Yiwei; Izutsu, Hiroshi; Kodama, Keisuke; Nakada, Mitsutaka; Wakai, Toshifumi

    2016-11-01

    Recently, targeted drugs have been developed for the treatment of colorectal cancer(CRC). Among targets, it is well known that KRAS mutations are associated with resistance to epidermal growth factor receptor(EGFR)monoclonal antibodies. However, response rates using anti-EGFR monotherapy for CRC were less than 20-30% in previous clinical studies. Thus, because the RAS/MAP2K/MAPK and PI3K/AKT pathways are associated with CRC resistance to chemotherapy, we analyzed gene mutations in Stage IV CRC patients using a genomic test(CancerPlex®). Medical records were reviewed for 112 patients who received treatment for CRC between 2007 and 2015 in Niigata University Medical and Dental Hospital or Niigata Cancer Center Hospital. There were 66 male and 46 female patients, and their median age was 62.5(range, 30-86) years. Cluster analyses were performed in 110 non-hypermutated Japanese CRC patients using Euclidean distance and Ward's clustering method, and 6 typical groups were identified. Among these, patients with all wild-type actionable genes benefited from anti-EGFR therapies. The expense of targeted drugs warrants consideration of cost-effectiveness during treatment decision-making for advanced CRC patients. To this end, based on the genetic information on CRC, it is possible to develop precision medicine using CancerPlex®.

  8. Career development initiatives in biomedical health informatics.

    PubMed

    Wagholikar, Amol

    2012-01-01

    The disciplines of biomedical engineering and health informatics complement each other. These two scientific fields sometimes strive independently to deliver better health care services. The rapid evolution in data-intensive methods has made practitioners to think about reviewing the educational needs of the biomedical health informatics workforces. This paper discusses the changing skills requirements in biomedical health informatics discipline. The author reports on the challenges faced by IEEE Engineering in Medicine and Biology (EMBS) in the context of continuous career development of the EMBS members. This paper discusses Queensland chapter's initiative towards an integrated career development to address challenges faced by IEEE EMBS.

  9. A National Agenda for Public Health Informatics

    PubMed Central

    Yasnoff, William A.; Overhage, J. Marc; Humphreys, Betsy L.; LaVenture, Martin

    2001-01-01

    The AMIA 2001 Spring Congress brought together members of the the public health and informatics communities to develop a national agenda for public health informatics. Discussions of funding and governance; architecture and infrastructure; standards and vocabulary; research, evaluation, and best practices; privacy, confidentiality, and security; and training and workforce resulted in 74 recommendations with two key themes—that all stakeholders need to be engaged in coordinated activities related to public health information architecture, standards, confidentiality, best practices, and research; and that informatics training is needed throughout the public health workforce. Implementation of this consensus agenda will help promote progress in the application of information technology to improve public health. PMID:11687561

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2015-10-01

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

  12. Medical Informatics in Croatia – a Historical Survey

    PubMed Central

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

    2014-01-01

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

  13. Biochemical informatics methods for diagnosis and disease management.

    PubMed

    Hudson, Samuel E

    2007-01-01

    New technological advances are beginning to have a direct impact on many aspects of healthcare, including screening, diagnosis, treatment, and disease management. A multidisciplinary approach permits the development of sophisticated patient-centered models that rely on bioinformatics, molecular biology, analytical and biochemistry, and healthcare informatics. In the work described here, a decision support model based on neural networks is used to combine results from laboratory tests with clinical parameters to produce a prognostic model for metastatic carcinoma. In addition, techniques for drug design and development are presented that can lead to medications that target specific cancer cells.

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

    ERIC Educational Resources Information Center

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

    2014-01-01

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

  15. Phytozome Comparative Plant Genomics Portal

    SciTech Connect

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

    2014-09-09

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

  16. Bioimage Informatics in the context of Drosophila research.

    PubMed

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

    2014-06-15

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

  17. Nursing Informatics Competencies: Psychometric Validation, Dissemination, and Maintenance of Self-Assessment Tool for Nurse Leaders.

    PubMed

    Collins, Sarah

    2016-01-01

    Due to rapid advances in technology, HIT competencies for nursing leaders require frequent attention and updating from experts in the field to ensure relevance to nursing leaders' work. This workshop will target nursing informatics researchers and leaders to: 1) learn methods and findings from a study validating a Self-Assessment Scale for Nursing Informatics Competencies for Nurse Leaders, 2) generate awareness of the Self-Assessment scale, 3) discuss strategies for maintenance of competencies overtime and 4) identify strategies to engage nursing leaders in this pursuit.

  18. Biomedical informatics in Switzerland: need for action.

    PubMed

    Lovis, Christian; Blaser, Jürg

    2015-01-01

    Biomedical informatics (BMI) is an umbrella scientific field that covers many domains, as defined several years ago by the International Medical Informatics Association and the American Medical Informatics Association, two leading players in the field. For example, one of the domains of BMI is clinical informatics, which has been formally recognised as a medical subspecialty by the American Board of Medical Specialty since 2011. Most OECD (Organisation for Economic Co-operation and Development) countries offer very strong curricula in the field of BMI, strong research and development funding with clear tracks and, for most of them, inclusion of BMI in the curricula of health professionals, but BMI remains only marginally recognised in Switzerland. Recent major changes, however, such as the future federal law on electronic patient records, the personalised health initiative or the growing empowerment of citizens towards their health data, are adding much weight to the need for BMI capacity-building in Switzerland.

  19. Big data from small samples: Informatics of next-generation sequencing in cytopathology.

    PubMed

    Roy-Chowdhuri, Sinchita; Roy, Somak; Monaco, Sara E; Routbort, Mark J; Pantanowitz, Liron

    2016-12-05

    The rapid adoption of next-generation sequencing (NGS) in clinical molecular laboratories has redefined the practice of cytopathology. Instead of simply being used as a diagnostic tool, cytopathology has evolved into a practice providing important genomic information that guides clinical management. The recent emphasis on maximizing limited-volume cytology samples for ancillary molecular studies, including NGS, requires cytopathologists not only to be more involved in specimen collection and processing techniques but also to be aware of downstream testing and informatics issues. For the integration of molecular informatics into the clinical workflow, it is important to understand the computational components of the NGS workflow by which raw sequence data are transformed into clinically actionable genomic information and to address the challenges of having a robust and sustainable informatics infrastructure for NGS-based testing in a clinical environment. Adapting to needs ranging from specimen procurement to report delivery is crucial for the optimal utilization of cytology specimens to accommodate requests from clinicians to improve patient care. This review presents a broad overview of the various aspects of informatics in the context of NGS-based testing of cytology specimens. Cancer Cytopathol 2016. © 2016 American Cancer Society.

  20. Comprehensive embryo analysis of advanced maternal age-related aneuploidies and mosaicism by short comparative genomic hybridization.

    PubMed

    Rius, Mariona; Daina, Gemma; Obradors, Albert; Ramos, Laia; Velilla, Esther; Fernández, Sílvia; Martínez-Passarell, Olga; Benet, Jordi; Navarro, Joaquima

    2011-01-01

    The short comparative genomic hybridization (short-CGH) method was used to perform a comprehensive cytogenetic study of isolated blastomeres from advanced maternal age embryos, discarded after fluorescent in situ hybridization (FISH) preimplantation genetic screening (PGS), detecting aneuploidies (38.5% of which corresponded to chromosomes not screened by 9-chromosome FISH), structural aberrations (31.8%), and mosaicism (77.3%). The short-CGH method was subsequently applied in one PGS, achieving a twin pregnancy.

  1. Evolution of Trends in European Medical Informatics

    PubMed Central

    I. Mihalas, George

    2014-01-01

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

  2. Leveraging Health Informatics to a Foster Smart Systems Response to Health Disparities and Health Equity Challenges.

    PubMed

    Jay Carney, Timothy; Kong, Amanda Y

    2017-02-15

    Informaticians are challenged to design health IT solutions for complex problems like health disparities but are only achieving mixed results in demonstrating a direct impact on health outcomes. This presentation of collective intelligence and the corresponding terms of smart health, knowledge ecosystem, enhanced health disparities informatics capacities, knowledge exchange, big-data, and situational awareness are means of demonstrating the complex challenges informatics professional face in trying to model, measure, and manage an intelligence and a smart systems response to health disparities. A critical piece in our understanding of collective intelligence for public and population health rests in our understanding of any public and population health as a living and evolving network of individuals, organizations, and resources. This discussion represents a step in advancing the conversation of what a smart response to health disparities should represent and how informatics can drive the design of intelligent systems to assist in eliminating health disparities and achieving health equity.

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

    PubMed

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

    2016-07-01

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

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

    PubMed

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

    2014-04-01

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

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

    PubMed

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

    2012-01-01

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

  6. Development of Advanced Technologies for Complete Genomic and Proteomic Characterization of Quantized Human Tumor Cells

    DTIC Science & Technology

    2014-07-01

    biomarker discovery . To complete this aim, we need blood and PBMC cells from both patients and their family members. Our clinical collaborators at...selection and family history of samples submitted to Complete Genomics for WGS analysis. Table 2. CGI quality control template for 12 genomic DNA...from a few kb long to entire chromosomes – based on comparison of the genome coverage signal to a pre-computed “median coverage profile” of many

  7. Digital Libraries and Recent Medical Informatics Research. Findings from the IMIA Yearbook of Medical Informatics 2001.

    PubMed

    Ammenwerth, E; Knaup, P; Maier, C; Mludek, V; Singer, R; Skonetzki, S; Wolff, A C; Haux, R; Kulikowski, C

    2001-05-01

    The Yearbook of Medical Informatics is published annually by the International Medical Informatics Association (IMIA) and contains a selection of recent excellent papers on medical informatics research (http://www.med.uni-heidelberg.de/mi/yearbook/index.htm). The special topic of the just published Yearbook 2001 is "Digital Libraries and Medicine". Digital libraries have changed dramatically and will continue to change the way we work with medical knowledge. The selected papers present recent research and new results on digital libraries. As usual, the Yearbook 2001 also contains a variety of papers on other subjects relevant to medical informatics, such as Electronic Patient Records, Health Information Systems, Health and Clinical Management, Decision Support Systems, Education, as well as Image and Signal Processing. This paper will briefly introduce the contributions covering digital libraries and will show how medical informatics research contributes to this important topic.

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

    PubMed Central

    Dixon, B. E.; Kharrazi, H.

    2015-01-01

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

  9. CRISPR/Cas9: an advanced tool for editing plant genomes.

    PubMed

    Samanta, Milan Kumar; Dey, Avishek; Gayen, Srimonta

    2016-10-01

    To meet current challenges in agriculture, genome editing using sequence-specific nucleases (SSNs) is a powerful tool for basic and applied plant biology research. Here, we describe the principle and application of available genome editing tools, including zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs) and the clustered regularly interspaced short palindromic repeat associated CRISPR/Cas9 system. Among these SSNs, CRISPR/Cas9 is the most recently characterized and rapidly developing genome editing technology, and has been successfully utilized in a wide variety of organisms. This review specifically illustrates the power of CRISPR/Cas9 as a tool for plant genome engineering, and describes the strengths and weaknesses of the CRISPR/Cas9 technology compared to two well-established genome editing tools, ZFNs and TALENs.

  10. X-Informatics: Practical Semantic Science

    NASA Astrophysics Data System (ADS)

    Borne, K. D.

    2009-12-01

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

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

    PubMed

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

    2016-01-01

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

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed Central

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

    2015-01-01

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

  14. Computational and informatics strategies for identification of specific protein interaction partners in affinity purification mass spectrometry experiments

    PubMed Central

    Nesvizhskii, Alexey I.

    2013-01-01

    Analysis of protein interaction networks and protein complexes using affinity purification and mass spectrometry (AP/MS) is among most commonly used and successful applications of proteomics technologies. One of the foremost challenges of AP/MS data is a large number of false positive protein interactions present in unfiltered datasets. Here we review computational and informatics strategies for detecting specific protein interaction partners in AP/MS experiments, with a focus on incomplete (as opposite to genome-wide) interactome mapping studies. These strategies range from standard statistical approaches, to empirical scoring schemes optimized for a particular type of data, to advanced computational frameworks. The common denominator among these methods is the use of label-free quantitative information such as spectral counts or integrated peptide intensities that can be extracted from AP/MS data. We also discuss related issues such as combining multiple biological or technical replicates, and dealing with data generated using different tagging strategies. Computational approaches for benchmarking of scoring methods are discussed, and the need for generation of reference AP/MS datasets is highlighted. Finally, we discuss the possibility of more extended modeling of experimental AP/MS data, including integration with external information such as protein interaction predictions based on functional genomics data. PMID:22611043

  15. Advances in ecological genomics in forest trees and applications to genetic resources conservation and breeding.

    PubMed

    Holliday, Jason A; Aitken, Sally N; Cooke, Janice E K; Fady, Bruno; González-Martínez, Santiago C; Heuertz, Myriam; Jaramillo-Correa, Juan-Pablo; Lexer, Christian; Staton, Margaret; Whetten, Ross W; Plomion, Christophe

    2017-02-01

    Forest trees are an unparalleled group of organisms in their combined ecological, economic and societal importance. With widespread distributions, predominantly random mating systems and large population sizes, most tree species harbour extensive genetic variation both within and among populations. At the same time, demographic processes associated with Pleistocene climate oscillations and land-use change have affected contemporary range-wide diversity and may impinge on the potential for future adaptation. Understanding how these adaptive and neutral processes have shaped the genomes of trees species is therefore central to their management and conservation. As for many other taxa, the advent of high-throughput sequencing methods is expected to yield an understanding of the interplay between the genome and environment at a level of detail and depth not possible only a few years ago. An international conference entitled 'Genomics and Forest Tree Genetics' was held in May 2016, in Arcachon (France), and brought together forest geneticists with a wide range of research interests to disseminate recent efforts that leverage contemporary genomic tools to probe the population, quantitative and evolutionary genomics of trees. An important goal of the conference was to discuss how such data can be applied to both genome-enabled breeding and the conservation of forest genetic resources under land use and climate change. Here, we report discoveries presented at the meeting and discuss how the ecological genomic toolkit can be used to address both basic and applied questions in tree biology.

  16. Advances in translational bioinformatics and population genomics in the Asia-Pacific.

    PubMed

    Ranganathan, Shoba; Tongsima, Sissades; Chan, Jonathan; Tan, Tin Wee; Schönbach, Christian

    2012-01-01

    The theme of the 2012 International Conference on Bioinformatics (InCoB) in Bangkok, Thailand was "From Biological Data to Knowledge to Technological Breakthroughs." Besides providing a forum for life scientists and bioinformatics researchers in the Asia-Pacific region to meet and interact, the conference also hosted thematic sessions on the Pan-Asian Pacific Genome Initiative and immunoinformatics. Over the seven years of conference papers published in BMC Bioinformatics and four years in BMC Genomics, we note that there is increasing interest in the applications of -omics technologies to the understanding of diseases, as a forerunner to personalized genomic medicine.

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

    PubMed

    Döhlemann, Johannes; Brennecke, Meike; Becker, Anke

    2016-09-10

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

  18. Biomedical informatics training at Stanford in the 21st century.

    PubMed

    Altman, Russ B; Klein, Teri E

    2007-02-01

    The Stanford Biomedical Informatics training program began with a focus on clinical informatics, and has now evolved into a general program of biomedical informatics training, including clinical informatics, bioinformatics and imaging informatics. The program offers PhD, MS, distance MS, certificate programs, and is now affiliated with an undergraduate major in biomedical computation. Current dynamics include (1) increased activity in informatics within other training programs in biology and the information sciences (2) increased desire among informatics students to gain laboratory experience, (3) increased demand for computational collaboration among biomedical researchers, and (4) interaction with the newly formed Department of Bioengineering at Stanford University. The core focus on research training-the development and application of novel informatics methods for biomedical research-keeps the program centered in the midst of this period of growth and diversification.

  19. [Medical informatics--today and tomorrow].

    PubMed

    Dezelić, Gjuro

    2007-09-01

    The status of medical informatics, a comparatively new biomedical discipline beginning to develop in the second half of the 20th century, is described at the transition into the 21st century. The appearance of new information and communication technologies, among which Internet nas special importance, was a major impulse to the development of medical informatics in its different fields. Health information systems are integrating, while at the same time, by distribution of their parts, they become available to the individual healthcare user. These processes put the problems of interoperability and standardization into the focus of contemporary medical informatics. The electronic health record is recognized as a key instrument of modern healthcare systems, and its development and implementation are being planned at many places. Whereas the research and application of medical decision support systems are stagnating, new disciplines have emerged such as telemedicine, cybermedicine and bioinformatics. The perspectives of the future development of medical informatics are described. In the appendix, a chronology of the development of medical informatics from its beginning to the present time is given.

  20. Medical Informatics Education & Research in Greece

    PubMed Central

    Chouvarda, I.

    2015-01-01

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

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

    PubMed

    Lim, Kwang-il

    2015-01-01

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

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

    PubMed Central

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

    2013-01-01

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

  3. Core content for the subspecialty of clinical informatics.

    PubMed

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

    2009-01-01

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

  4. Health informatics: moving from a discipline to a science.

    PubMed

    Turley, James P

    2009-01-01

    This paper examines the historical definitions of Health (Biomedical) Informatics. It is clear that a majority of the definitions refer to Health Informatics as a discipline. Rather it can be argued that the maturation of Health Informatics is beginning to culminate in a distinct science. This progress need to be reflected in academic programs as well as our conferences and publications.

  5. Image informatics in systems biology applications

    NASA Astrophysics Data System (ADS)

    Wong, Stephen T. C.

    2005-02-01

    Digital optical microscopy, coupled with parallel processing and a large arsenal of labeling techniques, offers tremendous values to localize, identify, and characterize cells and molecules. This generates many image informatics challenges in requiring new algorithms and tools to extract, classify, correlate, and model image features and content from massive amounts of cellular and molecular images acquired. Image informatics aims to fill this gap. Coupling automated microscopy and image analysis with biostatistical and data mining techniques to provide a system biologic approach in studying the cells, the basic unit of life, potentially leads to many exciting applications in life and health sciences. In this presentation, we describe certain new system biology applications enabled by image informatics technology.

  6. NASA Biomedical Informatics Capabilities and Needs

    NASA Technical Reports Server (NTRS)

    Johnson-Throop, Kathy A.

    2009-01-01

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

  7. Community annotation and bioinformatics workforce development in concert--Little Skate Genome Annotation Workshops and Jamborees.

    PubMed

    Wang, Qinghua; Arighi, Cecilia N; King, Benjamin L; Polson, Shawn W; Vincent, James; Chen, Chuming; Huang, Hongzhan; Kingham, Brewster F; Page, Shallee T; Rendino, Marc Farnum; Thomas, William Kelley; Udwary, Daniel W; Wu, Cathy H

    2012-01-01

    Recent advances in high-throughput DNA sequencing technologies have equipped biologists with a powerful new set of tools for advancing research goals. The resulting flood of sequence data has made it critically important to train the next generation of scientists to handle the inherent bioinformatic challenges. The North East Bioinformatics Collaborative (NEBC) is undertaking the genome sequencing and annotation of the little skate (Leucoraja erinacea) to promote advancement of bioinformatics infrastructure in our region, with an emphasis on practical education to create a critical mass of informatically savvy life scientists. In support of the Little Skate Genome Project, the NEBC members have developed several annotation workshops and jamborees to provide training in genome sequencing, annotation and analysis. Acting as a nexus for both curation activities and dissemination of project data, a project web portal, SkateBase (http://skatebase.org) has been developed. As a case study to illustrate effective coupling of community annotation with workforce development, we report the results of the Mitochondrial Genome Annotation Jamborees organized to annotate the first completely assembled element of the Little Skate Genome Project, as a culminating experience for participants from our three prior annotation workshops. We are applying the physical/virtual infrastructure and lessons learned from these activities to enhance and streamline the genome annotation workflow, as we look toward our continuing efforts for larger-scale functional and structural community annotation of the L. erinacea genome.

  8. Informatics approaches to understanding TGFβ pathway regulation

    PubMed Central

    Kahlem, Pascal; Newfeld, Stuart J.

