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  1. Joint Genome Institute's Automation Approach and History

    SciTech Connect

    Roberts, Simon

    2006-07-05

    Department of Energy/Joint Genome Institute (DOE/JGI) collaborates with DOE national laboratories and community users, to advance genome science in support of the DOE missions of clean bio-energy, carbon cycling, and bioremediation.

  2. A Taste of Algal Genomes from the Joint Genome Institute

    SciTech Connect

    Kuo, Alan; Grigoriev, Igor

    2012-06-17

    Algae play profound roles in aquatic food chains and the carbon cycle, can impose health and economic costs through toxic blooms, provide models for the study of symbiosis, photosynthesis, and eukaryotic evolution, and are candidate sources for bio-fuels; all of these research areas are part of the mission of DOE's Joint Genome Institute (JGI). To date JGI has sequenced, assembled, annotated, and released to the public the genomes of 18 species and strains of algae, sampling almost all of the major clades of photosynthetic eukaryotes. With more algal genomes currently undergoing analysis, JGI continues its commitment to driving forward basic and applied algal science. Among these ongoing projects are the pan-genome of the dominant coccolithophore Emiliania huxleyi, the interrelationships between the 4 genomes in the nucleomorph-containing Bigelowiella natans and Guillardia theta, and the search for symbiosis genes of lichens.

  3. Microbial Genomics Data from the DOE Joint Genome Institute (JGI)

    DOE Data Explorer

    The JGI makes high-quality genome sequencing data freely available to the greater scientific community through its web portal. Having played a significant role in the federally funded Human Genome Project -- generating the complete sequences of Chromosomes 5, 16, and 19--the JGI has now moved on to contributing in other critical areas of genomics research. While NIH-funded genome sequencing activities continue to emphasize human biomedical targets and applications, the JGI has since shifted its focus to the non-human components of the biosphere, particularly those relevant to the science mission of the Department of Energy. With efficiencies of scale established at the PGF, and capacity now exceeding three billion bases generated on a monthly basis, the JGI has tackled scores of additional genomes. These include more than 60 microbial genomes and many important multicellular organisms and communities of microbes. In partnership with other federal institutions and universities, the JGI is in the process of sequencing a frog (Xenopus tropicalis), a green alga (Chlamydomonas reinhardtii), a diatom (Thalassiosira pseudonana) , the cottonwood tree (Populus trichocarpa), and a host of agriculturally important plants and plant pathogens. Microorganisms, for example those that thrive under extreme conditions such as high acidity, radiation, and metal contamination, are of particular interest to the DOE and JGI. Investigations by JGI and its partners are shedding light on the cellular machinery of microbes and how they can be harnessed to clean up contaminated soil or water, capture carbon from the atmosphere, and produce potentially important sources of energy such as hydrogen and methane. [Excerpt from the JGI page "Who We Are" at http://www.jgi.doe.gov/whoweare/whoweare.html] From the JGI webportal users can view a photo grid of organisims, check assemblies for status, access the Integrated Microbial Genomes (IMG) system to do comparative analysis of publicly available

  4. 76 FR 28056 - National Human Genome Research Institute; Notice of Closed Meetings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-05-13

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed... of Committee: National Human Genome Research Institute Initial Review Group, Genome Research Review... Scientific Review, National Human Genome Research Institute, National Institutes of Health, Bethesda,...

  5. Eukaryotic Genomics Data from the DOE Joint Genome Institute (JGI)

    DOE Data Explorer

    The JGI makes high-quality genome sequencing data freely available to the greater scientific community through its web portal. Having played a significant role in the federally funded Human Genome Project -- generating the complete sequences of Chromosomes 5, 16, and 19--the JGI has now moved on to contributing in other critical areas of genomics research. While NIH-funded genome sequencing activities continue to emphasize human biomedical targets and applications, the JGI has since shifted its focus to the non-human components of the biosphere, particularly those relevant to the science mission of the Department of Energy. With efficiencies of scale established at the PGF, and capacity now exceeding three billion bases generated on a monthly basis, the JGI has tackled scores of additional genomes. These include more than 60 microbial genomes and many important multicellular organisms and communities of microbes. In partnership with other federal institutions and universities, the JGI is in the process of sequencing a frog (Xenopus tropicalis), a green alga (Chlamydomonas reinhardtii), a diatom (Thalassiosira pseudonana) , the cottonwood tree (Populus trichocarpa), and a host of agriculturally important plants and plant pathogens. Microorganisms, for example those that thrive under extreme conditions such as high acidity, radiation, and metal contamination, are of particular interest to the DOE and JGI. Investigations by JGI and its partners are shedding light on the cellular machinery of microbes and how they can be harnessed to clean up contaminated soil or water, capture carbon from the atmosphere, and produce potentially important sources of energy such as hydrogen and methane. [Excerpt from the JGI page "Who We Are" at http://www.jgi.doe.gov/whoweare/whoweare.html] From the JGI webportal users can choose Eukaryotic genomes from a photo list, access the JGI FTP directories to download data files, use the Tree of Life navigation tool, or choose a genome and go

  6. 2013 Progress Report -- DOE Joint Genome Institute

    SciTech Connect

    2013-11-01

    In October 2012, we introduced a 10-Year Strategic Vision [http://bit.ly/JGI-Vision] for the Institute. A central focus of this Strategic Vision is to bridge the gap between sequenced genomes and an understanding of biological functions at the organism and ecosystem level. This involves the continued massive-scale generation of sequence data, complemented by orthogonal new capabilities to functionally annotate these large sequence data sets. Our Strategic Vision lays out a path to guide our decisions and ensure that the evolving set of experimental and computational capabilities available to DOE JGI users will continue to enable groundbreaking science.

  7. DOE Joint Genome Institute 2008 Progress Report

    SciTech Connect

    Gilbert, David

    2009-03-12

    While initially a virtual institute, the driving force behind the creation of the DOE Joint Genome Institute in Walnut Creek, California in the Fall of 1999 was the Department of Energy's commitment to sequencing the human genome. With the publication in 2004 of a trio of manuscripts describing the finished 'DOE Human Chromosomes', the Institute successfully completed its human genome mission. In the time between the creation of the Department of Energy Joint Genome Institute (DOE JGI) and completion of the Human Genome Project, sequencing and its role in biology spread to fields extending far beyond what could be imagined when the Human Genome Project first began. Accordingly, the targets of the DOE JGI's sequencing activities changed, moving from a single human genome to the genomes of large numbers of microbes, plants, and other organisms, and the community of users of DOE JGI data similarly expanded and diversified. Transitioning into operating as a user facility, the DOE JGI modeled itself after other DOE user facilities, such as synchrotron light sources and supercomputer facilities, empowering the science of large numbers of investigators working in areas of relevance to energy and the environment. The JGI's approach to being a user facility is based on the concept that by focusing state-of-the-art sequencing and analysis capabilities on the best peer-reviewed ideas drawn from a broad community of scientists, the DOE JGI will effectively encourage creative approaches to DOE mission areas and produce important science. This clearly has occurred, only partially reflected in the fact that the DOE JGI has played a major role in more than 45 papers published in just the past three years alone in Nature and Science. The involvement of a large and engaged community of users working on important problems has helped maximize the impact of JGI science. A seismic technological change is presently underway at the JGI. The Sanger capillary-based sequencing process that

  8. 77 FR 60706 - National Human Genome Research Institute; Notice of Closed Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-10-04

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed.... Name of Committee: National Human Genome Research Institute Special Emphasis Panel; Special Emphasis... Officer, Scientific Review Branch, National Human Genome Research Institute, National Institutes of...

  9. 75 FR 8374 - National Human Genome Research Institute; Notice of Closed Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-02-24

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed... of Committee: National Human Genome Research Institute Special Emphasis Panel, Revolutionary..., National Human Genome Research Institute, National Institutes of Health, 5635 Fishers Lane, Suite 4076, MSC...

  10. Conceptualizing a Genomics Software Institute (GSI).

    PubMed

    Gilbert, Jack A; Catlett, Charlie; Desai, Narayan; Knight, Rob; White, Owen; Robbins, Robert; Sankaran, Rajesh; Sansone, Susanna-Assunta; Field, Dawn; Meyer, Folker

    2012-03-19

    Microbial ecology has been enhanced greatly by the ongoing 'omics revolution, bringing half the world's biomass and most of its biodiversity into analytical view for the first time; indeed, it feels almost like the invention of the microscope and the discovery of the new world at the same time. With major microbial ecology research efforts accumulating prodigious quantities of sequence, protein, and metabolite data, we are now poised to address environmental microbial research at macro scales, and to begin to characterize and understand the dimensions of microbial biodiversity on the planet. What is currently impeding progress is the need for a framework within which the research community can develop, exchange and discuss predictive ecosystem models that describe the biodiversity and functional interactions. Such a framework must encompass data and metadata transparency and interoperation; data and results validation, curation, and search; application programming interfaces for modeling and analysis tools; and human and technical processes and services necessary to ensure broad adoption. Here we discuss the need for focused community interaction to augment and deepen established community efforts, beginning with the Genomic Standards Consortium (GSC), to create a science-driven strategic plan for a Genomic Software Institute (GSI).

  11. Conceptualizing a Genomics Software Institute (GSI)

    PubMed Central

    Gilbert, Jack A.; Catlett, Charlie; Desai, Narayan; Knight, Rob; White, Owen; Robbins, Robert; Sankaran, Rajesh; Sansone, Susanna-Assunta; Field, Dawn; Meyer, Folker

    2012-01-01

    Microbial ecology has been enhanced greatly by the ongoing ‘omics revolution, bringing half the world's biomass and most of its biodiversity into analytical view for the first time; indeed, it feels almost like the invention of the microscope and the discovery of the new world at the same time. With major microbial ecology research efforts accumulating prodigious quantities of sequence, protein, and metabolite data, we are now poised to address environmental microbial research at macro scales, and to begin to characterize and understand the dimensions of microbial biodiversity on the planet. What is currently impeding progress is the need for a framework within which the research community can develop, exchange and discuss predictive ecosystem models that describe the biodiversity and functional interactions. Such a framework must encompass data and metadata transparency and interoperation; data and results validation, curation, and search; application programming interfaces for modeling and analysis tools; and human and technical processes and services necessary to ensure broad adoption. Here we discuss the need for focused community interaction to augment and deepen established community efforts, beginning with the Genomic Standards Consortium (GSC), to create a science-driven strategic plan for a Genomic Software Institute (GSI). PMID:22675605

  12. Implementing genomics and pharmacogenomics in the clinic: The National Human Genome Research Institute's genomic medicine portfolio.

    PubMed

    Manolio, Teri A

    2016-10-01

    Increasing knowledge about the influence of genetic variation on human health and growing availability of reliable, cost-effective genetic testing have spurred the implementation of genomic medicine in the clinic. As defined by the National Human Genome Research Institute (NHGRI), genomic medicine uses an individual's genetic information in his or her clinical care, and has begun to be applied effectively in areas such as cancer genomics, pharmacogenomics, and rare and undiagnosed diseases. In 2011 NHGRI published its strategic vision for the future of genomic research, including an ambitious research agenda to facilitate and promote the implementation of genomic medicine. To realize this agenda, NHGRI is consulting and facilitating collaborations with the external research community through a series of "Genomic Medicine Meetings," under the guidance and leadership of the National Advisory Council on Human Genome Research. These meetings have identified and begun to address significant obstacles to implementation, such as lack of evidence of efficacy, limited availability of genomics expertise and testing, lack of standards, and difficulties in integrating genomic results into electronic medical records. The six research and dissemination initiatives comprising NHGRI's genomic research portfolio are designed to speed the evaluation and incorporation, where appropriate, of genomic technologies and findings into routine clinical care. Actual adoption of successful approaches in clinical care will depend upon the willingness, interest, and energy of professional societies, practitioners, patients, and payers to promote their responsible use and share their experiences in doing so.

  13. 78 FR 64222 - National Human Genome Research Institute; Notice of Closed Meetings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-10-28

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed... of Committee: National Human Genome Research Institute Initial Review Group; Genome Research Review..., Ph.D., Scientific Review Officer, Office of Scientific Review, National Human Genome...

  14. 75 FR 10488 - National Human Genome Research Institute; Notice of Closed Meetings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-03-08

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed... of Committee: National Human Genome Research Institute Special Emphasis Panel; NHGRI MAP Review... Human Genome Research Institute Special Emphasis Panel; LRP 2010 Teleconference. Date: April 7,...

  15. 75 FR 52538 - National Human Genome Research Institute; Notice of Closed Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-08-26

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed... of Committee: National Human Genome Research Institute Special Emphasis Panel. Date: November 19-20..., Scientific Review Officer, Scientific Review Branch, National Human Genome Research Institute,...

  16. 78 FR 20933 - National Human Genome Research Institute; Notice of Closed Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-04-08

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed... of Committee: National Human Genome Research Institute Special Emphasis Panel Loan Repayment Program... applications. Place: National Human Genome Research Institute, Room 3055, 5635 Fishers Lane, Rockville,...

  17. 78 FR 14806 - National Human Genome Research Institute; Notice of Closed Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-03-07

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed... of Committee: National Human Genome Research Institute Special Emphasis Panel: Clinically Relevant... grant applications. Place: National Human Genome Research Institute, 4th Floor Conference Room,...

  18. 76 FR 35223 - National Human Genome Research Institute; Notice of Closed Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-06-16

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed... of Committee: National Human Genome Research Institute Special Emphasis Panel, Sequencing Centers...D, Scientific Review Officer, Scientific Review Branch, National Human Genome Research Institute...

  19. 76 FR 65204 - National Human Genome Research Institute; Notice of Closed Meetings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-10-20

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed... of Committee: National Human Genome Research Institute Special Emphasis Panel; Genomic Resource...: Rudy O. Pozzatti, Ph.D., Scientific Review Officer, Scientific Review Branch, National Human...

  20. Plant database resources at The Institute for Genomic Research.

    PubMed

    Chan, Agnes P; Rabinowicz, Pablo D; Quackenbush, John; Buell, C Robin; Town, Chris D

    2007-01-01

    With the completion of the genome sequences of the model plants Arabidopsis and rice, and the continuing sequencing efforts of other economically important crop plants, an unprecedented amount of genome sequence data is now available for large-scale genomics studies and analyses, such as the identification and discovery of novel genes, comparative genomics, and functional genomics. Efficient utilization of these large data sets is critically dependent on the ease of access and organization of the data. The plant databases at The Institute for Genomic Research (TIGR) have been set up to maintain various data types including genomic sequence, annotation and analyses, expressed transcript assemblies and analyses, and gene expression profiles from microarray studies. We present here an overview of the TIGR database resources for plant genomics and describe methods to access the data.

  1. 76 FR 58023 - National Human Genome Research Institute; Notice of Closed Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-09-19

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed... of Committee: National Human Genome Research Institute Initial Review Group; Genome Research Review... Review, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, 301...

  2. 75 FR 2148 - National Human Genome Research Institute; Notice of Closed Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-01-14

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed... of Committee: National Human Genome Research Institute Initial Review Group, Genome Research Review... Domestic Assistance Program Nos. 93.172, Human Genome Research, National Institutes of Health, HHS)...

  3. 75 FR 52537 - National Human Genome Research Institute; Notice of Closed Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-08-26

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed... of Committee: National Human Genome Research Institute Initial Review Group; Genome Research Review... Domestic Assistance Program Nos. 93.172, Human Genome Research, National Institutes of Health, HHS)...

  4. 78 FR 24223 - National Human Genome Research Institute; Notice of Closed Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-04-24

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed... of Committee: National Human Genome Research Institute Initial Review Group; Genome Research Review... applications. Place: National Human Genome Research Institute, 3rd floor Conf. Room 3146, 5635 Fishers...

  5. 77 FR 28888 - National Human Genome Research Institute Notice of Closed Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-05-16

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute Notice of Closed... of Committee: National Human Genome Research Institute Initial Review Group; Genome Research Review... applications. Place: National Human Genome Research Institute, 3635 Fishers Lane, Suite 4076, ] Rockville, MD...

  6. 76 FR 3643 - National Human Genome Research Institute; Notice of Closed Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-01-20

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed... of Committee: National Human Genome Research Institute Initial Review Group; Genome Research Review... Assistance Program Nos. 93.172, Human Genome Research, National Institutes of Health, HHS) Dated: January 13...

  7. 77 FR 61770 - National Human Genome Research Institute; Notice of Closed Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-10-11

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed... of Committee: National Human Genome Research Institute Special Emphasis Panel; Genomic Medicine RFAs..., Human Genome Research, National Institutes of Health, HHS) ] Dated: October 4, 2012. David Clary...

  8. 75 FR 80509 - National Human Genome Research Institute; Notice of Closed Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-12-22

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed..., PhD, Scientific Review Officer, CIDR, National Human Genome Research Institute, National Institutes..., Human Genome Research, National Institutes of Health, HHS) Dated: December 16, 2010. Jennifer S....

  9. 78 FR 47715 - National Human Genome Research Institute; Notice of Closed Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-08-06

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed...., Scientific Review Officer, CIDR, National Human Genome Research Institute, National Institutes of Health... Federal Domestic Assistance Program Nos. 93.172, Human Genome Research, National Institutes of Health,...

  10. 76 FR 79199 - National Human Genome Research Institute; Notice of Closed Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-12-21

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed...., Scientific Review Officer, CIDR, National Human Genome Research Institute, National Institutes of Health... Federal Domestic Assistance Program Nos. 93.172, Human Genome Research, National Institutes of Health,...

  11. 76 FR 9031 - National Human Genome Research Institute; Notice of Closed Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-02-16

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed..., PhD, Scientific Review Officer, CIDR, National Human Genome Research Institute, National Institutes... . (Catalogue of Federal Domestic Assistance Program Nos. 93.172, Human Genome Research, National Institutes...

  12. 78 FR 107 - National Human Genome Research Institute; Notice of Closed Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-01-02

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed...: National Human Genome Research Institute, 3rd Floor Conference Room, 5635 Fishers Lane, Rockville, MD 20851... Review Branch, National Human Genome Research Institute, National Institutes of Health, 5635 Fishers...

  13. 75 FR 35821 - National Human Genome Research Institute; Notice of Closed Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-06-23

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed..., Scientific Review Officer, CIDR, National Human Genome Research Institute, National Institutes of Health... Federal Domestic Assistance Program Nos. 93.172, Human Genome Research, National Institutes of Health, HHS...

  14. 76 FR 19780 - National Human Genome Research Institute; Notice of Closed Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-04-08

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed... Officer, CIDR, National Human Genome Research Institute, National Institutes of Health, 5635 Fishers Lane... Assistance Program No. 93.172, Human Genome Research, National Institutes of Health, HHS) Dated: April 4...

  15. 75 FR 62548 - National Human Genome Research Institute; Notice of Closed Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-10-12

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed..., PhD, Scientific Review Officer, CIDR, National Human Genome Research Institute, National Institutes... . Catalogue of Federal Domestic Assistance Program Nos. 93.172, Human Genome Research, National Institutes of...

  16. 78 FR 68856 - National Human Genome Research Institute; Notice of Closed Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-11-15

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed... Review Officer, Scientific Review Branch, National Human Genome Research Institute, National Institutes... of Federal Domestic Assistance Program Nos. 93.172, Human Genome Research, National Institutes of...

  17. 77 FR 71604 - National Human Genome Research Institute; Notice of Closed Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-12-03

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed... of Committee: National Human Genome Research Institute Special Emphasis Panel. Date: January 11, 2013..., National Human Genome Research Institute, National Institutes of Health, 5635 Fishers Lane, Suite 4076, MSC...

  18. 77 FR 5035 - National Human Genome Research Institute; Notice of Closed Meetings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-02-01

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed... of Committee: National Human Genome Research Institute Special Emphasis Panel Sequencing Technology... Person: Ken D. Nakamura, Ph.D., Scientific Review Officer, Scientific Review Branch, National...

  19. The genome portal of the Department of Energy Joint Genome Institute: 2014 updates

    PubMed Central

    Nordberg, Henrik; Cantor, Michael; Dusheyko, Serge; Hua, Susan; Poliakov, Alexander; Shabalov, Igor; Smirnova, Tatyana; Grigoriev, Igor V.; Dubchak, Inna

    2014-01-01

    The U.S. Department of Energy (DOE) Joint Genome Institute (JGI), a national user facility, serves the diverse scientific community by providing integrated high-throughput sequencing and computational analysis to enable system-based scientific approaches in support of DOE missions related to clean energy generation and environmental characterization. The JGI Genome Portal (http://genome.jgi.doe.gov) provides unified access to all JGI genomic databases and analytical tools. The JGI maintains extensive data management systems and specialized analytical capabilities to manage and interpret complex genomic data. A user can search, download and explore multiple data sets available for all DOE JGI sequencing projects including their status, assemblies and annotations of sequenced genomes. Here we describe major updates of the Genome Portal in the past 2 years with a specific emphasis on efficient handling of the rapidly growing amount of diverse genomic data accumulated in JGI. PMID:24225321

  20. What does it mean to be genomically literate?: National Human Genome Research Institute Meeting Report.

    PubMed

    Hurle, Belen; Citrin, Toby; Jenkins, Jean F; Kaphingst, Kimberly A; Lamb, Neil; Roseman, Jo Ellen; Bonham, Vence L

    2013-08-01

    Genomic discoveries will increasingly advance the science of medicine. Limited genomic literacy may adversely impact the public's understanding and use of the power of genetics and genomics in health care and public health. In November 2011, a meeting was held by the National Human Genome Research Institute to examine the challenge of achieving genomic literacy for the general public, from kindergarten to grade 12 to adult education. The role of the media in disseminating scientific messages and in perpetuating or reducing misconceptions was also discussed. Workshop participants agreed that genomic literacy will be achieved only through active engagement between genomics experts and the varied constituencies that comprise the public. This report summarizes the background, content, and outcomes from this meeting, including recommendations for a research agenda to inform decisions about how to advance genomic literacy in our society.

  1. What Does it Mean to be Genomically Literate? National Human Genome Research Institute Meeting Report

    PubMed Central

    Hurle, Belen; Citrin, Toby; Jenkins, Jean F.; Kaphingst, Kimberly A.; Lamb, Neil; Roseman, Jo Ellen; Bonham, Vence L.