    2009-01-01

    Summary In recent years, informatics studies have predicted several new ways in which the transforming growth factor β (TGFβ) signaling pathway can be post-translationally regulated. Subsequently, many of these predictions were experimentally validated. These approaches include phylogenetic predictions for the phosphorylation, sumoylation and ubiquitylation of pathway components, as well as kinetic models of endocytosis, phosphorylation and nucleo-cytoplasmic shuttling. We review these studies and provide a brief `how to' guide for phylogenetics. Our hope is to stimulate experimental tests of informatics-based predictions for TGFβ signaling, as well as for other signaling pathways, and to expand the number of developmental pathways that are being analyzed computationally. PMID:19855015

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

    SciTech Connect

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

    2011-01-01

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

  10. The CRISPR-Cas system for plant genome editing: advances and opportunities.

    PubMed

    Kumar, Vinay; Jain, Mukesh

    2015-01-01

    Genome editing is an approach in which a specific target DNA sequence of the genome is altered by adding, removing, or replacing DNA bases. Artificially engineered hybrid enzymes, zinc-finger nucleases (ZFNs), and transcription activator-like effector nucleases (TALENs), and the CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR-associated protein) system are being used for genome editing in various organisms including plants. The CRISPR-Cas system has been developed most recently and seems to be more efficient and less time-consuming compared with ZFNs or TALENs. This system employs an RNA-guided nuclease, Cas9, to induce double-strand breaks. The Cas9-mediated breaks are repaired by cellular DNA repair mechanisms and mediate gene/genome modifications. Here, we provide a detailed overview of the CRISPR-Cas system and its adoption in different organisms, especially plants, for various applications. Important considerations and future opportunities for deployment of the CRISPR-Cas system in plants for numerous applications are also discussed. Recent investigations have revealed the implications of the CRISPR-Cas system as a promising tool for targeted genetic modifications in plants. This technology is likely to be more commonly adopted in plant functional genomics studies and crop improvement in the near future.

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

    PubMed Central

    2014-01-01

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

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

    PubMed Central

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

    2013-01-01

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

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

    PubMed

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

    2013-10-01

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

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

    PubMed

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

    2015-04-20

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

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

    PubMed Central

    Kilbridge, Peter M.; Classen, David C.

    2008-01-01

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

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

    PubMed

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

    2016-03-01

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

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

    PubMed Central

    Kameshwar, Ayyappa kumar Sista; Qin, Wensheng

    2016-01-01

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

  18. Comprehensive genomic sequencing and the molecular profiles of clinically advanced breast cancer.

    PubMed

    Ross, Jeffrey S; Gay, Laurie M

    2017-02-01

    Targeting specific mutations that have arisen within a tumour is a promising means of increasing the efficacy of treatments, and breast cancer is no exception to this new paradigm of personalised medicine. Traditional DNA sequencing methods used to characterise clinical cancer specimens and impact treatment decisions are highly sensitive, but are often limited in their scope to known mutational hot spots. Next-generation sequencing (NGS) technologies can also test for these well-known hot spots, as well as identifying insertions and deletions, copy number changes such as ERBB2 (HER2) gene amplification, and a wide array of fusion or rearrangement events. By rapidly analysing many genes in parallel, NGS technologies can make efficient use of precious biopsy material. Comprehensive genomic profiling (CGP) by NGS can reveal targetable, clinically relevant genomic alterations that can stratify tumours by predicted sensitivity to a variety of therapies, including HER2- or MTOR-targeted therapies, immunotherapies, and other kinase inhibitors. Many clinically relevant genomic alterations would not be identified by IHC or hotspot testing, but can be detected by NGS. In addition to the most common breast carcinoma subtypes, rare subtypes analysed with CGP also harbour clinically relevant genomic alterations that can potentially direct therapy selection, illustrating that CGP is a powerful tool for guiding treatment across all breast cancer subtypes.

  19. Ongoing efforts and future plans for phenotyping to complement genomic advances in peanut

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Ongoing and planned genomic research in the peanut community should lead to the development of additional molecular markers that will be useful in peanut cultivar development. However, to achieve this, much work will need to be done to associate these genetic markers with important phenotypic trait...

  20. Advances in genome-wide RNAi cellular screens: a case study using the Drosophila JAK/STAT pathway

    PubMed Central

    2012-01-01

    Background Genome-scale RNA-interference (RNAi) screens are becoming ever more common gene discovery tools. However, whilst every screen identifies interacting genes, less attention has been given to how factors such as library design and post-screening bioinformatics may be effecting the data generated. Results Here we present a new genome-wide RNAi screen of the Drosophila JAK/STAT signalling pathway undertaken in the Sheffield RNAi Screening Facility (SRSF). This screen was carried out using a second-generation, computationally optimised dsRNA library and analysed using current methods and bioinformatic tools. To examine advances in RNAi screening technology, we compare this screen to a biologically very similar screen undertaken in 2005 with a first-generation library. Both screens used the same cell line, reporters and experimental design, with the SRSF screen identifying 42 putative regulators of JAK/STAT signalling, 22 of which verified in a secondary screen and 16 verified with an independent probe design. Following reanalysis of the original screen data, comparisons of the two gene lists allows us to make estimates of false discovery rates in the SRSF data and to conduct an assessment of off-target effects (OTEs) associated with both libraries. We discuss the differences and similarities between the resulting data sets and examine the relative improvements in gene discovery protocols. Conclusions Our work represents one of the first direct comparisons between first- and second-generation libraries and shows that modern library designs together with methodological advances have had a significant influence on genome-scale RNAi screens. PMID:23006893

  1. Cognitive informatics in biomedicine and healthcare.

    PubMed

    Patel, Vimla L; Kannampallil, Thomas G

    2015-02-01

    Cognitive Informatics (CI) is a burgeoning interdisciplinary domain comprising of the cognitive and information sciences that focuses on human information processing, mechanisms and processes within the context of computing and computer applications. Based on a review of articles published in the Journal of Biomedical Informatics (JBI) between January 2001 and March 2014, we identified 57 articles that focused on topics related to cognitive informatics. We found that while the acceptance of CI into the mainstream informatics research literature is relatively recent, its impact has been significant - from characterizing the limits of clinician problem-solving and reasoning behavior, to describing coordination and communication patterns of distributed clinical teams, to developing sustainable and cognitively-plausible interventions for supporting clinician activities. Additionally, we found that most research contributions fell under the topics of decision-making, usability and distributed team activities with a focus on studying behavioral and cognitive aspects of clinical personnel, as they performed their activities or interacted with health information systems. We summarize our findings within the context of the current areas of CI research, future research directions and current and future challenges for CI researchers.

  2. Medical informatics and bioinformatics: a bibliometric study

    PubMed Central

    Bansard, Jean-Yves; Rebholz-Schuhman, Dietrich; Cameron, Graham; Clark, Dominic; van Mulligen, Erik; Beltrame, Francesco; Del Hoyo Barbolla, Eva; Martin-Sanchez, Fernando; Milanesi, Luciano; Tollis, Ioannis; Van der Lei, Johan; Coatrieux, Jean-Louis

    2007-01-01

    This paper reports on an analysis of the bioinformatics and medical informatics literature with the objective to identify upcoming trends that are shared among both research fields to derive benefits from potential collaborative initiatives for their future. Our results present the main characteristics of the two fields and show that these domains are still relatively separated. PMID:17521073

  3. Geo-Engineering through Internet Informatics (GEMINI)

    SciTech Connect

    Doveton, John H.; Watney, W. Lynn

    2003-03-06

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

  4. Informatics and Standards for Nanomedicine Technology

    PubMed Central

    Thomas, Dennis G.; Klaessig, Fred; Harper, Stacey L.; Fritts, Martin; Hoover, Mark D.; Gaheen, Sharon; Stokes, Todd H.; Reznik-Zellen, Rebecca; Freund, Elaine T.; Klemm, Juli D.; Paik, David S.; Baker, Nathan A.

    2011-01-01

    There are several issues to be addressed concerning the management and effective use of information (or data), generated from nanotechnology studies in biomedical research and medicine. These data are large in volume, diverse in content, and are beset with gaps and ambiguities in the description and characterization of nanomaterials. In this work, we have reviewed three areas of nanomedicine informatics: information resources; taxonomies, controlled vocabularies, and ontologies; and information standards. Informatics methods and standards in each of these areas are critical for enabling collaboration, data sharing, unambiguous representation and interpretation of data, semantic (meaningful) search and integration of data; and for ensuring data quality, reliability, and reproducibility. In particular, we have considered four types of information standards in this review, which are standard characterization protocols, common terminology standards, minimum information standards, and standard data communication (exchange) formats. Currently, due to gaps and ambiguities in the data, it is also difficult to apply computational methods and machine learning techniques to analyze, interpret and recognize patterns in data that are high dimensional in nature, and also to relate variations in nanomaterial properties to variations in their chemical composition, synthesis, characterization protocols, etc. Progress towards resolving the issues of information management in nanomedicine using informatics methods and standards discussed in this review will be essential to the rapidly growing field of nanomedicine informatics. PMID:21721140

  5. Pharmacy informatics in controlled substances research.

    PubMed

    Lin, Jia-Ling; Vahabzadeh, Massoud; Mezghanni, Mustapha; Na, Paul J; Leff, Michelle; Contoreggi, Carlo

    2008-11-06

    Pharmacies have become essential components in support of clinical research. Their operations become highly complex when preponderance of prescriptions is composed of controlled substances. Application of informatics will result in more efficient operations. We present the Pharmacy Information Management System (PIMS) that includes a set of decision support systems to address the pharmacy challenges and is integrated into our electronic health record system.

  6. Optimizing Clinical Research Participant Selection with Informatics.

    PubMed

    Weng, Chunhua

    2015-11-01

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

  7. Medical informatics and telemedicine: A vision

    NASA Technical Reports Server (NTRS)

    Clemmer, Terry P.

    1991-01-01

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

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

    PubMed Central

    Kneale, L.

    2015-01-01

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

  9. Current Status of Nursing Informatics Education in Korea

    PubMed Central

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

    2016-01-01

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

  10. Tetrahedron of medical academics: reasons for training in management, leadership and informatics.

    PubMed

    Martins, Henrique

    2009-06-01

    Medical school professors and lecturers are often called to be practicing clinicians, researchers in their own field, in addition to executing their education and curricular responsibilities. Some further accumulate healthcare management responsibilities. These areas pose conflicting demands on time and intellectual activity, but despite their apparent differences, knowledge and skills from management, leadership and informatics may prove useful in helping to smooth these conflicts and hence increase personal effectiveness in these areas. This article tries to clarify some concepts and advance why training in management, leadership and health informatics would seem particularly useful for the medical academic. As opposed to the idea of educational dispersion/specialization, the concept of an integrative tetrahedronal education framework is advanced as a way to plan workshops and other faculty development activities which could be implemented transnationally as well as locally.

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

    PubMed

    Stranieri, Andrew; Vaughan, Stephen

    2010-01-01

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

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

    PubMed

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

    2016-04-01

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

  13. The South African Astro-informatics Alliance (SA3)

    NASA Astrophysics Data System (ADS)

    Barway, S.

    South African astronomy is entering a new era of astronomical research with SALT and MeerKAT/SKA. These new facilities expected to produce huge amount of data and combined with multi wavelength databases that already exists, South African astronomers need to be equipped with latest technologies to deal with new challenges posed by SALT/MeerKAT/SKA. South African Astro-informatics Alliance (SA3) is a collaborative initiative lead by SAAO, SA-SKA and HartRAO to utilize the most recent advancements in IT technology to address many Terabytes of data volume generated by SALT/MeerKAT/SKA along with existing multi-wavelength data archives. In this talk, I present SA3 activities which include the development of a new generation of data archives and tools to address the many Terabytes of data that will be generated by the new South African observing facilities.

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

    PubMed Central

    Henry, S B

    1995-01-01

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

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

    PubMed

    Soberón, Jorge; Peterson, A Townsend

    2004-04-29

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

  16. Bits and bytes: the future of radiology lies in informatics and information technology.

    PubMed

    Brink, James A; Arenson, Ronald L; Grist, Thomas M; Lewin, Jonathan S; Enzmann, Dieter

    2017-03-09

    Advances in informatics and information technology are sure to alter the practice of medical imaging and image-guided therapies substantially over the next decade. Each element of the imaging continuum will be affected by substantial increases in computing capacity coincident with the seamless integration of digital technology into our society at large. This article focuses primarily on areas where this IT transformation is likely to have a profound effect on the practice of radiology.

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

    ERIC Educational Resources Information Center

    Lewis, Kadriye O.; Sincan, Murat

    2009-01-01

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

  18. Construction of BIBAC and BAC libraries from a variety of organisms for advanced genomics research.

    PubMed

    Zhang, Hong-Bin; Scheuring, Chantel F; Zhang, Meiping; Zhang, Yang; Wu, Cheng-Cang; Dong, Jennifer J; Li, Yaning

    2012-02-16

    Large-insert BAC (bacterial artificial chromosome) and BIBAC (binary BAC) libraries are essential for modern genomics research for all organisms. We helped pioneer the BAC and BIBAC technologies, and by using them we have constructed hundreds of BAC and BIBAC libraries for different species of plants, animals, marine animals, insects, algae and microbes. These libraries have been used globally for different aspects of genomics research. Here we describe the procedure with the latest improvements that we have made and used for construction of BIBAC libraries. The procedure includes the preparation of BIBAC vectors, the preparation of clonable fragments of the desired size from the source DNA, the construction and transformation of BIBACs and, finally, the characterization and assembly of BIBAC libraries. We also specify the modifications necessary for construction of BAC libraries using the protocol. The entire protocol takes ∼7 d.

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

    PubMed

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

    2013-06-01

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

  20. Development of Advanced Technologies for Complete Genomic and Proteomic Characterization of Quantized Human Tumor Cells

    DTIC Science & Technology

    2014-07-01

    determined Unmethylated 105mg TMZ, concurrent, 7 weeks. IMRT, 5940 cGy in 33 fractions, 7 weeks. 123 Table 1. Clinical diagnosis, treatment history ...cells) and were used for further analysis. Figure 4. Patient selection and family history of samples submitted for whole genome... chromosomal deletion is not observed in the PBMC sample, as expected. Similarly, we observed large-scale but partial losses in chromosomes 1, 9, 12

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

    PubMed Central

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

    2016-01-01

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

  2. Advances in the integration of transcriptional regulatory information into genome-scale metabolic models.

    PubMed

    Vivek-Ananth, R P; Samal, Areejit

    2016-09-01

    A major goal of systems biology is to build predictive computational models of cellular metabolism. Availability of complete genome sequences and wealth of legacy biochemical information has led to the reconstruction of genome-scale metabolic networks in the last 15 years for several organisms across the three domains of life. Due to paucity of information on kinetic parameters associated with metabolic reactions, the constraint-based modelling approach, flux balance analysis (FBA), has proved to be a vital alternative to investigate the capabilities of reconstructed metabolic networks. In parallel, advent of high-throughput technologies has led to the generation of massive amounts of omics data on transcriptional regulation comprising mRNA transcript levels and genome-wide binding profile of transcriptional regulators. A frontier area in metabolic systems biology has been the development of methods to integrate the available transcriptional regulatory information into constraint-based models of reconstructed metabolic networks in order to increase the predictive capabilities of computational models and understand the regulation of cellular metabolism. Here, we review the existing methods to integrate transcriptional regulatory information into constraint-based models of metabolic networks.

  3. Genomic similarity and kernel methods I: advancements by building on mathematical and statistical foundations.

    PubMed

    Schaid, Daniel J

    2010-01-01

    Measures of genomic similarity are the basis of many statistical analytic methods. We review the mathematical and statistical basis of similarity methods, particularly based on kernel methods. A kernel function converts information for a pair of subjects to a quantitative value representing either similarity (larger values meaning more similar) or distance (smaller values meaning more similar), with the requirement that it must create a positive semidefinite matrix when applied to all pairs of subjects. This review emphasizes the wide range of statistical methods and software that can be used when similarity is based on kernel methods, such as nonparametric regression, linear mixed models and generalized linear mixed models, hierarchical models, score statistics, and support vector machines. The mathematical rigor for these methods is summarized, as is the mathematical framework for making kernels. This review provides a framework to move from intuitive and heuristic approaches to define genomic similarities to more rigorous methods that can take advantage of powerful statistical modeling and existing software. A companion paper reviews novel approaches to creating kernels that might be useful for genomic analyses, providing insights with examples [1].

  4. Automated identification of depsipeptide natural products by an informatic search algorithm.

    PubMed

    Skinnider, Michael A; Johnston, Chad W; Zvanych, Rostyslav; Magarvey, Nathan A

    2015-01-19

    Nonribosomal depsipeptides are a class of potent microbial natural products, which include several clinically approved pharmaceutical agents. Genome sequencing has revealed a large number of uninvestigated natural-product biosynthetic gene clusters. However, while novel informatic search methods to access these gene clusters have been developed to identify peptide natural products, depsipeptide detection has proven challenging. Herein, we present an improved version of our informatic search algorithm for natural products (iSNAP), which facilitates the detection of known and genetically predicted depsipeptides in complex microbial culture extracts. We validated this technology by identifying several depsipeptides from novel producers, and located a large number of novel depsipeptide gene clusters for future study. This approach highlights the value of chemoinformatic search methods for the discovery of genetically encoded metabolites by targeting specific areas of chemical space.

  5. Human Genome Program

    SciTech Connect

    Not Available

    1993-01-01

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

  6. Human Genome Project

    SciTech Connect

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

    1998-01-04

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

  7. Systems Medicine: The Future of Medical Genomics, Healthcare, and Wellness.

    PubMed

    Saqi, Mansoor; Pellet, Johann; Roznovat, Irina; Mazein, Alexander; Ballereau, Stéphane; De Meulder, Bertrand; Auffray, Charles

    2016-01-01

    Recent advances in genomics have led to the rapid and relatively inexpensive collection of patient molecular data including multiple types of omics data. The integration of these data with clinical measurements has the potential to impact on our understanding of the molecular basis of disease and on disease management. Systems medicine is an approach to understanding disease through an integration of large patient datasets. It offers the possibility for personalized strategies for healthcare through the development of a new taxonomy of disease. Advanced computing will be an important component in effectively implementing systems medicine. In this chapter we describe three computational challenges associated with systems medicine: disease subtype discovery using integrated datasets, obtaining a mechanistic understanding of disease, and the development of an informatics platform for the mining, analysis, and visualization of data emerging from translational medicine studies.

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

    PubMed

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

    2016-09-01

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

  9. Advanced Cancer Genomics Institute: Genetic Signatures and Therapeutic Targets in Cancer Progression

    DTIC Science & Technology

    2015-04-01

    Covaris E210: DNA shearer used to produce next-gen libraries v) Caliper Sciclone: liquid handling robotic station vi) Autoloader-2: robotic platform...the NGS capabilities funded through the NFGC/TATRC mechanism have been published: 1. Hennon MW, Yendamuri S. Advances in lung cancer surgery . J

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

    PubMed

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

    2016-05-01

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

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

    PubMed Central

    2013-01-01

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

  12. Genomic damage in end-stage renal failure: potential involvement of advanced glycation end products and carbonyl stress.

    PubMed

    Stopper, Helga; Schupp, Nicole; Bahner, Udo; Sebekova, Katarina; Klassen, Andre; Heidland, August

    2004-09-01

    In patients with chronic renal failure, genomic damage has been shown by numerous biomarkers, such as micronuclei frequency and comet assay (single-cell gel electrophoresis) in peripheral lymphocytes, 8-hydroxy 2'-deoxyguanosine (8-OH-dG) content in leukocytes, mitochondrial DNA deletions in skeletal muscle tissue and hair follicles, as well as in DNA repair mechanisms in freshly isolated lymphocytes after ultraviolet light exposure. In the pathogenesis of DNA damage--besides genetic influences, enhanced reactive oxygen species (ROS), and lipid peroxidation-the genotoxic potential of advanced glycation end products (AGEs) and reactive carbonyl compounds deserve special attention. In fact, reactions of glucose with DNA can lead to mutagenic DNA AGEs. In vitro, incubation of tubulus cells with various AGEs and methylglyoxal induces DNA damage, which is suppressed by antioxidants. This underlines the role played by oxidative stress in DNA damage.

  13. The Open Microscopy Environment: open image informatics for the biological sciences

    NASA Astrophysics Data System (ADS)

    Blackburn, Colin; Allan, Chris; Besson, Sébastien; Burel, Jean-Marie; Carroll, Mark; Ferguson, Richard K.; Flynn, Helen; Gault, David; Gillen, Kenneth; Leigh, Roger; Leo, Simone; Li, Simon; Lindner, Dominik; Linkert, Melissa; Moore, Josh; Moore, William J.; Ramalingam, Balaji; Rozbicki, Emil; Rustici, Gabriella; Tarkowska, Aleksandra; Walczysko, Petr; Williams, Eleanor; Swedlow, Jason R.

    2016-07-01

    Despite significant advances in biological imaging and analysis, major informatics challenges remain unsolved: file formats are proprietary, storage and analysis facilities are lacking, as are standards for sharing image data and results. While the open FITS file format is ubiquitous in astronomy, astronomical imaging shares many challenges with biological imaging, including the need to share large image sets using secure, cross-platform APIs, and the need for scalable applications for processing and visualization. The Open Microscopy Environment (OME) is an open-source software framework developed to address these challenges. OME tools include: an open data model for multidimensional imaging (OME Data Model); an open file format (OME-TIFF) and library (Bio-Formats) enabling free access to images (5D+) written in more than 145 formats from many imaging domains, including FITS; and a data management server (OMERO). The Java-based OMERO client-server platform comprises an image metadata store, an image repository, visualization and analysis by remote access, allowing sharing and publishing of image data. OMERO provides a means to manage the data through a multi-platform API. OMERO's model-based architecture has enabled its extension into a range of imaging domains, including light and electron microscopy, high content screening, digital pathology and recently into applications using non-image data from clinical and genomic studies. This is made possible using the Bio-Formats library. The current release includes a single mechanism for accessing image data of all types, regardless of original file format, via Java, C/C++ and Python and a variety of applications and environments (e.g. ImageJ, Matlab and R).

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

    SciTech Connect

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

    2013-09-15

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

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

    PubMed Central

    Orkin, Stuart H.

    2015-01-01

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

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

    PubMed Central

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

    2012-01-01

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

  17. Advances in genome-wide protein expression using the wheat germ cell-free system.

    PubMed

    Endo, Yaeta; Sawasaki, Tatsuya

    2005-01-01

    In the current post-genomic era, cell-free translation platforms are gaining importance in structural as well as functional genomics. They are based on extracts prepared from Escherichia coli cells, wheat germ, or rabbit reticulocytes, and when programmed with any mRNA in the presence of energy sources and amino acids, can synthesize the respective protein in vitro. Among the cell-free systems, the wheat germ-based translation system is of special interest due to its eukaryotic nature and robustness. This chapter outlines the existing protein production platforms and their limitations, and describes the basic concept of the wheat germ-based cell-free system. It also demonstrates how the conventional wheat germ system can be improved by eliminating endogenous inhibitors, by using an expression vector specially designed for this system and polymerase chain reaction-directed protein synthesis directly from cDNAs in a bi-layer translation system. Finally, a robotic procedure for translation based on the wheat germ extract and bi-layer cell-free translation is described.

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

    PubMed

    Orkin, Stuart H

    2016-03-01

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

  19. Advanced yellow fever virus genome detection in point-of-care facilities and reference laboratories.

    PubMed

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

    2012-12-01

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

  20. Technological Advances in Bifidobacterial Molecular Genetics: Application to Functional Genomics and Medical Treatments

    PubMed Central

    FUKIYA, Satoru; HIRAYAMA, Yosuke; SAKANAKA, Mikiyasu; KANO, Yasunobu; YOKOTA, Atsushi

    2012-01-01

    Bifidobacteria are well known as beneficial intestinal bacteria that exert health-promoting effects in humans. In addition to physiological and immunological investigations, molecular genetic technologies have been developed and have recently started to be applied to clarify the molecular bases of host-Bifidobacterium interactions. These technologies include transformation technologies and Escherichia coli-Bifidobacterium shuttle vectors that enable heterologous gene expression. In this context, a plasmid artificial modification method that protects the introduced plasmid from the restriction system in host bifidobacteria has recently been developed to increase transformation efficiency. On the other hand, targeted gene inactivation systems, which are vital for functional genomics, seemed far from being practically applicable in bifidobacteria. However, remarkable progress in this technology has recently been achieved, enabling functional genomics in bifidobacteria. Integrated use of these molecular genetic technologies with omics-based analyses will surely boost characterization of the molecular basis underlying beneficial effects of bifidobacteria. Applications of recombinant bifidobacteria to medical treatments have also progressed. PMID:24936345

  1. Informatics and public health at CDC.

    PubMed

    McNabb, Scott J N; Koo, D; Seligman, J

    2006-12-22

    Since CDC acquired its first mainframe computer in 1964, the use of information technology in public health practice has grown steadily and, during the past 2 decades, dramatically. Public health informatics (PHI) arrived on the scene during the 1990s after medical informatics (intersecting information technology, medicine, and health care) and bioinformatics (intersecting mathematics, statistics, computer science, and molecular biology). Similarly, PHI merged the disciplines of information science and computer science to public health practice, research, and learning. Using strategies and standards, practitioners employ PHI tools and training to maximize health impacts at local, state, and national levels. They develop and deploy information technology solutions that provide accurate, timely, and secure information to guide public health action.

  2. Distributed medical informatics education using internet2.

    PubMed

    Tidmarsh, Patrica J; Cummings, Joseph; Hersh, William R; Freidman, Charles P

    2002-01-01

    The curricula of most medical informatics training programs are incomplete. We used Internet2-based videoconferencing to expand the educational opportunities of medical informatics students at Oregon Health & Science University and the University of Pittsburgh. Students and faculty in both programs shared extra-curricular research conferences and journal club meetings. A course in Information Retrieval was made available to students in both programs. The conferences, meetings and class were well accepted by participants. A few problems were experienced with the technology, some of which were resolved, and some non-technical challenges to distributing academic conferences, meetings and coursework were also uncovered. We plan to continue our efforts with expanded course and extra-curricular offerings and a more comprehensive evaluation strategy.

  3. Distributed Medical Informatics Education Using Internet2

    PubMed Central

    Cummings, Joseph; Tidmarsh, Patricia; Hersh, William; Friedman, Charles

    2001-01-01

    The subject expertise of most medical informatics training programs funded by the National Library of Medicine (NLM) is incomplete. This not only limits the topical content students from individual sites are taught, but also restricts the project work they can undertake. This goal of this pilot project is to enable students in the informatics programs at two different sites - Oregon Health Sciences University (OHSU) and University of Pittsburgh (UP) - to have access to a broader range of faculty, their subject expertise, and other students with whom to collaborate using high-speed networking and distance learning modalities. Students at OHSU and UP participate in real time training program activities via IP-based/Internet2 videoconferences.

  4. Distributed medical informatics education using internet2.

    PubMed Central

    Tidmarsh, Patrica J.; Cummings, Joseph; Hersh, William R.; Freidman, Charles P.

    2002-01-01

    The curricula of most medical informatics training programs are incomplete. We used Internet2-based videoconferencing to expand the educational opportunities of medical informatics students at Oregon Health & Science University and the University of Pittsburgh. Students and faculty in both programs shared extra-curricular research conferences and journal club meetings. A course in Information Retrieval was made available to students in both programs. The conferences, meetings and class were well accepted by participants. A few problems were experienced with the technology, some of which were resolved, and some non-technical challenges to distributing academic conferences, meetings and coursework were also uncovered. We plan to continue our efforts with expanded course and extra-curricular offerings and a more comprehensive evaluation strategy. PMID:12463932

  5. The young person's guide to biomedical informatics.

    PubMed

    van Bemmel, Jan H

    2006-01-01

    In a retrospective review, a parallel is drawn between the challenges by which a research department in biomedical informatics is confronted and those of a symphony orchestra. In both areas, different disciplines and different groups of instruments can be discerned. The importance of mastering one's instrument and the harmony between the team members is stressed. The conductor has to stimulate the individual players so that they can all have a successful career. Competition between orchestras and performance assessments determine survival and success. A record of refereed publications is crucial for continued existence. Conclusions are that biomedical informatics is typically multidisciplinary, that hypotheses underlying research should be carefully formulated, that the time from research to application may easily take 20 years or more, that mutual trust and knowing each other's competences is essential for success, that a good leader gives enough room to all team members to develop their careers, and that the outcomes of assessment studies are related to the quality of publications.

  6. Curricula Challenges and Informatics Competencies for Nurse Educators.

    PubMed

    Kinnunen, Ulla-Mari; Rajalahti, Elina; Cummings, Elizabeth; Borycki, Elizabeth M

    2017-01-01

    Nursing informatics competencies are fundamental to nursing practice in all areas of nursing work, including direct patient care, administration and education. The recent activity relating to the development of nursing informatics competencies for beginning level nurses has exposed a paucity of understanding of the requirements for nursing informatics competencies for nurse educators. So, whilst the challenge of educating faculty to teach informatics has been limited, research into such competencies is required to meet this challenge. This paper describes the challenges and issues associated with nursing informatics competency development for faculty, outlines the capabilities of faculty, and presents a vision for the future of informatics education for faculty. The final requirement of the introduction of new competencies is to determine appropriate evaluation measures that reflect the requirements of all stakeholders.

  7. Current advances in DNA repair: regulation of enzymes and pathways involved in maintaining genomic stability.

    PubMed

    Neher, Tracy M; Turchi, John J

    2011-06-15

    Novel discoveries in the DNA repair field have lead to continuous and rapid advancement of our understanding of not only DNA repair but also DNA replication and recombination. Research in the field transcends numerous areas of biology, biochemistry, physiology, and medicine, making significant connections across these broad areas of study. From early studies conducted in bacterial systems to current analyses in eukaryotic systems and human disease, the innovative research into the mechanisms of repair machines and the consequences of ineffective DNA repair has impacted a wide scientific community. This Forum contains a select mix of primary research articles in addition to a number of timely reviews covering a subset of DNA repair pathways where recent advances and novel discoveries are improving our understanding of DNA repair, its regulation, and implications to human disease.

  8. Development of Advanced Technologies for Complete Genomic and Proteomic Characterization of Quantized Human Tumor Cells

    DTIC Science & Technology

    2013-07-01

    extending the period of performance soon. The Ivy Center for Advanced Brain Tumor Treatment at the Swedish Neuroscience Institute (SNI) has...markers: (A) GFAP/astrocytes, (B), TUJ-1/neurons and (C) O4/oligodendrocytes. Cells were grown in NSA media without growth factors (EGF and FGF-2...Treatment at the Swedish Neuroscience Institute (SNI) has collected potentially eligible tumor tissue from over forty GBM patients. • Primary GBM cell

  9. Informatics, machine learning and computational medicinal chemistry.

    PubMed

    Mitchell, John B O

    2011-03-01

    This article reviews the use of informatics and computational chemistry methods in medicinal chemistry, with special consideration of how computational techniques can be adapted and extended to obtain more and higher-quality information. Special consideration is given to the computation of protein-ligand binding affinities, to the prediction of off-target bioactivities, bioactivity spectra and computational toxicology, and also to calculating absorption-, distribution-, metabolism- and excretion-relevant properties, such as solubility.

  10. Materials Informatics: Statistical Modeling in Material Science.

    PubMed

    Yosipof, Abraham; Shimanovich, Klimentiy; Senderowitz, Hanoch

    2016-12-01

    Material informatics is engaged with the application of informatic principles to materials science in order to assist in the discovery and development of new materials. Central to the field is the application of data mining techniques and in particular machine learning approaches, often referred to as Quantitative Structure Activity Relationship (QSAR) modeling, to derive predictive models for a variety of materials-related "activities". Such models can accelerate the development of new materials with favorable properties and provide insight into the factors governing these properties. Here we provide a comparison between medicinal chemistry/drug design and materials-related QSAR modeling and highlight the importance of developing new, materials-specific descriptors. We survey some of the most recent QSAR models developed in materials science with focus on energetic materials and on solar cells. Finally we present new examples of material-informatic analyses of solar cells libraries produced from metal oxides using combinatorial material synthesis. Different analyses lead to interesting physical insights as well as to the design of new cells with potentially improved photovoltaic parameters.

  11. Building strong relationships between conservation genetics and primary industry leads to mutually beneficial genomic advances.

    PubMed

    Galla, Stephanie J; Buckley, Thomas R; Elshire, Rob; Hale, Marie L; Knapp, Michael; McCallum, John; Moraga, Roger; Santure, Anna W; Wilcox, Phillip; Steeves, Tammy E

    2016-11-01

    Several reviews in the past decade have heralded the benefits of embracing high-throughput sequencing technologies to inform conservation policy and the management of threatened species, but few have offered practical advice on how to expedite the transition from conservation genetics to conservation genomics. Here, we argue that an effective and efficient way to navigate this transition is to capitalize on emerging synergies between conservation genetics and primary industry (e.g., agriculture, fisheries, forestry and horticulture). Here, we demonstrate how building strong relationships between conservation geneticists and primary industry scientists is leading to mutually-beneficial outcomes for both disciplines. Based on our collective experience as collaborative New Zealand-based scientists, we also provide insight for forging these cross-sector relationships.

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2016-02-01

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

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

    PubMed Central

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

    2011-01-01

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

  15. The future of biomedical informatics: a perspective from academia.

    PubMed

    Shortliffe, Edward H

    2012-01-01

    Academic biomedical informatics has achieved great successes through research contributions over several decades, now reflected in a thriving commercial marketplace for electronic health records and other informatics tools. That very success, coupled with changes in the ability of governments to support research at past levels, is forcing a reconsideration of the directions and emphases for faculty members in informatics academic units. This paper discusses those forces and proposes areas of emphasis that will strengthen the academic discipline as it evolves in the years ahead. The focus is on the role of academic informaticians as practitioners of informatics, as researchers, and as educators.

  16. Crossing the chasm: information technology to biomedical informatics.

    PubMed

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

    2011-06-01

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

  17. Crossing the Chasm: Information Technology to Biomedical Informatics

    PubMed Central

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

    2011-01-01

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

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2016-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

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

    SciTech Connect

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

    2015-12-26

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

  2. Functional Reconstitution of a Fungal Natural Product Gene Cluster by Advanced Genome Editing.

    PubMed

    Weber, Jakob; Valiante, Vito; Nødvig, Christina S; Mattern, Derek J; Slotkowski, Rebecca A; Mortensen, Uffe H; Brakhage, Axel A

    2017-01-20

    Filamentous fungi produce varieties of natural products even in a strain dependent manner. However, the genetic basis of chemical speciation between strains is still widely unknown. One example is trypacidin, a natural product of the opportunistic human pathogen Aspergillus fumigatus, which is not produced among different isolates. Combining computational analysis with targeted gene editing, we could link a single nucleotide insertion in the polyketide synthase of the trypacidin biosynthetic pathway and reconstitute its production in a nonproducing strain. Thus, we present a CRISPR/Cas9-based tool for advanced molecular genetic studies in filamentous fungi, exploiting selectable markers separated from the edited locus.

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

    PubMed Central

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

    2013-01-01

    Imaging has become a prevalent tool in the diagnosis and treatment of many diseases, providing a unique in vivo, multi-scale view of anatomic and physiologic processes. With the increased use of imaging and its progressive technical advances, the role of imaging informatics is now evolving—from one of managing images, to one of integrating the full scope of clinical information needed to contextualize and link observations across phenotypic and genotypic scales. Several challenges exist for imaging informatics, including the need for methods to transform clinical imaging studies and associated data into structured information that can be organized and analyzed. We examine some of these challenges in establishing imaging-based observational databases that can support the creation of comprehensive disease models. The development of these databases and ensuing models can aid in medical decision making and knowledge discovery and ultimately, transform the use of imaging to support individually-tailored patient care. PMID:23775172

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

    NASA Astrophysics Data System (ADS)

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

    2009-02-01

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

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

    PubMed Central

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

    2016-01-01

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

  6. Advancement in genetic variants conferring obesity susceptibility from genome-wide association studies.

    PubMed

    Wang, Tao; Jia, Weiping; Hu, Cheng

    2015-06-01

    Obesity prevalence has increased in recent years. Lifestyle change fuels obesity, but genetic factors cause more than 50% of average variations in obesity. The advent of genome-wide association studies (GWAS) has hastened the progress of polygenic obesity research. As of this writing, more than 73 obesity susceptibility loci have been identified in ethnic groups through GWAS. The identified loci explain only 2% to 4% of obesity heritability, thereby indicating that a large proportion of loci remain undiscovered. Thus, the next step is to identify and confirm novel loci, which may exhibit smaller effects and lower allele frequencies than established loci. However, achieving these tasks has been difficult for researchers. GWAS help researchers discover the causal loci. Moreover, numerous biological studies have been performed on the polygenic effects on obesity, such as studies on fat mass- and obesity-associated gene (FTO), but the role of these polygenic effects in the mechanism of obesity remains unclear. Thus, obesity-causing variations should be identified, and insights into the biology of polygenic effects on obesity are needed.

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

    PubMed

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

    2012-10-01

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

  8. Informatics for RNA Sequencing: A Web Resource for Analysis on the Cloud

    PubMed Central

    Griffith, Malachi; Walker, Jason R.; Spies, Nicholas C.; Ainscough, Benjamin J.; Griffith, Obi L.

    2015-01-01

    Massively parallel RNA sequencing (RNA-seq) has rapidly become the assay of choice for interrogating RNA transcript abundance and diversity. This article provides a detailed introduction to fundamental RNA-seq molecular biology and informatics concepts. We make available open-access RNA-seq tutorials that cover cloud computing, tool installation, relevant file formats, reference genomes, transcriptome annotations, quality-control strategies, expression, differential expression, and alternative splicing analysis methods. These tutorials and additional training resources are accompanied by complete analysis pipelines and test datasets made available without encumbrance at www.rnaseq.wiki. PMID:26248053

  9. Creating a pipeline of talent for informatics: STEM initiative for high school students in computer science, biology, and biomedical informatics

    PubMed Central

    Dutta-Moscato, Joyeeta; Gopalakrishnan, Vanathi; Lotze, Michael T.; Becich, Michael J.

    2014-01-01

    This editorial provides insights into how informatics can attract highly trained students by involving them in science, technology, engineering, and math (STEM) training at the high school level and continuing to provide mentorship and research opportunities through the formative years of their education. Our central premise is that the trajectory necessary to be expert in the emergent fields in front of them requires acceleration at an early time point. Both pathology (and biomedical) informatics are new disciplines which would benefit from involvement by students at an early stage of their education. In 2009, Michael T Lotze MD, Kirsten Livesey (then a medical student, now a medical resident at University of Pittsburgh Medical Center (UPMC)), Richard Hersheberger, PhD (Currently, Dean at Roswell Park), and Megan Seippel, MS (the administrator) launched the University of Pittsburgh Cancer Institute (UPCI) Summer Academy to bring high school students for an 8 week summer academy focused on Cancer Biology. Initially, pathology and biomedical informatics were involved only in the classroom component of the UPCI Summer Academy. In 2011, due to popular interest, an informatics track called Computer Science, Biology and Biomedical Informatics (CoSBBI) was launched. CoSBBI currently acts as a feeder program for the undergraduate degree program in bioinformatics at the University of Pittsburgh, which is a joint degree offered by the Departments of Biology and Computer Science. We believe training in bioinformatics is the best foundation for students interested in future careers in pathology informatics or biomedical informatics. We describe our approach to the recruitment, training and research mentoring of high school students to create a pipeline of exceptionally well-trained applicants for both the disciplines of pathology informatics and biomedical informatics. We emphasize here how mentoring of high school students in pathology informatics and biomedical informatics

  10. Creating a pipeline of talent for informatics: STEM initiative for high school students in computer science, biology, and biomedical informatics.

    PubMed

    Dutta-Moscato, Joyeeta; Gopalakrishnan, Vanathi; Lotze, Michael T; Becich, Michael J

    2014-01-01

    This editorial provides insights into how informatics can attract highly trained students by involving them in science, technology, engineering, and math (STEM) training at the high school level and continuing to provide mentorship and research opportunities through the formative years of their education. Our central premise is that the trajectory necessary to be expert in the emergent fields in front of them requires acceleration at an early time point. Both pathology (and biomedical) informatics are new disciplines which would benefit from involvement by students at an early stage of their education. In 2009, Michael T Lotze MD, Kirsten Livesey (then a medical student, now a medical resident at University of Pittsburgh Medical Center (UPMC)), Richard Hersheberger, PhD (Currently, Dean at Roswell Park), and Megan Seippel, MS (the administrator) launched the University of Pittsburgh Cancer Institute (UPCI) Summer Academy to bring high school students for an 8 week summer academy focused on Cancer Biology. Initially, pathology and biomedical informatics were involved only in the classroom component of the UPCI Summer Academy. In 2011, due to popular interest, an informatics track called Computer Science, Biology and Biomedical Informatics (CoSBBI) was launched. CoSBBI currently acts as a feeder program for the undergraduate degree program in bioinformatics at the University of Pittsburgh, which is a joint degree offered by the Departments of Biology and Computer Science. We believe training in bioinformatics is the best foundation for students interested in future careers in pathology informatics or biomedical informatics. We describe our approach to the recruitment, training and research mentoring of high school students to create a pipeline of exceptionally well-trained applicants for both the disciplines of pathology informatics and biomedical informatics. We emphasize here how mentoring of high school students in pathology informatics and biomedical informatics

  11. The Recurrence Relations in Teaching Students of Informatics

    ERIC Educational Resources Information Center

    Bakoev, Valentin P.