    2014-01-01

    Genomic discoveries will increasingly advance the science of medicine. Limited genomic literacy may adversely impact the public’s understanding and use of the power of genetics and genomics in health care and public health. In November 2011, a meeting was held by the National Human Genome Research Institute to examine the challenge of achieving genomic literacy for the general public, from K-12 to adult education. The role of the media in disseminating scientific messages and in perpetuating, or reducing, misconceptions was also discussed. Workshop participants agreed that genomic literacy will only be achieved through active engagement between genomics experts and the varied constituencies that comprise the public. This report summarizes the background, content, and outcomes from this meeting, including recommendations for a research agenda to inform decisions about how to advance genomic literacy in our society. PMID:23448722

  2. The genome portal of the Department of Energy Joint Genome Institute: 2014 updates

    SciTech Connect

    Nordberg, Henrik; Cantor, Michael; Dusheyko, Serge; Hua, Susan; Poliakov, Alexander; Shabalov, Igor; Smirnova, Tatyana; Grigoriev, Igor V.; Dubchak, Inna

    2013-11-12

    The U.S. Department of Energy (DOE) Joint Genome Institute (JGI), a national user facility, serves the diverse scientific community by providing integrated high-throughput sequencing and computational analysis to enable system-based scientific approaches in support of DOE missions related to clean energy generation and environmental characterization. The JGI Genome Portal (http://genome.jgi.doe.gov) provides unified access to all JGI genomic databases and analytical tools. The JGI maintains extensive data management systems and specialized analytical capabilities to manage and interpret complex genomic data. A user can search, download and explore multiple data sets available for all DOE JGI sequencing projects including their status, assemblies and annotations of sequenced genomes. In this paper, we describe major updates of the Genome Portal in the past 2 years with a specific emphasis on efficient handling of the rapidly growing amount of diverse genomic data accumulated in JGI.

  3. The Genome Portal of the Department of Energy Joint Genome Institute

    PubMed Central

    Grigoriev, Igor V.; Nordberg, Henrik; Shabalov, Igor; Aerts, Andrea; Cantor, Mike; Goodstein, David; Kuo, Alan; Minovitsky, Simon; Nikitin, Roman; Ohm, Robin A.; Otillar, Robert; Poliakov, Alex; Ratnere, Igor; Riley, Robert; Smirnova, Tatyana; Rokhsar, Daniel; Dubchak, Inna

    2012-01-01

    The Department of Energy (DOE) Joint Genome Institute (JGI) is a national user facility with massive-scale DNA sequencing and analysis capabilities dedicated to advancing genomics for bioenergy and environmental applications. Beyond generating tens of trillions of DNA bases annually, the Institute develops and maintains data management systems and specialized analytical capabilities to manage and interpret complex genomic data sets, and to enable an expanding community of users around the world to analyze these data in different contexts over the web. The JGI Genome Portal (http://genome.jgi.doe.gov) provides a unified access point to all JGI genomic databases and analytical tools. A user can find all DOE JGI sequencing projects and their status, search for and download assemblies and annotations of sequenced genomes, and interactively explore those genomes and compare them with other sequenced microbes, fungi, plants or metagenomes using specialized systems tailored to each particular class of organisms. We describe here the general organization of the Genome Portal and the most recent addition, MycoCosm (http://jgi.doe.gov/fungi), a new integrated fungal genomics resource. PMID:22110030

  4. 77 FR 20646 - National Human Genome Research Institute; Notice of Closed Meetings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-04-05

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed... of Committee: National Human Genome Research Institute Special Emphasis Panel; Loan Repayment Program...: National Human Genome Research Institute, 5635 Fishers Lane, 3rd Floor Conference Room, Rockville, MD...

  5. 78 FR 11898 - National Human Genome Research Institute; Notice of Closed Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-02-20

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed.... Day, Ph.D., Scientific Review Officer CIDR, National Human Genome Research Institute, National... . (Catalogue of Federal Domestic Assistance Program Nos. 93.172, Human Genome Research, National Institutes...

  6. 77 FR 12604 - National Human Genome Research Institute; Notice of Closed Meetings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-03-01

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed.... >Name of Committee: National Human Genome Research Institute Special Emphasis Panel, CIDR Contract. Date...: National Human Genome Reseach Institute, 5635 Fishers Lane, Room 4076, Rockville, MD 20852,...

  7. 78 FR 31953 - National Human Genome Research Institute; Notice of Closed Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-05-28

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed... of Committee: National Human Genome Research Institute Special Emphasis Panel; SEP-UDN Coordinating... applications. Place: National Human Genome Research Institute, 3rd Floor Conference Room, 3146, 5635...

  8. 75 FR 60467 - National Human Genome Research Institute; Notice of Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-09-30

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Meeting... hereby given of a meeting of the Board of Scientific Counselors, National Human Genome Research Institute... intramural programs and projects conducted by the National Human Genome Research Institute,...

  9. 78 FR 77477 - National Human Genome Research Institute; Notice of Closed Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-12-23

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed...: Camilla E. Day, Ph.D., Scientific Review Officer, CIDR, National Human Genome Research Institute, National... . (Catalogue of Federal Domestic Assistance Program Nos. 93.172, Human Genome Research, National Institutes...

  10. 77 FR 6810 - National Human Genome Research Institute; Notice of Closed Meetings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-02-09

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed... of Committee: National Human Genome Research Institute Special Emphasis Panel; CIDR Contract Renewal... Branch, National Human Genome Research Institute, 5635 Fishers Lane, Suite 4076, MSC 9306, Rockville,...

  11. 76 FR 50486 - National Human Genome Research Institute; Notice of Closed Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-08-15

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed.... Day, PhD, Scientific Review Officer, CIDR, National Human Genome Research Institute, National... . (Catalogue of Federal Domestic Assistance Program Nos. 93.172, Human Genome Research, National Institutes...

  12. 77 FR 31863 - National Human Genome Research Institute; Notice of Closed Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-05-30

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed... of Committee: National Human Genome Research Institute Special Emphasis Panel DAP R25 Eppig.... (Catalogue of Federal Domestic Assistance Program Nos. 93.172, Human Genome Research, National Institutes...

  13. 77 FR 59933 - National Human Genome Research Institute; Notice of Closed Meetings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-10-01

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed... of Committee: National Human Genome Research Institute Special Emphasis Panel; ELSI CEERS RFA (SEP... Branch, National Human Genome Research Institute, 5635 Fishers Lane, Suite 4076, MSC 9306, Rockville,...

  14. 77 FR 22332 - National Human Genome Research Institute; Notice of Closed Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-04-13

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed... of Committee: National Human Genome Research Institute Special Emphasis Panel, H3Africa Biorepository... applications. Place: National Human Genome Research Institute, 5635 Fishers Lane, 4076, Rockville, MD...

  15. 76 FR 22407 - National Human Genome Research Institute; Notice of Closed Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-04-21

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed... of Committee: National Human Genome Research Institute Special Emphasis Panel; Loan Repayment Program....172, Human Genome Research, National Institutes of Health, HHS) Dated: April 12, 2011. Jennifer...

  16. 77 FR 58402 - National Human Genome Research Institute; Notice of Closed Meetings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-09-20

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed... of Committee: National Human Genome Research Institute Special Emphasis Panel; R25 DAP Sept. 2012...: National Human Genome Research Institute, 5635 Fishers Lane, 3rd Floor Conference Room, Rockville, MD...

  17. 77 FR 64816 - National Human Genome Research Institute; Notice of Closed Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-10-23

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed...: Camilla E. Day, Ph.D., Scientific Review Officer, CIDR, National Human Genome Research Institute, National... . (Catalogue of Federal Domestic Assistance Program Nos. 93.172, Human Genome Research, National Institutes...

  18. 75 FR 32957 - National Human Genome Research Institute; Notice of Closed Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-06-10

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed... of Committee: National Human Genome Research Institute Special Emphasis Panel, Protein Resource RFA... of Federal Domestic Assistance Program Nos. 93.172, Human Genome Research, National Institutes...

  19. 75 FR 8977 - National Human Genome Research Institute; Notice of Closed Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-02-26

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed...: Camilla E. Day, PhD, Scientific Review Officer, CIDR, National Human Genome Research Institute, National... . (Catalogue of Federal Domestic Assistance Program Nos. 93.172, Human Genome Research, National Institutes...

  20. 75 FR 8373 - National Human Genome Research Institute; Notice of Closed Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-02-24

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed... of Committee: National Human Genome Research Institute Special Emphasis Panel, GWAS Comparing Design... of Federal Domestic Assistance Program Nos. 93.172, Human Genome Research, National Institutes of...

  1. 76 FR 35224 - National Human Genome Research Institute; Notice of Closed Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-06-16

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed.... Day, PhD, Scientific Review Officer, CIR, National Human Genome Research Institute, National... . (Catalogue of Federal Domestic Assistance Program Nos. 93.172, Human Genome Research, National Institutes of...

  2. 76 FR 66076 - National Human Genome Research Institute; Notice of Closed Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-10-25

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed...: Camilla E. Day, PhD, Scientific Review Officer, CIDR, National Human Genome Research Institute, National..., Human Genome Research, National Institutes of Health, HHS) Dated: October 19, 2011. Jennifer S. Spaeth...

  3. 77 FR 50140 - National Human Genome Research Institute; Notice of Closed Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-08-20

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed.... Day, Ph.D., Scientific Review Officer, CIDR, National Human Genome Research Institute, National... . (Catalogue of Federal Domestic Assistance Program Nos. 93.172, Human Genome Research, National Institutes of...

  4. 77 FR 35991 - National Human Genome Research Institute; Notice of Closed Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-06-15

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed...: Camilla E. Day, Ph.D., Scientific Review Officer, CIDR, National Human Genome Research Institute, National... . (Catalogue of Federal Domestic Assistance Program Nos. 93.172, Human Genome Research, National Institutes of...

  5. 75 FR 48977 - National Human Genome Research Institute; Notice of Closed Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-08-12

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed.... Day, PhD, Scientific Review Officer, CIDR, National Human Genome Research Institute, National... . (Catalogue of Federal Domestic Assistance Program Nos. 93.172, Human Genome Research, National Institutes of...

  6. 78 FR 9707 - National Human Genome Research Institute; Notice of Closed Meetings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-02-11

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed... of Committee: National Human Genome Research Institute Special Emphasis Panel; H3Africa (RM-006, RM... Human Genome Research Institute, 5635 Fishers Lane, Suite 4076, MSC 9306, Rockville, MD 20852, (301) 402...

  7. 76 FR 63932 - National Human Genome Research Institute; Notice of Closed Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-10-14

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed... of Committee: National Human Genome Research Institute Special Emphasis Panel, ENCODE Technology RFA... Genome Research, National Institutes of Health, HHS) Dated: October 7, 2011 . Jennifer S. Spaeth...

  8. 76 FR 5390 - National Human Genome Research Institute; Notice of Closed Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-01-31

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed... privacy. Place: National Human Genome Research Institute Special Emphasis Panel; NHGRI Sample Repository..., National Human Genome Research Institute, 5635 Fishers Lane, Suite 4076, MSC 9306, Rockville, MD 20852...

  9. 75 FR 56115 - National Human Genome Research Institute; Notice of Closed Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-09-15

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed... of Committee: National Human Genome Research Institute Special Emphasis Panel; CEGS DAP. Date... Assistance Program Nos. 93.172, Human Genome Research, National Institutes of Health, HHS) Dated: September 9...

  10. 76 FR 22112 - National Human Genome Research Institute; Notice of Closed Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-04-20

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed... of Committee: National Human Genome Research Institute Special Emphasis Panel, Special Emphasis Panel... Assistance Program Nos. 93.172, Human Genome Research, National Institutes of Health, HHS) Dated: April 14...

  11. 78 FR 56905 - National Human Genome Research Institute; Notice of Closed Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-09-16

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed... of Committee: National Human Genome Research Institute Special Emphasis Panel; H3AFRICA ELSI Research.... Place: National Human Genome Research Institute, Suite 3055, 5635 Fishers Lane, Rockville, MD 20852...

  12. 76 FR 17930 - National Human Genome Research Institute; Notice of Closed Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-03-31

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed... privacy. Name of Committee: National Human Genome Research Institute Special Emphasis Panel; Genetic... Branch, National Human Genome Research Institute, 5635 Fishers Lane, Suite 4076, MSC 9306, Rockville, MD...

  13. 77 FR 64816 - National Human Genome Research Institute; Notice of Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-10-23

    ... intramural programs and projects conducted by the National Human Genome Research Institute, including... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Meeting... hereby given of a meeting of the Board of Scientific Counselors, National Human Genome Research Institute...

  14. 78 FR 55752 - National Human Genome Research Institute; Notice of Closed Meetings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-09-11

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed... of Committee: National Human Genome Research Institute Special Emphasis Panel; Clinical Sites for..., Scientific Review Branch, National Human Genome Research Institute, 5635 Fishers Lane, Suite 4076, MSC 9306...

  15. 76 FR 65204 - National Human Genome Research Institute; Notice of Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-10-20

    ... intramural programs and projects conducted by the National Human Genome Research Institute, including... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Meeting... hereby given of a meeting of the Board of Scientific Counselors, National Human Genome Research Institute...

  16. 76 FR 36930 - National Human Genome Research Institute; Notice of Closed Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-06-23

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed... of Committee: National Human Genome Research Institute Special Emphasis Panel, DAP R-25. Date: July...@mail.nih.gov . (Catalogue of Federal Domestic Assistance Program Nos. 93.172, Human Genome...

  17. 77 FR 2304 - National Human Genome Research Institute; Notice of Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-01-17

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Meeting... given that the National Human Genome Research Institute (NHGRI) will host a series of meetings to enable... for Human Genome Research. Background materials on the proposed reorganization and...

  18. 77 FR 74676 - National Human Genome Research Institute; Notice of Closed Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-12-17

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed... Person: Camilla E. Day, Ph.D., Scientific Review Officer, CIDR, National Human Genome Research Institute...@nih.gov . (Catalogue of Federal Domestic Assistance Program Nos. 93.172, Human Genome...

  19. 75 FR 67380 - National Human Genome Research Institute; Notice of Closed Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-11-02

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed...: Ken D. Nakamura, PhD, Scientific Review Officer, Scientific Review Branch, National Human Genome... Program Nos. 93.172, Human Genome Research, National Institutes of Health, HHS) Dated: October 26, 2010...

  20. 76 FR 3917 - National Human Genome Research Institute; Notice of Closed Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-01-21

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed... privacy. Name of Committee: National Human Genome Research Institute Special Emphasis Panel, TRND--RFP... Person: Rudy O. Pozzatti, PhD, Scientific Review Officer, Scientific Review Branch, National Human Genome...

  1. 76 FR 66731 - National Human Genome Research Institute; Notice of Closed Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-10-27

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed... of Committee: National Human Genome Research Institute Special Emphasis Panel, DAP for CEGS-SEP. Date...@mail.nih.gov . (Catalogue of Federal Domestic Assistance Program Nos. 93.172, Human Genome Research...

  2. 75 FR 53703 - National Human Genome Research Institute; Notice of Closed Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-09-01

    ... National Human Genome Research Institute; Notice of Closed Meeting Pursuant to section 10(d) of the Federal... Review Officer, Scientific Review Branch, National Human Genome Research Institute, National Institutes... review and funding cycle. (Catalogue of Federal Domestic Assistance Program Nos. 93.172, Human Genome...

  3. 76 FR 50486 - National Human Genome Research Institute; Notice of Closed Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-08-15

    ... individual intramural programs and projects conducted by the National Human Genome Research Institute... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed....), notice is hereby given of a meeting of the Board of Scientific Counselors, National Human Genome Research...

  4. 75 FR 13558 - National Human Genome Research Institute; Notice of Closed Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-03-22

    ... individual intramural programs and projects conducted by the National Human Genome Research Institute... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed....), notice is hereby given of a meeting of the Board of Scientific Counselors, National Human Genome Research...

  5. 76 FR 3642 - National Human Genome Research Institute; Notice of Closed Meetings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-01-20

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed... of Committee: National Human Genome Research Institute Special Emphasis Panel, KOMP (KNOCK-OUT MOUSE..., MD 20814, 301-594- 4280, mckenneyk@mail.nih.gov . Name of Committee: National Human Genome Research...

  6. 76 FR 28056 - National Human Genome Research Institute; Notice of Closed Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-05-13

    ... individual intramural programs and projects conducted by the National Human Genome Research Institute... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed....), notice is hereby given of a meeting of the Board of Scientific Counselors, National Human Genome Research...

  7. 78 FR 70063 - National Human Genome Research Institute; Notice of Closed Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-11-22

    ... individual intramural programs and projects conducted by the NATIONAL HUMAN GENOME RESEARCH INSTITUTE... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed....), notice is hereby given of a meeting of the Board of Scientific Counselors, National Human Genome Research...

  8. Integrated Microbial Genomes (IMG) System from the DOE Joint Genome Institute (JGI)

    DOE Data Explorer

    The integrated microbial genomes (IMG) system is a data management, analysis and annotation platform for all publicly available genomes. IMG contains both draft and complete JGI microbial genomes integrated with all other publicly available genomes from all three domains of life, together with a large number of plasmids and viruses. IMG provides tools and viewers for analyzing and annotating genomes, genes and functions, individually or in a comparative context. Since its first release in 2005, IMG's data content and analytical capabilities have been constantly expanded through quarterly releases. IMG is provided by the DOE-Joint Genome Institute (JGI) and is available from http://img.jgi.doe.gov. [Abstract from The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions; Victor M. Markowitz, Ernest Szeto, Krishna Palaniappan, Yuri Grechkin, Ken Chu, I-Min A. Chen, Inna Dubchak, Iain Anderson, Athanasios Lykidis, Konstantinos Mavromatis, Natalia N. Ivanova and Nikos C. Kyrpides; Nucleic Acids Research, 2008, Vol. 36. (Database Issue) See also the companion system, Integrated Microbial Genomes with Microbiome Samples.

  9. 75 FR 2147 - National Human Genome Research Institute; Notice of Meetings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-01-14

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of....), notice is hereby given of meetings of the National Advisory Council for Human Genome Research. The... of Committee: National Advisory Council for Human Genome Research. Date: February 8-9, 2010....

  10. 77 FR 8268 - National Human Genome Research Institute; Notice of Closed Meetings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-02-14

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed...:30 a.m. to 1 p.m. Agenda: To review and evaluate grant applications. Place: National Human Genome...). Contact Person: Camilla E. Day, Ph.D., Scientific Review Officer, CIDR, National Human Genome...

  11. 75 FR 8977 - National Human Genome Research Institute; Notice of Closed Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-02-26

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed.... Nakamura, PhD, Scientific Review Officer, Scientific Review Branch, National Human Genome Research...-402-0838. (Catalogue of Federal Domestic Assistance Program Nos. 93.172, Human Genome...

  12. 78 FR 21382 - National Human Genome Research Institute; Notice of Closed Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-04-10

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed...:00 p.m. to 4:00 p.m. Agenda: To review and evaluate grant applications. Place: National Human Genome... Person: Camilla E. Day, PhD., Scientific Review Officer, CIDR, National Human Genome Research...

  13. 76 FR 10909 - National Human Genome Research Institute; Notice of Closed Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-02-28

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed.... Nakamura, PhD, Scientific Review Officer, Scientific Review Branch, National Human Genome Research...-402-0838. (Catalogue of Federal Domestic Assistance Program Nos. 93.172, Human Genome...

  14. 75 FR 44800 - National Human Genome Research Institute; Notice of Closed Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-07-29

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed....), notice is hereby given of a meeting of the National Advisory Council for Human Genome Research. The... Genome Research. Date: August 18, 2010. Time: 1 p.m. to 3 p.m. Agenda: To review and evaluate grant...

  15. 78 FR 66752 - National Human Genome Research Institute; Amended Notice of Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-11-06

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Amended Notice of Meeting Notice is hereby given of a change in the meeting of the National Human Genome Research Institute Special Emphasis Panel, October 15, 2013, 01:00 p.m. to October 15, 2013, 02:30 p.m., National...

  16. 75 FR 19984 - National Human Genome Research Institute; Notice of Closed Meetings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-04-16

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed... of Committee: Center for Inherited Disease Research Access Committee. Date: April 30, 2010. Time: 11...: Camilla E. Day, PhD, Scientific Review Officer, CIDR, National Human Genome Research Institute, National...

  17. 76 FR 65738 - National Human Genome Research Institute; Amended Notice of Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-10-24

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Amended Notice of Meeting Notice is hereby given of a change in the meeting of the National Human Genome Research Institute...

  18. 76 FR 71581 - National Human Genome Research Institute; Amended Notice of Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-11-18

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Amended Notice of Meeting Notice is hereby given of a change in the meeting of the National Human Genome Research...

  19. 78 FR 65342 - National Human Genome Research Institute; Amended Notice of Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-10-31

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Amended Notice of Meeting Notice is hereby given of a change in the meeting of the National Human Genome Research...

  20. 77 FR 67385 - National Human Genome Research Institute; Amended Notice of Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-11-09

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Amended Notice of Meeting Notice is hereby given of a change in the meeting of the National Human Genome Research...

  1. 78 FR 47715 - National Human Genome Research Institute; Notice of Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-08-06

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Meeting... hereby given of a meeting of the National Advisory Council for Human Genome Research. The meeting will be... unwarranted invasion of personal privacy. Name of Committee: National Advisory Council for Human...

  2. 78 FR 61851 - National Human Genome Research Institute; Notice of Closed Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-10-04

    ... No: 2013-24289] DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human... clearly unwarranted invasion of personal privacy. Name of Committee: National Human Genome Research... Human Genome Research Institute, 4076 Conference Room, 5635 Fishers Lane, Rockville, MD...

  3. Genomics, public health and developing countries: the case of the Mexican National Institute of Genomic Medicine (INMEGEN).

    PubMed

    Séguin, Béatrice; Hardy, Billie-Jo; Singer, Peter A; Daar, Abdallah S

    2008-10-01

    In 2004, the government of Mexico established the National Institute of Genomic Medicine (INMEGEN), to carry out disease-related genomic studies that will address national health problems and stimulate scientific and technological development by generating new commercial products and services in genomic medicine. Towards this end, INMEGEN is carrying out a large-scale genotyping project to map genomic variation within its own population. The initiative is expected to generate a key resource for local researchers to understand disease susceptibility and variation in drug responses, which will contribute to Mexico's goal of developing public health genomics - a field in which Mexico is proving to be a leader amongst emerging economies.

  4. Dana-Farber Cancer Institute | Office of Cancer Genomics

    Cancer.gov

    Functional Annotation of Cancer Genomes Principal Investigator: William C. Hahn, M.D., Ph.D. The comprehensive characterization of cancer genomes has and will continue to provide an increasingly complete catalog of genetic alterations in specific cancers. However, most epithelial cancers harbor hundreds of genetic alterations as a consequence of genomic instability. Therefore, the functional consequences of the majority of mutations remain unclear.

  5. 75 FR 26762 - National Human Genome Research Institute; Notice of Closed Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-05-12

    ... No: 2010-11051] DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human... clearly unwarranted invasion of personal privacy. Name of Committee: National Human Genome Research....nih.gov . (Catalogue of Federal Domestic Assistance Program Nos. 93.172, Human Genome Research...

  6. 77 FR 27471 - National Human Genome Research Institute Amended Notice of Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-05-10

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome Research Institute Amended Notice of Meeting Notice is hereby given of a change in the meeting of the National Advisory Council for...