    2010-01-01

    The topic "Recurrence relations" and its place in teaching students of Informatics is discussed in this paper. We represent many arguments about the importance, the necessity and the benefit of studying this subject by Informatics students. They are based on investigation of some fundamental books and textbooks on Discrete Mathematics,…

  12. Characteristics of Information Systems and Business Informatics Study Programs

    ERIC Educational Resources Information Center

    Helfert, Markus

    2011-01-01

    Over the last decade there is an intensive discussion within the Information Systems (IS) and Informatics community about the characteristics and identity of the discipline. Simultaneously with the discussion, there is an ongoing debate on essential skills and capabilities of IS and Business Informatics graduates as well as the profile of IS…

  13. Publication trends and impact factors in the Medical Informatics literature.

    PubMed

    Lavallie, Donna L; Wolf, Fredric M

    2005-01-01

    We survey the "evolution" of the field of Medical Informatics by describing trends in volume(quantity) of Medical Informatics-indexed publications, identifying major journals of publication and their focus areas and presenting trends in impact factor scores during the 1994-2003 period. Changes in total impact-scores suggest an increasing trend of publication in journals of higher impact.

  14. Genome-Wide Association Mapping for Intelligence in Military Working Dogs: Development of Advanced Classification Algorithm for Genome-Wide Single Nucleotide Polymorphism (SNP) Data Analysis

    DTIC Science & Technology

    2011-04-01

    distribution unlimited. QC – quality control QTL – quantitative trait loci SNP – single nucleotide polymorphism TE – Tris + EDTA TBE – Tris + Boric Acid + EDTA WGSA – whole genome sampling assay ...canine intelligence testing protocol EDTA – ethylenediaminetetraacetic acid GWAS – genome-wide association study LD – linkage disequilibrium MWD

  15. Improving Bridging from Informatics Theory to Practice

    PubMed Central

    Haux, R.

    2015-01-01

    Background In 1962, Methods of Information in Medicine (MIM) began to publish papers on the methodology and scientific fundamentals of managing data, information, and knowledge in biomedicine and health care. Meeting an increasing demand for research about practical implementation of health information systems, the journal Applied Clinical Informatics (ACI) was launched in 2009. Both journals are official journals of the International Medical Informatics Association (IMIA). Objectives Based on prior analyses, we aimed to describe major topics published in MIM during 2014 and to explore whether theory of MIM influenced practice of ACI. Our objectives were further to describe lessons learned and to discuss possible editorial policies to improve bridging from theory to practice. Methods We conducted a retrospective, observational study reviewing MIM articles published during 2014 (N=61) and analyzing reference lists of ACI articles from 2014 (N=70). Lessons learned and opinions about MIM editorial policies were developed in consensus by the two authors. These have been influenced by discussions with the journal’s associate editors and editorial board members. Results The publication topics of MIM in 2014 were broad, covering biomedical and health informatics, medical biometry and epidemiology. Important topics discussed were biosignal interpretation, boosting methodologies, citation analysis, health-enabling and ambient assistive technologies, health record banking, safety, and standards. Nine ACI practice articles from 2014 cited eighteen MIM theory papers from any year. These nine ACI articles covered mainly the areas of clinical documentation and medication-related decision support. The methodological basis they cited from was almost exclusively related to evaluation. We could show some direct links where theory impacted practice. These links are however few in relation to the total amount of papers published. Conclusions Editorial policies such as publishing

  16. [Standards in Medical Informatics: Fundamentals and Applications].

    PubMed

    Suárez-Obando, Fernando; Camacho Sánchez, Jhon

    2013-09-01

    The use of computers in medical practice has enabled novel forms of communication to be developed in health care. The optimization of communication processes is achieved through the use of standards to harmonize the exchange of information and provide a common language for all those involved. This article describes the concept of a standard applied to medical informatics and its importance in the development of various applications, such as computational representation of medical knowledge, disease classification and coding systems, medical literature searches and integration of biological and clinical sciences.

  17. Integrating problem-based learning in a nursing informatics curriculum.

    PubMed

    Demiris, George; Zierler, Brenda

    2010-02-01

    In recent years employers in health care organizations have been recognizing the need for nurses to enter the workforce with a set of informatics competencies. Numerous nursing informatics programs have been established worldwide. The challenge becomes to explore innovative tools that will equip nurses with the appropriate skills to utilize information technology to improve health care quality and patient safety and redesign health care services. This paper presents the introduction of problem-based learning (PBL) modules into an existing nursing informatics curriculum, the Clinical Informatics and Patient Centered Technologies Master program at the School of Nursing, University of Washington. Additionally, we discuss recommendations and challenges associated with the integration of PBL in nursing informatics graduate education including the need for facilitators, flexible technology platforms, promotion and documentation of group work, faculty training and supervision by a program committee.

  18. Exploring the biomedical and health informatics educational programs in europe.

    PubMed

    Manifava, Eirini; Kolokathi, Aikaterini; Mantas, John

    2014-01-01

    The Health Information Technology can improve public health, quality of health care etc. Thus, it is important for professionals to be well educated by training programs. The aim of this paper is to record all the educational programs with specializations in Health Informatics, Medical Informatics, Bioinformatics, Biomedical Informatics and Biomedical Engineering in European Universities and Institutions. An on-line research was conducted on Scopus, PubMed, Scholar Google, and Google. More than 150 universities and colleges in Europe conduct educational programs for these domains. The majority them, expertise in Biomedical Engineering (31%), 22% of the educational programs correspond to Bioinformatics, while Health Informatics studies have 18%. On the last few years, a growth of Health informatics professionals has been observed in Europe.

  19. [Medical informatics education at the Medical School in Tuzla].

    PubMed

    Sabanović, Zekerijah; Mujcinagić, Alija

    2004-01-01

    Medical informatics is a specific and interdisciplinary science which involves many participants of the health system like: patients, physicians, nurses, managers, administrators, computer experts, students, with the different level of education and understanding, different approaches and expectations. Education of medical informatics requests organization solutions of high quality and necessary equipment for its realization. Educational programs are also limited by student's basic knowledge of informatics from secondary schools. For assessment of this knowledge we have conducted special designed questionnaire at the first year of undergraduate study which results confirm our thesis that great number of students entered the faculty with the lack of basic knowledge from informatics area. In this paper was presented level of organization and education of medical informatics at the Medical faculty and University Clinical Center of Tuzla, with its characteristics through which this system has been passed since 1990.

  20. High throughput instruments, methods, and informatics for systems biology.

    SciTech Connect

    Sinclair, Michael B.; Cowie, Jim R.; Van Benthem, Mark Hilary; Wylie, Brian Neil; Davidson, George S.; Haaland, David Michael; Timlin, Jerilyn Ann; Aragon, Anthony D.; Keenan, Michael Robert; Boyack, Kevin W.; Thomas, Edward Victor; Werner-Washburne, Margaret C.; Mosquera-Caro, Monica P.; Martinez, M. Juanita; Martin, Shawn Bryan; Willman, Cheryl L.

    2003-12-01

    High throughput instruments and analysis techniques are required in order to make good use of the genomic sequences that have recently become available for many species, including humans. These instruments and methods must work with tens of thousands of genes simultaneously, and must be able to identify the small subsets of those genes that are implicated in the observed phenotypes, or, for instance, in responses to therapies. Microarrays represent one such high throughput method, which continue to find increasingly broad application. This project has improved microarray technology in several important areas. First, we developed the hyperspectral scanner, which has discovered and diagnosed numerous flaws in techniques broadly employed by microarray researchers. Second, we used a series of statistically designed experiments to identify and correct errors in our microarray data to dramatically improve the accuracy, precision, and repeatability of the microarray gene expression data. Third, our research developed new informatics techniques to identify genes with significantly different expression levels. Finally, natural language processing techniques were applied to improve our ability to make use of online literature annotating the important genes. In combination, this research has improved the reliability and precision of laboratory methods and instruments, while also enabling substantially faster analysis and discovery.

  1. Impact of sperm genome decay on Day-3 embryo chromosomal abnormalities from advanced-maternal-age patients.

    PubMed

    Kaarouch, Ismail; Bouamoud, Nouzha; Louanjli, Noureddine; Madkour, Aicha; Copin, Henri; Benkhalifa, Moncef; Sefrioui, Omar

    2015-10-01

    Infertile male patients often exhibit unconventional semen parameters, including DNA fragmentation, chromatin dispersion, and aneuploidy-collectively referred to as sperm genome decay (SGD). We investigated the correlation of SGD to embryo chromosomal abnormalities and its effect on clinical pregnancy rates in patients with advanced maternal age (AMA) (>40 years) who were undergoing intracytoplasmic sperm injection-preimplantation genetic screening (ICSI-PGS). Three groups were assessed: patients with AMA and male partners with normal sperm (AMA-N); AMA patients and male partners presenting with SGD (AMA-SGD); and young fertile female patients and male partners with SGD (Y-SGD). We found a significant increase in embryonic chromosomal abnormalities-polyploidy, nullisomy, mosaicism, and chaotic anomaly rates-when semen parameters are altered (76% vs. 67% and 66% in AMA-SGD vs. AMA-N and Y-SGD groups, respectively). Statistical analysis showed a correlation between SGD and aneuploidies of embryonic chromosomes 13, 16, 21, X, and Y, as well as negative clinical outcomes. Incorporation of molecular sperm analyses should therefore significantly minimize the risk of transmission of chromosomal anomalies from spermatozoa to embryos, and may provide better predictors of pregnancy than conventional sperm analyses. We also demonstrated that an ICSI-PGS program should be implemented for SGD patients in order to limit transmission of chromosomal paternal anomalies and to improve clinical outcome.

  2. Health Informatics via Machine Learning for the Clinical Management of Patients

    PubMed Central

    Niehaus, K. E.; Charlton, P.; Colopy, G. W.

    2015-01-01

    Summary Objectives To review how health informatics systems based on machine learning methods have impacted the clinical management of patients, by affecting clinical practice. Methods We reviewed literature from 2010-2015 from databases such as Pubmed, IEEE xplore, and INSPEC, in which methods based on machine learning are likely to be reported. We bring together a broad body of literature, aiming to identify those leading examples of health informatics that have advanced the methodology of machine learning. While individual methods may have further examples that might be added, we have chosen some of the most representative, informative exemplars in each case. Results Our survey highlights that, while much research is taking place in this high-profile field, examples of those that affect the clinical management of patients are seldom found. We show that substantial progress is being made in terms of methodology, often by data scientists working in close collaboration with clinical groups. Conclusions Health informatics systems based on machine learning are in their infancy and the translation of such systems into clinical management has yet to be performed at scale. PMID:26293849

  3. Mouse Genome Database (MGD)-2017: community knowledge resource for the laboratory mouse

    PubMed Central

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

    2017-01-01

    The Mouse Genome Database (MGD: http://www.informatics.jax.org) is the primary community data resource for the laboratory mouse. It provides a highly integrated and highly curated system offering a comprehensive view of current knowledge about mouse genes, genetic markers and genomic features as well as the associations of those features with sequence, phenotypes, functional and comparative information, and their relationships to human diseases. MGD continues to enhance access to these data, to extend the scope of data content and visualizations, and to provide infrastructure and user support that ensures effective and efficient use of MGD in the advancement of scientific knowledge. Here, we report on recent enhancements made to the resource and new features. PMID:27899570

  4. An academic-business partnership for advancing clinical informatics.

    PubMed

    Connors, Helen R; Weaver, Charlotte; Warren, Judith; Miller, Karen L

    2002-01-01

    A jointly funded partnership between the school of nursing at a large midwestern university and a premier health care information technology supplier represents a pioneering event for education and for the health care information technology industry. The impetus for this partnership arose from Institute of Medicine reports published in late 1999 and early 2001 addressing the quality, error, and waste in the health care system in the United States. The Simulated E-hEalth Delivery System (SEEDS) provides opportunities based on best practices in education to learn and practice clinical skills in a state-of-the-art environment using a live-production, clinical information system designed for care delivery. A pilot project that began with a small cohort of baccalaureate nursing students has been implemented and extended. SEEDS will also be extended to other health professional programs.

  5. Health informatics model for helminthiasis in Thailand.

    PubMed

    Nithikathkul, C; Trevanich, A; Wongsaroj, T; Wongsawad, C; Reungsang, P

    2016-09-26

    At the beginning of the new millennium, helminth infections continue to be prevalent, particularly among impoverished populations. This study attempts to create the first health informatics model of helminthiasis in Thailand. The authors investigate how a health informatics model could be used to predict the control and eradication in a national control campaign. Fish-borne helminthiasis caused by Opisthorchis viverrini remains a major public health problem in many parts of South-East Asia, including Thailand, Lao PDR, Vietnam and Cambodia. The epicentre of this disease is located in north-east Thailand, where high prevalence coexists with a high incidence of cholangiocarcinoma (CHCA). The current report was conducted to determine a mathematical model of surveillance for helminthiasis while also using a geographic information system. The fish-borne helminthiasis model or the predicted equation was Y1 = 3.028 + 0.020 (elevation) - 2.098 (clay). For soil-transmitted helminthiasis, the mathematical model or the predicted equation was Y2 = -1.559 + 0.005 (rainfall) + 0.004 (elevation) - 2.198 (clay). The Ministry of Public Health has concluded that mass treatment for helminthiasis in the Thai population, targeting high-risk individuals, may be a cost-effective way to allocate limited funds. This type of approach, as well as further study on the correlation of clinical symptoms with environmental and geographic information, may offer a novel strategy to the helminth crisis.

  6. Contemporary issues in transfusion medicine informatics

    PubMed Central

    Sharma, Gaurav; Parwani, Anil V.; Raval, Jay S.; Triulzi, Darrell J.; Benjamin, Richard J.; Pantanowitz, Liron

    2011-01-01

    The Transfusion Medicine Service (TMS) covers diverse clinical and laboratory-based services that must be delivered with accuracy, efficiency and reliability. TMS oversight is shared by multiple regulatory agencies that cover product manufacturing and validation standards geared toward patient safety. These demands present significant informatics challenges. Over the past few decades, TMS information systems have improved to better handle blood product manufacturing, inventory, delivery, tracking and documentation. Audit trails and access to electronic databases have greatly facilitated product traceability and biovigilance efforts. Modern blood bank computing has enabled novel applications such as the electronic crossmatch, kiosk-based blood product delivery systems, and self-administered computerized blood donor interview and eligibility determination. With increasing use of barcoding technology, there has been a marked improvement in patient and specimen identification. Moreover, the emergence of national and international labeling standards such as ISBT 128 have facilitated the availability, movement and tracking of blood products across national and international boundaries. TMS has only recently begun to leverage the electronic medical record to address quality issues in transfusion practice and promote standardized documentation within institutions. With improved technology, future growth is expected in blood bank automation and product labeling with applications such as radio frequency identification devices. This article reviews several of these key informatics issues relevant to the contemporary practice of TMS. PMID:21383927

  7. Fractal Image Informatics: from SEM to DEM

    NASA Astrophysics Data System (ADS)

    Oleschko, K.; Parrot, J.-F.; Korvin, G.; Esteves, M.; Vauclin, M.; Torres-Argüelles, V.; Salado, C. Gaona; Cherkasov, S.

    2008-05-01

    In this paper, we introduce a new branch of Fractal Geometry: Fractal Image Informatics, devoted to the systematic and standardized fractal analysis of images of natural systems. The methods of this discipline are based on the properties of multiscale images of selfaffine fractal surfaces. As proved in the paper, the image inherits the scaling and lacunarity of the surface and of its reflectance distribution [Korvin, 2005]. We claim that the fractal analysis of these images must be done without any smoothing, thresholding or binarization. Two new tools of Fractal Image Informatics, firmagram analysis (FA) and generalized lacunarity (GL), are presented and discussed in details. These techniques are applicable to any kind of image or to any observed positive-valued physical field, and can be used to correlate between images. It will be shown, by a modified Grassberger-Hentschel-Procaccia approach [Phys. Lett. 97A, 227 (1983); Physica 8D, 435 (1983)] that GL obeys the same scaling law as the Allain-Cloitre lacunarity [Phys. Rev. A 44, 3552 (1991)] but is free of the problems associated with gliding boxes. Several applications are shown from Soil Physics, Surface Science, and other fields.

  8. Translational Research from an Informatics Perspective

    NASA Technical Reports Server (NTRS)

    Bernstam, Elmer; Meric-Bernstam, Funda; Johnson-Throop, Kathy A.; Turley, James P.; Smith, Jack W.

    2007-01-01

    Clinical and translational research (CTR) is an essential part of a sustainable global health system. Informatics is now recognized as an important en-abler of CTR and informaticians are increasingly called upon to help CTR efforts. The US National Institutes of Health mandated biomedical informatics activity as part of its new national CTR grant initiative, the Clinical and Translational Science Award (CTSA). Traditionally, translational re-search was defined as the translation of laboratory discoveries to patient care (bench to bedside). We argue, however, that there are many other kinds of translational research. Indeed, translational re-search requires the translation of knowledge dis-covered in one domain to another domain and is therefore an information-based activity. In this panel, we will expand upon this view of translational research and present three different examples of translation to illustrate the point: 1) bench to bedside, 2) Earth to space and 3) academia to community. We will conclude with a discussion of our local translational research efforts that draw on each of the three examples.

  9. Bayesian Analysis of the Pattern Informatics Technique

    NASA Astrophysics Data System (ADS)

    Cho, N.; Tiampo, K.; Klein, W.; Rundle, J.

    2007-12-01

    The pattern informatics (PI) [Rundle et al., 2000; Tiampo et al., 2002; Holliday et al., 2005] is a technique that uses phase dynamics in order to quantify temporal variations in seismicity patterns. This technique has shown interesting results for forecasting earthquakes with magnitude greater than or equal to 5 in southern California from 2000 to 2010 [Rundle et al., 2002]. In this work, a Bayesian approach is used to obtain a modified updated version of the PI called Bayesian pattern informatics (BPI). This alternative method uses the PI result as a prior probability and models such as ETAS [Ogata, 1988, 2004; Helmstetter and Sornette, 2002] or BASS [Turcotte et al., 2007] in order to obtain the likelihood. Its result is similar to the one obtained by the PI: the determination of regions, known as hotspots, that are most susceptible to the occurrence of events with M=5 and larger during the forecast period. As an initial test, retrospective forecasts for the southern California region from 1990 to 2000 were made with both the BPI and the PI techniques, and the results are discussed in this work.

  10. Empowered Consumers and the Health Care Team: A Dynamic Model of Health Informatics.

    PubMed

    Mancuso, Peggy J; Myneni, Sahiti

    2016-01-01

    This article presents a dynamic new model of health informatics. Within the model, the focus of health informatics changes from the provider to the consumer and incorporates the dynamic relationship of technological change to health care. Bioinformatics is the scientific discipline that is translated into care through the practice of health informatics. The loci of health informatics practices are the consumer (consumer informatics), the patient (clinical informatics), and the community (public health informatics). The continuum from individual to community interacts with and contributes to health care technology, which is represented as a constantly changing progressive wave.

  11. High-throughput neuro-imaging informatics.

    PubMed

    Miller, Michael I; Faria, Andreia V; Oishi, Kenichi; Mori, Susumu

    2013-01-01

    This paper describes neuroinformatics technologies at 1 mm anatomical scale based on high-throughput 3D functional and structural imaging technologies of the human brain. The core is an abstract pipeline for converting functional and structural imagery into their high-dimensional neuroinformatic representation index containing O(1000-10,000) discriminating dimensions. The pipeline is based on advanced image analysis coupled to digital knowledge representations in the form of dense atlases of the human brain at gross anatomical scale. We demonstrate the integration of these high-dimensional representations with machine learning methods, which have become the mainstay of other fields of science including genomics as well as social networks. Such high-throughput facilities have the potential to alter the way medical images are stored and utilized in radiological workflows. The neuroinformatics pipeline is used to examine cross-sectional and personalized analyses of neuropsychiatric illnesses in clinical applications as well as longitudinal studies. We demonstrate the use of high-throughput machine learning methods for supporting (i) cross-sectional image analysis to evaluate the health status of individual subjects with respect to the population data, (ii) integration of image and personal medical record non-image information for diagnosis and prognosis.

  12. High-throughput neuro-imaging informatics

    PubMed Central

    Miller, Michael I.; Faria, Andreia V.; Oishi, Kenichi; Mori, Susumu

    2013-01-01

    This paper describes neuroinformatics technologies at 1 mm anatomical scale based on high-throughput 3D functional and structural imaging technologies of the human brain. The core is an abstract pipeline for converting functional and structural imagery into their high-dimensional neuroinformatic representation index containing O(1000–10,000) discriminating dimensions. The pipeline is based on advanced image analysis coupled to digital knowledge representations in the form of dense atlases of the human brain at gross anatomical scale. We demonstrate the integration of these high-dimensional representations with machine learning methods, which have become the mainstay of other fields of science including genomics as well as social networks. Such high-throughput facilities have the potential to alter the way medical images are stored and utilized in radiological workflows. The neuroinformatics pipeline is used to examine cross-sectional and personalized analyses of neuropsychiatric illnesses in clinical applications as well as longitudinal studies. We demonstrate the use of high-throughput machine learning methods for supporting (i) cross-sectional image analysis to evaluate the health status of individual subjects with respect to the population data, (ii) integration of image and personal medical record non-image information for diagnosis and prognosis. PMID:24381556

  13. The history of pathology informatics: A global perspective

    PubMed Central

    Park, Seung; Parwani, Anil V.; Aller, Raymond D.; Banach, Lech; Becich, Michael J.; Borkenfeld, Stephan; Carter, Alexis B.; Friedman, Bruce A.; Rojo, Marcial Garcia; Georgiou, Andrew; Kayser, Gian; Kayser, Klaus; Legg, Michael; Naugler, Christopher; Sawai, Takashi; Weiner, Hal; Winsten, Dennis; Pantanowitz, Liron

    2013-01-01

    Pathology informatics has evolved to varying levels around the world. The history of pathology informatics in different countries is a tale with many dimensions. At first glance, it is the familiar story of individuals solving problems that arise in their clinical practice to enhance efficiency, better manage (e.g., digitize) laboratory information, as well as exploit emerging information technologies. Under the surface, however, lie powerful resource, regulatory, and societal forces that helped shape our discipline into what it is today. In this monograph, for the first time in the history of our discipline, we collectively perform a global review of the field of pathology informatics. In doing so, we illustrate how general far-reaching trends such as the advent of computers, the Internet and digital imaging have affected pathology informatics in the world at large. Major drivers in the field included the need for pathologists to comply with national standards for health information technology and telepathology applications to meet the scarcity of pathology services and trained people in certain countries. Following trials by a multitude of investigators, not all of them successful, it is apparent that innovation alone did not assure the success of many informatics tools and solutions. Common, ongoing barriers to the widespread adoption of informatics devices include poor information technology infrastructure in undeveloped areas, the cost of technology, and regulatory issues. This review offers a deeper understanding of how pathology informatics historically developed and provides insights into what the promising future might hold. PMID:23869286

  14. Use of statistical analysis in the biomedical informatics literature.

    PubMed

    Scotch, Matthew; Duggal, Mona; Brandt, Cynthia; Lin, Zhenqui; Shiffman, Richard

    2010-01-01

    Statistics is an essential aspect of biomedical informatics. To examine the use of statistics in informatics research, a literature review of recent articles in two high-impact factor biomedical informatics journals, the Journal of American Medical Informatics Association (JAMIA) and the International Journal of Medical Informatics was conducted. The use of statistical methods in each paper was examined. Articles of original investigations from 2000 to 2007 were reviewed. For each journal, the results by statistical methods were analyzed as: descriptive, elementary, multivariable, other regression, machine learning, and other statistics. For both journals, descriptive statistics were most often used. Elementary statistics such as t tests, chi(2), and Wilcoxon tests were much more frequent in JAMIA, while machine learning approaches such as decision trees and support vector machines were similar in occurrence across the journals. Also, the use of diagnostic statistics such as sensitivity, specificity, precision, and recall, was more frequent in JAMIA. These results highlight the use of statistics in informatics and the need for biomedical informatics scientists to have, as a minimum, proficiency in descriptive and elementary statistics.

  15. WE-E-12A-01: Medical Physics 1.0 to 2.0: MRI, Displays, Informatics

    SciTech Connect

    Pickens, D; Flynn, M; Peck, D

    2014-06-15

    , effective implementation of that oversight has been challenging due to the number and extend of medical displays in use at a facility. The advent of color display and mobile displays has added additional challenges to the task of the medical physicist. This informatics display lecture first addresses the current display guidelines (the 1.0 paradigm) and further outlines the initiatives and prospects for color and mobile displays (the 2.0 paradigm). Informatics Management 1.0 to 2.0: Imaging informatics is part of every radiology practice today. Imaging informatics covers everything from the ordering of a study, through the data acquisition and processing, display and archiving, reporting of findings and the billing for the services performed. The standardization of the processes used to manage the information and methodologies to integrate these standards is being developed and advanced continuously. These developments are done in an open forum and imaging organizations and professionals all have a part in the process. In the Informatics Management presentation, the flow of information and the integration of the standards used in the processes will be reviewed. The role of radiologists and physicists in the process will be discussed. Current methods (the 1.0 paradigm) and evolving methods (the 2.0 paradigm) for validation of informatics systems function will also be discussed. Learning Objectives: Identify requirements for improving quality assurance and compliance tools for advanced and hybrid MRI systems. Identify the need for new quality assurance metrics and testing procedures for advanced systems. Identify new hardware systems and new procedures needed to evaluate MRI systems. Understand the components of current medical physics expectation for medical displays. Understand the role and prospect fo medical physics for color and mobile display devices. Understand different areas of imaging informatics and the methodology for developing informatics standards. Understand

  16. Genome cartography: charting the apicomplexan genome.

    PubMed

    Kissinger, Jessica C; DeBarry, Jeremy

    2011-08-01

    Genes reside in particular genomic contexts that can be mapped at many levels. Historically, 'genetic maps' were used primarily to locate genes. Recent technological advances in the determination of genome sequences have made the analysis and comparison of whole genomes possible and increasingly tractable. What do we see if we shift our focus from gene content (the 'inventory' of genes contained within a genome) to the composition and organization of a genome? This review examines what has been learned about the evolution of the apicomplexan genome as well as the significance and impact of genomic location on our understanding of the eukaryotic genome and parasite biology.

  17. Consumer health informatics: a consensus description and commentary from American Medical Informatics Association members.

    PubMed Central

    Houston, T. K.; Chang, B. L.; Brown, S.; Kukafka, R.

    2001-01-01

    BACKGROUND: Although interest in Consumer Health Informatics (CHI) has increased, a consensus definition of CHI does not yet exist. PURPOSE: To conduct a hypothesis-generating survey of AMIA members regarding definition and research agenda for CHI. METHODS: We solicited participation among AMIA members in an Internet-based survey focusing on issues related to a definition of CHI. RESULTS: One hundred thirty-five AMIA members responded. Participants indicated a broad spectrum of topics important to CHI including "self-help for disease management" and "patient access to their own medical records." CHI research was felt to rely heavily on public health methods such as epidemiology and outcomes research, a paradigm shift from traditional medical informatics. Responses indicated a perceived lack of funding and need for further research in CHI. CONCLUSIONS: A working definition should emphasize the multidisciplinary nature of CHI, include consumer input into CHI design, and focus on public health approaches to evaluation. PMID:11825193

  18. Nursing Informatics Beyond 2020; An Interactive Workshop Exploring Our Futures.

    PubMed

    Murray, Peter J

    2016-01-01

    This interactive workshop will reflect on and update participants' views on possible future scenarios for the development of health and nursing informatics. The NI2006 Post Congress Conference discussed the future nature and scope of nursing informatics, nursing and healthcare, as viewed from likely developments between 2006 and 2020 [1]. Brief synposes from the NI2006 conference will be presented, with summaries of speakers' views on changes and progress since. Workshop participants will discuss major themes and changes, with a view to updating views on possible futures for nursing, healthcare and informatics.

  19. Gap analysis of biomedical informatics graduate education competencies.

    PubMed

    Ritko, Anna L; Odlum, Michelle

    2013-01-01

    Graduate training in biomedical informatics (BMI) is evolving rapidly. BMI graduate programs differ in informatics domain, delivery method, degrees granted, as well as breadth and depth of curricular competencies. Using the current American Medical Informatics Association (AMIA) definition of BMI core competencies as a framework, we identified and labeled course offerings within graduate programs. From our qualitative analysis, gaps between defined competencies and curricula emerged. Topics missing from existing graduate curricula include community health, translational and clinical research, knowledge representation, data mining, communication and evidence-based practice.

  20. The Medical Informatics Program at the National University of Singapore.

    PubMed

    Lun, K C; Leong, T Y; Ong, K; Raghavan, R; Pung, H K

    1998-01-01

    The Medical Informatics Program at the National University of Singapore was established in September 1996 with a $4 million joint funding from the National Science and Technology Board and the Ministry of Education. The primary aims of the research program are to undertake upstream basic research in medical informatics and to build a critical mass of medical informatics expertise to meet long-term research goals and to effect technology transfer to the health sector of Singapore. Research projects fall into five groups: Clinical Decision Systems, Health Information Systems, Biomedical Datamining Systems, Medical Education Systems and Medical Networking, Applications Development and Integration Systems.

  1. Gap Analysis of Biomedical Informatics Graduate Education Competencies

    PubMed Central

    Ritko, Anna L.; Odlum, Michelle

    2013-01-01

    Graduate training in biomedical informatics (BMI) is evolving rapidly. BMI graduate programs differ in informatics domain, delivery method, degrees granted, as well as breadth and depth of curricular competencies. Using the current American Medical Informatics Association (AMIA) definition of BMI core competencies as a framework, we identified and labeled course offerings within graduate programs. From our qualitative analysis, gaps between defined competencies and curricula emerged. Topics missing from existing graduate curricula include community health, translational and clinical research, knowledge representation, data mining, communication and evidence-based practice. PMID:24551403

  2. Exposome informatics: considerations for the design of future biomedical research information systems.

    PubMed

    Martin Sanchez, Fernando; Gray, Kathleen; Bellazzi, Riccardo; Lopez-Campos, Guillermo

    2014-01-01

    The environment's contribution to health has been conceptualized as the exposome. Biomedical research interest in environmental exposures as a determinant of physiopathological processes is rising as such data increasingly become available. The panoply of miniaturized sensing devices now accessible and affordable for individuals to use to monitor a widening range of parameters opens up a new world of research data. Biomedical informatics (BMI) must provide a coherent framework for dealing with multi-scale population data including the phenome, the genome, the exposome, and their interconnections. The combination of these more continuous, comprehensive, and personalized data sources requires new research and development approaches to data management, analysis, and visualization. This article analyzes the implications of a new paradigm for the discipline of BMI, one that recognizes genome, phenome, and exposome data and their intricate interactions as the basis for biomedical research now and for clinical care in the near future.

  3. NCI Workshop Report: Clinical and Computational Requirements for Correlating Imaging Phenotypes with Genomics Signatures

    PubMed Central

    Colen, Rivka; Foster, Ian; Gatenby, Robert; Giger, Mary Ellen; Gillies, Robert; Gutman, David; Heller, Matthew; Jain, Rajan; Madabhushi, Anant; Madhavan, Subha; Napel, Sandy; Rao, Arvind; Saltz, Joel; Tatum, James; Verhaak, Roeland; Whitman, Gary

    2014-01-01

    The National Cancer Institute (NCI) Cancer Imaging Program organized two related workshops on June 26–27, 2013, entitled “Correlating Imaging Phenotypes with Genomics Signatures Research” and “Scalable Computational Resources as Required for Imaging-Genomics Decision Support Systems.” The first workshop focused on clinical and scientific requirements, exploring our knowledge of phenotypic characteristics of cancer biological properties to determine whether the field is sufficiently advanced to correlate with imaging phenotypes that underpin genomics and clinical outcomes, and exploring new scientific methods to extract phenotypic features from medical images and relate them to genomics analyses. The second workshop focused on computational methods that explore informatics and computational requirements to extract phenotypic features from medical images and relate them to genomics analyses and improve the accessibility and speed of dissemination of existing NIH resources. These workshops linked clinical and scientific requirements of currently known phenotypic and genotypic cancer biology characteristics with imaging phenotypes that underpin genomics and clinical outcomes. The group generated a set of recommendations to NCI leadership and the research community that encourage and support development of the emerging radiogenomics research field to address short-and longer-term goals in cancer research. PMID:25389451

  4. Informatics Enabled Behavioral Medicine in Oncology

    PubMed Central

    Hesse, Bradford W.; Suls, Jerry M.

    2011-01-01

    For the practicing physician, the behavioral implications of preventing, diagnosing, and treating cancer are many and varied. Fortunately, an enhanced capacity in informatics may help create a redesigned ecosystem in which applying evidence-based principles from behavioral medicine will become a routine part of care. Innovation to support this evolution will be spurred by the “meaningful use” criteria stipulated by the Health Information Technology for Economic and Clinical Health (HITECH) Act of 2009, and by focused research and development efforts within the broader health information ecosystem. The implications for how to better integrate evidence-based principles in behavioral medicine into oncology care through both spheres of development are discussed within the framework of the cancer control continuum. The promise of using the data collected through these tools to accelerate discovery in psycho-oncology is also discussed. If nurtured appropriately, these developments should help accelerate successes against cancer by altering the behavioral milieu. PMID:21799329

  5. [Looking for evidence-based medical informatics].

    PubMed

    Coiera, Enrico

    2016-03-01

    e-Health is experiencing a difficult time. On the one side, the forecast is for a bright digital health future created by precision medicine and smart devices. On the other hand, most large scale e-health projects struggle to make a difference and are often controversial. Both futures fail because they are not evidence-based. Medical informatics should follow the example of evidence-based medicine, i.e. conduct rigorous research that gives us evidence to solve real world problems, synthesise that evidence and then apply it strictly. We already have the tools for creating a different universe. What we need is evidence, will, a culture of learning, and hard work.

  6. Eco-informatics and natural resource management

    USGS Publications Warehouse

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

    2006-01-01

    This project highlight reports on the 2004 workshop [1], as well as follow-up activities in 2005 and 2006, regarding how informatics tools can help manage natural resources and decide policy. The workshop was sponsored jointly by sponsored by the NSF, NBII, NASA, and EPA, and attended by practitioners from government and non-government agencies, and university researchers from the computer, social, and ecological sciences. The workshop presented the significant information technology (IT) problems that resource managers face when integrating ecological or environmental information to make decisions. These IT problems fall into five categories: data presentation, data gaps, tools, indicators, and policy making and implementation. To alleviate such problems, we recommend informatics research in four IT areas, as defined in this abstract and our final report: modeling and simulation, data quality, information integration and ontologies, and social and human aspects. Additionally, we recommend that funding agencies provide infrastructure and some changes in funding habits to assure cycles of innovation in the domain were addressed. Follow-on activities to the workshop subsequent to dg.o 2005 included: an invited talk presenting workshop results at DILS 2005, publication of the workshop final report by the NBII [1], and a poster at the NBII All Hands Meeting (Oct. 2005). We also expect a special issue of the JIIS to appear in 2006 that addresses some of these questions. As we go to press, no solicitation by funding agencies has as yet been published, but various NASA and NBII, and NSF cyber-infrastructure and DG research efforts now underway address the above issues.

  7. Genomics spurs rapid advances in our understanding of the biology of vascular wilt pathogens in the genus Verticillium

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The availability of genomic sequences from Verticillium species has spawned a surge in functional genomics analyses, addressing a range of fundamental questions on the genes controlling the Verticillium lifecycle and disease process. These studies have also revealed evolutionary mechanisms, like hyb...

  8. Genomics and Bioinformatics in Undergraduate Curricula: Contexts for Hybrid Laboratory/Lecture Courses for Entering and Advanced Science Students

    ERIC Educational Resources Information Center

    Temple, Louise; Cresawn, Steven G.; Monroe, Jonathan D.

    2010-01-01

    Emerging interest in genomics in the scientific community prompted biologists at James Madison University to create two courses at different levels to modernize the biology curriculum. The courses are hybrids of classroom and laboratory experiences. An upper level class uses raw sequence of a genome (plasmid or virus) as the subject on which to…

  9. Identification of Novel Drug Targets and Lead Compounds for Advanced Prostate Cancer through Genomic and Cheminformatic Analyses

    DTIC Science & Technology

    2015-08-01

    Proteomics, Cheminformatics, Computer- aided drug design, Small molecule inhibitors, biological assays, Compound validation. 16. SECURITY...aberrations Genomics Transcriptomics Proteomics Bioinformatics Cheminformatics Computer- aided drug design Small molecule inhibitors In silico compound...using the combined power of genomic analyses, protein structural modeling, computer- aided drug design and biological screening to develop new

  10. A Short History of Medical Informatics in Bosnia and Herzegovina

    PubMed Central

    Masic, Izet

    2014-01-01

    The health informatics profession in Bosnia and Herzegovina has relatively long history. Thirty five years from the introduction of the first automatic manipulation of data, thirty years from the establishment of Society for Medical Informatics BiH, twenty years from the establishment of the Scientific journal “Acta Informatica Medica (Acta Inform Med”, indexed in PubMed, PubMed Central Scopus, Embase, etc.), twenty years on from the establishment of the first Cathedra for Medical Informatics on Biomedical Faculties in Bosnia and Herzegovina, ten years on from the introduction of the method of “Distance learning” in medical curriculum. The author of this article is eager to mark the importance of the above mentioned Anniversaries in the development of Health informatics in Bosnia and Herzegovina and have attempted, very briefly, to present the most significant events and persons with essential roles throughout this period. PMID:24648621

  11. Visualizing simulated learning experiences through the use of informatics tools.

    PubMed

    Thompson, Teri L; Warren, Judith J

    2009-01-01

    High-fidelity simulation technology is a growing educational technology. Designing effective simulations requires the use of informatics tools such as UML modeling. This poster demonstrates the steps in modeling a simulation exercise.

  12. SWOT Analysis on Medical Informatics and Development Strategies

    ERIC Educational Resources Information Center

    Ma, Xiaoyan; Han, Zhongdong; Ma, Hua

    2015-01-01

    This article aims at clarifying the strategic significance of developing medical informatics, conducting SWOT analysis on this discipline and hence establishing the strategic objectives and focal points for its development.

  13. [HYGIENIC ASSESSMENT OF INFORMATIZATION OF EDUCATION AND UP-BRINGING].

    PubMed

    Kuchma, V R; Tkachuk, E A

    2015-01-01

    During the last decade the quality of children's health declined, the level of children's aggression and aggressiveness increased. The consistent trend to increasing the quantity of children with the signs of motor disinhibition in different forms and manifestations was noted. In a study on the example of educational institutions of Irkutsk there was made an assessment of the impact of the intensification and informatization of education and up-bringing with the use of the index of the level of informatization. In preschool children over the information period mental performance was found to be characterized by an increase in the speed and decline in the quality of information processing, there are dominated increased aggressive background and unmotivated fears "out home", there are reduced values of endurance ratio of the cardiovascular system, higher levels of morbidity rate were noted. There was proposed a hygienic assessment of informatization of education and up-bringing with the use of the index of the level of informatization.

  14. Antecedents of the People and Organizational Aspects of Medical Informatics

    PubMed Central

    Lorenzi, Nancy M.; Riley, Robert T.; Blyth, Andrew J. C.; Southon, Gray; Dixon, Bradley J.