  7. 77 FR 55853 - National Human Genome Research Institute; Amended Notice of Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-09-11

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Amended Notice of Meeting Notice is hereby given of a change in the meeting of the National Advisory Council for...

  8. Complete Genome Sequences of Four Bordetella pertussis Vaccine Reference Strains from Serum Institute of India

    PubMed Central

    Peng, Yanhui; Loparev, Vladimir; Johnson, Taccara; Juieng, Phalasy; Gairola, Sunil; Kumar, Rakesh; Shaligram, Umesh; Gowrishankar, Ramnath; Moura, Hercules; Rees, Jon; Schieltz, David M.; Williamson, Yulanda; Woolfitt, Adrian; Barr, John; Tondella, M. Lucia; Williams, Margaret M.

    2016-01-01

    Serum Institute of India is among the world’s largest vaccine producers. Here, we report the complete genome sequences for four Bordetella pertussis strains used by Serum Institute of India in the production of whole-cell pertussis vaccines. PMID:28007855

  9. Translational Genomics Research Institute: Quantified Cancer Cell Line Encyclopedia (CCLE) RNA-seq Data | Office of Cancer Genomics

    Cancer.gov

    Many applications analyze quantified transcript-level abundances to make inferences.  Having completed this computation across the large sample set, the CTD2 Center at the Translational Genomics Research Institute presents the quantified data in a straightforward, consolidated form for these types of analyses.

  10. 2012 U.S. Department of Energy: Joint Genome Institute: Progress Report

    SciTech Connect

    Gilbert, David

    2013-01-01

    The mission of the U.S. Department of Energy Joint Genome Institute (DOE JGI) is to serve the diverse scientific community as a user facility, enabling the application of large-scale genomics and analysis of plants, microbes, and communities of microbes to address the DOE mission goals in bioenergy and the environment. The DOE JGI's sequencing efforts fall under the Eukaryote Super Program, which includes the Plant and Fungal Genomics Programs; and the Prokaryote Super Program, which includes the Microbial Genomics and Metagenomics Programs. In 2012, several projects made news for their contributions to energy and environment research.

  11. Challenges and Opportunities for Genomics Education: Insights from an Institute of Medicine Roundtable Activity.

    PubMed

    Dougherty, Michael J; Wicklund, Catherine; Johansen Taber, Katherine A

    2016-01-01

    Despite the growing availability of genomic tools for clinical care, many health care providers experience gaps in genomics knowledge and skills that serve as impediments to widespread and appropriate integration of genomics into routine care. A workshop recently held by the Institute of Medicine (IOM) Roundtable on Translating Genomics-Based Research for Health explored 1) the barriers that result in a perception among health care providers that the need for genomics education is not urgent and 2) the drivers that may spur a change in that attitude. This commentary promotes continuing and graduate education-informed by an awareness of barriers, drivers, and best practices-as the most effective approaches for preparing the workforce for genomic medicine and ultimately improving patient care, and argues that the time for education is now.

  12. The Genome Portal of the Department of Energy Joint Genome Institute

    SciTech Connect

    Nordberg, Henrik; Cantor, Michael; Dushekyo, Serge; Hua, Susan; Poliakov, Alexander; Smirnova, Tatyana; Dubchak, Inna

    2014-03-14

    The JGI Genome Portal (http://genome.jgi.doe.gov) provides unified access to all JGI genomic databases and analytical tools. A user can search, download and explore multiple data sets available for all DOE JGI sequencing projects including their status, assemblies and annotations of sequenced genomes. Genome Portal in the past 2 years was significantly updated, with a specific emphasis on efficient handling of the rapidly growing amount of diverse genomic data accumulated in JGI. A critical aspect of handling big data in genomics is the development of visualization and analysis tools that allow scientists to derive meaning from what are otherwise terrabases of inert sequence. An interactive visualization tool developed in the group allows us to explore contigs resulting from a single metagenome assembly. Implemented with modern web technologies that take advantage of the power of the computer's graphical processing unit (gpu), the tool allows the user to easily navigate over a 100,000 data points in multiple dimensions, among many biologically meaningful parameters of a dataset such as relative abundance, contig length, and G+C content.

  13. 75 FR 51828 - National Human Genome Research Institute; Notice of Meetings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-08-23

    ... No: 2010-20858] DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human... for Human Genome Research. The meetings will be open to the public as indicated below, with attendance... clearly unwarranted invasion of personal privacy. Name of Committee: National Advisory Council for...

  14. Researcher and Institutional Review Board Chair Perspectives on Incidental Findings in Genomic Research

    PubMed Central

    Daack-Hirsch, Sandra; Driessnack, Martha; Downing, Nancy; Shinkunas, Laura; Brandt, Debra; Simon, Christian

    2012-01-01

    Aims: Genomic research can produce findings unrelated to a study's aims. The purpose of this study was to examine researcher and Institutional Review Board (IRB) chair perspectives on genomic incidental findings (GIFs). Methods: Nineteen genomic researchers and 34 IRB chairs from 42 institutions participated in semi-structured telephone interviews. Researchers and chairs described GIFs within their respective roles. Few had direct experience with disclosure of GIFs. Researchers favored policies where a case by case determination regarding whether GIF disclosure would be offered after discovery, whereas IRB chairs preferred policies where procedures for disclosure would be determined prior to approval of the research. Conclusions: Researcher and IRB chair perspectives on management of GIFs overlap, but each group provides a unique perspective on decisions regarding disclosure of GIFs in research. Engagement of both groups is essential in efforts to provide guidance for researchers and IRBs regarding disclosure of GIFs in research. PMID:22352737

  15. Development of Structural Neurobiology and Genomics Programs in the Neurogenetic Institute

    SciTech Connect

    Henderson, Brian E., M.D.

    2006-11-10

    The purpose of the DOE equipment-only grant was to purchase instrumentation in support of structural biology and genomics core facilities in the Zilkha Neurogenetic Institute (ZNI). The ZNI, a new laboratory facility (125,000 GSF) and a center of excellence at the Keck School of Medicine of USC, was opened in 2003. The goal of the ZNI is to recruit upwards of 30 new faculty investigators engaged in interdisciplinary research programs that will add breadth and depth to existing school strengths in neuroscience, epidemiology and genetics. Many of these faculty, and other faculty researchers at the Keck School will access structural biology and genomics facilities developed in the ZNI.

  16. Dana-Farber Cancer Institute: Identification of Therapeutic Targets Across Cancer Types | Office of Cancer Genomics

    Cancer.gov

    The Dana Farber Cancer Institute CTD2 Center focuses on the use of high-throughput genetic and bioinformatic approaches to identify and credential oncogenes and co-dependencies in cancers. This Center aims to provide the cancer research community with information that will facilitate the prioritization of targets based on both genomic and functional evidence, inform the most appropriate genetic context for downstream mechanistic and validation studies, and enable the translation of this information into therapeutics and diagnostics.

  17. Illumina Production Sequencing at the DOE Joint Genome Institute - Workflow and Optimizations

    SciTech Connect

    Tarver, Angela; Fern, Alison; Diego, Matthew San; Kennedy, Megan; Zane, Matthew; Daum, Christopher; Hack, Christopher; Tang, Eric; Deshpande, Shweta; Cheng, Jan-Fang; Roberts, Simon; Alexandre, Melanie; Harmon-Smith, Miranda; Lucas, Susan

    2010-06-18

    The U.S. Department of Energy (DOE) Joint Genome Institute?s (JGI) Production Sequencing group is committed to the generation of high-quality genomic DNA sequence to support the DOE mission areas of renewable energy generation, global carbon management, and environmental characterization and clean-up. Within the JGI?s Production Sequencing group, the Illumina Genome Analyzer pipeline has been established as one of three sequencing platforms, along with Roche/454 and ABI/Sanger. Optimization of the Illumina pipeline has been ongoing with the aim of continual process improvement of the laboratory workflow. These process improvement projects are being led by the JGI?s Process Optimization, Sequencing Technologies, Instrumentation& Engineering, and the New Technology Production groups. Primary focus has been on improving the procedural ergonomics and the technicians? operating environment, reducing manually intensive technician operations with different tools, reducing associated production costs, and improving the overall process and generated sequence quality. The U.S. DOE JGI was established in 1997 in Walnut Creek, CA, to unite the expertise and resources of five national laboratories? Lawrence Berkeley, Lawrence Livermore, Los Alamos, Oak Ridge, and Pacific Northwest ? along with HudsonAlpha Institute for Biotechnology. JGI is operated by the University of California for the U.S. DOE.

  18. The Ethical, Legal, and Social Implications Research Program at the National Human Genome Research Institute.

    PubMed

    Meslin, Eric M; Thomson, Elizabeth J; Boyer, Joy T

    1997-09-01

    Organizers of the Human Genome Project (HGP) understood from the beginning that the scientific activities of mapping and sequencing the human genome would raise ethical, legal, and social issues that would require careful attention by scientists, health care professionals, government officials, and the public. The establishment of the ELSI (ethical, legal, and social implications) programs at the National Human Genome Research Institute (NHGRI) and the Department of Energy (DOE) was thought to be vital to the success of the HGP in the United States. It also provided a novel approach to the simultaneous study of ethical, legal, and social issues and basic scientific issues. Eric Juengst, the first director of the ELSI program, described its origins in a previous issue of the Kennedy Institute of Ethics Journal (Juengst 1991). Now in its seventh year, the ELSI program has accomplished much. This article summarizes the evolution and goals of the ELSI program at NHGRI, outlines the program's current research priorities with examples of activities within each priority area, and provides a look to the future, including the initiation of a strategic planning process.

  19. Spanning the genomics era: the vital role of a single institution biorepository for childhood cancer research over a decade

    PubMed Central

    Zhou, Li

    2015-01-01

    The ‘genomics era’ is considered to have begun with the commencement of the Human Genome Project. As translational genomic studies can only be established when human tissue samples are available for analysis, biospecimens are now proven to be an essential element for their success. During the genomics era the necessity for more extensive biobanking infrastructure has been highlighted. With the increased number of genomic studies into cancer, it is considered that the availability of biospecimens will become the rate limiting step. Despite the efforts in international biobanking, translational genomics is hampered when there low numbers of biospecimens for a particular rare diseases and is most apparent for paediatric cancer. As there is a call for biobanking practice to be responsive to the current experimental needs of the time and for more expansive systems of tissue procurement to be established we have asked the question what role does a single institution biorepository play in the current highly networked world of translational genomics. Here we describe such a case. The Tumour Bank at The Children’s Hospital at Westmead (TB-CHW) in the western suburbs of Sydney was formally established in 1998 as a key resource for translational paediatric cancer research. During the genomics era, we show that the TB-CHW has developed into a key biospecimen repository for the cancer research community, during which time it has increasingly found itself having a vital role in the establishment of translational genomics for paediatric cancer. Here we detail metrics that demonstrate how as a single institution biorepository, the TB-CHW has been a strong participant in the advancement of translational genomics throughout the genomics era. This paper describes the significant contribution of a single institutional hospital embedded tumour biobank to the genomic research community. Despite the increased stringencies placed on biobanking practice, the TB-CHW has shown that a

  20. Prokaryotic Super Program Advisory Committee DOE Joint Genome Institute, Walnut Creek, CA, March 27, 2013.

    PubMed

    Garrity, George M; Banfield, Jill; Eisen, Jonathan; van der Lelie, Niels; McMahon, Trina; Rusch, Doug; Delong, Edward; Moran, Mary Ann; Currie, Cameron; Furhman, Jed; Hallam, Steve; Hugenholtz, Phil; Moran, Nancy; Nelson, Karen; Roberts, Richard; Stepanauskas, Ramunas

    2013-07-30

    The Prokaryotic Super Program Advisory Committee met on March 27, 2013 for their annual review the Prokaryotic Super Program at the DOE Joint Genome Institute. As is the case with any site visit or program review, the objective is to evaluate progress in meeting organizational objectives, provide feedback to from the user-community and to assist the JGI in formulating plans for the coming year. The advisors want to commend the JGI for its central role in developing new technologies and capabilities, and for catalyzing the formation of new collaborative user communities. Highlights of the post-meeting exchanges among the advisors focused on the importance of programmatic initiatives including: • GEBA, which serves as a phylogenetic "base-map" on which our knowledge of functional diversity can be layered. • FEBA, which promises to provide new insights into the physiological capabilities of prokaryotes under highly standardized conditions. • Single-cell genomics technology, which is seen to significantly enhance our ability to interpret genomic and metagenomic data and broaden the scope of the GEBA program to encompass at least a part of the microbial "dark-matter". • IMG, which is seen to play a central role in JGI programs and is viewed as a strategically important asset in the JGI portfolio. On this latter point, the committee encourages the formation of a strategic relationship between IMG and the Kbase to ensure that the intelligence, deep knowledge and experience captured in the former is not lost. The committee strongly urges the DOE to continue its support for maintaining this critical resource.

  1. Prokaryotic Super Program Advisory Committee DOE Joint Genome Institute, Walnut Creek, CA, March 27, 2013

    PubMed Central

    Garrity, George M.; Banfield, Jill; Eisen, Jonathan; van der Lelie, Niels; McMahon, Trina; Rusch, Doug; DeLong, Edward; Moran, Mary Ann; Currie, Cameron; Furhman, Jed; Hallam, Steve; Hugenholtz, Phil; Moran, Nancy; Nelson, Karen; Roberts, Richard; Stepanauskas, Ramunas

    2013-01-01

    The Prokaryotic Super Program Advisory Committee met on March 27, 2013 for their annual review the Prokaryotic Super Program at the DOE Joint Genome Institute. As is the case with any site visit or program review, the objective is to evaluate progress in meeting organizational objectives, provide feedback to from the user-community and to assist the JGI in formulating plans for the coming year. The advisors want to commend the JGI for its central role in developing new technologies and capabilities, and for catalyzing the formation of new collaborative user communities. Highlights of the post-meeting exchanges among the advisors focused on the importance of programmatic initiatives including: • GEBA, which serves as a phylogenetic “base-map” on which our knowledge of functional diversity can be layered. • FEBA, which promises to provide new insights into the physiological capabilities of prokaryotes under highly standardized conditions. • Single-cell genomics technology, which is seen to significantly enhance our ability to interpret genomic and metagenomic data and broaden the scope of the GEBA program to encompass at least a part of the microbial “dark-matter”. • IMG, which is seen to play a central role in JGI programs and is viewed as a strategically important asset in the JGI portfolio. On this latter point, the committee encourages the formation of a strategic relationship between IMG and the Kbase to ensure that the intelligence, deep knowledge and experience captured in the former is not lost. The committee strongly urges the DOE to continue its support for maintaining this critical resource. PMID:24501639

  2. The Ethical, Legal, and Social Implications Program of the National Human Genome Research Institute: reflections on an ongoing experiment.

    PubMed

    McEwen, Jean E; Boyer, Joy T; Sun, Kathie Y; Rothenberg, Karen H; Lockhart, Nicole C; Guyer, Mark S

    2014-01-01

    For more than 20 years, the Ethical, Legal, and Social Implications (ELSI) Program of the National Human Genome Research Institute has supported empirical and conceptual research to anticipate and address the ethical, legal, and social implications of genomics. As a component of the agency that funds much of the underlying science, the program has always been an experiment. The ever-expanding number of issues the program addresses and the relatively low level of commitment on the part of other funding agencies to support such research make setting priorities especially challenging. Program-supported studies have had a significant impact on the conduct of genomics research, the implementation of genomic medicine, and broader public policies. The program's influence is likely to grow as ELSI research, genomics research, and policy development activities become increasingly integrated. Achieving the benefits of increased integration while preserving the autonomy, objectivity, and intellectual independence of ELSI investigators presents ongoing challenges and new opportunities.

  3. Institutional Responsibility and the Flawed Genomic Biomarkers at Duke University: A Missed Opportunity for Transparency and Accountability.

    PubMed

    DeMets, David L; Fleming, Thomas R; Geller, Gail; Ransohoff, David F

    2016-11-23

    When there have been substantial failures by institutional leadership in their oversight responsibility to protect research integrity, the public should demand that these be recognized and addressed by the institution itself, or the funding bodies. This commentary discusses a case of research failures in developing genomic predictors for cancer risk assessment and treatment at a leading university. In its review of this case, the Office of Research Integrity, an agency within the US Department of Health and Human Services, focused their report entirely on one individual faculty member and made no comment on the institution's responsibility and its failure to provide adequate oversight and investigation. These actions missed an important opportunity to emphasize the institution's critical responsibilities in oversight of research integrity and the importance of institutional transparency and accountability.

  4. Post-Genome Era Pedagogy: How a BS Biotechnology Program Benefits the Liberal Arts Institution

    ERIC Educational Resources Information Center

    Eden, Peter

    2005-01-01

    Genomics profoundly affects society, because genome sequence information is widely used in such areas as genetic testing, genomic medicine/vaccine development, and so forth. Therefore, a responsibility to modernize science curricula exists for "post-genome era" educators. At my university, we developed a BS biotechnology program within a…

  5. Post-Genome Era Pedagogy: How a BS Biotechnology Program Benefits the Liberal Arts Institution

    ERIC Educational Resources Information Center

    Eden, Peter

    2005-01-01

    Genomics profoundly affects society, because genome sequence information is widely used in such areas as genetic testing, genomic medicine/vaccine development, and so forth. Therefore, a responsibility to modernize science curricula exists for "post-genome era" educators. At my university, we developed a BS biotechnology program within a…

  6. Robotic Enrichment Processing of Roche 454 Titanium Emlusion PCR at the DOE Joint Genome Institute

    SciTech Connect

    Hamilton, Matthew; Wilson, Steven; Bauer, Diane; Miller, Don; Duffy-Wei, Kecia; Hammon, Nancy; Lucas, Susan; Pollard, Martin; Cheng, Jan-Fang

    2010-05-28

    Enrichment of emulsion PCR product is the most laborious and pipette-intensive step in the 454 Titanium process, posing the biggest obstacle for production-oriented scale up. The Joint Genome Institute has developed a pair of custom-made robots based on the Microlab Star liquid handling deck manufactured by Hamilton to mediate the complexity and ergonomic demands of the 454 enrichment process. The robot includes a custom built centrifuge, magnetic deck positions, as well as heating and cooling elements. At present processing eight emulsion cup samples in a single 2.5 hour run, these robots are capable of processing up to 24 emulsion cup samples. Sample emulsions are broken using the standard 454 breaking process and transferred from a pair of 50ml conical tubes to a single 2ml tube and loaded on the robot. The robot performs the enrichment protocol and produces beads in 2ml tubes ready for counting. The robot follows the Roche 454 enrichment protocol with slight exceptions to the manner in which it resuspends beads via pipette mixing rather than vortexing and a set number of null bead removal washes. The robotic process is broken down in similar discrete steps: First Melt and Neutralization, Enrichment Primer Annealing, Enrichment Bead Incubation, Null Bead Removal, Second Melt and Neutralization and Sequencing Primer Annealing. Data indicating our improvements in enrichment efficiency and total number of bases per run will also be shown.

  7. Implementing a genomic data management system using iRODS in the Wellcome Trust Sanger Institute

    PubMed Central

    2011-01-01

    Background Increasingly large amounts of DNA sequencing data are being generated within the Wellcome Trust Sanger Institute (WTSI). The traditional file system struggles to handle these increasing amounts of sequence data. A good data management system therefore needs to be implemented and integrated into the current WTSI infrastructure. Such a system enables good management of the IT infrastructure of the sequencing pipeline and allows biologists to track their data. Results We have chosen a data grid system, iRODS (Rule-Oriented Data management systems), to act as the data management system for the WTSI. iRODS provides a rule-based system management approach which makes data replication much easier and provides extra data protection. Unlike the metadata provided by traditional file systems, the metadata system of iRODS is comprehensive and allows users to customize their own application level metadata. Users and IT experts in the WTSI can then query the metadata to find and track data. The aim of this paper is to describe how we designed and used (from both system and user viewpoints) iRODS as a data management system. Details are given about the problems faced and the solutions found when iRODS was implemented. A simple use case describing how users within the WTSI use iRODS is also introduced. Conclusions iRODS has been implemented and works as the production system for the sequencing pipeline of the WTSI. Both biologists and IT experts can now track and manage data, which could not previously be achieved. This novel approach allows biologists to define their own metadata and query the genomic data using those metadata. PMID:21906284

  8. Dana-Farber Cancer Institute: Identification of Therapeutic Targets in KRAS Driven Lung Cancer | Office of Cancer Genomics

    Cancer.gov

    The CTD2 Center at Dana Farber Cancer Institute focuses on the use of high-throughput genetic and bioinformatic approaches to identify and credential oncogenes and co-dependencies in cancers. This Center aims to provide the cancer research community with information that will facilitate the prioritization of targets based on both genomic and functional evidence, inform the most appropriate genetic context for downstream mechanistic and validation studies, and enable the translation of this information into therapeutics and diagnostics.

  9. Illumina GA IIx& HiSeq 2000 Production Sequenccing and QC Analysis Pipelines at the DOE Joint Genome Institute

    SciTech Connect

    Daum, Christopher; Zane, Matthew; Han, James; Kennedy, Megan; San Diego, Matthew; Copeland, Alex; Li, Mingkun; Lucas, Susan

    2011-01-31

    The U.S. Department of Energy (DOE) Joint Genome Institute's (JGI) Production Sequencing group is committed to the generation of high-quality genomic DNA sequence to support the mission areas of renewable energy generation, global carbon management, and environmental characterization and clean-up. Within the JGI's Production Sequencing group, a robust Illumina Genome Analyzer and HiSeq pipeline has been established. Optimization of the sesequencer pipelines has been ongoing with the aim of continual process improvement of the laboratory workflow, reducing operational costs and project cycle times to increases ample throughput, and improving the overall quality of the sequence generated. A sequence QC analysis pipeline has been implemented to automatically generate read and assembly level quality metrics. The foremost of these optimization projects, along with sequencing and operational strategies, throughput numbers, and sequencing quality results will be presented.

  10. Cardiovascular genomics, personalized medicine, and the National Heart, Lung, and Blood Institute: part I: the beginning of an era.