    1997-01-01

    Abstract People and organizational issues are critical in both implementing medical informatics systems and in dealing with the altered organizations that new systems often create. The people and organizational issues area—like medical informatics itself—is a blend of many disciplines. The academic disciplines of psychology, sociology, social psychology, social anthropology, organizational behavior and organizational development, management, and cognitive sciences are rich with research with significant potential to ease the introduction and on-going use of information technology in today's complex health systems. These academic areas contribute research data and core information for better understanding of such issues as the importance of and processes for creating future direction; managing a complex change process; effective strategies for involving individuals and groups in the informatics effort; and effectively managing the altered organization. This article reviews the behavioral and business referent disciplines that can potentially contribute to improved implementations and on-going management of change in the medical informatics arena. PMID:9067874

  15. Developing a Capstone Course within a Health Informatics Program

    PubMed Central

    Hackbarth, Gary; Cata, Teuta; Cole, Laura

    2012-01-01

    This article discusses the ongoing development of a health informatics capstone program in a Midwest university from the hiring of a program coordinator to the development of a capstone course, through initial student results. University health informatics programs require a strong academic program to be successful but also require a spirited program coordinator to manage resources and organize an effective capstone course. This is particularly true of health informatics master's programs that support health industry career fields, whereby employers can locate and work with a pool of qualified applicants. The analysis of students’ logs confirms that students’ areas of focus and concern are consistent with course objectives and company work requirements during the work-study portion of the student capstone project. The article further discusses lessons learned and future improvements to be made in the health informatics capstone course. PMID:22783150

  16. A short history of medical informatics in bosnia and herzegovina.

    PubMed

    Masic, Izet

    2014-02-01

    The health informatics profession in Bosnia and Herzegovina has relatively long history. Thirty five years from the introduction of the first automatic manipulation of data, thirty years from the establishment of Society for Medical Informatics BiH, twenty years from the establishment of the Scientific journal "Acta Informatica Medica (Acta Inform Med", indexed in PubMed, PubMed Central Scopus, Embase, etc.), twenty years on from the establishment of the first Cathedra for Medical Informatics on Biomedical Faculties in Bosnia and Herzegovina, ten years on from the introduction of the method of "Distance learning" in medical curriculum. The author of this article is eager to mark the importance of the above mentioned Anniversaries in the development of Health informatics in Bosnia and Herzegovina and have attempted, very briefly, to present the most significant events and persons with essential roles throughout this period.

  17. Climate Informatics: Accelerating Discovering in Climate Science with Machine Learning

    NASA Technical Reports Server (NTRS)

    Monteleoni, Claire; Schmidt, Gavin A.; McQuade, Scott

    2014-01-01

    The goal of climate informatics, an emerging discipline, is to inspire collaboration between climate scientists and data scientists, in order to develop tools to analyze complex and ever-growing amounts of observed and simulated climate data, and thereby bridge the gap between data and understanding. Here, recent climate informatics work is presented, along with details of some of the field's remaining challenges. Given the impact of climate change, understanding the climate system is an international priority. The goal of climate informatics is to inspire collaboration between climate scientists and data scientists, in order to develop tools to analyze complex and ever-growing amounts of observed and simulated climate data, and thereby bridge the gap between data and understanding. Here, recent climate informatics work is presented, along with details of some of the remaining challenges.

  18. New study program: Interdisciplinary Postgraduate Specialist Study in Medical Informatics.

    PubMed

    Hercigonja-Szekeres, Mira; Simić, Diana; Božikov, Jadranka; Vondra, Petra

    2014-01-01

    Paper presents an overview of the EU funded Project of Curriculum Development for Interdisciplinary Postgraduate Specialist Study in Medical Informatics named MEDINFO to be introduced in Croatia. The target group for the program is formed by professionals in any of the areas of medicine, IT professionals working on applications of IT for health and researchers and teachers in medical informatics. In addition to Croatian students, the program will also provide opportunity for enrolling students from a wider region of Southeast Europe. Project partners are two faculties of the University of Zagreb - Faculty of Organization and Informatics from Varaždin and School of Medicine, Andrija Štampar School of Public Health from Zagreb with the Croatian Society for Medical Informatics, Croatian Chamber of Economy, and Ericsson Nikola Tesla Company as associates.

  19. Excellence in Computational Biology and Informatics — EDRN Public Portal

    Cancer.gov

    9th Early Detection Research Network (EDRN) Scientific Workshop. Excellence in Computational Biology and Informatics: Sponsored by the EDRN Data Sharing Subcommittee Moderator: Daniel Crichton, M.S., NASA Jet Propulsion Laboratory

  20. Genomics spurs rapid advances in our understanding of the biology of vascular wilt pathogens in the genus Verticillium.

    PubMed

    Klimes, Anna; Dobinson, Katherine F; Thomma, Bart P H J; Klosterman, Steven J

    2015-01-01

    The availability of genomic sequences of several Verticillium species triggered an explosion of genome-scale investigations of mechanisms fundamental to the Verticillium life cycle and disease process. Comparative genomics studies have revealed evolutionary mechanisms, such as hybridization and interchromosomal rearrangements, that have shaped these genomes. Functional analyses of a diverse group of genes encoding virulence factors indicate that successful host xylem colonization relies on specific Verticillium responses to various stresses, including nutrient deficiency and host defense-derived oxidative stress. Regulatory pathways that control responses to changes in nutrient availability also appear to positively control resting structure development. Conversely, resting structure development seems to be repressed by pathways, such as those involving effector secretion, which promote responses to host defenses. The genomics-enabled functional characterization of responses to the challenges presented by the xylem environment, accompanied by identification of novel virulence factors, has rapidly expanded our understanding of niche adaptation in Verticillium species.

  1. TU-F-BRD-01: Biomedical Informatics for Medical Physicists

    SciTech Connect

    Phillips, M; Kalet, I; McNutt, T; Smith, W

    2014-06-15

    Biomedical informatics encompasses a very large domain of knowledge and applications. This broad and loosely defined field can make it difficult to navigate. Physicists often are called upon to provide informatics services and/or to take part in projects involving principles of the field. The purpose of the presentations in this symposium is to help medical physicists gain some knowledge about the breadth of the field and how, in the current clinical and research environment, they can participate and contribute. Three talks have been designed to give an overview from the perspective of physicists and to provide a more in-depth discussion in two areas. One of the primary purposes, and the main subject of the first talk, is to help physicists achieve a perspective about the range of the topics and concepts that fall under the heading of 'informatics'. The approach is to de-mystify topics and jargon and to help physicists find resources in the field should they need them. The other talks explore two areas of biomedical informatics in more depth. The goal is to highlight two domains of intense current interest--databases and models--in enough depth into current approaches so that an adequate background for independent inquiry is achieved. These two areas will serve as good examples of how physicists, using informatics principles, can contribute to oncology practice and research. Learning Objectives: To understand how the principles of biomedical informatics are used by medical physicists. To put the relevant informatics concepts in perspective with regard to biomedicine in general. To use clinical database design as an example of biomedical informatics. To provide a solid background into the problems and issues of the design and use of data and databases in radiation oncology. To use modeling in the service of decision support systems as an example of modeling methods and data use. To provide a background into how uncertainty in our data and knowledge can be

  2. The golden era of biomedical informatics has begun.

    PubMed

    Moore, Jason H; Holmes, John H

    2016-01-01

    Biomedical informatics has become a central focus for many academic medical centers and universities as biomedical research because increasingly reliant on the processing, analysis, and interpretation of large volumes of data, information, and knowledge. We posit here that this is the beginning of the golden era of biomedical informatics with opportunity for this maturing discipline to have a substantial impact on the biggest questions and challenges facing efforts to improve human health and the healthcare system.

  3. Accelerating discovery for complex neurological and behavioral disorders through systems genetics and integrative genomics in the laboratory mouse.

    PubMed

    Bubier, Jason A; Chesler, Elissa J

    2012-04-01

    Recent advances in systems genetics and integrative functional genomics have greatly improved the study of complex neurological and behavioral traits. The methods developed for the integrated characterization of new, high-resolution mouse genetic reference populations and systems genetics enable behavioral geneticists an unprecedented opportunity to address questions of the molecular basis of neurological and psychiatric disorders and their comorbidities. Integrative genomics augment these strategies by enabling rapid informatics-assisted candidate gene prioritization, cross-species translation, and mechanistic comparison across related disorders from a wealth of existing data in mouse and other model organisms. Ultimately, through these complementary approaches, finding the mechanisms and sources of genetic variation underlying complex neurobehavioral disease related traits is becoming tractable. Furthermore, these methods enable categorization of neurobehavioral disorders through their underlying biological basis. Together, these model organism-based approaches can lead to a refinement of diagnostic categories and targeted treatment of neurological and psychiatric disease.

  4. Diverse convergent evidence in the genetic analysis of complex disease: coordinating omic, informatic, and experimental evidence to better identify and validate risk factors

    PubMed Central

    2014-01-01

    In omic research, such as genome wide association studies, researchers seek to repeat their results in other datasets to reduce false positive findings and thus provide evidence for the existence of true associations. Unfortunately this standard validation approach cannot completely eliminate false positive conclusions, and it can also mask many true associations that might otherwise advance our understanding of pathology. These issues beg the question: How can we increase the amount of knowledge gained from high throughput genetic data? To address this challenge, we present an approach that complements standard statistical validation methods by drawing attention to both potential false negative and false positive conclusions, as well as providing broad information for directing future research. The Diverse Convergent Evidence approach (DiCE) we propose integrates information from multiple sources (omics, informatics, and laboratory experiments) to estimate the strength of the available corroborating evidence supporting a given association. This process is designed to yield an evidence metric that has utility when etiologic heterogeneity, variable risk factor frequencies, and a variety of observational data imperfections might lead to false conclusions. We provide proof of principle examples in which DiCE identified strong evidence for associations that have established biological importance, when standard validation methods alone did not provide support. If used as an adjunct to standard validation methods this approach can leverage multiple distinct data types to improve genetic risk factor discovery/validation, promote effective science communication, and guide future research directions. PMID:25071867

  5. The Methods Behind 2015 Informatics Capacity and Needs Assessment Study

    PubMed Central

    2016-01-01

    The 2015 Informatics Needs and Capacity of Local Health Departments (LHDs) survey is the most recent comprehensive source of quantitative data on LHD informatics. Conducted by the National Association of County & City Health Officials (NACCHO), this is the third nationally representative quantitative study of LHD informatics since 2009. The previous 2 comprehensive quantitative assessments were conducted by NACCHO in 2009-2010 and 2011. Given that public health informatics is rapidly evolving, the 2015 Informatics survey is a much-needed country-wide assessment of the current informatics needs and capacities of LHDs. This article outlines detailed methodology used in the 2015 Informatics survey, including instrument development, pretesting, sampling design and sample size, survey administration, and sampling weights. A 9-member advisory committee representing federal, state, and local health agency representatives guided the design and implementation of this study. The survey instrument was organized into 6 topic areas: demographics, physical infrastructure, skills and capacity available, public health workforce development needs, electronic health records, and health information exchange. The instrument was pretested with a sample of 20 LHDs and subsequently pilot-tested with 30 LHDs. The survey was administered via the Qualtrics survey software to the sample of 650 LHDs, selected using stratified random sampling. The survey was fielded for approximately 8 weeks and 324 usable responses were received, constituting a response rate of 50%. Statistical weights were developed to account for 3 factors: (a) disproportionate response rate by population size (using 7 population strata), (b) oversampling of LHDs with larger population sizes, and (c) sampling rather than a census approach. PMID:27684627

  6. A locally funded Puerto Rican parrot (Amazona vittata) genome sequencing project increases avian data and advances young researcher education

    PubMed Central

    2012-01-01

    Background Amazona vittata is a critically endangered Puerto Rican endemic bird, the only surviving native parrot species in the United States territory, and the first parrot in the large Neotropical genus Amazona, to be studied on a genomic scale. Findings In a unique community-based funded project, DNA from an A. vittata female was sequenced using a HiSeq Illumina platform, resulting in a total of ~42.5 billion nucleotide bases. This provided approximately 26.89x average coverage depth at the completion of this funding phase. Filtering followed by assembly resulted in 259,423 contigs (N50 = 6,983 bp, longest = 75,003 bp), which was further scaffolded into 148,255 fragments (N50 = 19,470, longest = 206,462 bp). This provided ~76% coverage of the genome based on an estimated size of 1.58 Gb. The assembled scaffolds allowed basic genomic annotation and comparative analyses with other available avian whole-genome sequences. Conclusions The current data represents the first genomic information from and work carried out with a unique source of funding. This analysis further provides a means for directed training of young researchers in genetic and bioinformatics analyses and will facilitate progress towards a full assembly and annotation of the Puerto Rican parrot genome. It also adds extensive genomic data to a new branch of the avian tree, making it useful for comparative analyses with other avian species. Ultimately, the knowledge acquired from these data will contribute to an improved understanding of the overall population health of this species and aid in ongoing and future conservation efforts. PMID:23587420

  7. Nursing informatics: state of the science.

    PubMed

    Henry, S B

    1995-12-01

    The phenomena of interest in nursing informatics are nursing data, nursing information and nursing knowledge. The current state of knowledge related to these phenomena suggests four implications for the development of systems to support nursing. First, research has provided evidence that knowledge and experience is related to the quality of nursing assessment, diagnosis or clinical inference, and planning of nursing care, and also that knowledge is task-specific. Information technology can provide access to a variety of information resources, such as knowledge bases and decision support systems, to increase the level of knowledge of the nurse decision-maker. Second, structured patient assessment forms with linkages to knowledge bases of diagnoses have the potential to improve the quality of the patient assessment and the accuracy of the diagnosis or clinical inference. Third, studies on planning care have demonstrated the complexity of the task when a number of options are potentially appropriate. Model-based decision support applications such as decision analysis and multi-attribute utility theory can assist the clinicians and patients to analyse and compare the treatment alternatives in a systematic manner. Fourth, there is modest support for demonstrating the relationship between the process and outcomes of clinical decision making. Large databases built upon nursing data are needed to further examine this relationship.

  8. Enabling functional genomics with genome engineering.

    PubMed

    Hilton, Isaac B; Gersbach, Charles A

    2015-10-01

    Advances in genome engineering technologies have made the precise control over genome sequence and regulation possible across a variety of disciplines. These tools can expand our understanding of fundamental biological processes and create new opportunities for therapeutic designs. The rapid evolution of these methods has also catalyzed a new era of genomics that includes multiple approaches to functionally characterize and manipulate the regulation of genomic information. Here, we review the recent advances of the most widely adopted genome engineering platforms and their application to functional genomics. This includes engineered zinc finger proteins, TALEs/TALENs, and the CRISPR/Cas9 system as nucleases for genome editing, transcription factors for epigenome editing, and other emerging applications. We also present current and potential future applications of these tools, as well as their current limitations and areas for future advances.

  9. Enabling functional genomics with genome engineering

    PubMed Central

    Hilton, Isaac B.; Gersbach, Charles A.

    2015-01-01

    Advances in genome engineering technologies have made the precise control over genome sequence and regulation possible across a variety of disciplines. These tools can expand our understanding of fundamental biological processes and create new opportunities for therapeutic designs. The rapid evolution of these methods has also catalyzed a new era of genomics that includes multiple approaches to functionally characterize and manipulate the regulation of genomic information. Here, we review the recent advances of the most widely adopted genome engineering platforms and their application to functional genomics. This includes engineered zinc finger proteins, TALEs/TALENs, and the CRISPR/Cas9 system as nucleases for genome editing, transcription factors for epigenome editing, and other emerging applications. We also present current and potential future applications of these tools, as well as their current limitations and areas for future advances. PMID:26430154

  10. Bioinformatics Methods and Tools to Advance Clinical Care

    PubMed Central

    Lecroq, T.

    2015-01-01

    Summary Objectives To summarize excellent current research in the field of Bioinformatics and Translational Informatics with application in the health domain and clinical care. Method We provide a synopsis of the articles selected for the IMIA Yearbook 2015, from which we attempt to derive a synthetic overview of current and future activities in the field. As last year, a first step of selection was performed by querying MEDLINE with a list of MeSH descriptors completed by a list of terms adapted to the section. Each section editor has evaluated separately the set of 1,594 articles and the evaluation results were merged for retaining 15 articles for peer-review. Results The selection and evaluation process of this Yearbook’s section on Bioinformatics and Translational Informatics yielded four excellent articles regarding data management and genome medicine that are mainly tool-based papers. In the first article, the authors present PPISURV a tool for uncovering the role of specific genes in cancer survival outcome. The second article describes the classifier PredictSNP which combines six performing tools for predicting disease-related mutations. In the third article, by presenting a high-coverage map of the human proteome using high resolution mass spectrometry, the authors highlight the need for using mass spectrometry to complement genome annotation. The fourth article is also related to patient survival and decision support. The authors present datamining methods of large-scale datasets of past transplants. The objective is to identify chances of survival. Conclusions The current research activities still attest the continuous convergence of Bioinformatics and Medical Informatics, with a focus this year on dedicated tools and methods to advance clinical care. Indeed, there is a need for powerful tools for managing and interpreting complex, large-scale genomic and biological datasets, but also a need for user-friendly tools developed for the clinicians in their

  11. Relationship of smoking status to genomic profile, chemotherapy response and clinical outcome in patients with advanced urothelial carcinoma

    PubMed Central

    Joshi, Monika; Vasekar, Monali; Grivas, Petros; Emamekhoo, Hamid; Hsu, JoAnn; Miller, Vincent A.; Stephens, Philip J.; Ali, Siraj M.; Ross, Jeffrey S.; Zhu, Junjia; Warrick, Joshua; Drabick, Joseph J.; Holder, Sheldon L.; Kaag, Matthew; Li, Min; Pal, Sumanta Kumar

    2016-01-01

    Smoking has been linked to urothelial carcinoma (UC), but the implications on genomic profile and therapeutic response are poorly understood. To determine how smoking history impacts genomic profile and chemotherapy response, clinicopathologic data was collected for patients with metastatic UC (mUC) across 3 academic medical centers and comprehensive genomic profiling (CGP) was performed through a CLIA-certified lab. Unsupervised hierarchical clustering based on smoking status was used to categorize the frequency of genomic alterations (GAs) amongst current smokers (CS), ex-smokers (ES) and non-smokers (NS), and survival was compared in these subsets. Fisher's exact test identified significant associations between GAs and smoking status. Amongst 83 patients, 23%, 55% and 22% were CS, ES, and NS, respectively, and 95% of patients had stage IV disease. With a median follow up of 14.4 months, the median overall survival (OS) was significantly higher in NS and ES (combined) as compared to CS (51.6 vs 15.6 months; P = 0.04). Of 315 cancer-related genes and 31 genes often related to rearrangement tested, heatmaps show some variations amongst the subsets. GAs in NSD1 were more frequent in CS as compared to other groups (P < 0.001). CS status negatively impacts OS in patients with mUC and is associated with genomic alterations that could have therapeutic implications. PMID:27213592

  12. Functional Genomic and Advanced Genetic Studies Reveal Novel Insights into the Metabolism, Regulation, and Biology of Haloferax volcanii

    PubMed Central

    Soppa, Jörg

    2011-01-01

    The genome sequence of Haloferax volcanii is available and several comparative genomic in silico studies were performed that yielded novel insight for example into protein export, RNA modifications, small non-coding RNAs, and ubiquitin-like Small Archaeal Modifier Proteins. The full range of functional genomic methods has been established and results from transcriptomic, proteomic and metabolomic studies are discussed. Notably, Hfx. volcanii is together with Halobacterium salinarum the only prokaryotic species for which a translatome analysis has been performed. The results revealed that the fraction of translationally-regulated genes in haloarchaea is as high as in eukaryotes. A highly efficient genetic system has been established that enables the application of libraries as well as the parallel generation of genomic deletion mutants. Facile mutant generation is complemented by the possibility to culture Hfx. volcanii in microtiter plates, allowing the phenotyping of mutant collections. Genetic approaches are currently used to study diverse biological questions–from replication to posttranslational modification—and selected results are discussed. Taken together, the wealth of functional genomic and genetic tools make Hfx. volcanii a bona fide archaeal model species, which has enabled the generation of important results in recent years and will most likely generate further breakthroughs in the future. PMID:22190865

  13. Nanomanufacturing and characterization modalities for bio-nano-informatics systems.

    PubMed

    Ho, Dean; Garcia, Dan; Ho, Chih-Ming

    2006-04-01

    In the next decade or two, the feature size of microelectronic devices will continue to decrease and is eventually expected to reach fabrication and material limits. With the field of microelectronics rapidly approaching the end of its roadmap, the National Nanotechnology Initiative (NNI) was created for the purpose of creating new technologies and to maintain the momentum of continuous scientific and technological progress. Primarily, the fields of nanoscience and nanotechnology aim to synthesize, characterize, apply, and control macro functional molecules and consist of three areas. First, the area of bio-nanotechnologies concerns that of biological molecules such as DNA, the molecule that serves as the blueprint of all living organisms. Harnessing the intrinsic functionality of these nano-sized biological molecules, i.e., DNA/RNA and proteins, will yield enormous potential for a wide array of applications (biomedical, energy, sensing, etc.) Second, diminishing electronic device feature sizes has spurred the development of new techniques for nanoelectronics and has emerged as a critical area of research. Third, these macro functional molecules possess rich potential for various new nanomaterials that have applications in bio-nano and nanoelectronics industries. Given the range of devices and applications that may be generated and addressed, respectively, through the fruition of these areas, development of novel and advanced core characterization and nanomanufacturing technologies will serve as a requisite strategy toward the realization of the potential underlying nanotechnological development. As such, this review will address how these novel technologies will be used to achieve a true coalescence of nanoscience and nanotechnology. This, in turn, will ultimately benefit the human condition by using the building blocks and fundamental findings of nanoscience to develop systems based on the fusion of biology, nanotechnology, and informatics, with embedded

  14. Use of Modern Chemical Protein Synthesis and Advanced Fluorescent Assay Techniques to Experimentally Validate the Functional Annotation of Microbial Genomes

    SciTech Connect

    Kent, Stephen

    2012-07-20

    The objective of this research program was to prototype methods for the chemical synthesis of predicted protein molecules in annotated microbial genomes. High throughput chemical methods were to be used to make large numbers of predicted proteins and protein domains, based on microbial genome sequences. Microscale chemical synthesis methods for the parallel preparation of peptide-thioester building blocks were developed; these peptide segments are used for the parallel chemical synthesis of proteins and protein domains. Ultimately, it is envisaged that these synthetic molecules would be ‘printed’ in spatially addressable arrays. The unique ability of total synthesis to precision label protein molecules with dyes and with chemical or biochemical ‘tags’ can be used to facilitate novel assay technologies adapted from state-of-the art single molecule fluorescence detection techniques. In the future, in conjunction with modern laboratory automation this integrated set of techniques will enable high throughput experimental validation of the functional annotation of microbial genomes.