    PubMed

    O'Donnell, Christopher J; Nabel, Elizabeth G

    2008-10-01

    The inaugural issue of Circulation: Cardiovascular Genetics arrives at a remarkable time in the history of genetic research and cardiovascular medicine. Despite tremendous progress in knowledge gained, cardiovascular disease(CVD) remains the leading cause of death in the United States,1 and it has overcome infectious diseases as the leading cause of death worldwide.2 In addition, rates of CVD remain higher in black and Hispanic populations in the United States.1 The recent Strategic Plan of the National Heart, Lung,and Blood Institute (NHLBI) emphasizes research areas to fill the significant knowledge gaps needed to improve the diagnosis,treatment, and control of known risk factors and clinically apparent disease. Simultaneously, the NHLBI Strategic Plan recognizes a tremendous opportunity that is available for use of genetic and genomic research to generate new knowledge that might reduce the morbidity and mortality from CVD in US populations.3 Public availability of vast amounts of detailed sequence information about the human genome, completed sequence data on dozens of other animal genomes, and private sector development of high-throughput genetic technologies has transformed in a few short years the conduct of cardiovascular genetics and genomics research from a primary focus on mendelian disorders to a current emphasis on genome-wide association studies (GWAS; Figure1). In this review, we describe the rationale for the current emphasis on large-scale genomic studies, summarize the evolving approaches and progress to date, and identify immediate-term research needs. The National Institutes of Health (NIH) and the NHLBI are supporting a portfolio of large-scale genetic and genomic programs in diverse US populations with the longer-term objective of translating knowledge into the prediction, prevention, and preemption of CVD, as well as lung, sleep, and blood disorders. Underlying this portfolio is a strong commitment to make available participant-level data and

  11. 77 FR 2735 - National Human Genome Research Institute; Notice of Meetings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-01-19

    ..., Terrace Level Conference Room, Rockville, MD 20892. Contact Person: Mark S. Guyer, Ph.D., Director for... Institutes of Health, 5635 Fishers Lane, Terrace Level Conference Room, Rockville, MD 20892. Closed: February...: National Institutes of Health, 5635 Fishers Lane Terrace Level Conference Room, Rockville, MD 20892. Closed...

  12. 75 FR 46951 - National Human Genome Research Institute; Notice of Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-08-04

    ... Health, 5635 Fishers Lane, Terrace Level Conference Room, Bethesda, MD 20892. Closed: September 13, 2010... Institutes of Health, 5635 Fishers Lane, Terrace Level Conference Room, Bethesda, MD 20892. Closed: September.... Place: National Institutes of Health, 5635 Fishers Lane, Terrace Level Conference Room, Bethesda, MD...

  13. Genome-wide scan and conditional analysis in bipolar disorder: evidence for genomic interaction in the National Institute of Mental Health genetics initiative bipolar pedigrees.

    PubMed

    McInnis, Melvin G; Dick, Danielle M; Willour, Virginia L; Avramopoulos, Dimitrios; MacKinnon, Dean F; Simpson, Sylvia G; Potash, James B; Edenberg, Howard J; Bowman, Elizabeth S; McMahon, Francis J; Smiley, Carrie; Chellis, Jennifer L; Huo, Yuqing; Diggs, Tyra; Meyer, Eric T; Miller, Marvin; Matteini, Amy T; Rau, N Leela; DePaulo, J Raymond; Gershon, Elliot S; Badner, Judith A; Rice, John P; Goate, Alison M; Detera-Wadleigh, Sevilla D; Nurnberger, John I; Reich, Theodore; Zandi, Peter P; Foroud, Tatiana M

    2003-12-01

    In 1989 the National Institute of Mental Health began a collaborative effort to identify genes for bipolar disorder. The first 97 pedigrees showed evidence of linkage to chromosomes 1, 6, 7, 10, 16, and 22 (Nurnberger et al 1997). An additional 56 bipolar families have been genotyped, and the combined sample of 153 pedigrees studied. Three hierarchical affection status models were analyzed with 513 simple sequence repeat markers; 298 were common across all pedigrees. The primary analysis was a nonparametric genome-wide scan. We performed conditional analyses based on epistasis or heterogeneity for five regions. One region, on 16p13, was significant at the genome-wide p <.05 level. Four additional chromosomal regions (20p12, 11p15, 6q24, and 10p12) showed nominally significant linkage findings (p genome-wide scan aimed to identify single gene effects.

  14. Dana Farber Cancer Institute: Discovery of Novel Oncogenes | Office of Cancer Genomics

    Cancer.gov

    Widespread recurrent copy number alterations are observed across the majority of human cancers, yet the specific targets of such amplified or deleted regions remain undefined. Here, the CTD2 Center at the Dana Farber Cancer Institute took a systematic approach using cDNA overexpression screening to identify and validate oncogenes residing in such amplified regions. In representative examples, these experiments have identified the adaptor proteins CRKL, GAB2, FRS2 and the TLOC and SKIL proteins as novel amplified oncogenes.

  15. Dana Farber Cancer Institute: Discovery of Resistance Mechanisms | Office of Cancer Genomics

    Cancer.gov

    Resistance to targeted therapy is emerging as a bottleneck to achieving durable drug responses in cancer. The goal of the CTD2 Center at Dana Farber Cancer Institute is to identify mechanisms of resistance for both existing therapeutics as well as for emerging targets even prior to the identification of lead compounds. They aim to use this information to inform combinatorial treatments. In representative examples they have found that YAP1 leads to resistance after KRAS targeting and that PRKACA mediates resistance to HER2 therapy.

  16. Algal Functional Annotation Tool from the DOE-UCLA Institute for Genomics and Proteomics

    DOE Data Explorer

    Lopez, David

    The Algal Functional Annotation Tool is a bioinformatics resource to visualize pathway maps, identify enriched biological terms, or convert gene identifiers to elucidate biological function in silico. These types of analysis have been catered to support lists of gene identifiers, such as those coming from transcriptome gene expression analysis. By analyzing the functional annotation of an interesting set of genes, common biological motifs may be elucidated and a first-pass analysis can point further research in the right direction. Currently, the following databases have been parsed, processed, and added to the tool: 1( Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathways Database, 2) MetaCyc Encyclopedia of Metabolic Pathways, 3) Panther Pathways Database, 4) Reactome Pathways Database, 5) Gene Ontology, 6) MapMan Ontology, 7) KOG (Eukaryotic Clusters of Orthologous Groups), 5)Pfam, 6) InterPro.

  17. Radiogenomic analysis of lower grade glioma: a pilot multi-institutional study shows an association between quantitative image features and tumor genomics

    NASA Astrophysics Data System (ADS)

    Mazurowski, Maciej A.; Clark, Kal; Czarnek, Nicholas M.; Shamsesfandabadi, Parisa; Peters, Katherine B.; Saha, Ashirbani

    2017-03-01

    Recent studies showed that genomic analysis of lower grade gliomas can be very effective for stratification of patients into groups with different prognosis and proposed specific genomic classifications. In this study, we explore the association of one of those genomic classifications with imaging parameters to determine whether imaging could serve a similar role to genomics in cancer patient treatment. Specifically, we analyzed imaging and genomics data for 110 patients from 5 institutions from The Cancer Genome Atlas and The Cancer Imaging Archive datasets. The analyzed imaging data contained preoperative FLAIR sequence for each patient. The images were analyzed using the in-house algorithms which quantify 2D and 3D aspects of the tumor shape. Genomic data consisted of a cluster of clusters classification proposed in a very recent and leading publication in the field of lower grade glioma genomics. Our statistical analysis showed that there is a strong association between the tumor cluster-of-clusters subtype and two imaging features: bounding ellipsoid volume ratio and angular standard deviation. This result shows high promise for the potential use of imaging as a surrogate measure for genomics in the decision process regarding treatment of lower grade glioma patients.

  18. Klebsiella pneumoniae Carbapenemase (KPC)-Producing K. pneumoniae at a Single Institution: Insights into Endemicity from Whole-Genome Sequencing

    PubMed Central

    Stoesser, Nicole; Sheppard, Anna E.; Pankhurst, Louise; Giess, Adam; Yeh, Anthony J.; Didelot, Xavier; Turner, Stephen D.; Sebra, Robert; Kasarskis, Andrew; Peto, Tim; Crook, Derrick; Sifri, Costi D.

    2015-01-01

    The global emergence of Klebsiella pneumoniae carbapenemase-producing K. pneumoniae (KPC-Kp) multilocus sequence type ST258 is widely recognized. Less is known about the molecular and epidemiological details of non-ST258 K. pneumoniae in the setting of an outbreak mediated by an endemic plasmid. We describe the interplay of blaKPC plasmids and K. pneumoniae strains and their relationship to the location of acquisition in a U.S. health care institution. Whole-genome sequencing (WGS) analysis was applied to KPC-Kp clinical isolates collected from a single institution over 5 years following the introduction of blaKPC in August 2007, as well as two plasmid transformants. KPC-Kp from 37 patients yielded 16 distinct sequence types (STs). Two novel conjugative blaKPC plasmids (pKPC_UVA01 and pKPC_UVA02), carried by the hospital index case, accounted for the presence of blaKPC in 21/37 (57%) subsequent cases. Thirteen (35%) isolates represented an emergent lineage, ST941, which contained pKPC_UVA01 in 5/13 (38%) and pKPC_UVA02 in 6/13 (46%) cases. Seven (19%) isolates were the epidemic KPC-Kp strain, ST258, mostly imported from elsewhere and not carrying pKPC_UVA01 or pKPC_UVA02. Using WGS-based analysis of clinical isolates and plasmid transformants, we demonstrate the unexpected dispersal of blaKPC to many non-ST258 lineages in a hospital through spread of at least two novel blaKPC plasmids. In contrast, ST258 KPC-Kp was imported into the institution on numerous occasions, with other blaKPC plasmid vectors and without sustained transmission. Instead, a newly recognized KPC-Kp strain, ST941, became associated with both novel blaKPC plasmids and spread locally, making it a future candidate for clinical persistence and dissemination. PMID:25561339

  19. The Genomics Education Partnership: Successful Integration of Research into Laboratory Classes at a Diverse Group of Undergraduate Institutions

    ERIC Educational Resources Information Center

    Shaffer, Christopher D.; Alvarez, Consuelo; Bailey, Cheryl; Barnard, Daron; Bhalla, Satish; Chandrasekaran, Chitra; Chandrasekaran, Vidya; Chung, Hui-Min; Dorer, Douglas R.; Du, Chunguang; Eckdahl, Todd T.; Poet, Jeff L.; Frohlich, Donald; Goodman, Anya L.; Gosser, Yuying; Hauser, Charles; Hoopes, Laura L. M.; Johnson, Diana; Jones, Christopher J.; Kaehler, Marian; Kokan, Nighat; Kopp, Olga R.; Kuleck, Gary A.; McNeil, Gerard; Moss, Robert; Myka, Jennifer L.; Nagengast, Alexis; Morris, Robert; Overvoorde, Paul J.; Shoop, Elizabeth; Parrish, Susan; Reed, Kelynne; Regisford, E. Gloria; Revie, Dennis; Rosenwald, Anne G.; Saville, Ken; Schroeder, Stephanie; Shaw, Mary; Skuse, Gary; Smith, Christopher; Smith, Mary; Spana, Eric P.; Spratt, Mary; Stamm, Joyce; Thompson, Jeff S.; Wawersik, Matthew; Wilson, Barbara A.; Youngblom, Jim; Leung, Wilson; Buhler, Jeremy; Mardis, Elaine R.; Lopatto, David; Elgin, Sarah C. R.

    2010-01-01

    Genomics is not only essential for students to understand biology but also provides unprecedented opportunities for undergraduate research. The goal of the Genomics Education Partnership (GEP), a collaboration between a growing number of colleges and universities around the country and the Department of Biology and Genome Center of Washington…

  20. The Genomics Education Partnership: Successful Integration of Research into Laboratory Classes at a Diverse Group of Undergraduate Institutions

    ERIC Educational Resources Information Center

    Shaffer, Christopher D.; Alvarez, Consuelo; Bailey, Cheryl; Barnard, Daron; Bhalla, Satish; Chandrasekaran, Chitra; Chandrasekaran, Vidya; Chung, Hui-Min; Dorer, Douglas R.; Du, Chunguang; Eckdahl, Todd T.; Poet, Jeff L.; Frohlich, Donald; Goodman, Anya L.; Gosser, Yuying; Hauser, Charles; Hoopes, Laura L. M.; Johnson, Diana; Jones, Christopher J.; Kaehler, Marian; Kokan, Nighat; Kopp, Olga R.; Kuleck, Gary A.; McNeil, Gerard; Moss, Robert; Myka, Jennifer L.; Nagengast, Alexis; Morris, Robert; Overvoorde, Paul J.; Shoop, Elizabeth; Parrish, Susan; Reed, Kelynne; Regisford, E. Gloria; Revie, Dennis; Rosenwald, Anne G.; Saville, Ken; Schroeder, Stephanie; Shaw, Mary; Skuse, Gary; Smith, Christopher; Smith, Mary; Spana, Eric P.; Spratt, Mary; Stamm, Joyce; Thompson, Jeff S.; Wawersik, Matthew; Wilson, Barbara A.; Youngblom, Jim; Leung, Wilson; Buhler, Jeremy; Mardis, Elaine R.; Lopatto, David; Elgin, Sarah C. R.

    2010-01-01

    Genomics is not only essential for students to understand biology but also provides unprecedented opportunities for undergraduate research. The goal of the Genomics Education Partnership (GEP), a collaboration between a growing number of colleges and universities around the country and the Department of Biology and Genome Center of Washington…

  1. The Scientific Foundation for Personal Genomics: Recommendations from a National Institutes of Health–Centers for Disease Control and Prevention Multidisciplinary Workshop

    PubMed Central

    Khoury, Muin J.; McBride, Colleen M.; Schully, Sheri D.; Ioannidis, John P. A.; Feero, W. Gregory; Janssens, A. Cecile J. W.; Gwinn, Marta; Simons-Morton, Denise G.; Bernhardt, Jay M.; Cargill, Michele; Chanock, Stephen J.; Church, George M.; Coates, Ralph J.; Collins, Francis S.; Croyle, Robert T.; Davis, Barry R.; Downing, Gregory J.; DuRoss, Amy; Friedman, Susan; Gail, Mitchell H.; Ginsburg, Geoffrey S.; Green, Robert C.; Greene, Mark H.; Greenland, Philip; Gulcher, Jeffrey R.; Hsu, Andro; Hudson, Kathy L.; Kardia, Sharon L. R.; Kimmel, Paul L.; Lauer, Michael S.; Miller, Amy M.; Offit, Kenneth; Ransohoff, David F.; Roberts, J. Scott; Rasooly, Rebekah S.; Stefansson, Kari; Terry, Sharon F.; Teutsch, Steven M.; Trepanier, Angela; Wanke, Kay L.; Witte, John S.; Xu, Jianfeng

    2010-01-01

    The increasing availability of personal genomic tests has led to discussions about the validity and utility of such tests and the balance of benefits and harms. A multidisciplinary workshop was convened by the National Institutes of Health and the Centers for Disease Control and Prevention to review the scientific foundation for using personal genomics in risk assessment and disease prevention and to develop recommendations for targeted research. The clinical validity and utility of personal genomics is a moving target with rapidly developing discoveries but little translation research to close the gap between discoveries and health impact. Workshop participants made recommendations in five domains: (1) developing and applying scientific standards for assessing personal genomic tests; (2) developing and applying a multidisciplinary research agenda, including observational studies and clinical trials to fill knowledge gaps in clinical validity and utility; (3) enhancing credible knowledge synthesis and information dissemination to clinicians and consumers; (4) linking scientific findings to evidence-based recommendations for use of personal genomics; and (5) assessing how the concept of personal utility can affect health benefits, costs, and risks by developing appropriate metrics for evaluation. To fulfill the promise of personal genomics, a rigorous multidisciplinary research agenda is needed. PMID:19617843

  2. The Scientific Foundation for personal genomics: recommendations from a National Institutes of Health-Centers for Disease Control and Prevention multidisciplinary workshop.

    PubMed

    Khoury, Muin J; McBride, Colleen M; Schully, Sheri D; Ioannidis, John P A; Feero, W Gregory; Janssens, A Cecile J W; Gwinn, Marta; Simons-Morton, Denise G; Bernhardt, Jay M; Cargill, Michele; Chanock, Stephen J; Church, George M; Coates, Ralph J; Collins, Francis S; Croyle, Robert T; Davis, Barry R; Downing, Gregory J; Duross, Amy; Friedman, Susan; Gail, Mitchell H; Ginsburg, Geoffrey S; Green, Robert C; Greene, Mark H; Greenland, Philip; Gulcher, Jeffrey R; Hsu, Andro; Hudson, Kathy L; Kardia, Sharon L R; Kimmel, Paul L; Lauer, Michael S; Miller, Amy M; Offit, Kenneth; Ransohoff, David F; Roberts, J Scott; Rasooly, Rebekah S; Stefansson, Kari; Terry, Sharon F; Teutsch, Steven M; Trepanier, Angela; Wanke, Kay L; Witte, John S; Xu, Jianfeng

    2009-08-01

    The increasing availability of personal genomic tests has led to discussions about the validity and utility of such tests and the balance of benefits and harms. A multidisciplinary workshop was convened by the National Institutes of Health and the Centers for Disease Control and Prevention to review the scientific foundation for using personal genomics in risk assessment and disease prevention and to develop recommendations for targeted research. The clinical validity and utility of personal genomics is a moving target with rapidly developing discoveries but little translation research to close the gap between discoveries and health impact. Workshop participants made recommendations in five domains: (1) developing and applying scientific standards for assessing personal genomic tests; (2) developing and applying a multidisciplinary research agenda, including observational studies and clinical trials to fill knowledge gaps in clinical validity and utility; (3) enhancing credible knowledge synthesis and information dissemination to clinicians and consumers; (4) linking scientific findings to evidence-based recommendations for use of personal genomics; and (5) assessing how the concept of personal utility can affect health benefits, costs, and risks by developing appropriate metrics for evaluation. To fulfill the promise of personal genomics, a rigorous multidisciplinary research agenda is needed.

  3. The Genomics Education Partnership: Successful Integration of Research into Laboratory Classes at a Diverse Group of Undergraduate Institutions

    PubMed Central

    Shaffer, Christopher D.; Alvarez, Consuelo; Bailey, Cheryl; Barnard, Daron; Bhalla, Satish; Chandrasekaran, Chitra; Chandrasekaran, Vidya; Chung, Hui-Min; Dorer, Douglas R.; Du, Chunguang; Eckdahl, Todd T.; Poet, Jeff L.; Frohlich, Donald; Goodman, Anya L.; Gosser, Yuying; Hauser, Charles; Hoopes, Laura L.M.; Johnson, Diana; Jones, Christopher J.; Kaehler, Marian; Kokan, Nighat; Kopp, Olga R.; Kuleck, Gary A.; McNeil, Gerard; Moss, Robert; Myka, Jennifer L.; Nagengast, Alexis; Morris, Robert; Overvoorde, Paul J.; Shoop, Elizabeth; Parrish, Susan; Reed, Kelynne; Regisford, E. Gloria; Revie, Dennis; Rosenwald, Anne G.; Saville, Ken; Schroeder, Stephanie; Shaw, Mary; Skuse, Gary; Smith, Christopher; Smith, Mary; Spana, Eric P.; Spratt, Mary; Stamm, Joyce; Thompson, Jeff S.; Wawersik, Matthew; Wilson, Barbara A.; Youngblom, Jim; Leung, Wilson; Buhler, Jeremy; Mardis, Elaine R.; Lopatto, David

    2010-01-01

    Genomics is not only essential for students to understand biology but also provides unprecedented opportunities for undergraduate research. The goal of the Genomics Education Partnership (GEP), a collaboration between a growing number of colleges and universities around the country and the Department of Biology and Genome Center of Washington University in St. Louis, is to provide such research opportunities. Using a versatile curriculum that has been adapted to many different class settings, GEP undergraduates undertake projects to bring draft-quality genomic sequence up to high quality and/or participate in the annotation of these sequences. GEP undergraduates have improved more than 2 million bases of draft genomic sequence from several species of Drosophila and have produced hundreds of gene models using evidence-based manual annotation. Students appreciate their ability to make a contribution to ongoing research, and report increased independence and a more active learning approach after participation in GEP projects. They show knowledge gains on pre- and postcourse quizzes about genes and genomes and in bioinformatic analysis. Participating faculty also report professional gains, increased access to genomics-related technology, and an overall positive experience. We have found that using a genomics research project as the core of a laboratory course is rewarding for both faculty and students. PMID:20194808

  4. Use of Comparative Genomics To Characterize the Diversity of Acinetobacter baumannii Surveillance Isolates in a Health Care Institution.

    PubMed

    Wallace, Lalena; Daugherty, Sean C; Nagaraj, Sushma; Johnson, J Kristie; Harris, Anthony D; Rasko, David A

    2016-10-01

    Despite the increasing prevalence of the nosocomial pathogen Acinetobacter baumannii, little is known about which genomic components contribute to clinical presentation of this important pathogen. Most whole-genome comparisons of A. baumannii have focused on specific genomic regions associated with phenotypes in a limited number of genomes. In this work, we describe the results of a whole-genome comparative analysis of 254 surveillance isolates of Acinetobacter species, 203 of which were A. baumannii, isolated from perianal swabs and sputum samples collected as part of an infection control active surveillance program at the University of Maryland Medical Center. The collection of surveillance isolates includes both carbapenem-susceptible and -resistant isolates. Based on the whole-genome phylogeny, the A. baumannii isolates collected belong to two major phylogenomic lineages. Results from multilocus sequence typing indicated that one of the major phylogenetic groups of A. baumannii was comprised solely of strains from the international clonal lineage 2. The genomic content of the A. baumannii isolates was examined using large-scale BLAST score ratio analysis to identify genes that are associated with carbapenem-susceptible and -resistant isolates, as well as genes potentially associated with the source of isolation. This analysis revealed a number of genes that were exclusive or at greater frequency in each of these classifications. This study is the most comprehensive genomic comparison of Acinetobacter isolates from a surveillance study to date and provides important information that will contribute to our understanding of the success of A. baumannii as a human pathogen.

  5. Frontiers in cancer epidemiology: a challenge to the research community from the Epidemiology and Genomics Research Program at the National Cancer Institute.

    PubMed

    Khoury, Muin J; Freedman, Andrew N; Gillanders, Elizabeth M; Harvey, Chinonye E; Kaefer, Christie; Reid, Britt C; Rogers, Scott; Schully, Sheri D; Seminara, Daniela; Verma, Mukesh

    2012-07-01

    The Epidemiology and Genomics Research Program (EGRP) at the National Cancer Institute (NCI) is developing scientific priorities for cancer epidemiology research in the next decade. We would like to engage the research community and other stakeholders in a planning effort that will include a workshop in December 2012 to help shape new foci for cancer epidemiology research. To facilitate the process of defining the future of cancer epidemiology, we invite the research community to join in an ongoing web-based conversation at http://blog-epi.grants.cancer.gov/ to develop priorities and the next generation of high-impact studies. ©2012 AACR

  6. One Thousand Genomes Imputation in the National Cancer Institute Breast and Prostate Cancer Cohort Consortium Aggressive Prostate Cancer Genome-wide Association Study

    PubMed Central

    Machiela, Mitchell J.; Chen, Constance; Liang, Liming; Diver, W. Ryan; Stevens, Victoria L.; Tsilidis, Konstantinos K.; Haiman, Christopher A.; Chanock, Stephen J.; Hunter, David J.; Kraft, Peter

    2014-01-01

    BACKGROUND Genotype imputation substantially increases available markers for analysis in genome-wide association studies (GWAS) by leveraging linkage disequilibrium from a reference panel. We sought to (i) investigate the performance of imputation from the August 2010 release of the 1000 Genomes Project (1000GP) in an existing GWAS of prostate cancer, (ii) look for novel associations with prostate cancer risk, (iii) fine-map known prostate cancer susceptibility regions using an approximate Bayesian framework and stepwise regression, and (iv) compare power and efficiency of imputation and de novo sequencing. METHODS We used 2,782 aggressive prostate cancer cases and 4,458 controls from the NCI Breast and Prostate Cancer Cohort Consortium aggressive prostate cancer GWAS to infer 5.8 million well-imputed autosomal single nucleotide polymorphisms. RESULTS Imputation quality, as measured by correlation between imputed and true allele counts, was higher among common variants than rare variants. We found no novel prostate cancer associations among a subset of 1.2 million well-imputed low-frequency variants. At a genome-wide sequencing cost of $2,500, imputation from SNP arrays is a more powerful strategy than sequencing for detecting disease associations of SNPs with minor allele frequencies above 1%. CONCLUSIONS 1000GP imputation provided dense coverage of previously-identified prostate cancer susceptibility regions, highlighting its potential as an inexpensive first-pass approach to fine-mapping in regions such as 5p15 and 8q24. Our study shows 1000GP imputation can accurately identify low-frequency variants and stresses the importance of large sample size when studying these variants. PMID:23255287

  7. One thousand genomes imputation in the National Cancer Institute Breast and Prostate Cancer Cohort Consortium aggressive prostate cancer genome-wide association study.

    PubMed

    Machiela, Mitchell J; Chen, Constance; Liang, Liming; Diver, W Ryan; Stevens, Victoria L; Tsilidis, Konstantinos K; Haiman, Christopher A; Chanock, Stephen J; Hunter, David J; Kraft, Peter

    2013-05-01

    Genotype imputation substantially increases available markers for analysis in genome-wide association studies (GWAS) by leveraging linkage disequilibrium from a reference panel. We sought to (i) investigate the performance of imputation from the August 2010 release of the 1000 Genomes Project (1000GP) in an existing GWAS of prostate cancer, (ii) look for novel associations with prostate cancer risk, (iii) fine-map known prostate cancer susceptibility regions using an approximate Bayesian framework and stepwise regression, and (iv) compare power and efficiency of imputation and de novo sequencing. We used 2,782 aggressive prostate cancer cases and 4,458 controls from the NCI Breast and Prostate Cancer Cohort Consortium aggressive prostate cancer GWAS to infer 5.8 million well-imputed autosomal single nucleotide polymorphisms (SNPs). Imputation quality, as measured by correlation between imputed and true allele counts, was higher among common variants than rare variants. We found no novel prostate cancer associations among a subset of 1.2 million well-imputed low-frequency variants. At a genome-wide sequencing cost of $2,500, imputation from SNP arrays is a more powerful strategy than sequencing for detecting disease associations of SNPs with minor allele frequencies (MAF) above 1%. 1000GP imputation provided dense coverage of previously identified prostate cancer susceptibility regions, highlighting its potential as an inexpensive first-pass approach to fine mapping in regions such as 5p15 and 8q24. Our study shows 1000GP imputation can accurately identify low-frequency variants and stresses the importance of large sample size when studying these variants. Copyright © 2012 Wiley Periodicals, Inc.

  8. Integration of Genomic and Other Epidemiologic Data to Investigate and Control a Cross-Institutional Outbreak of Streptococcus pyogenes

    PubMed Central

    Chalker, Victoria J.; Smith, Alyson; Al-Shahib, Ali; Botchway, Stella; Macdonald, Emily; Daniel, Roger; Phillips, Sarah; Platt, Steven; Doumith, Michel; Tewolde, Rediat; Coelho, Juliana; Jolley, Keith A.; Underwood, Anthony

    2016-01-01

    Single-strain outbreaks of Streptococcus pyogenes infections are common and often go undetected. In 2013, two clusters of invasive group A Streptococcus (iGAS) infection were identified in independent but closely located care homes in Oxfordshire, United Kingdom. Investigation included visits to each home, chart review, staff survey, microbiologic sampling, and genome sequencing. S. pyogenes emm type 1.0, the most common circulating type nationally, was identified from all cases yielding GAS isolates. A tailored whole-genome reference population comprising epidemiologically relevant contemporaneous isolates and published isolates was assembled. Data were analyzed independently using whole-genome multilocus sequencing and single-nucleotide polymorphism analyses. Six isolates from staff and residents of the homes formed a single cluster that was separated from the reference population by both analytical approaches. No further cases occurred after mass chemoprophylaxis and enhanced infection control. Our findings demonstrate the ability of 2 independent analytical approaches to enable robust conclusions from nonstandardized whole-genome analysis to support public health practice. PMID:27192043

  9. The Broad Institute: Screening for Dependencies in Cancer Cell Lines Using Small Molecules | Office of Cancer Genomics

    Cancer.gov

    Using cancer cell-line profiling, we established an ongoing resource to identify, as comprehensively as possible, the drug-targetable dependencies that specific genomic alterations impart on human cancers. We measured the sensitivity of hundreds of genetically characterized cancer cell lines to hundreds of small-molecule probes and drugs that have highly selective interactions with their targets, and that collectively modulate many distinct nodes in cancer cell circuitry.

  10. ZipperDB: Predictions of Fibril-forming Segments within Proteins Identified by the 3D Profile Method (from the UCLA-DOE Institute for Genomics and Proteomics)

    DOE Data Explorer

    Goldschmidt, L.; Teng, P. K.; Riek, R.; Eisenberg, D.

    ZipperDB contains predictions of fibril-forming segments within proteins identified by the 3D Profile Method. The UCLA-DOE Institute for Genomics and Proteomics has analyzed over 20,000 putative protein sequences for segments with high fibrillation propensity that could form a "steric zipper"ùtwo self-complementary beta sheets, giving rise to the spine of an amyloid fibril. The approach is unique in that structural information is used to evaluate the likelihood that a particular sequence can form fibrils. [copied with edits from http://www.doe-mbi.ucla.edu/]. In addition to searching the database, academic and non-profit users may also submit their protein sequences to the database.

  11. The Future of Microbial Genomics

    SciTech Connect

    Kyrpides, Nikos

    2010-06-02

    Nikos Kyrpides, head of the Genome Biology group at the DOE Joint Genome Institute discusses current challenges in the field of microbial genomics on June 2, 2010 at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM

  12. National Human Genome Research Institute

    MedlinePlus

    ... Resources NHGRI-Related News Journal Articles from NHGRI Social Media Careers Educational Programs Health Professional Education Intramural Training Office Online Careers & Training Resources Training ...

  13. Interactions Between Genome-Wide Significant Genetic Variants and Circulating Concentrations of 25-Hydroxyvitamin D in Relation to Prostate Cancer Risk in the National Cancer Institute BPC3.

    PubMed

    Dimitrakopoulou, Vasiliki I; Travis, Ruth C; Shui, Irene M; Mondul, Alison; Albanes, Demetrius; Virtamo, Jarmo; Agudo, Antonio; Boeing, Heiner; Bueno-de-Mesquita, H Bas; Gunter, Marc J; Johansson, Mattias; Khaw, Kay-Tee; Overvad, Kim; Palli, Domenico; Trichopoulou, Antonia; Giovannucci, Edward; Hunter, David J; Lindström, Sara; Willett, Walter; Gaziano, J Michael; Stampfer, Meir; Berg, Christine; Berndt, Sonja I; Black, Amanda; Hoover, Robert N; Kraft, Peter; Key, Timothy J; Tsilidis, Konstantinos K

    2017-03-15

    Genome-wide association studies (GWAS) have identified over 100 single nucleotide polymorphisms (SNPs) associated with prostate cancer. However, information on the mechanistic basis for some associations is limited. Recent research has been directed towards the potential association of vitamin D concentrations and prostate cancer, but little is known about whether the aforementioned genetic associations are modified by vitamin D. We investigated the associations of 46 GWAS-identified SNPs, circulating concentrations of 25-hydroxyvitamin D (25(OH)D), and prostate cancer (3,811 cases, 511 of whom died from the disease, compared with 2,980 controls-from 5 cohort studies that recruited participants over several periods beginning in the 1980s). We used logistic regression models with data from the National Cancer Institute Breast and Prostate Cancer Cohort Consortium (BPC3) to evaluate interactions on the multiplicative and additive scales. After allowing for multiple testing, none of the SNPs examined was significantly associated with 25(OH)D concentration, and the SNP-prostate cancer associations did not differ by these concentrations. A statistically significant interaction was observed for each of 2 SNPs in the 8q24 region (rs620861 and rs16902094), 25(OH)D concentration, and fatal prostate cancer on both multiplicative and additive scales (P ≤ 0.001). We did not find strong evidence that associations between GWAS-identified SNPs and prostate cancer are modified by circulating concentrations of 25(OH)D. The intriguing interactions between rs620861 and rs16902094, 25(OH)D concentration, and fatal prostate cancer warrant replication. © The Author 2017. Published by Oxford University Press on behalf of the Johns Hopkins Bloomberg School of Public Health. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  14. MIPS plant genome information resources.

    PubMed

    Spannagl, Manuel; Haberer, Georg; Ernst, Rebecca; Schoof, Heiko; Mayer, Klaus F X

    2007-01-01

    The Munich Institute for Protein Sequences (MIPS) has been involved in maintaining plant genome databases since the Arabidopsis thaliana genome project. Genome databases and analysis resources have focused on individual genomes and aim to provide flexible and maintainable data sets for model plant genomes as a backbone against which experimental data, for example from high-throughput functional genomics, can be organized and evaluated. In addition, model genomes also form a scaffold for comparative genomics, and much can be learned from genome-wide evolutionary studies.

  15. Center for Cancer Genomics | Office of Cancer Genomics

    Cancer.gov

    The Center for Cancer Genomics (CCG) was established to unify the National Cancer Institute's activities in cancer genomics, with the goal of advancing genomics research and translating findings into the clinic to improve the precise diagnosis and treatment of cancers. In addition to promoting genomic sequencing app

  16. Genomic Encyclopedia of Fungi

    SciTech Connect

    Grigoriev, Igor

    2012-08-10

    Genomes of fungi relevant to energy and environment are in focus of the Fungal Genomic Program at the US Department of Energy Joint Genome Institute (JGI). Its key project, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts), and explores fungal diversity by means of genome sequencing and analysis. Over 150 fungal genomes have been sequenced by JGI to date and released through MycoCosm (www.jgi.doe.gov/fungi), a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supported by functional genomics leads to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such parts suggested by comparative genomics and functional analysis in these areas are presented here.

  17. JGI Fungal Genomics Program

    SciTech Connect

    Grigoriev, Igor V.

    2011-03-14

    Genomes of energy and environment fungi are in focus of the Fungal Genomic Program at the US Department of Energy Joint Genome Institute (JGI). Its key project, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts), and explores fungal diversity by means of genome sequencing and analysis. Over 50 fungal genomes have been sequenced by JGI to date and released through MycoCosm (www.jgi.doe.gov/fungi), a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supported by functional genomics leads to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such 'parts' suggested by comparative genomics and functional analysis in these areas are presented here

  18. Biomarkers for Early Detection of Clinically Relvant Prostate Cancer: A Multi-Institutional Validation Trial - Genomic Health, Inc. — EDRN Public Portal

    Cancer.gov

    Validate a panel of tissue-based biomarkers to determine the presence of or progression to clinically relevant prostate cancer at the time of diagnosis. Utilize a novel, biopsy based multi-gene quantitative RT-PCR assay developed by Genomic Health, Oncotype DX Prostate Cancer Assay, which discriminates aggressive from indolent cancer on multivariate modeling of PCa patients.

  19. Genome Informatics

    PubMed Central

    Winslow, Raimond L.; Boguski, Mark S.

    2005-01-01

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

  20. 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

  1. Epidemiology & Genomics Research Program

    Cancer.gov

    The Epidemiology and Genomics Research Program, in the National Cancer Institute's Division of Cancer Control and Population Sciences, funds research in human populations to understand the determinants of cancer occurrence and outcomes.

  2. Automated Microbial Genome Annotation

    SciTech Connect

    Land, Miriam

    2009-05-29

    Miriam Land of the DOE Joint Genome Institute at Oak Ridge National Laboratory gives a talk on the current state and future challenges of moving toward automated microbial genome annotation at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM

  3. Genomic Advances to Improve Biomass for Biofuels (Genomics and Bioenergy)

    SciTech Connect

    Rokhsar, Daniel

    2008-02-11

    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.

  4. Genome-wide linkage scan in a large bipolar disorder sample from the National Institute of Mental Health genetics initiative suggests putative loci for bipolar disorder, psychosis, suicide, and panic disorder.

    PubMed

    Cheng, R; Juo, S H; Loth, J E; Nee, J; Iossifov, I; Blumenthal, R; Sharpe, L; Kanyas, K; Lerer, B; Lilliston, B; Smith, M; Trautman, K; Gilliam, T C; Endicott, J; Baron, M

    2006-03-01

    We conducted a 9-cM genome scan in a large bipolar pedigree sample from the National Institute of Mental Health genetics initiative (1060 individuals from 154 multiplex families). We performed parametric and nonparametric analyses using both standard diagnostic models and comorbid conditions thought to identify phenotypic subtypes: psychosis, suicidal behavior, and panic disorder. Our strongest linkage signals (genome-wide significance) were observed on chromosomes 10q25, 10p12, 16q24, 16p13, and 16p12 using standard diagnostic models, and on 6q25 (suicidal behavior), 7q21 (panic disorder) and 16p12 (psychosis) using phenotypic subtypes. Several other regions were suggestive of linkage, including 1p13 (psychosis), 1p21 (psychosis), 1q44, 2q24 (suicidal behavior), 2p25 (psychosis), 4p16 (psychosis, suicidal behavior), 5p15, 6p25 (psychosis), 8p22 (psychosis), 8q24, 10q21, 10q25 (suicidal behavior), 10p11 (psychosis), 13q32 and 19p13 (psychosis). Over half the implicated regions were identified using phenotypic subtypes. Several regions - 1p, 1q, 6q, 8p, 13q and 16p - have been previously reported to be linked to bipolar disorder. Our results suggest that dissection of the disease phenotype can enrich the harvest of linkage signals and expedite the search for susceptibility genes. This is the first large-scale linkage scan of bipolar disorder to analyze simultaneously bipolar disorder, psychosis, suicidal behavior, and panic disorder.

  5. Haemonchus contortus: Genome Structure, Organization and Comparative Genomics.

    PubMed

    Laing, R; Martinelli, A; Tracey, A; Holroyd, N; Gilleard, J S; Cotton, J A

    2016-01-01

    One of the first genome sequencing projects for a parasitic nematode was that for Haemonchus contortus. The open access data from the Wellcome Trust Sanger Institute provided a valuable early resource for the research community, particularly for the identification of specific genes and genetic markers. Later, a second sequencing project was initiated by the University of Melbourne, and the two draft genome sequences for H. contortus were published back-to-back in 2013. There is a pressing need for long-range genomic information for genetic mapping, population genetics and functional genomic studies, so we are continuing to improve the Wellcome Trust Sanger Institute assembly to provide a finished reference genome for H. contortus. This review describes this process, compares the H. contortus genome assemblies with draft genomes from other members of the strongylid group and discusses future directions for parasite genomics using the H. contortus model. Copyright © 2016 Elsevier Ltd. All rights reserved.

  6. Center for Cancer Genomics | Office of Cancer Genomics

    Cancer.gov

    The Center for Cancer Genomics (CCG) was established to unify the National Cancer Institute's activities in cancer genomics, with the goal of advancing genomics research and translating findings into the clinic to improve the precise diagnosis and treatment of cancers. In addition to promoting genomic sequencing approaches, CCG aims to accelerate structural, functional and computational research to explore cancer mechanisms, discover new cancer targets, and develop new therapeutics.

  7. TCGA Workshop: Genomics and Biology of Glioblastoma Multiforme (GBM) - TCGA

    Cancer.gov

    The National Cancer Institute (NCI) and National Human Genome Research Institute (NHGRI) held a workshop entitled, “Genomics and Biology of Glioblastoma Multiforme (GBM),” to review the initial GBM data from the TCGA pilot project.

  8. Evolutionary institutionalism.

    PubMed

    Fürstenberg, Dr Kai

    Institutions are hard to define and hard to study. Long prominent in political science have been two theories: Rational Choice Institutionalism (RCI) and Historical Institutionalism (HI). Arising from the life sciences is now a third: Evolutionary Institutionalism (EI). Comparative strengths and weaknesses of these three theories warrant review, and the value-to-be-added by expanding the third beyond Darwinian evolutionary theory deserves consideration. Should evolutionary institutionalism expand to accommodate new understanding in ecology, such as might apply to the emergence of stability, and in genetics, such as might apply to political behavior? Core arguments are reviewed for each theory with more detailed exposition of the third, EI. Particular attention is paid to EI's gene-institution analogy; to variation, selection, and retention of institutional traits; to endogeneity and exogeneity; to agency and structure; and to ecosystem effects, institutional stability, and empirical limitations in behavioral genetics. RCI, HI, and EI are distinct but complementary. Institutional change, while amenable to rational-choice analysis and, retrospectively, to criticaljuncture and path-dependency analysis, is also, and importantly, ecological. Stability, like change, is an emergent property of institutions, which tend to stabilize after change in a manner analogous to allopatric speciation. EI is more than metaphorically biological in that institutional behaviors are driven by human behaviors whose evolution long preceded the appearance of institutions themselves.

  9. Institution Closures.

    ERIC Educational Resources Information Center

    Hayden, Mary F., Ed.; And Others

    1995-01-01

    This newsletter theme issue focuses on the need to accelerate the closing of institutions for people with mental retardation. Articles are by both current and former residents of institutions and by professionals, and include: "The Realities of Institutions" (Tia Nelis); "I Cry Out So That I Won't Go Insane" (Mary F. Hayden); "Trends in…

  10. Overview | Office of Cancer Genomics

    Cancer.gov

    The Human Cancer Model Initiative (HCMI) is an international consortium that is generating novel human tumor-derived culture models with associated genomic and clinical data. The HCMI consortium includes the US-National Cancer Institute, part of the National Institutes of Health, Cancer Research UK, foundation Hubrecht Organoid Technology, and Wellcome Trust Sanger Institute (more on the Consortium).

  11. Genotyping serotonin transporter polymorphisms 5-HTTLPR and rs25531 in European- and African-American subjects from the National Institute of Mental Health's Collaborative Center for Genomic Studies.

    PubMed

    Odgerel, Z; Talati, A; Hamilton, S P; Levinson, D F; Weissman, M M

    2013-09-24

    A number of studies have suggested DNA sequence variability in the serotonin transporter gene (SLC6A4) between European-American (EA) and African-American (AA) populations, which could be clinically important, given the central role SLC6A4 has in serotonin transmission. However, these studies have had relatively small samples, used self-reported measures of race, and have only tested the promoter-linked polymorphism 5-HTTLPR. Here we genotype 5-HTTLPR and rs25531, a neighboring functional polymorphism, in 954 AA and 2622EA subjects from a National Institute of Mental Health repository sample. Genotyping was performed using fragment analysis by capillary electrophoresis. AA, as compared with EA, groups had lower frequencies of the S allele (0.25 vs 0.43) and SS genotype (0.06 vs 0.19) at 5-HTTLPR, and higher rates of the G allele at rs25531 (0.21 vs 0.075). A rare xL variant at 5-HTTLPR was also more common among AAs (0.017 vs 0.008). When the polymorphisms were redefined into a high- and low-transcription haplotypes, the AA group showed significantly fewer low-transcription variants (χ(2)=4.8, P=0.03). No genotypes were associated with major depression, any anxiety disorder, or neuroticism in either EA or AA populations. This is the largest study to show SLC6A4 genotype differences between EA and AA populations, and the first to include rs25531. Lack of associations with clinical outcomes may reflect untested moderating environmental influences.

  12. Institutional paranoia.

    PubMed

    Kulenović, M

    1995-01-01

    Taken separately, the concepts of institution and paranoia have no bearing on this work. They acquire their full new meaning as "institutional paranoia" only when they are taken together. Institutional paranoia is not a mental illness in the ordinary sense. It is a state, a condition, which exists in all associations and communities which have the same goal and concurrent intentions. The author's analysis of the problem is based on observation and monitoring of circumstances, discussions and content analysis, as well as on the use of questionnaires in several health institutions over a long period of time. He focuses his attention primarily on health, political, and economic institutions. The results of observation and analysis point to some interesting phenomena which require further study, regardless of their positive or negative outcome. With additional interventions, the content and dynamics of this process in institutions can contribute to the gradual diminishing of institutional paranoia, and sometimes its complete disappearance over a long time.

  13. [Institutional Renewal].

    ERIC Educational Resources Information Center

    Brown, Peggy, Ed.

    1983-01-01

    The theme of this journal issue is "Institutional Renewal." Projects designed to address the issues of the 1980s at 18 colleges are described, and 15 definitions of institutional renewal are presented. Participating colleges were provided expert advice through the Association of American College's (AAC) Project Lodestar (renamed…

  14. 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.

  15. Collaborators | Office of Cancer Genomics

    Cancer.gov

    The TARGET initiative is jointly managed within the National Cancer Institute (NCI) by the Office of Cancer Genomics (OCG)Opens in a New Tab and the Cancer Therapy Evaluation Program (CTEP)Opens in a New Tab.

  16. Genomic Datasets for Cancer Research

    Cancer.gov

    A variety of datasets from genome-wide association studies of cancer and other genotype-phenotype studies, including sequencing and molecular diagnostic assays, are available to approved investigators through the Extramural National Cancer Institute Data Access Committee.

  17. Collaborators | Office of Cancer Genomics

    Cancer.gov

    The TARGET initiative is jointly managed within the National Cancer Institute (NCI) by the Office of Cancer Genomics (OCG)Opens in a New Tab and the Cancer Therapy Evaluation Program (CTEP)Opens in a New Tab.

  18. The snail (Biomphalaria glabrata) genome project.

    PubMed

    Raghavan, Nithya; Knight, Matty

    2006-04-01

    In 2001, ideas for a snail genome project were discussed at the American Society of Parasitologists meeting (New Mexico) and a snail genome consortium was subsequently established (the first consortium meeting was held in 2005). A proposal for sequencing the snail genome was submitted to the National Human Genome Research Institute, and Biomphalaria glabrata was prioritized as a non-mammalian sequencing target in 2004. The sequencing of the genome of this medically important snail is now underway.