  15. Transforming consumer health informatics through a patient work framework: connecting patients to context.

    PubMed

    Valdez, Rupa S; Holden, Richard J; Novak, Laurie L; Veinot, Tiffany C

    2015-01-01

    Designing patient-centered consumer health informatics (CHI) applications requires understanding and creating alignment with patients' and their family members' health-related activities, referred to here as 'patient work'. A patient work approach to CHI draws on medical social science and human factors engineering models and simultaneously attends to patients, their family members, activities, and context. A patient work approach extends existing approaches to CHI design that are responsive to patients' biomedical realities and personal skills and behaviors. It focuses on the embeddedness of patients' health management in larger processes and contexts and prioritizes patients' perspectives on illness management. Future research is required to advance (1) theories of patient work, (2) methods for assessing patient work, and (3) techniques for translating knowledge of patient work into CHI application design. Advancing a patient work approach within CHI is integral to developing and deploying consumer-facing technologies that are integrated with patients' everyday lives.

  16. Transforming consumer health informatics through a patient work framework: connecting patients to context

    PubMed Central

    Valdez, Rupa S; Holden, Richard J; Novak, Laurie L; Veinot, Tiffany C

    2015-01-01

    Designing patient-centered consumer health informatics (CHI) applications requires understanding and creating alignment with patients’ and their family members’ health-related activities, referred to here as ‘patient work’. A patient work approach to CHI draws on medical social science and human factors engineering models and simultaneously attends to patients, their family members, activities, and context. A patient work approach extends existing approaches to CHI design that are responsive to patients’ biomedical realities and personal skills and behaviors. It focuses on the embeddedness of patients’ health management in larger processes and contexts and prioritizes patients’ perspectives on illness management. Future research is required to advance (1) theories of patient work, (2) methods for assessing patient work, and (3) techniques for translating knowledge of patient work into CHI application design. Advancing a patient work approach within CHI is integral to developing and deploying consumer-facing technologies that are integrated with patients’ everyday lives. PMID:25125685

  17. Detection and phasing of single base de novo mutations in biopsies from human in vitro fertilized embryos by advanced whole-genome sequencing.

    PubMed

    Peters, Brock A; Kermani, Bahram G; Alferov, Oleg; Agarwal, Misha R; McElwain, Mark A; Gulbahce, Natali; Hayden, Daniel M; Tang, Y Tom; Zhang, Rebecca Yu; Tearle, Rick; Crain, Birgit; Prates, Renata; Berkeley, Alan; Munné, Santiago; Drmanac, Radoje

    2015-03-01

    Currently, the methods available for preimplantation genetic diagnosis (PGD) of in vitro fertilized (IVF) embryos do not detect de novo single-nucleotide and short indel mutations, which have been shown to cause a large fraction of genetic diseases. Detection of all these types of mutations requires whole-genome sequencing (WGS). In this study, advanced massively parallel WGS was performed on three 5- to 10-cell biopsies from two blastocyst-stage embryos. Both parents and paternal grandparents were also analyzed to allow for accurate measurements of false-positive and false-negative error rates. Overall, >95% of each genome was called. In the embryos, experimentally derived haplotypes and barcoded read data were used to detect and phase up to 82% of de novo single base mutations with a false-positive rate of about one error per Gb, resulting in fewer than 10 such errors per embryo. This represents a ∼ 100-fold lower error rate than previously published from 10 cells, and it is the first demonstration that advanced WGS can be used to accurately identify these de novo mutations in spite of the thousands of false-positive errors introduced by the extensive DNA amplification required for deep sequencing. Using haplotype information, we also demonstrate how small de novo deletions could be detected. These results suggest that phased WGS using barcoded DNA could be used in the future as part of the PGD process to maximize comprehensiveness in detecting disease-causing mutations and to reduce the incidence of genetic diseases.

  18. Molecular studies in olive (Olea europaea L.): overview on DNA markers applications and recent advances in genome analysis.

    PubMed

    Bracci, T; Busconi, M; Fogher, C; Sebastiani, L

    2011-04-01

    Olive (Olea europaea L.) is one of the oldest agricultural tree crops worldwide and is an important source of oil with beneficial properties for human health. This emblematic tree crop of the Mediterranean Basin, which has conserved a very wide germplasm estimated in more than 1,200 cultivars, is a diploid species (2n = 2x = 46) that is present in two forms, namely wild (Olea europaea subsp. europaea var. sylvestris) and cultivated (Olea europaea subsp. europaea var. europaea). In spite of its economic and nutritional importance, there are few data about the genetic of olive if compared with other fruit crops. Available molecular data are especially related to the application of molecular markers to the analysis of genetic variability in Olea europaea complex and to develop efficient molecular tools for the olive oil origin traceability. With regard to genomic research, in the last years efforts are made for the identification of expressed sequence tag, with particular interest in those sequences expressed during fruit development and in pollen allergens. Very recently the sequencing of chloroplast genome provided new information on the olive nucleotide sequence, opening the olive genomic era. In this article, we provide an overview of the most relevant results in olive molecular studies. A particular attention was given to DNA markers and their application that constitute the most part of published researches. The first important results in genome analysis were reported.

  19. Programmatic Role of Education Libraries in Informatics to Support Preservice Teacher Preparation Programs

    ERIC Educational Resources Information Center

    Farmer, Lesley S. J.

    2010-01-01

    Background/Context: The management, processing, and transformation of information constitute central tasks in education. Education informatics intersects the theories and practices of both informatics and education. In particular, informatics aids in the systematic incorporation of technology as educational stakeholders represent, process, and…

  20. Enhancing "Mathematics for Informatics" and its Correlation with Student Pass Rates

    ERIC Educational Resources Information Center

    Divjak, B.; Erjavec, Z.

    2008-01-01

    In this article, changes in "Mathematics for Informatics" at the Faculty of Organisation and Informatics in the University of Zagreb are described, and correlated with students pass rates. Students at the Faculty work in an interdisciplinary field, studying Informatics within a business context. The main reason for introducing the…

  1. Interpreting concept learning in cognitive informatics and granular computing.

    PubMed

    Yao, Yiyu

    2009-08-01

    Cognitive informatics and granular computing are two emerging fields of study concerning information and knowledge processing. A central notion to this processing is information and knowledge granularity. Concepts, as the basic units of thought underlying human intelligence and communication, may play a fundamental role when integrating the results from the two fields in terms of information and knowledge coding, representation, communication, and processing. While cognitive informatics focuses on information processing in the abstract, in machines, and in the brain, granular computing models such processing at multiple levels of granularity. In this paper, we examine a conceptual framework for concept learning from the viewpoints of cognitive informatics and granular computing. Within the framework, we interpret concept learning based on a layered model of knowledge discovery.

  2. The Question Concerning Narration of Self in Health Informatics.

    PubMed

    Botin, Lars

    2015-01-01

    Narration is central, even crucial, when it comes to embracing the whole individual, continuity of care, and responsible (ethical) handling of the technological construction of the self that takes place in health informatics. This paper will deal with the role of narratives in the construction of health informatics platforms and how different voices should have space for speech on these platforms. Theoretically the paper takes an outset in the actant model for narratives by the French-Lithuanian theorist of linguistics and literature A.-J. Greimas and post-phenomenological readings of human-technology interactions. The main assumption is that certain interactions and voices are absent from the construction of health informatics platforms, because regarded as outside the text of computational and medical practice and expertise. This has implications for what concerns meaning and understanding regarding both the actual users (physicians and medical staff) and excluded users (patients and citizens).

  3. Effect of advanced intercrossing on genome structure and on the power to detect linked quantitative trait loci in a multi-parent population: a simulation study in rice

    PubMed Central

    2014-01-01

    Background In genetic analysis of agronomic traits, quantitative trait loci (QTLs) that control the same phenotype are often closely linked. Furthermore, many QTLs are localized in specific genomic regions (QTL clusters) that include naturally occurring allelic variations in different genes. Therefore, linkage among QTLs may complicate the detection of each individual QTL. This problem can be resolved by using populations that include many potential recombination sites. Recently, multi-parent populations have been developed and used for QTL analysis. However, their efficiency for detection of linked QTLs has not received attention. By using information on rice, we simulated the construction of a multi-parent population followed by cycles of recurrent crossing and inbreeding, and we investigated the resulting genome structure and its usefulness for detecting linked QTLs as a function of the number of cycles of recurrent crossing. Results The number of non-recombinant genome segments increased linearly with an increasing number of cycles. The mean and median lengths of the non-recombinant genome segments decreased dramatically during the first five to six cycles, then decreased more slowly during subsequent cycles. Without recurrent crossing, we found that there is a risk of missing QTLs that are linked in a repulsion phase, and a risk of identifying linked QTLs in a coupling phase as a single QTL, even when the population was derived from eight parental lines. In our simulation results, using fewer than two cycles of recurrent crossing produced results that differed little from the results with zero cycles, whereas using more than six cycles dramatically improved the power under most of the conditions that we simulated. Conclusion Our results indicated that even with a population derived from eight parental lines, fewer than two cycles of crossing does not improve the power to detect linked QTLs. However, using six cycles dramatically improved the power, suggesting

  4. Imaging informatics: essential tools for the delivery of imaging services.

    PubMed

    Mendelson, David S; Rubin, Daniel L

    2013-10-01

    There are rapid changes occurring in the health care environment. Radiologists face new challenges but also new opportunities. The purpose of this report is to review how new informatics tools and developments can help the radiologist respond to the drive for safety, quality, and efficiency. These tools will be of assistance in conducting research and education. They not only provide greater efficiency in traditional operations but also open new pathways for the delivery of new services and imaging technologies. Our future as a specialty is dependent on integrating these informatics solutions into our daily practice.

  5. Role of Informatics in Patient Safety and Quality Assurance.

    PubMed

    Nakhleh, Raouf E

    2015-06-01

    Quality assurance encompasses monitoring daily processes for accurate, timely, and complete reports in surgical pathology. Quality assurance also includes implementation of policies and procedures that prevent or detect errors in a timely manner. This article presents uses of informatics in quality assurance. Three main foci are critical to the general improvement of diagnostic surgical pathology. First is the application of informatics to specimen identification with lean methods for real-time statistical control of specimen receipt and processing. Second is the development of case reviews before sign-out. Third is the development of information technology in communication of results to assure treatment in a timely manner.

  6. Observations on sustainable and ubiquitous healthcare informatics from Florence Nightingale.

    PubMed

    Betts, Helen J; Wright, Graham

    2009-01-01

    As nurses around the world prepare to celebrate the centenary of the death of Florence Nightingale in 2010 this paper reviews her work on using information, especially statistics, to analyze and manage patient care and links that to current developments in informatics. It then examines assistive technologies and how they may impact on nursing practice in the future and links these developments to the writings of Florence Nightingale. The paper concludes by suggesting that in progressing towards sustainable and ubiquitous healthcare informatics we need to study history in order to learn from the lessons of Florence Nightingale and other healthcare pioneers.

  7. A Primer on Aspects of Cognition for Medical Informatics

    PubMed Central

    Patel, Vimla L.; Arocha, José F.; Kaufman, David R.

    2001-01-01

    As a multidisciplinary field, medical informatics draws on a range of disciplines, such as computer science, information science, and the social and cognitive sciences. The cognitive sciences can provide important insights into the nature of the processes involved in human– computer interaction and help improve the design of medical information systems by providing insight into the roles that knowledge, memory, and strategies play in a variety of cognitive activities. In this paper, the authors survey literature on aspects of medical cognition and provide a set of claims that they consider to be important in medical informatics. PMID:11418539

  8. Summative evaluation of a baccalaureate nursing informatics curriculum.

    PubMed Central

    Travis, L. L.; Hudak, C. A.; Brennan, P. F.

    1995-01-01

    This paper describes the fifth stage in the process of designing, implementing and evaluating the nursing informatics courses incorporated into a baccalaureate nursing program. The challenge is to construct an evolving nursing informatics curriculum so as to provide nursing professionals with the foundations for affecting health care delivery. The basic components of the curriculum framework are information, technology, and clinical care process. Information on the two groups of graduates who have completed the four course sequence and the one group of graduates who have been in practice will be discussed. PMID:8563330

  9. Behavioral Informatics and Computational Modeling in Support of Proactive Health Management and Care.

    PubMed

    Pavel, Misha; Jimison, Holly B; Korhonen, Ilkka; Gordon, Christine M; Saranummi, Niilo

    2015-12-01

    Health-related behaviors are among the most significant determinants of health and quality of life. Improving health behavior is an effective way to enhance health outcomes and mitigate the escalating challenges arising from an increasingly aging population and the proliferation of chronic diseases. Although it has been difficult to obtain lasting improvements in health behaviors on a wide scale, advances at the intersection of technology and behavioral science may provide the tools to address this challenge. In this paper, we describe a vision and an approach to improve health behavior interventions using the tools of behavioral informatics, an emerging transdisciplinary research domain based on system-theoretic principles in combination with behavioral science and information technology. The field of behavioral informatics has the potential to optimize interventions through monitoring, assessing, and modeling behavior in support of providing tailored and timely interventions. We describe the components of a closed-loop system for health interventions. These components range from fine grain sensor characterizations to individual-based models of behavior change. We provide an example of a research health coaching platform that incorporates a closed-loop intervention based on these multiscale models. Using this early prototype, we illustrate how the optimized and personalized methodology and technology can support self-management and remote care. We note that despite the existing examples of research projects and our platform, significant future research is required to convert this vision to full-scale implementations.

  10. Behavioral Informatics and Computational Modeling in Support of Proactive Health Management and Care

    PubMed Central

    Jimison, Holly B.; Korhonen, Ilkka; Gordon, Christine M.; Saranummi, Niilo

    2016-01-01

    Health-related behaviors are among the most significant determinants of health and quality of life. Improving health behavior is an effective way to enhance health outcomes and mitigate the escalating challenges arising from an increasingly aging population and the proliferation of chronic diseases. Although it has been difficult to obtain lasting improvements in health behaviors on a wide scale, advances at the intersection of technology and behavioral science may provide the tools to address this challenge. In this paper, we describe a vision and an approach to improve health behavior interventions using the tools of behavioral informatics, an emerging transdisciplinary research domain based on system-theoretic principles in combination with behavioral science and information technology. The field of behavioral informatics has the potential to optimize interventions through monitoring, assessing, and modeling behavior in support of providing tailored and timely interventions. We describe the components of a closed-loop system for health interventions. These components range from fine grain sensor characterizations to individual-based models of behavior change. We provide an example of a research health coaching platform that incorporates a closed-loop intervention based on these multiscale models. Using this early prototype, we illustrate how the optimized and personalized methodology and technology can support self-management and remote care. We note that despite the existing examples of research projects and our platform, significant future research is required to convert this vision to full-scale implementations. PMID:26441408

  11. A bioimage informatics based reconstruction of breast tumor microvasculature with computational blood flow predictions.

    PubMed

    Stamatelos, Spyros K; Kim, Eugene; Pathak, Arvind P; Popel, Aleksander S

    2014-01-01

    Induction of tumor angiogenesis is among the hallmarks of cancer and a driver of metastatic cascade initiation. Recent advances in high-resolution imaging enable highly detailed three-dimensional geometrical representation of the whole-tumor microvascular architecture. This enormous increase in complexity of image-based data necessitates the application of informatics methods for the analysis, mining and reconstruction of these spatial graph data structures. We present a novel methodology that combines ex-vivo high-resolution micro-computed tomography imaging data with a bioimage informatics algorithm to track and reconstruct the whole-tumor vasculature of a human breast cancer model. The reconstructed tumor vascular network is used as an input of a computational model that estimates blood flow in each segment of the tumor microvascular network. This formulation involves a well-established biophysical model and an optimization algorithm that ensures mass balance and detailed monitoring of all the vessels that feed and drain blood from the tumor microvascular network. Perfusion maps for the whole-tumor microvascular network are computed. Morphological and hemodynamic indices from different regions are compared to infer their role in overall tumor perfusion.

  12. Design, implementation and operation of a multimodality research imaging informatics repository

    PubMed Central

    2015-01-01

    Background Biomedical imaging research increasingly involves acquiring, managing and processing large amounts of distributed imaging data. Integrated systems that combine data, meta-data and workflows are crucial for realising the opportunities presented by advances in imaging facilities. Methods This paper describes the design, implementation and operation of a multi-modality research imaging data management system that manages imaging data obtained from biomedical imaging scanners operated at Monash Biomedical Imaging (MBI), Monash University in Melbourne, Australia. In addition to Digital Imaging and Communications in Medicine (DICOM) images, raw data and non-DICOM biomedical data can be archived and distributed by the system. Imaging data are annotated with meta-data according to a study-centric data model and, therefore, scientific users can find, download and process data easily. Results The research imaging data management system ensures long-term usability, integrity inter-operability and integration of large imaging data. Research users can securely browse and download stored images and data, and upload processed data via subject-oriented informatics frameworks including the Distributed and Reflective Informatics System (DaRIS), and the Extensible Neuroimaging Archive Toolkit (XNAT). PMID:25870760

  13. The United States National Center for Interprofessional Practice and Education: Integrating an informatics approach to interprofessional work.

    PubMed

    Brandt, Barbara F; Cerra, Frank B; Delaney, Connie White

    2015-01-01

    The National Center for Interprofessional Practice and Education, a United States public-private partnership, was formed to provide national leadership, scholarship, evidence, and coordination to advance interprofessional education (IPE) and practice. Many external drivers led to the creation of the partnership that culminated in the National Center: patient safety initiatives, the need for care coordination and transitions efforts, quality improvement imperatives, calls for teamwork and workforce optimization, newly defined national core competencies for interprofessional collaborative practice, practice redesign, escalating health care costs, and state and federal policies. The National Center principals who have served in a variety of senior leadership roles--a clinician, educationalist, and informaticist--recognized the opportunity to leverage the potential that informatics could bring not only to the center but also to the field of IPECP. An informatics approach focuses on collaborative processes and works to address information processing, communications, and data collection. To do so, the National Center created multiple platforms: informatics education, a resource exchange, communication strategy, incubator network, national data repository, and learning system.

  14. Cognitive and learning sciences in biomedical and health instructional design: A review with lessons for biomedical informatics education.

    PubMed

    Patel, Vimla L; Yoskowitz, Nicole A; Arocha, Jose F; Shortliffe, Edward H

    2009-02-01

    Theoretical and methodological advances in the cognitive and learning sciences can greatly inform curriculum and instruction in biomedicine and also educational programs in biomedical informatics. It does so by addressing issues such as the processes related to comprehension of medical information, clinical problem-solving and decision-making, and the role of technology. This paper reviews these theories and methods from the cognitive and learning sciences and their role in addressing current and future needs in designing curricula, largely using illustrative examples drawn from medical education. The lessons of this past work are also applicable, however, to biomedical and health professional curricula in general, and to biomedical informatics training, in particular. We summarize empirical studies conducted over two decades on the role of memory, knowledge organization and reasoning as well as studies of problem-solving and decision-making in medical areas that inform curricular design. The results of this research contribute to the design of more informed curricula based on empirical findings about how people learn and think, and more specifically, how expertise is developed. Similarly, the study of practice can also help to shape theories of human performance, technology-based learning, and scientific and professional collaboration that extend beyond the domain of medicine. Just as biomedical science has revolutionized health care practice, research in the cognitive and learning sciences provides a scientific foundation for education in biomedicine, the health professions, and biomedical informatics.