  19. AutoGenomics, Inc.

    PubMed

    Vairavan, Ram

    2004-07-01

    AutoGenomics has created an automated multiplexing microarray platform to make genomic and proteomic analyses routine and efficient for clinical and research laboratories. While the emergence of microarrays has advanced genomic analyses, a number of underlying issues, such as cross-hybridization, poor spot morphology and intrinsic fluorescence of the solid substrate, have yet to be fully resolved. Current methods use discrete instrumentation, are manual and require highly skilled labor, which leads to inconsistent results. AutoGenomics' automated platform uses a three-dimensional BioFilmChip microarray to circumvent these issues, providing optimal spot morphology and utilizing solution-based hybridization with allele-specific primer extension to improve single-base discrimination. AutoGenomics is developing applications for the early detection and management of complex disease states in oncology, cardiology, and mental disorders. Customers include clinical reference laboratories, hospitals, academic institutions, and pharmaceutical and biotech companies. Founded in 1999, the company is headquartered in Carlsbad, California, USA.

  20. Burn Institute

    MedlinePlus

    ... a resource to the community. Learn more The Burn Institute reaches thousands of children and adults each year through fire and burn prevention education, burn survivor support programs and the ...

  1. Genetics, Genomics and Breeding in Soybean

    USDA-ARS?s Scientific Manuscript database

    The soybean (Glycine max) genome sequencing project began as an interagency project with the DOE’s Joint Genome Institute providing the production sequencing throughput with the NSF and USDA funded groups providing genomic resources and soybean expertise to the project (Jackson et al, 2006). The go...

  2. Institution Morphisms

    NASA Technical Reports Server (NTRS)

    Goguen, Joseph; Rosu, Grigore; Norvig, Peter (Technical Monitor)

    2001-01-01

    Institutions formalize the intuitive notion of logical system, including both syntax and semantics. A surprising number of different notions of morphisim have been suggested for forming categories with institutions as objects, and a surprising variety of names have been proposed for them. One goal of this paper is to suggest a terminology that is both uniform and informative to replace the current rather chaotic nomenclature. Another goal is to investigate the properties and interrelations of these notions. Following brief expositions of indexed categories, twisted relations, and Kan extensions, we demonstrate and then exploit the duality between institution morphisms in the original sense of Goguen and Burstall, and the 'plain maps' of Meseguer, obtaining simple uniform proofs of completeness and cocompleteness for both resulting categories; because of this duality, we prefer the name 'comorphism' over 'plain map.' We next consider 'theoroidal' morphisms and comorphisims, which generalize signatures to theories, finding that the 'maps' of Meseguer are theoroidal comorphisms, while theoroidal morphisms are a new concept. We then introduce 'forward' and 'semi-natural' morphisms, and appendices discuss institutions for hidden algebra, universal algebra, partial equational logic, and a variant of order sorted algebra supporting partiality.

  3. Institutional Censorship

    ERIC Educational Resources Information Center

    Burke, John Gordon; Bowers, H. Paxton

    1970-01-01

    The difficulty an individual who has been denied access to library material faces in obtaining a remedy in the courts dictates that the library profession go on record against all forms of institutional censorship or unreasonable restrictions on use of library materials. (Author/JS)

  4. Institutional Paralysis

    ERIC Educational Resources Information Center

    Yarmolinsky, Adam

    1975-01-01

    Institutional paralysis of higher education is the result of the disjunction between faculty and administration; the disjunction between substantive planning and bugetary decision-making; the disjunction between departmental structures and functional areas of university concern; and the disjunction between the theory of direct democracy and its…

  5. Institutional Change.

    ERIC Educational Resources Information Center

    Smith, Hayden R., Ed.

    1978-01-01

    This publication's theme, "Institutional Change," is broadly examined in fourteen articles that range from research and opinion to allegory and satire. A student teacher, a dean, and a state education director are among the authors. Articles concern: 1) key elements of change; 2) relationships between local, county, state, and federal educational…

  6. Institutional betrayal.

    PubMed

    Smith, Carly Parnitzke; Freyd, Jennifer J

    2014-09-01

    A college freshman reports a sexual assault and is met with harassment and insensitive investigative practices leading to her suicide. Former grade school students, now grown, come forward to report childhood abuse perpetrated by clergy, coaches, and teachers--first in trickles and then in waves, exposing multiple perpetrators with decades of unfettered access to victims. Members of the armed services elect to stay quiet about sexual harassment and assault during their military service or risk their careers by speaking up. A Jewish academic struggles to find a name for the systematic destruction of his people in Nazi Germany during the Holocaust. These seemingly disparate experiences have in common trusted and powerful institutions (schools, churches, military, government) acting in ways that visit harm upon those dependent on them for safety and well-being. This is institutional betrayal. The purpose of this article is to describe psychological research that examines the role of institutions in traumatic experiences and psychological distress following these experiences. We demonstrate the ways in which institutional betrayal has been left unseen by both the individuals being betrayed as well as the field of psychology and introduce means by which to identify and address this betrayal.

  7. International Summer School, ‘ From Genome to Life’

    PubMed Central

    2002-01-01

    This report from the International Summer School ‘From Genome to Life’, held at the Institute d'Etudes Scientifiques de Cargèse in Corsica in July 2002, covers the talks of the invited speakers. The topics of the talks can be broadly grouped into the areas of genome annotation, comparative and evolutionary genomics, functional genomics, proteomics, structural genomics, pharmacogenomics, and organelle genomes, epigenetics and RNA. PMID:18629253

  8. 78 FR 55083 - Submission for OMB Review; 30-day Comment Request; Genomics and Society Public Surveys in...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-09-09

    ... an additional 30 days for public comment. The National Human Genome Research Institute (NHGRI..., 0925--NEW, National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH). Need and Use of Information Collection: The National Human Genome Research Institute's (NHGRI) strategic...

  9. Genomics of Climate Resilience (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

    SciTech Connect

    Bermingham, Eldredge

    2013-03-27

    Eldredge Bermingham of the Smithsonian Tropical Research Institute-Panama on "Genomics of climate resilience" at the 8th Annual Genomics of Energy & Environment Meeting on March 27, 2013 in Walnut Creek, Calif.

  10. Institute news

    NASA Astrophysics Data System (ADS)

    1999-11-01

    Joining the team A new member of staff has recently joined the Institute of Physics Education Department (Schools and Colleges) team. (Dr) Steven Chapman will have managerial responsibility for physics education issues in the 11 - 16 age range, particularly on the policy side. He will work closely with Mary Wood, who spends much of her time out and about doing the practical things to support physics education pre-16. Catherine Wilson will be spending more of her time working to support the Post-16 Physics Initiative but retains overall responsibility for the department. Steven graduated in Physics and Astronomy and then went on to do his doctorate at Sussex University. He stayed in the research field for a while, including a period at NPL. Then, having decided to train as a teacher, he taught for the last five years, most recently at a brand new school in Sutton where he was Head of Physics. Physics update Dates for `Physics Update' courses in 2000, intended for practising science teachers, are as follows: 1 - 3 April: Malvern College 9 - 10 June: Stirling University 8 - 10 July: York University 8 - 10 December: Oxford University The deadline for applications for the course to be held on 11 - 13 December 1999 at the School of Physics, Exeter University, is 12 November, so any late enquiries should be sent to Leila Solomon at The Institute of Physics, 76 Portland Place, London W1N 3DH (tel: 020 7470 4821) right away. Name that teacher! Late nominations are still welcome for the Teachers of Physics/Teachers of Primary Science awards for the year 2000. Closing date for nominations is `the last week in November'. Further details can be obtained from Catherine Wilson or Barbara Hill in the Institute's Education Department. Forward and back! The Education Group's one-day meeting on 13 November is accepting bookings until almost the last minute, so don't delay your application! The day is entitled `Post-16 physics: Looking forward, learning from the past' and it aims to

  11. How the genome folds

    NASA Astrophysics Data System (ADS)

    Lieberman Aiden, Erez

    2012-02-01

    I describe Hi-C, a novel technology for probing the three-dimensional architecture of whole genomes by coupling proximity-based ligation with massively parallel sequencing. Working with collaborators at the Broad Institute and UMass Medical School, we used Hi-C to construct spatial proximity maps of the human genome at a resolution of 1Mb. These maps confirm the presence of chromosome territories and the spatial proximity of small, gene-rich chromosomes. We identified an additional level of genome organization that is characterized by the spatial segregation of open and closed chromatin to form two genome-wide compartments. At the megabase scale, the chromatin conformation is consistent with a fractal globule, a knot-free conformation that enables maximally dense packing while preserving the ability to easily fold and unfold any genomic locus. The fractal globule is distinct from the more commonly used globular equilibrium model. Our results demonstrate the power of Hi-C to map the dynamic conformations of whole genomes.

  12. Contact | Office of Cancer Genomics

    Cancer.gov

    For more information about the Office of Cancer Genomics, please contact: Office of Cancer Genomics National Cancer Institute 31 Center Drive, 10A07 Bethesda, Maryland 20892-2580 Phone: (240) 781-3280 Fax: (240) 541-4510 Email: ocg@mail.nih.gov *Please note that this site will not function properly in Internet Explorer unless you completely turn off the Compatibility View*

  13. Capturing prokaryotic dark matter genomes.

    PubMed

    Gasc, Cyrielle; Ribière, Céline; Parisot, Nicolas; Beugnot, Réjane; Defois, Clémence; Petit-Biderre, Corinne; Boucher, Delphine; Peyretaillade, Eric; Peyret, Pierre

    2015-12-01

    Prokaryotes are the most diverse and abundant cellular life forms on Earth. Most of them, identified by indirect molecular approaches, belong to microbial dark matter. The advent of metagenomic and single-cell genomic approaches has highlighted the metabolic capabilities of numerous members of this dark matter through genome reconstruction. Thus, linking functions back to the species has revolutionized our understanding of how ecosystem function is sustained by the microbial world. This review will present discoveries acquired through the illumination of prokaryotic dark matter genomes by these innovative approaches. Copyright © 2015 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

  14. Prophage Genomics

    PubMed Central

    Canchaya, Carlos; Proux, Caroline; Fournous, Ghislain; Bruttin, Anne; Brüssow, Harald

    2003-01-01

    The majority of the bacterial genome sequences deposited in the National Center for Biotechnology Information database contain prophage sequences. Analysis of the prophages suggested that after being integrated into bacterial genomes, they undergo a complex decay process consisting of inactivating point mutations, genome rearrangements, modular exchanges, invasion by further mobile DNA elements, and massive DNA deletion. We review the technical difficulties in defining such altered prophage sequences in bacterial genomes and discuss theoretical frameworks for the phage-bacterium interaction at the genomic level. The published genome sequences from three groups of eubacteria (low- and high-G+C gram-positive bacteria and γ-proteobacteria) were screened for prophage sequences. The prophages from Streptococcus pyogenes served as test case for theoretical predictions of the role of prophages in the evolution of pathogenic bacteria. The genomes from further human, animal, and plant pathogens, as well as commensal and free-living bacteria, were included in the analysis to see whether the same principles of prophage genomics apply for bacteria living in different ecological niches and coming from distinct phylogenetical affinities. The effect of selection pressure on the host bacterium is apparently an important force shaping the prophage genomes in low-G+C gram-positive bacteria and γ-proteobacteria. PMID:12794192

  15. Human genome project: Past, present, and future

    SciTech Connect

    Watson, J.D.

    1990-04-06

    The article presents a short discussion of the development of the human genome program in the United States, a summary of the current status of the organization and administration of the National Institutes of Health component of the program, and some prospects for the future directions of the program and the applications of genome information.

  16. Cancer Genome Anatomy Project | Office of Cancer Genomics

    Cancer.gov

    The National Cancer Institute (NCI) Cancer Genome Anatomy Project (CGAP) is an online resource designed to provide the research community access to biological tissue characterization data. Request a free copy of the CGAP Website Virtual Tour CD from ocg@mail.nih.gov.

  17. Cancer Genome Anatomy Project | Office of Cancer Genomics

    Cancer.gov

    The National Cancer Institute (NCI) Cancer Genome Anatomy Project (CGAP) is an online resource designed to provide the research community access to biological tissue characterization data. Request a free copy of the CGAP Website Virtual Tour CD from ocg@mail.nih.gov.

  18. Building International Genomics Collaboration for Global Health Security

    PubMed Central

    Cui, Helen H.; Erkkila, Tracy; Chain, Patrick S. G.; Vuyisich, Momchilo

    2015-01-01

    Genome science and technologies are transforming life sciences globally in many ways and becoming a highly desirable area for international collaboration to strengthen global health. The Genome Science Program at the Los Alamos National Laboratory is leveraging a long history of expertise in genomics research to assist multiple partner nations in advancing their genomics and bioinformatics capabilities. The capability development objectives focus on providing a molecular genomics-based scientific approach for pathogen detection, characterization, and biosurveillance applications. The general approaches include introduction of basic principles in genomics technologies, training on laboratory methodologies and bioinformatic analysis of resulting data, procurement, and installation of next-generation sequencing instruments, establishing bioinformatics software capabilities, and exploring collaborative applications of the genomics capabilities in public health. Genome centers have been established with public health and research institutions in the Republic of Georgia, Kingdom of Jordan, Uganda, and Gabon; broader collaborations in genomics applications have also been developed with research institutions in many other countries. PMID:26697418

  19. Building international genomics collaboration for global health security

    SciTech Connect

    Cui, Helen H.; Erkkila, Tracy; Chain, Patrick S. G.; Vuyisich, Momchilo

    2015-12-07

    Genome science and technologies are transforming life sciences globally in many ways and becoming a highly desirable area for international collaboration to strengthen global health. The Genome Science Program at the Los Alamos National Laboratory is leveraging a long history of expertise in genomics research to assist multiple partner nations in advancing their genomics and bioinformatics capabilities. The capability development objectives focus on providing a molecular genomics-based scientific approach for pathogen detection, characterization, and biosurveillance applications. The general approaches include introduction of basic principles in genomics technologies, training on laboratory methodologies and bioinformatic analysis of resulting data, procurement, and installation of next-generation sequencing instruments, establishing bioinformatics software capabilities, and exploring collaborative applications of the genomics capabilities in public health. Genome centers have been established with public health and research institutions in the Republic of Georgia, Kingdom of Jordan, Uganda, and Gabon; broader collaborations in genomics applications have also been developed with research institutions in many other countries.

  20. Building International Genomics Collaboration for Global Health Security.

    PubMed

    Cui, Helen H; Erkkila, Tracy; Chain, Patrick S G; Vuyisich, Momchilo

    2015-01-01

    Genome science and technologies are transforming life sciences globally in many ways and becoming a highly desirable area for international collaboration to strengthen global health. The Genome Science Program at the Los Alamos National Laboratory is leveraging a long history of expertise in genomics research to assist multiple partner nations in advancing their genomics and bioinformatics capabilities. The capability development objectives focus on providing a molecular genomics-based scientific approach for pathogen detection, characterization, and biosurveillance applications. The general approaches include introduction of basic principles in genomics technologies, training on laboratory methodologies and bioinformatic analysis of resulting data, procurement, and installation of next-generation sequencing instruments, establishing bioinformatics software capabilities, and exploring collaborative applications of the genomics capabilities in public health. Genome centers have been established with public health and research institutions in the Republic of Georgia, Kingdom of Jordan, Uganda, and Gabon; broader collaborations in genomics applications have also been developed with research institutions in many other countries.

  1. Aquaculture Genomics

    USDA-ARS?s Scientific Manuscript database

    The genomics chapter covers the basics of genome mapping and sequencing and the current status of several relevant species. The chapter briefly describes the development and use of (cDNA, BAC, etc.) libraries for mapping and obtaining specific sequence information. Other topics include comparative ...

  2. Fueling Future with Algal Genomics

    SciTech Connect

    Grigoriev, Igor

    2012-07-05

    Algae constitute a major component of fundamental eukaryotic diversity, play profound roles in the carbon cycle, and are prominent candidates for biofuel production. The US Department of Energy Joint Genome Institute (JGI) is leading the world in algal genome sequencing (http://jgi.doe.gov/Algae) and contributes of the algal genome projects worldwide (GOLD database, 2012). The sequenced algal genomes offer catalogs of genes, networks, and pathways. The sequenced first of its kind genomes of a haptophyte E.huxleyii, chlorarachniophyte B.natans, and cryptophyte G.theta fill the gaps in the eukaryotic tree of life and carry unique genes and pathways as well as molecular fossils of secondary endosymbiosis. Natural adaptation to conditions critical for industrial production is encoded in algal genomes, for example, growth of A.anophagefferens at very high cell densities during the harmful algae blooms or a global distribution across diverse environments of E.huxleyii, able to live on sparse nutrients due to its expanded pan-genome. Communications and signaling pathways can be derived from simple symbiotic systems like lichens or complex marine algae metagenomes. Collectively these datasets derived from algal genomics contribute to building a comprehensive parts list essential for algal biofuel development.

  3. Future Health Applications of Genomics

    PubMed Central

    McBride, Colleen M.; Bowen, Deborah; Brody, Lawrence C.; Condit, Celeste M.; Croyle, Robert T.; Gwinn, Marta; Khoury, Muin J.; Koehly, Laura M.; Korf, Bruce R.; Marteau, Theresa M.; McLeroy, Kenneth; Patrick, Kevin; Valente, Thomas W.

    2014-01-01

    Despite the quickening momentum of genomic discovery, the communication, behavioral, and social sciences research needed for translating this discovery into public health applications has lagged behind. The National Human Genome Research Institute held a 2-day workshop in October 2008 convening an interdisciplinary group of scientists to recommend forward-looking priorities for translational research. This research agenda would be designed to redress the top three risk factors (tobacco use, poor diet, and physical inactivity) that contribute to the four major chronic diseases (heart disease, type 2 diabetes, lung disease, and many cancers) and account for half of all deaths worldwide. Three priority research areas were identified: (1) improving the public’s genetic literacy in order to enhance consumer skills; (2) gauging whether genomic information improves risk communication and adoption of healthier behaviors more than current approaches; and (3) exploring whether genomic discovery in concert with emerging technologies can elucidate new behavioral intervention targets. Important crosscutting themes also were identified, including the need to: (1) anticipate directions of genomic discovery; (2) take an agnostic scientific perspective in framing research questions asking whether genomic discovery adds value to other health promotion efforts; and (3) consider multiple levels of influence and systems that contribute to important public health problems. The priorities and themes offer a framework for a variety of stakeholders, including those who develop priorities for research funding, interdisciplinary teams engaged in genomics research, and policymakers grappling with how to use the products born of genomics research to address public health challenges. PMID:20409503

  4. Institute Study Report

    NASA Technical Reports Server (NTRS)

    Whitaker, Ann; Steadman, Jackie; Little, Sally; Underwood, Debra; Blackman, Mack; Simonds, Judy

    1997-01-01

    This report documents a study conducted by the MSFC working group on Institutes in 1995 on the structure, organization and business arrangements of Institutes at a time when the agency was considering establishing science institutes. Thirteen institutes, ten science centers associated with the state of Georgia, Stanford Research Institute (SRI), and IIT Research Institute (IITRI), and general data on failed institutes were utilized to form this report. The report covers the working group's findings on institute mission, structure, director, board of directors/advisors, the working environment, research arrangements, intellectual property rights, business management, institute funding, and metrics.

  5. Genomes to Proteomes

    SciTech Connect

    Panisko, Ellen A.; Grigoriev, Igor; Daly, Don S.; Webb-Robertson, Bobbie-Jo; Baker, Scott E.

    2009-03-01

    Biologists are awash with genomic sequence data. In large part, this is due to the rapid acceleration in the generation of DNA sequence that occurred as public and private research institutes raced to sequence the human genome. In parallel with the large human genome effort, mostly smaller genomes of other important model organisms were sequenced. Projects following on these initial efforts have made use of technological advances and the DNA sequencing infrastructure that was built for the human and other organism genome projects. As a result, the genome sequences of many organisms are available in high quality draft form. While in many ways this is good news, there are limitations to the biological insights that can be gleaned from DNA sequences alone; genome sequences offer only a bird's eye view of the biological processes endemic to an organism or community. Fortunately, the genome sequences now being produced at such a high rate can serve as the foundation for other global experimental platforms such as proteomics. Proteomic methods offer a snapshot of the proteins present at a point in time for a given biological sample. Current global proteomics methods combine enzymatic digestion, separations, mass spectrometry and database searching for peptide identification. One key aspect of proteomics is the prediction of peptide sequences from mass spectrometry data. Global proteomic analysis uses computational matching of experimental mass spectra with predicted spectra based on databases of gene models that are often generated computationally. Thus, the quality of gene models predicted from a genome sequence is crucial in the generation of high quality peptide identifications. Once peptides are identified they can be assigned to their parent protein. Proteins identified as expressed in a given experiment are most useful when compared to other expressed proteins in a larger biological context or biochemical pathway. In this chapter we will discuss the automatic

  6. 77 FR 6812 - National Institute of Nursing Research; Notice of Closed Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-02-09

    ... HUMAN SERVICES National Institutes of Health National Institute of Nursing Research; Notice of Closed... of Committee: National Institute of Nursing Research Special Emphasis Panel Genomic Advances to Wound...: Tamizchelvi Thyagarajan, Ph.D., Scientific Review Officer, National Institute of Nursing Research, National...

  7. The Nostoc punctiforme Genome

    SciTech Connect

    John C. Meeks

    2001-12-31

    Nostoc punctiforme is a filamentous cyanobacterium with extensive phenotypic characteristics and a relatively large genome, approaching 10 Mb. The phenotypic characteristics include a photoautotrophic, diazotrophic mode of growth, but N. punctiforme is also facultatively heterotrophic; its vegetative cells have multiple development alternatives, including terminal differentiation into nitrogen-fixing heterocysts and transient differentiation into spore-like akinetes or motile filaments called hormogonia; and N. punctiforme has broad symbiotic competence with fungi and terrestrial plants, including bryophytes, gymnosperms and an angiosperm. The shotgun-sequencing phase of the N. punctiforme strain ATCC 29133 genome has been completed by the Joint Genome Institute. Annotation of an 8.9 Mb database yielded 7432 open reading frames, 45% of which encode proteins with known or probable known function and 29% of which are unique to N. punctiforme. Comparative analysis of the sequence indicates a genome that is highly plastic and in a state of flux, with numerous insertion sequences and multilocus repeats, as well as genes encoding transposases and DNA modification enzymes. The sequence also reveals the presence of genes encoding putative proteins that collectively define almost all characteristics of cyanobacteria as a group. N. punctiforme has an extensive potential to sense and respond to environmental signals as reflected by the presence of more than 400 genes encoding sensor protein kinases, response regulators and other transcriptional factors. The signal transduction systems and any of the large number of unique genes may play essential roles in the cell differentiation and symbiotic interaction properties of N. punctiforme.

  8. [RadGenomics project].

    PubMed

    Iwakawa, Mayumi; Imai, Takashi; Harada, Yoshinobu; Ban, Sadayuki; Michikawa, Yu-ichi; Saegusa, Kumiko; Sagara, Masasi; Tsuji, Atsushi; Noda, Shuhei; Ishikawa, Atsuko

    2002-08-01

    Human health conditions are largely determined by a complex interplay among genetic susceptibility, environmental factors, and aging. The RadGenomics project, which began in April 2001, promotes analysis of genes in response to irradiation, identification of their allelic variants in the human population, development of an effective procedure for quantitating individual radio-sensitivity, and analysis of the interrelationship between genetic heterogeneity and susceptibility to irradiation. Major groups of genes with which the project will concern itself include DNA repair genes, cell cycle genes, oncogenes, tumor suppressor genes, genes for programmed cell death, genes for signal transduction, and genes for oxidative processes. The outcome of the RadGenomics project should lead to improved protocols for personalized radiotherapy and reduce the possible side effects of treatment. The project will contribute to future research on the molecular mechanisms of radiation sensitivity in humans and stimulate the development of new high-throughput technology for a broader application of the biological and medical sciences. Identification of functionally important polymorphisms in the radiation response genes may determine individual differences in sensitivity to radiation exposure. The staff members, who are specialists in a variety of fields including genome science, radiation biology, medical science, molecular biology, and bioinformatics, have come to the RadGenomics project from various universities, companies, and research institutes.

  9. Antarctic Genomics

    PubMed Central

    Clarke, Andrew; Cockell, Charles S.; Convey, Peter; Detrich III, H. William; Fraser, Keiron P. P.; Johnston, Ian A.; Methe, Barbara A.; Murray, Alison E.; Peck, Lloyd S.; Römisch, Karin; Rogers, Alex D.

    2004-01-01

    With the development of genomic science and its battery of technologies, polar biology stands on the threshold of a revolution, one that will enable the investigation of important questions of unprecedented scope and with extraordinary depth and precision. The exotic organisms of polar ecosystems are ideal candidates for genomic analysis. Through such analyses, it will be possible to learn not only the novel features that enable polar organisms to survive, and indeed thrive, in their extreme environments, but also fundamental biological principles that are common to most, if not all, organisms. This article aims to review recent developments in Antarctic genomics and to demonstrate the global context of such studies. PMID:18629155

  10. New Approaches and Technologies to Sequence de novo Plant reference Genomes (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

    SciTech Connect

    Schmutz, Jeremy

    2013-03-01

    Jeremy Schmutz of the HudsonAlpha Institute for Biotechnology on "New approaches and technologies to sequence de novo plant reference genomes" at the 8th Annual Genomics of Energy & Environment Meeting on March 27, 2013 in Walnut Creek, Calif.

  11. National Cancer Institute

    MedlinePlus

    ... Partners & Collaborators Spotlight on Scientists Research Areas Cancer Biology Research Cancer Genomics Research Research on Causes of ... Collaborators Spotlight on Scientists NCI Research Areas Cancer Biology Cancer Genomics Causes of Cancer Diagnosis Prevention Screening & ...

  12. PGSB/MIPS Plant Genome Information Resources and Concepts for the Analysis of Complex Grass Genomes.

    PubMed

    Spannagl, Manuel; Bader, Kai; Pfeifer, Matthias; Nussbaumer, Thomas; Mayer, Klaus F X

    2016-01-01

    PGSB (Plant Genome and Systems Biology; formerly MIPS-Munich Institute for Protein Sequences) has been involved in developing, implementing and maintaining plant genome databases for more than a decade. Genome databases and analysis resources have focused on individual genomes and aim to provide flexible and maintainable datasets for model plant genomes as a backbone against which experimental data, e.g., from high-throughput functional genomics, can be organized and analyzed. In addition, genomes from both model and crop plants form a scaffold for comparative genomics, assisted by specialized tools such as the CrowsNest viewer to explore conserved gene order (synteny) between related species on macro- and micro-levels.The genomes of many economically important Triticeae plants such as wheat, barley, and rye present a great challenge for sequence assembly and bioinformatic analysis due to their enormous complexity and large genome size. Novel concepts and strategies have been developed to deal with these difficulties and have been applied to the genomes of wheat, barley, rye, and other cereals. This includes the GenomeZipper concept, reference-guided exome assembly, and "chromosome genomics" based on flow cytometry sorted chromosomes.

  13. Genome databases

    SciTech Connect

    Courteau, J.

    1991-10-11

    Since the Genome Project began several years ago, a plethora of databases have been developed or are in the works. They range from the massive Genome Data Base at Johns Hopkins University, the central repository of all gene mapping information, to small databases focusing on single chromosomes or organisms. Some are publicly available, others are essentially private electronic lab notebooks. Still others limit access to a consortium of researchers working on, say, a single human chromosome. An increasing number incorporate sophisticated search and analytical software, while others operate as little more than data lists. In consultation with numerous experts in the field, a list has been compiled of some key genome-related databases. The list was not limited to map and sequence databases but also included the tools investigators use to interpret and elucidate genetic data, such as protein sequence and protein structure databases. Because a major goal of the Genome Project is to map and sequence the genomes of several experimental animals, including E. coli, yeast, fruit fly, nematode, and mouse, the available databases for those organisms are listed as well. The author also includes several databases that are still under development - including some ambitious efforts that go beyond data compilation to create what are being called electronic research communities, enabling many users, rather than just one or a few curators, to add or edit the data and tag it as raw or confirmed.

  14. Genome Sequencing.

    PubMed

    Verma, Mansi; Kulshrestha, Samarth; Puri, Ayush

    2017-01-01

    Genome sequencing is an important step toward correlating genotypes with phenotypic characters. Sequencing technologies are important in many fields in the life sciences, including functional genomics, transcriptomics, oncology, evolutionary biology, forensic sciences, and many more. The era of sequencing has been divided into three generations. First generation sequencing involved sequencing by synthesis (Sanger sequencing) and sequencing by cleavage (Maxam-Gilbert sequencing). Sanger sequencing led to the completion of various genome sequences (including human) and provided the foundation for development of other sequencing technologies. Since then, various techniques have been developed which can overcome some of the limitations of Sanger sequencing. These techniques are collectively known as "Next-generation sequencing" (NGS), and are further classified into second and third generation technologies. Although NGS methods have many advantages in terms of speed, cost, and parallelism, the accuracy and read length of Sanger sequencing is still superior and has confined the use of NGS mainly to resequencing genomes. Consequently, there is a continuing need to develop improved real time sequencing techniques. This chapter reviews some of the options currently available and provides a generic workflow for sequencing a genome.

  15. Genome Improvement at JGI-HAGSC

    SciTech Connect

    Grimwood, Jane; Schmutz, Jeremy J.; Myers, Richard M.

    2012-03-03

    Since the completion of the sequencing of the human genome, the Joint Genome Institute (JGI) has rapidly expanded its scientific goals in several DOE mission-relevant areas. At the JGI-HAGSC, we have kept pace with this rapid expansion of projects with our focus on assessing, assembling, improving and finishing eukaryotic whole genome shotgun (WGS) projects for which the shotgun sequence is generated at the Production Genomic Facility (JGI-PGF). We follow this by combining the draft WGS with genomic resources generated at JGI-HAGSC or in collaborator laboratories (including BAC end sequences, genetic maps and FLcDNA sequences) to produce an improved draft sequence. For eukaryotic genomes important to the DOE mission, we then add further information from directed experiments to produce reference genomic sequences that are publicly available for any scientific researcher. Also, we have continued our program for producing BAC-based finished sequence, both for adding information to JGI genome projects and for small BAC-based sequencing projects proposed through any of the JGI sequencing programs. We have now built our computational expertise in WGS assembly and analysis and have moved eukaryotic genome assembly from the JGI-PGF to JGI-HAGSC. We have concentrated our assembly development work on large plant genomes and complex fungal and algal genomes.

  16. Fungal Genomics for Energy and Environment

    SciTech Connect

    Grigoriev, Igor V.

    2013-03-11

    Genomes of fungi relevant to energy and environment are in focus of the Fungal Genomic Program at the US Department of Energy Joint Genome Institute (JGI). One of its projects, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts) by means of genome sequencing and analysis. New chapters of the Encyclopedia can be opened with user proposals to the JGI Community Sequencing Program (CSP). Another JGI project, the 1000 fungal genomes, explores fungal diversity on genome level at scale and is open for users to nominate new species for sequencing. Over 200 fungal genomes have been sequenced by JGI to date and released through MycoCosm (www.jgi.doe.gov/fungi), a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supported by functional genomics leads to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such parts suggested by comparative genomics and functional analysis in these areas are presented here.

  17. Interactions Between Genome-wide Significant Genetic Variants and Circulating Concentrations of Insulin-like Growth Factor 1, Sex Hormones, and Binding Proteins in Relation to Prostate Cancer Risk in the National Cancer Institute Breast and Prostate Cancer Cohort Consortium

    PubMed Central

    Tsilidis, Konstantinos K.; Travis, Ruth C.; Appleby, Paul N.; Allen, Naomi E.; Lindstrom, Sara; Schumacher, Fredrick R.; Cox, David; Hsing, Ann W.; Ma, Jing; Severi, Gianluca; Albanes, Demetrius; Virtamo, Jarmo; Boeing, Heiner; Bueno-de-Mesquita, H. Bas; Johansson, Mattias; Quirós, J. Ramón; Riboli, Elio; Siddiq, Afshan; Tjønneland, Anne; Trichopoulos, Dimitrios; Tumino, Rosario; Gaziano, J. Michael; Giovannucci, Edward; Hunter, David J.; Kraft, Peter; Stampfer, Meir J.; Giles, Graham G.; Andriole, Gerald L.; Berndt, Sonja I.; Chanock, Stephen J.; Hayes, Richard B.; Key, Timothy J.

    2012-01-01

    Genome-wide association studies (GWAS) have identified many single nucleotide polymorphisms (SNPs) associated with prostate cancer risk. There is limited information on the mechanistic basis of these associations, particularly about whether they interact with circulating concentrations of growth factors and sex hormones, which may be important in prostate cancer etiology. Using conditional logistic regression, the authors compared per-allele odds ratios for prostate cancer for 39 GWAS-identified SNPs across thirds (tertile groups) of circulating concentrations of insulin-like growth factor 1 (IGF-1), insulin-like growth factor binding protein 3 (IGFBP-3), testosterone, androstenedione, androstanediol glucuronide, estradiol, and sex hormone-binding globulin (SHBG) for 3,043 cases and 3,478 controls in the Breast and Prostate Cancer Cohort Consortium. After allowing for multiple testing, none of the SNPs examined were significantly associated with growth factor or hormone concentrations, and the SNP-prostate cancer associations did not differ by these concentrations, although 4 interactions were marginally significant (MSMB-rs10993994 with androstenedione (uncorrected P = 0.008); CTBP2-rs4962416 with IGFBP-3 (uncorrected P = 0.003); 11q13.2-rs12418451 with IGF-1 (uncorrected P = 0.006); and 11q13.2-rs10896449 with SHBG (uncorrected P = 0.005)). The authors found no strong evidence that associations between GWAS-identified SNPs and prostate cancer are modified by circulating concentrations of IGF-1, sex hormones, or their major binding proteins. PMID:22459122

  18. Listeria Genomics

    NASA Astrophysics Data System (ADS)

    Cabanes, Didier; Sousa, Sandra; Cossart, Pascale

    The opportunistic intracellular foodborne pathogen Listeria monocytogenes has become a paradigm for the study of host-pathogen interactions and bacterial adaptation to mammalian hosts. Analysis of L. monocytogenes infection has provided considerable insight into how bacteria invade cells, move intracellularly, and disseminate in tissues, as well as tools to address fundamental processes in cell biology. Moreover, the vast amount of knowledge that has been gathered through in-depth comparative genomic analyses and in vivo studies makes L. monocytogenes one of the most well-studied bacterial pathogens. This chapter provides an overview of progress in the exploration of genomic, transcriptomic, and proteomic data in Listeria spp. to understand genome evolution and diversity, as well as physiological aspects of metabolism used by bacteria when growing in diverse environments, in particular in infected hosts.

  19. Mapping the human genome

    SciTech Connect

    Cantor, Charles R.

    1989-06-01

    The following pages aim to lay a foundation for understanding the excitement surrounding the ''human genome project,'' as well as to convey a flavor of the ongoing efforts and plans at the Human Genome Center at the Lawrence Berkeley Laboratory. Our own work, of course, is only part of a broad international effort that will dramatically enhance our understanding of human molecular genetics before the end of this century. In this country, the bulk of the effort will be carried out under the auspices of the Department of Energy and the National Institutes of Health, but significant contributions have already been made both by nonprofit private foundations and by private corporation. The respective roles of the DOE and the NIH are being coordinated by an inter-agency committee, the aims of which are to emphasize the strengths of each agency, to facilitate cooperation, and to avoid unnecessary duplication of effort. The NIH, for example, will continue its crucial work in medical genetics and in mapping the genomes of nonhuman species. The DOE, on the other hand, has unique experience in managing large projects, and its national laboratories are repositories of expertise in physics, engineering, and computer science, as well as the life sciences. The tools and techniques the project will ultimately rely on are thus likely to be developed in multidisciplinary efforts at laboratories like LBL. Accordingly, we at LBL take great pride in this enterprise -- an enterprise that will eventually transform our understanding of ourselves.

  20. Genome mapping

    USDA-ARS?s Scientific Manuscript database

    Genome maps can be thought of much like road maps except that, instead of traversing across land, they traverse across the chromosomes of an organism. Genetic markers serve as landmarks along the chromosome and provide researchers information as to how close they may be to a gene or region of inter...

  1. The Genomic CDS Sandbox: An Assessment Among Domain Experts

    PubMed Central

    Aziz, Ayesha; Kawamoto, Kensaku; Eilbeck, Karen; Williams, Marc S.; Freimuth, Robert R.; Hoffman, Mark A.; Rasmussen, Luke V.; Overby, Casey L.; Shirts, Brian H.; Hoffman, James M.; Welch, Brandon M.

    2016-01-01

    Genomics is a promising tool that is becoming more widely available to improve the care and treatment of individuals. While there is much assertion, genomics will most certainly require the use of clinical decision support (CDS) to be fully realized in the routine clinical setting. The National Human Genome Research Institute (NHGRI) of the National Institutes of Health recently convened an in-person, multi-day meeting on this topic. It was widely recognized that there is a need to promote the innovation and development of resources for genomic CDS such as a CDS sandbox. The purpose of this study was to evaluate a proposed approach for such a genomic CDS sandbox among domain experts and potential users. Survey results indicate a significant interest and desire for a genomic CDS sandbox environment among domain experts. These results will be used to guide the development of a genomic CDS sandbox. PMID:26778834

  2. A GSC Global Genome Census (GSC8 Meeting)

    ScienceCinema

    Kyrpides, Nikos [DOE JGI

    2016-07-12

    The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding "Research Coordination Network" from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. Nikos Kyrpides of the DOE Joint Genome Institute discusses the notion of a global genome census at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, Calif. on Sept. 9, 2009.

  3. A GSC Global Genome Census (GSC8 Meeting)

    SciTech Connect

    Kyrpides, Nikos

    2009-09-09

    The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding "Research Coordination Network" from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. Nikos Kyrpides of the DOE Joint Genome Institute discusses the notion of a global genome census at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, Calif. on Sept. 9, 2009.

  4. Genome Analyses and Supplement Data from the International Populus Genome Consortium (IPGC)

    DOE Data Explorer

    International Populus Genome Consortium (IPGC)

    The sequencing of the first tree genome, that of Populus, was a project initiated by the Office of Biological and Environmental Research in DOE’s Office of Science. The International Populus Genome Consortium (IPGC) was formed to help develop and guide post-sequence activities. The IPGC website, hosted at the Oak Ridge National Laboratory, provides draft sequence data as it is made available from DOE Joint Genome Institute, genome analyses for Populus, lists of related publications and resources, and the science plan. The data are available at http://www.ornl.gov/sci/ipgc/ssr_resource.htm.

  5. Swimmer-Training Institutions

    ERIC Educational Resources Information Center

    O'Donnell, R. W.

    1972-01-01

    This satirical essay proposes an institution of higher learning that would prepare students to become swimmers" and swimming instructors. Curriculum, teaching methods, student selection and evaluation are modelled on certain contemporary teacher-training institutes. (PD)

  6. Proteomics Data on UCSC Genome Browser - Office of Cancer Clinical Proteomics Research

    Cancer.gov

    The National Cancer Institute's Clinical Proteomic Tumor Analysis Consortium scientists are working together with the University of California, Santa Cruz (UCSC) Genomics Institute to provide public access to cancer proteomics data.

  7. Canadian institute honours Hawking

    NASA Astrophysics Data System (ADS)

    Durrani, Matin

    2009-11-01

    The Perimeter Institute for Theoretical Physics in Waterloo, Canada, has announced that a major new extension to its campus will be known as the Stephen Hawking Centre. The extension, which is currently being built, is due to open in 2011 and will double the size of the institute. It will also provide a home for the institute's Masters students, the first of whom joined the Perimeter Institute this autumn as part of its Perimeter Scholars international programme.

  8. Implementing Institutional Research Findings.

    ERIC Educational Resources Information Center

    Blai, Boris, Jr.

    Although many agree that institutional research in higher education has come of age and is accepted as a part of institutional management, great variations exist in the extent to which institutional research findings are synthesized and utilized in management decision-making. A number of reasons can be identified as accounting for this phenomenon,…

  9. Astronomical Institute of Athens

    NASA Astrophysics Data System (ADS)

    Murdin, P.

    2000-11-01

    The Astronomical Institute of Athens is the oldest research institute of modern Greece (it faces the Parthenon). The Astronomical Institute (AI) of the National Observatory of Athens (NOA) started its observational projects in 1847. The modern computer and research center are housed at the Penteli Astronomical Station with major projects and international collaborations focused on extragalactic ...

  10. Netherlands Maritime Institute

    ERIC Educational Resources Information Center

    Hoefsmit, R. G. A.

    1976-01-01

    Account of the aims and activities of the Netherlands Maritime Institute provided by the Secretary to the Institute's Board of Directors, The Institute's intent is "to promote maritime activities, including the shipbuilding-shipping relationship, in the broadest sense of the word." (Editor/RK)

  11. Herzberg Institute of Astrophysics

    NASA Astrophysics Data System (ADS)

    Murdin, P.

    2000-11-01

    The Herzberg Institute of Astrophysics (HIA) is the Institute within the NATIONAL RESEARCH COUNCIL of Canada responsible for providing astronomical facilities, and developing related instrumentation and software for Canadian researchers. The Institute was established in 1975, and now operates 1.8 m and 1.2 m optical telescopes at the DOMINION ASTROPHYSICAL OBSERVATORY close to Victoria, BC, as we...

  12. Personal genomics services: whose genomes?

    PubMed Central

    Gurwitz, David; Bregman-Eschet, Yael

    2009-01-01

    New companies offering personal whole-genome information services over the internet are dynamic and highly visible players in the personal genomics field. For fees currently ranging from US$399 to US$2500 and a vial of saliva, individuals can now purchase online access to their individual genetic information regarding susceptibility to a range of chronic diseases and phenotypic traits based on a genome-wide SNP scan. Most of the companies offering such services are based in the United States, but their clients may come from nearly anywhere in the world. Although the scientific validity, clinical utility and potential future implications of such services are being hotly debated, several ethical and regulatory questions related to direct-to-consumer (DTC) marketing strategies of genetic tests have not yet received sufficient attention. For example, how can we minimize the risk of unauthorized third parties from submitting other people's DNA for testing? Another pressing question concerns the ownership of (genotypic and phenotypic) information, as well as the unclear legal status of customers regarding their own personal information. Current legislation in the US and Europe falls short of providing clear answers to these questions. Until the regulation of personal genomics services catches up with the technology, we call upon commercial providers to self-regulate and coordinate their activities to minimize potential risks to individual privacy. We also point out some specific steps, along the trustee model, that providers of DTC personal genomics services as well as regulators and policy makers could consider for addressing some of the concerns raised below. PMID:19259127

  13. Mapping Hispanic-Serving Institutions: A Typology of Institutional Diversity

    ERIC Educational Resources Information Center

    Núñez, Anne-Marie; Crisp, Gloria; Elizondo, Diane

    2016-01-01

    Hispanic-Serving Institutions (HSIs), institutions that enroll at least 25% Hispanic students, are institutionally diverse, including a much wider array of institutional types than other Minority-Serving Institutions (MSIs). Furthermore, they have distinctive institutional characteristics from those typically emphasized in institutional typologies…

  14. Citrus Genomics

    PubMed Central

    Talon, Manuel; Gmitter Jr., Fred G.

    2008-01-01

    Citrus is one of the most widespread fruit crops globally, with great economic and health value. It is among the most difficult plants to improve through traditional breeding approaches. Currently, there is risk of devastation by diseases threatening to limit production and future availability to the human population. As technologies rapidly advance in genomic science, they are quickly adapted to address the biological challenges of the citrus plant system and the world's industries. The historical developments of linkage mapping, markers and breeding, EST projects, physical mapping, an international citrus genome sequencing project, and critical functional analysis are described. Despite the challenges of working with citrus, there has been substantial progress. Citrus researchers engaged in international collaborations provide optimism about future productivity and contributions to the benefit of citrus industries worldwide and to the human population who can rely on future widespread availability of this health-promoting and aesthetically pleasing fruit crop. PMID:18509486

  15. Imaging genomics.

    PubMed

    Hariri, Ahmad R; Weinberger, Daniel R

    2003-01-01

    The recent completion of a working draft of the human genome sequence promises to provide unprecedented opportunities to explore the genetic basis of individual differences in complex behaviours and vulnerability to neuropsychiatric illness. Functional neuroimaging, because of its unique ability to assay information processing at the level of brain within individuals, provides a powerful approach to such functional genomics. Recent fMRI studies have established important physiological links between functional genetic polymorphisms and robust differences in information processing within distinct brain regions and circuits that have been linked to the manifestation of various disease states such as Alzheimer's disease, schizophrenia and anxiety disorders. Importantly, all of these biological relationships have been revealed in relatively small samples of healthy volunteers and in the absence of observable differences at the level of behaviour, underscoring the power of a direct assay of brain physiology like fMRI in exploring the functional impact of genetic variation.