  15. Current Advances in the Identification and Characterization of Putative Drug and Vaccine Targets in the Bacterial Genomes.

    PubMed

    Shahbaaz, Mohd; Bisetty, Krishna; Ahmad, Faizan; Hassan, Md Imtaiyaz

    2016-01-01

    The development in sequencing technologies over the past few decades have increased the pace of decoding genetic and functional information present in the genomes of pathogenic microorganisms. The knowledge obtained through sequencing projects facilitated the identification of genes that codes for virulence factors. A major portion of genomes of pathogenic of bacteria contains genes which are classified as "hypothetical or uncharacterized". Due to unavailability of precise information about the functionality of these genes, the pathogenic mechanisms utilized by varieties of microorganisms are not fully understood. This respective class of proteins draws a significant interest of pharmaceutical research as they have potential to provide new clues regarding the development of novel therapeutics particularly against the multidrug resistant strains of bacteria. The in silico identification of putative drug and vaccine targets in the set of uncharacterized proteins through comparative and subtractive genome analyses facilitates the increase usability and efficiency of the present drugs. The functional annotation of these characterized target proteins can uncover varieties of biochemical pathways important for the survival and pathogenesis of bacteria. This review focuses on the current protocols available for identification and functional annotations of these uncharacterized potential therapeutic targets.

  16. Making the genomic leap in HCT: application of second-generation sequencing to clinical advances in hematopoietic cell transplantation.

    PubMed

    Li, Yun R; Levine, John E; Hakonarson, Hakon; Keating, Brendan J

    2014-06-01

    Recent developments in second-generation sequencing (SGS) technologies provide an avenue for achieving rapid and accurate high-throughput analysis of human and microbial genomic diversity. SGS technologies have the potential to transform existing medical management of complex and life-threatening medical conditions by enabling clinicians to develop disease-targeted clinical care plans for each patient. In this review, we outline how innovative SGS-based approaches can improve the care of recipients of allogeneic hematopoietic cell transplantation (HCT), a life-saving procedure that carries a 1-year mortality risk of over 30%. We specifically evaluate foreseeable applications of SGS-based technology in facilitating rapid, phase-sensitive human leukocyte antigen (HLA) typing, assessment of non-HLA genomic compatibility, identifying patients at high risk for adverse drug reactions, and post-HCT monitoring for engraftment, minimal residual disease and infection. We conclude that innovative SGS approaches have the capacity to revolutionize the HCT recipient risk assessment process, support non-invasive clinical monitoring and improve patient outcomes, thereby setting the stage for a new era of genomically informed patient-centered medicine.

  17. Deconstructing Mus gemischus: advances in understanding ancestry, structure, and variation in the genome of the laboratory mouse

    PubMed Central

    2013-01-01

    The laboratory mouse is an artificial construct with a complex relationship to its natural ancestors. In 2002, the mouse became the first mammalian model organism with a reference genome. Importantly, the mouse genome sequence was assembled from data on a single inbred laboratory strain, C57BL/6. Several large-scale genetic variant discovery efforts have been conducted, resulting in a catalog of tens of millions of SNPs and structural variants. High-density genotyping arrays covering a subset of those variants have been used to produce hundreds of millions of genotypes in laboratory stocks and a small number of wild mice. These landmark resources now enable us to determine relationships among laboratory mice, assign local ancestry at fine scale, resolve important controversies, and identify a new set of challenges—most importantly, the troubling scarcity of genetic data on the very natural populations from which the laboratory mouse was derived. Our aim with this review is to provide the reader with an historical context for the mouse as a model organism and to explain how practical decisions made in the past have influenced both the architecture of the laboratory mouse genome and the design and execution of current large-scale resources. We also provide examples on how the accomplishments of the past decade can be used by researchers to streamline the use of mice in their experiments and correctly interpret results. Finally, we propose future steps that will enable the mouse community to extend its successes in the decade to come. PMID:23223940

  18. 5th International ACC Symposium: Classification of Adrenocortical Cancers from Pathology to Integrated Genomics: Real Advances or Lost in Translation?

    PubMed

    de Krijger, Ronald E; Bertherat, Jérôme

    2016-02-01

    For the clinician, despite its rarity, adrenocortical cancer is a heterogeneous tumor both in term of steroid excess and tumor evolution. For patient management, it is crucial to have an accurate vision of this heterogeneity, in order to use a correct tumor classification. Pathology is the best way to classify operated adrenocortical tumors: to recognize their adrenocortical nature and to differentiate benign from malignant tumors. Among malignant tumors pathology also aims at prognosis assessment. Although progress has being made for prognosis assessment, there is still a need for improvement. Recent studies have established the value of Ki67 for adrenocortical cancer (ACC) prognostication, aiming also at standardization to reduce variability. The use of genomics to study adrenocortical tumors gives a very new insight in their pathogenesis and molecular classification. Genomics studies of ACC give now a clear description of the mRNA (transcriptome) and miRNA expression profile, as well as chromosomal and methylation alterations. Exome sequencing also established firmly the list of the main ACC driver genes. Interestingly, genomics study of ACC also revealed subtypes of malignant tumors with different pattern of molecular alterations, associated with different outcome. This leads to a new vision of adrenocortical tumors classification based on molecular analysis. Interestingly, these molecular classifications meet also the results of pathological analysis. This opens new perspectives on the development and use of various molecular tools to classify, along with pathological analysis, ACC, and guides patient management at the area of precision medicine.

  19. A blow to the fly - Lucilia cuprina draft genome and transcriptome to support advances in biology and biotechnology.

    PubMed

    Anstead, Clare A; Batterham, Philip; Korhonen, Pasi K; Young, Neil D; Hall, Ross S; Bowles, Vernon M; Richards, Stephen; Scott, Maxwell J; Gasser, Robin B

    2016-01-01

    The blow fly, Lucilia cuprina (Wiedemann, 1830) is a parasitic insect of major global economic importance. Maggots of this fly parasitize the skin of animal hosts, feed on excretions and tissues, and cause severe disease (flystrike or myiasis). Although there has been considerable research on L. cuprina over the years, little is understood about the molecular biology, biochemistry and genetics of this parasitic fly, as well as its relationship with its hosts and the disease that it causes. This situation might change with the recent report of the draft genome and transcriptome of this blow fly, which has given new and global insights into its biology, interactions with the host animal and aspects of insecticide resistance at the molecular level. This genomic resource will likely enable many fundamental and applied research areas in the future. The present article gives a background on L. cuprina and myiasis, a brief account of past and current treatment, prevention and control approaches, and provides a perspective on the impact that the L. cuprina genome should have on future research of this and related parasitic flies, and the design of new and improved interventions for myiasis.

  20. Office of Cancer Genomics |

    Cancer.gov

    The mission of the NCI’s Office of Cancer Genomics (OCG) is to enhance the understanding of the molecular mechanisms of cancer, advance and accelerate genomics science and technology development, and efficiently translate the genomics data to improve cancer research, prevention, early detection, diagnosis and treatment.

  1. Metropolis revisited: the evolving role of librarians in informatics education for the health professions

    PubMed Central

    King, Samuel B.; Lapidus, Mariana

    2015-01-01

    Objective: The authors' goal was to assess changes in the role of librarians in informatics education from 2004 to 2013. This is a follow-up to “Metropolis Redux: The Unique Importance of Library Skills in Informatics,” a 2004 survey of informatics programs. Methods: An electronic survey was conducted in January 2013 and sent to librarians via the MEDLIB-L email discussion list, the library section of the American Association of Colleges of Pharmacy, the Medical Informatics Section of the Medical Library Association, the Information Technology Interest Group of the Association of College and Research Libraries/New England Region, and various library directors across the country. Results: Librarians from fifty-five institutions responded to the survey. Of these respondents, thirty-four included librarians in nonlibrary aspects of informatics training. Fifteen institutions have librarians participating in leadership positions in their informatics programs. Compared to the earlier survey, the role of librarians has evolved. Conclusions: Librarians possess skills that enable them to participate in informatics programs beyond a narrow library focus. Librarians currently perform significant leadership roles in informatics education. There are opportunities for librarian interdisciplinary collaboration in informatics programs. Implications: Informatics is much more than the study of technology. The information skills that librarians bring to the table enrich and broaden the study of informatics in addition to adding value to the library profession itself. PMID:25552939

  2. MAKER-P: a tool kit for the rapid creation, management, and quality control of plant genome annotations.

    PubMed

    Campbell, Michael S; Law, MeiYee; Holt, Carson; Stein, Joshua C; Moghe, Gaurav D; Hufnagel, David E; Lei, Jikai; Achawanantakun, Rujira; Jiao, Dian; Lawrence, Carolyn J; Ware, Doreen; Shiu, Shin-Han; Childs, Kevin L; Sun, Yanni; Jiang, Ning; Yandell, Mark

    2014-02-01

    We have optimized and extended the widely used annotation engine MAKER in order to better support plant genome annotation efforts. New features include better parallelization for large repeat-rich plant genomes, noncoding RNA annotation capabilities, and support for pseudogene identification. We have benchmarked the resulting software tool kit, MAKER-P, using the Arabidopsis (Arabidopsis thaliana) and maize (Zea mays) genomes. Here, we demonstrate the ability of the MAKER-P tool kit to automatically update, extend, and revise the Arabidopsis annotations in light of newly available data and to annotate pseudogenes and noncoding RNAs absent from The Arabidopsis Informatics Resource 10 build. Our results demonstrate that MAKER-P can be used to manage and improve the annotations of even Arabidopsis, perhaps the best-annotated plant genome. We have also installed and benchmarked MAKER-P on the Texas Advanced Computing Center. We show that this public resource can de novo annotate the entire Arabidopsis and maize genomes in less than 3 h and produce annotations of comparable quality to those of the current The Arabidopsis Information Resource 10 and maize V2 annotation builds.

  3. Complete Genomic Sequence and Mass Spectrometric Analysis of Highly Diverse, Atypical Bacillus thuringiensis phage 0305φ8-36

    PubMed Central

    Thomas, Julie A.; Hardies, Stephen C.; Rolando, Mandy; Hayes, Shirley J.; Lieman, Karen; Carroll, Christopher A.; Weintraub, Susan T.; Serwer, Philip

    2007-01-01

    To investigate the apparent genomic complexity of long-genome bacteriophages, we have sequenced the 218,948-bp genome (6479 bp terminal repeat), and identified the virion proteins (55), of Bacillus thuringiensis bacteriophage 0305φ8-36. Phage 0305φ8-36 is an atypical myovirus with three large curly tail fibers. An accurate mode of DNA pyrosequencing was used to sequence the genome and mass spectrometry was used to accomplish the comprehensive virion protein survey. Advanced informatic techniques were used to identify classical morphogenesis genes. The 0305φ8-36 genes were highly diverged; 19% of 247 closely spaced genes have similarity to proteins with known functions. Genes for virion-associated, apparently fibrous proteins in a new class were found, in addition to strong candidates for the curly fiber genes. Phage 0305φ8-36 has twice the virion protein coding sequence of T4. Based on its genomic isolation, 0305φ8-36 is a resource for future studies of vertical gene transmission. PMID:17673272

  4. A solo hospital librarian's experience in clinical informatics.

    PubMed

    Miles, Alisha

    2015-01-01

    This column reviews some of a solo librarian's experiences that led to involvement with the hospital Clinical Informatics Team. This included work on the electronic health record (EHR), computerized physician order entry (CPOE) system, development of order sets, and participation in the Physician Technology Committee.

  5. Score Calculation in Informatics Contests Using Multiple Criteria Decision Methods

    ERIC Educational Resources Information Center

    Skupiene, Jurate

    2011-01-01

    The Lithuanian Informatics Olympiad is a problem solving contest for high school students. The work of each contestant is evaluated in terms of several criteria, where each criterion is measured according to its own scale (but the same scale for each contestant). Several jury members are involved in the evaluation. This paper analyses the problem…

  6. Improving the Evaluation Model for the Lithuanian Informatics Olympiads

    ERIC Educational Resources Information Center

    Skupiene, Jurate

    2010-01-01

    The Lithuanian Informatics Olympiads (LitIO) is a problem solving programming contest for students in secondary education. The work of the student to be evaluated is an algorithm designed by the student and implemented as a working program. The current evaluation process involves both automated (for correctness and performance of programs with the…

  7. A stimulus to define informatics and health information technology

    PubMed Central

    2009-01-01

    Background Despite the growing interest by leaders, policy makers, and others, the terminology of health information technology as well as biomedical and health informatics is poorly understood and not even agreed upon by academics and professionals in the field. Discussion The paper, presented as a Debate to encourage further discussion and disagreement, provides definitions of the major terminology used in biomedical and health informatics and health information technology. For informatics, it focuses on the words that modify the term as well as individuals who practice the discipline. Other categories of related terms are covered as well, from the associated disciplines of computer science, information technolog and health information management to the major application categories of applications used. The discussion closes with a classification of individuals who work in the largest segment of the field, namely clinical informatics. Summary The goal of presenting in Debate format is to provide a starting point for discussion to reach a documented consensus on the definition and use of these terms. PMID:19445665

  8. An Informatics Approach to Establishing a Sustainable Public Health Community

    ERIC Educational Resources Information Center

    Kriseman, Jeffrey Michael

    2012-01-01

    This work involved the analysis of a public health system, and the design, development and deployment of enterprise informatics architecture, and sustainable community methods to address problems with the current public health system. Specifically, assessment of the Nationally Notifiable Disease Surveillance System (NNDSS) was instrumental in…

  9. A current perspective on medical informatics and health sciences librarianship

    PubMed Central

    Perry, Gerald J.; Roderer, Nancy K.; Assar, Soraya

    2005-01-01

    Objective: The article offers a current perspective on medical informatics and health sciences librarianship. Narrative: The authors: (1) discuss how definitions of medical informatics have changed in relation to health sciences librarianship and the broader domain of information science; (2) compare the missions of health sciences librarianship and health sciences informatics, reviewing the characteristics of both disciplines; (3) propose a new definition of health sciences informatics; (4) consider the research agendas of both disciplines and the possibility that they have merged; and (5) conclude with some comments about actions and roles for health sciences librarians to flourish in the biomedical information environment of today and tomorrow. Summary: Boundaries are disappearing between the sources and types of and uses for health information managed by informaticians and librarians. Definitions of the professional domains of each have been impacted by these changes in information. Evolving definitions reflect the increasingly overlapping research agendas of both disciplines. Professionals in these disciplines are increasingly functioning collaboratively as “boundary spanners,” incorporating human factors that unite technology with health care delivery. PMID:15858622

  10. The Integration of Nursing Informatics in Delaware Nursing Education Programs

    ERIC Educational Resources Information Center

    Wheeler, Bernadette

    2016-01-01

    Over the past decade, there has been a conversion to electronic health records (EHRs) in an effort to improve patient care, access, and efficiency. The goal, which has been supported by federal initiatives, is to meaningfully use informatics to improve the safety and quality of patient care as a major force in improving healthcare. How nurses…

  11. An Abridged History of Medical Informatics Education in Europe

    PubMed Central

    Hasman, Arie; Mantas, John; Zarubina, Tatyana

    2014-01-01

    This contribution presents the development of medical informatics education in Europe. It does not discuss all developments that took place. Rather it discerns several themes that indicate the progress in the field, starting from the initiation phase to the final quality control phase. PMID:24648617

  12. School Subject Informatics (Computer Science) in Russia: Educational Relevant Areas

    ERIC Educational Resources Information Center

    Khenner, Evgeniy; Semakin, Igor

    2014-01-01

    This article deals with some aspects of studying Informatics in Russian schools. Those aspects are part of the "third dimension" of the Darmstadt model (they are also projected on the other two dimensions of this model) and include evolution of the subject, regulatory norms conforming to the Federal Educational Standards, the learning…

  13. Pre-School Teachers' Informatics and Information Literacy

    ERIC Educational Resources Information Center

    Tatkovic, Nevenka; Ruzic, Maja; Pecaric, Dilda

    2006-01-01

    The life and activities of every man in the period of transition from the second into the third millennium have been marked by epochal changes which appear as the consequence of scientific and technological revolution dominated by highly developed information and communication technology. Informatics and information education based on information…

  14. Informatics Teaching from the Students' Point of View

    ERIC Educational Resources Information Center

    Zahorec, Jan; Haskova, Alena

    2013-01-01

    Branches of science and technical/engineering study have for a long time been the less favoured disciplines and students have not been interested in studying them. Informatics/computer education, based on its character, belongs to these disciplines, but on the contrary it belongs rather to the group of popular school subjects. The paper presents…

  15. Informatics--Preparation for the Realities of the Future.

    ERIC Educational Resources Information Center

    Kotze, Paula

    The paper describes the informatics curriculum (the study of computer hardware and software as a tool in problem solving) in a special school for gifted children in South Africa. The program's aims (including development of a structured approach to general problem solving and stimulation of pupil interest in technology) are listed and discussed. A…

  16. Designing Biomedical Informatics Infrastructure for Clinical and Translational Science

    ERIC Educational Resources Information Center

    La Paz Lillo, Ariel Isaac

    2009-01-01

    Clinical and Translational Science (CTS) rests largely on information flowing smoothly at multiple levels, in multiple directions, across multiple locations. Biomedical Informatics (BI) is seen as a backbone that helps to manage information flows for the translation of knowledge generated and stored in silos of basic science into bedside…

  17. Human Genome Program Report. Part 2, 1996 Research Abstracts

    DOE R&D Accomplishments Database

    1997-11-01

    This report contains Part 2 of a two-part report to reflect research and progress in the US Department of Energy Human Genome Program from 1994 through 1996, with specified updates made just before publication. Part 2 consists of 1996 research abstracts. Attention is focused on the following: sequencing; mapping; informatics; ethical, legal, and social issues; infrastructure; and small business innovation research.

  18. Human genome program report. Part 2, 1996 research abstracts

    SciTech Connect

    1997-11-01

    This report contains Part 2 of a two-part report to reflect research and progress in the US Department of Energy Human Genome Program from 1994 through 1996, with specified updates made just before publication. Part 2 consists of 1996 research abstracts. Attention is focused on the following: sequencing; mapping; informatics; ethical, legal, and social issues; infrastructure; and small business innovation research.

  19. DOE Human Genome Program contractor-grantee workshop

    SciTech Connect

    1996-01-01

    This volume contains the proceedings for the DOE Human Genome Program`s Contractor-Grantee Workshop V held in Sante Fe, New Mexico January 28, February 1, 1996. Presentations were divided into sessions entitled Sequencing; Mapping; Informatics; Ethical, Legal, and Social Issues; and Infrastructure. Reports of individual projects described herein are separately indexed and abstracted for the database.

  20. Ensembl comparative genomics resources.

    PubMed

    Herrero, Javier; Muffato, Matthieu; Beal, Kathryn; Fitzgerald, Stephen; Gordon, Leo; Pignatelli, Miguel; Vilella, Albert J; Searle, Stephen M J; Amode, Ridwan; Brent, Simon; Spooner, William; Kulesha, Eugene; Yates, Andrew; Flicek, Paul

    2016-01-01

    Evolution provides the unifying framework with which to understand biology. The coherent investigation of genic and genomic data often requires comparative genomics analyses based on whole-genome alignments, sets of homologous genes and other relevant datasets in order to evaluate and answer evolutionary-related questions. However, the complexity and computational requirements of producing such data are substantial: this has led to only a small number of reference resources that are used for most comparative analyses. The Ensembl comparative genomics resources are one such reference set that facilitates comprehensive and reproducible analysis of chordate genome data. Ensembl computes pairwise and multiple whole-genome alignments from which large-scale synteny, per-base conservation scores and constrained elements are obtained. Gene alignments are used to define Ensembl Protein Families, GeneTrees and homologies for both protein-coding and non-coding RNA genes. These resources are updated frequently and have a consistent informatics infrastructure and data presentation across all supported species. Specialized web-based visualizations are also available including synteny displays, collapsible gene tree plots, a gene family locator and different alignment views. The Ensembl comparative genomics infrastructure is extensively reused for the analysis of non-vertebrate species by other projects including Ensembl Genomes and Gramene and much of the information here is relevant to these projects. The consistency of the annotation across species and the focus on vertebrates makes Ensembl an ideal system to perform and support vertebrate comparative genomic analyses. We use robust software and pipelines to produce reference comparative data and make it freely available. Database URL: http://www.ensembl.org.