  16. Ancient genomics

    PubMed Central

    Der Sarkissian, Clio; Allentoft, Morten E.; Ávila-Arcos, María C.; Barnett, Ross; Campos, Paula F.; Cappellini, Enrico; Ermini, Luca; Fernández, Ruth; da Fonseca, Rute; Ginolhac, Aurélien; Hansen, Anders J.; Jónsson, Hákon; Korneliussen, Thorfinn; Margaryan, Ashot; Martin, Michael D.; Moreno-Mayar, J. Víctor; Raghavan, Maanasa; Rasmussen, Morten; Velasco, Marcela Sandoval; Schroeder, Hannes; Schubert, Mikkel; Seguin-Orlando, Andaine; Wales, Nathan; Gilbert, M. Thomas P.; Willerslev, Eske; Orlando, Ludovic

    2015-01-01

    The past decade has witnessed a revolution in ancient DNA (aDNA) research. Although the field's focus was previously limited to mitochondrial DNA and a few nuclear markers, whole genome sequences from the deep past can now be retrieved. This breakthrough is tightly connected to the massive sequence throughput of next generation sequencing platforms and the ability to target short and degraded DNA molecules. Many ancient specimens previously unsuitable for DNA analyses because of extensive degradation can now successfully be used as source materials. Additionally, the analytical power obtained by increasing the number of sequence reads to billions effectively means that contamination issues that have haunted aDNA research for decades, particularly in human studies, can now be efficiently and confidently quantified. At present, whole genomes have been sequenced from ancient anatomically modern humans, archaic hominins, ancient pathogens and megafaunal species. Those have revealed important functional and phenotypic information, as well as unexpected adaptation, migration and admixture patterns. As such, the field of aDNA has entered the new era of genomics and has provided valuable information when testing specific hypotheses related to the past. PMID:25487338

  17. Ancient genomics.

    PubMed

    Der Sarkissian, Clio; Allentoft, Morten E; Ávila-Arcos, María C; Barnett, Ross; Campos, Paula F; Cappellini, Enrico; Ermini, Luca; Fernández, Ruth; da Fonseca, Rute; Ginolhac, Aurélien; Hansen, Anders J; Jónsson, Hákon; Korneliussen, Thorfinn; Margaryan, Ashot; Martin, Michael D; Moreno-Mayar, J Víctor; Raghavan, Maanasa; Rasmussen, Morten; Velasco, Marcela Sandoval; Schroeder, Hannes; Schubert, Mikkel; Seguin-Orlando, Andaine; Wales, Nathan; Gilbert, M Thomas P; Willerslev, Eske; Orlando, Ludovic

    2015-01-19

    The past decade has witnessed a revolution in ancient DNA (aDNA) research. Although the field's focus was previously limited to mitochondrial DNA and a few nuclear markers, whole genome sequences from the deep past can now be retrieved. This breakthrough is tightly connected to the massive sequence throughput of next generation sequencing platforms and the ability to target short and degraded DNA molecules. Many ancient specimens previously unsuitable for DNA analyses because of extensive degradation can now successfully be used as source materials. Additionally, the analytical power obtained by increasing the number of sequence reads to billions effectively means that contamination issues that have haunted aDNA research for decades, particularly in human studies, can now be efficiently and confidently quantified. At present, whole genomes have been sequenced from ancient anatomically modern humans, archaic hominins, ancient pathogens and megafaunal species. Those have revealed important functional and phenotypic information, as well as unexpected adaptation, migration and admixture patterns. As such, the field of aDNA has entered the new era of genomics and has provided valuable information when testing specific hypotheses related to the past.

  18. Toward a Comprehensive Genomic Analysis of Cancer - TCGA

    Cancer.gov

    The National Cancer Institute (NCI) and National Human Genome Research Institute (NHGRI) convened a "Toward a Comprehensive Genomic Analysis of Cancer" workshop in Washington, D.C. This workshop brought together physicians, basic scientists and other members of the U.S. and international cancer communities to assist in outlining the most effective strategies for the development of a successful project. Information about this workshop is reported in the Executive Summary.

  19. GOLD: The Genomes Online Database

    DOE Data Explorer

    Kyrpides, Nikos; Liolios, Dinos; Chen, Amy; Tavernarakis, Nektarios; Hugenholtz, Philip; Markowitz, Victor; Bernal, Alex

    Since its inception in 1997, GOLD has continuously monitored genome sequencing projects worldwide and has provided the community with a unique centralized resource that integrates diverse information related to Archaea, Bacteria, Eukaryotic and more recently Metagenomic sequencing projects. As of September 2007, GOLD recorded 639 completed genome projects. These projects have their complete sequence deposited into the public archival sequence databases such as GenBank EMBL,and DDBJ. From the total of 639 complete and published genome projects as of 9/2007, 527 were bacterial, 47 were archaeal and 65 were eukaryotic. In addition to the complete projects, there were 2158 ongoing sequencing projects. 1328 of those were bacterial, 59 archaeal and 771 eukaryotic projects. Two types of metadata are provided by GOLD: (i) project metadata and (ii) organism/environment metadata. GOLD CARD pages for every project are available from the link of every GOLD_STAMP ID. The information in every one of these pages is organized into three tables: (a) Organism information, (b) Genome project information and (c) External links. [The Genomes On Line Database (GOLD) in 2007: Status of genomic and metagenomic projects and their associated metadata, Konstantinos Liolios, Konstantinos Mavromatis, Nektarios Tavernarakis and Nikos C. Kyrpides, Nucleic Acids Research Advance Access published online on November 2, 2007, Nucleic Acids Research, doi:10.1093/nar/gkm884]

    The basic tables in the GOLD database that can be browsed or searched include the following information:

    • Gold Stamp ID
    • Organism name
    • Domain
    • Links to information sources
    • Size and link to a map, when available
    • Chromosome number, Plas number, and GC content
    • A link for downloading the actual genome data
    • Institution that did the sequencing
    • Funding source
    • Database where information resides
    • Publication status and information

    • The Structural Genomics Consortium

      PubMed Central

      Jones, Molly Morgan; Castle-Clarke, Sophie; Brooker, Daniel; Nason, Edward; Huzair, Farah; Chataway, Joanna

      2014-01-01

      Abstract The Structural Genomics Consortium (SGC) supports drug discovery efforts through a unique, open access model of public-private collaboration. This study presents the results of an independent evaluation of the Structural Genomics Consortium, conducted by RAND Europe with the Institute on Governance. The evaluation aimed to establish the role of the SGC within the wider drug discovery and PPP landscape, assessing the merits of the SGC open access model relative to alternative models of funding R&D in this space, as well as the key trends and opportunities in the external environment that may impact on the future of the SGC. It also established the incentives and disincentives for investment, strengths and weaknesses of the SGC's model, and the opportunities and threats the SGC will face in the future. This enabled us to assess the most convincing arguments for funding the SGC at present; important trade-offs or limitations that should be addressed in moving towards the next funding phase; and whether funders are anticipating changes either to the SGC or the wider PPP landscape. Finally, we undertook a quantitative analysis to ascertain what judgements can be made about the SGC's past and current performance track record, before unpacking the role of the external environment and particular actors within the SGC in developing scenarios for the future. PMID:28560088

  1. Texas Heart Institute

    MedlinePlus

    ... Texas Heart Institute, The University of Texas Health Science Center at Houston, MD Anderson Cancer Center, and The University of Houston. Held most ... for Physicians Fellowships & Residencies School ...

  2. The human genome project: Past, present, and future

    SciTech Connect

    Watson, J.D. )

    1990-04-06

    This article presents a short discussion of the development of the human genome program in the United States, a summary of the current status of the organization and administration of the National Institutes of Health component of the program, and some prospects for the future directions of the program and the applications of genome information.

  3. Musings on genome medicine: the Obama effect redux.

    PubMed

    Nathan, David G; Orkin, Stuart H

    2009-09-11

    From the point of view of genome medicine, Barack Obama has made two vital policy decisions: he has chosen a new director of the National Institutes of Health, and his proposed change in United States healthcare policy will have profound effects on genome medicine and, indeed, all of academic medicine.

  4. Musings on genome medicine: the Obama effect redux

    PubMed Central

    2009-01-01

    From the point of view of genome medicine, Barack Obama has made two vital policy decisions: he has chosen a new director of the National Institutes of Health, and his proposed change in United States healthcare policy will have profound effects on genome medicine and, indeed, all of academic medicine. PMID:19769781

  5. Almost finished: the complete genome sequence of Mycosphaerella graminicola

    USDA-ARS?s Scientific Manuscript database

    Mycosphaerella graminicola causes septoria tritici blotch of wheat. An 8.9x shotgun sequence of bread wheat strain IPO323 was generated through the Community Sequencing Program of the U.S. Department of Energy’s Joint Genome Institute (JGI), and was finished at the Stanford Human Genome Center. The ...

  6. The Human Genome Project: Past, Present, and Future

    NASA Astrophysics Data System (ADS)

    Watson, James D.

    1990-04-01

    This article presents a short discussion of the development of the human genome program in the United States, a summary of the current status of the organization and administration of the National Institutes of Health component of the program, and some prospects for the future directions of the program and the applications of genome information.

  7. Brad Ozenberger, Ph.D., Presents the Achievements of The Cancer Genome Atlas During its Early Years - TCGA

    Cancer.gov

    Dr. Brad Ozenberger, former TCGA Program Director for the National Human Genome Research Institute, describes the goals and achievements of TCGA during its pilot phase, which involved the genomic characterization of brain, ovarian, and lung cancers.

  8. Complete Genome Sequence of Pigmentation Negative Yersinia Pestis strain Cadman Running head: Complete Genome Sequence of Y. pestis strain Cadman

    DTIC Science & Technology

    2016-10-27

    Institute of Infectious Diseases, Fort Detrick, Frederick, Maryland, USA 9 10 11 Running head: Complete Genome Sequence of Y. pestis strain Cadman...1 Complete Genome Sequence of Pigmentation Negative Yersinia pestis strain Cadman 1 2 3 Sean Lovetta, Kitty Chaseb, Galina Korolevaa, Gustavo...we report the genome sequence of Yersinia pestis strain Cadman, an attenuated strain 25 lacking the pgm locus. Y. pestis is the causative agent of

  9. Mining the genomes of exceptional responders.

    PubMed

    Chang, David K; Grimmond, Sean M; Evans, T R Jeffry; Biankin, Andrew V

    2014-05-01

    The National Cancer Institute of the United States recently announced a major new initiative in understanding the genomes or, more broadly, the molecular phenotypes of exceptional responders. What can we expect to learn from exceptional responders? What are the potential benefits, and how do we approach studying them?

  10. Engagement and Institutional Advancement

    ERIC Educational Resources Information Center

    Weerts, David; Hudson, Elizabeth

    2009-01-01

    Research suggests that institutional commitment to community engagement can be understood by examining levels of student, faculty, and community involvement in engagement; organizational structure, rewards, and campus publications supporting engagement; and compatibility of an institution's mission with this work (Holland, 1997). Underlying all of…

  11. Educational Institutions: Terminology. Turkey.

    ERIC Educational Resources Information Center

    Council for Cultural Cooperation, Strasbourg (France).

    Prepared from interviews with personnel of the Turkish Ministry of National Education, and other educational administrators in that country, this publication provides a guide to the terminology used to name the types of public educational institutions found in Turkey. Private educational institutions, military schools, higher schools attached to…

  12. Institutional Long Range Planning.

    ERIC Educational Resources Information Center

    Caldwell Community Coll. and Technical Inst., Lenoir, NC.

    Long-range institutional planning has been in effect at Caldwell Community College and Technical Institute since 1973. The first step in the process was the identification of planning areas: administration, organization, educational programs, learning resources, student services, faculty, facilities, maintenance/operation, and finances. The major…

  13. Educational Institutions: Terminology. Turkey.

    ERIC Educational Resources Information Center

    Council for Cultural Cooperation, Strasbourg (France).

    Prepared from interviews with personnel of the Turkish Ministry of National Education, and other educational administrators in that country, this publication provides a guide to the terminology used to name the types of public educational institutions found in Turkey. Private educational institutions, military schools, higher schools attached to…

  14. What Is Institutional Research?

    ERIC Educational Resources Information Center

    Lyons, Paul R.

    Institutional research (IR), defined as inquiry "directed toward data useful or necessary [for] intelligent decisions and/or for the successful maintenance, operation and/or improvement of a given collegiate institution," can be directly applied to soaring enrollment, greater administrative complexity, rising costs. The junior college…

  15. "Canterbury Tales" Institute.

    ERIC Educational Resources Information Center

    Ruud, Jay

    Northern State University (South Dakota) held a 4-week institute on Chaucer's "Canterbury Tales" for high school English teachers from South Dakota and four neighboring states (North Dakota, Minnesota, Iowa, and Nebraska) in summer 1989. The institute provided an opportunity for high school teachers inadequately trained in this area to…

  16. Institutionalism "Old" and "New."

    ERIC Educational Resources Information Center

    Selznick, Philip

    1996-01-01

    Explores the new institutionalism's ethos and direction. Drawing a sharp line between old and new inhibits the contribution of institutional theory to major issues of bureaucracy and social policy. Problems of accountability and responsiveness, public and private bureaucracy, regulation and self-regulation, and management and governance will…

  17. Institutional Inbreeding Reexamined.

    ERIC Educational Resources Information Center

    Wyer, Jean C.; Conrad, Clifton F.

    1984-01-01

    Data from the 1977 Survey of the American Professoriate were used to examine the relationship among institutional origin, productivity, and institutional rewards. When an adjustment was made for time allocation, inbred faculty were found to be more productive but are paid significantly less than noninbred faculty. (Author/BW)

  18. Guiding Institutional Change.

    ERIC Educational Resources Information Center

    Adams, Frank G.

    1997-01-01

    Looks at several ways that change comes about over which the institution has little or no control: by mandate, through legislation, or through the accreditation process. Offers the CAP method (Communication, Alternatives selection, and Participation) to guide the institution through the change process. (JOW)

  19. Astrophysical Institute, Potsdam

    NASA Astrophysics Data System (ADS)

    Murdin, P.

    2000-11-01

    Built upon a tradition of almost 300 years, the Astrophysical Institute Potsdam (AIP) is in an historical sense the successor of one of the oldest astronomical observatories in Germany. It is the first institute in the world which incorporated the term `astrophysical' in its name, and is connected with distinguished scientists such as Karl Schwarzschild and Albert Einstein. The AIP constitutes on...

  20. Problems with Institutional Surveys.

    ERIC Educational Resources Information Center

    Frey, James H.

    1979-01-01

    A survey done properly by accepted and scientifically justifiable techniques can provide information on behalf of the goals of institutional advancement in academe. Deficiencies in institutional research are seen as the result of the lack of guidance on survey design, questionnaire construction, or problem definition in education research texts.…

  1. Engagement and Institutional Advancement

    ERIC Educational Resources Information Center

    Weerts, David; Hudson, Elizabeth

    2009-01-01

    Research suggests that institutional commitment to community engagement can be understood by examining levels of student, faculty, and community involvement in engagement; organizational structure, rewards, and campus publications supporting engagement; and compatibility of an institution's mission with this work (Holland, 1997). Underlying all of…

  2. Dr. Marco Marra: Pioneer and Visionary in Cancer Genomics Research | Office of Cancer Genomics

    Cancer.gov

    Dr. Marco Marra is a highly distinguished genomics and bioinformatics researcher. He is the Director of Canada’s Michael Smith Genome Sciences Centre at the BC Cancer Agency and holds a faculty position at the University of British Columbia. The Centre is a state-of-the-art sequencing facility in Vancouver, Canada, with a major focus on the study of cancers.  Many of their research projects are undertaken in collaborations with other Canadian and international institutions.

  3. Whole Genome Sequencing

    MedlinePlus

    ... you want to learn. Search form Search Whole Genome Sequencing You are here Home Testing & Services Testing ... the full story, click here . What is whole genome sequencing? Whole genome sequencing is the mapping out ...

  4. The platypus genome unraveled.

    PubMed

    O'Brien, Stephen J

    2008-06-13

    The genome of the platypus has been sequenced, assembled, and annotated by an international genomics team. Like the animal itself the platypus genome contains an amalgam of mammal, reptile, and bird-like features.

  5. HGVA: the Human Genome Variation Archive

    PubMed Central

    Coll, Jacobo; Haimel, Matthias; Kandasamy, Swaathi; Tarraga, Joaquin; Furio-Tari, Pedro; Bari, Wasim; Bleda, Marta; Rueda, Antonio; Gräf, Stefan; Rendon, Augusto

    2017-01-01

    Abstract High-profile genomic variation projects like the 1000 Genomes project or the Exome Aggregation Consortium, are generating a wealth of human genomic variation knowledge which can be used as an essential reference for identifying disease-causing genotypes. However, accessing these data, contrasting the various studies and integrating those data in downstream analyses remains cumbersome. The Human Genome Variation Archive (HGVA) tackles these challenges and facilitates access to genomic data for key reference projects in a clean, fast and integrated fashion. HGVA provides an efficient and intuitive web-interface for easy data mining, a comprehensive RESTful API and client libraries in Python, Java and JavaScript for fast programmatic access to its knowledge base. HGVA calculates population frequencies for these projects and enriches their data with variant annotation provided by CellBase, a rich and fast annotation solution. HGVA serves as a proof-of-concept of the genome analysis developments being carried out by the University of Cambridge together with UK's 100 000 genomes project and the National Institute for Health Research BioResource Rare-Diseases, in particular, deploying open-source for Computational Biology (OpenCB) software platform for storing and analyzing massive genomic datasets. PMID:28535294

  6. Genome evolution: the dynamics of static genomes.

    PubMed

    Stechmann, Alexandra

    2004-06-22

    A random survey of a microsporidian genome has revealed some striking features. Although the genomes of microsporidians are among the smallest known for eukaryotes, their organisation appears to be well conserved.

  7. 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. Copyright © 2011 Elsevier Ltd. All rights reserved.

  8. Genomic selection requires genomic control of inbreeding.

    PubMed

    Sonesson, Anna K; Woolliams, John A; Meuwissen, Theo H E

    2012-08-16

    In the past, pedigree relationships were used to control and monitor inbreeding because genomic relationships among selection candidates were not available until recently. The aim of this study was to understand the consequences for genetic variability across the genome when genomic information is used to estimate breeding values and in managing the inbreeding generated in the course of selection on genome-enhanced estimated breeding values. These consequences were measured by genetic gain, pedigree- and genome-based rates of inbreeding, and local inbreeding across the genome. Breeding schemes were compared by simulating truncation selection or optimum contribution selection with a restriction on pedigree- or genome-based inbreeding, and with selection using estimated breeding values based on genome- or pedigree-based BLUP. Trait information was recorded on full-sibs of the candidates. When the information used to estimate breeding values and to constrain rates of inbreeding were either both pedigree-based or both genome-based, rates of genomic inbreeding were close to the desired values and the identical-by-descent profiles were reasonably uniform across the genome. However, with a pedigree-based inbreeding constraint and genome-based estimated breeding values, genomic rates of inbreeding were much higher than expected. With pedigree-instead of genome-based estimated breeding values, the impact of the largest QTL on the breeding values was much smaller, resulting in a more uniform genome-wide identical-by-descent profile but genomic rates of inbreeding were still higher than expected based on pedigree relationships, because they measure the inbreeding at a neutral locus not linked to any QTL. Neutral loci did not exist here, where there were 100 QTL on each chromosome. With a pedigree-based inbreeding constraint and genome-based estimated breeding values, genomic rates of inbreeding substantially exceeded the value of its constraint. In contrast, with a genome

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

    SciTech Connect

    Rokhsar, Daniel

    2008-02-11

    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.

  10. 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.

  11. Complete Genome Sequence of the Hyperthermophilic Sulfate-Reducing Bacterium Thermodesulfobacterium geofontis OPF15T.

    PubMed

    Elkins, James G; Hamilton-Brehm, Scott D; Lucas, Susan; Han, James; Lapidus, Alla; Cheng, Jan-Fang; Goodwin, Lynne A; Pitluck, Sam; Peters, Lin; Mikhailova, Natalia; Davenport, Karen W; Detter, John C; Han, Cliff S; Tapia, Roxanne; Land, Miriam L; Hauser, Loren; Kyrpides, Nikos C; Ivanova, Natalia N; Pagani, Ioanna; Bruce, David; Woyke, Tanja; Cottingham, Robert W

    2013-04-11

    Thermodesulfobacterium geofontis OPF15(T) (ATCC BAA-2454, JCM 18567) was isolated from Obsidian Pool, Yellowstone National Park, and grows optimally at 83°C. The 1.6-Mb genome sequence was finished at the Joint Genome Institute and has been deposited for future genomic studies pertaining to microbial processes and nutrient cycles in high-temperature environments.

  12. Complete Genome Sequence of the hyperthermophilic sulfate-reducing bacterium Thermodesulfobacterium geofontis OPF15T

    SciTech Connect

    Elkins, James G.; Hamilton-Brehm, Scott; Lucas, Susan; Han, James; Lapidus, Alla; Cheng, Jan-Fang; Goodwin, Lynne A.; Pitluck, Sam; Peters, Lin; Mikhailova, Natalia; Walston Davenport, Karen; Detter, John C.; Han, Cliff S.; Tapia, Roxanne; Land, Miriam L.; Hauser, Loren; Kyrpides, Nikos C.; Ivanova, Natalia N.; Pagani, Ioanna; Bruce, David; Woyke, Tanja; Cottingham, Robert W.

    2013-04-11

    Thermodesulfobacterium geofontis OPF15T was isolated from Obsidian Pool, Yellowstone National Park and grows optimally at 83 oC. The OPF15T genome was finished at the Joint Genome Institute and the 1.6 Mb sequence has been annotated and deposited for future genomic studies aimed at understanding microbial processes and nutrient cycles in high-temperature environments.

  13. A Review of the Accomplishments of the CTD² Network | Office of Cancer Genomics

    Cancer.gov

    The Office of Cancer Genomics (OCG) Cancer Target Discovery and Development or CTD2 initiative was established by the National Cancer Institute (NCI) to accelerate the “translation” of high-throughput, high-content genomic data to the bedside through functional genomics. The CTD2 initiative is a collaborative network of 13 different research teams, or Centers.

  14. Complete Genome Sequence of the Hyperthermophilic Sulfate-Reducing Bacterium Thermodesulfobacterium geofontis OPF15T

    PubMed Central

    Hamilton-Brehm, Scott D.; Lucas, Susan; Han, James; Lapidus, Alla; Cheng, Jan-Fang; Goodwin, Lynne A.; Pitluck, Sam; Peters, Lin; Mikhailova, Natalia; Davenport, Karen W.; Detter, John C.; Han, Cliff S.; Tapia, Roxanne; Land, Miriam L.; Hauser, Loren; Kyrpides, Nikos C.; Ivanova, Natalia N.; Pagani, Ioanna; Bruce, David; Woyke, Tanja; Cottingham, Robert W.

    2013-01-01

    Thermodesulfobacterium geofontis OPF15T (ATCC BAA-2454, JCM 18567) was isolated from Obsidian Pool, Yellowstone National Park, and grows optimally at 83°C. The 1.6-Mb genome sequence was finished at the Joint Genome Institute and has been deposited for future genomic studies pertaining to microbial processes and nutrient cycles in high-temperature environments. PMID:23580711

  15. Mapping and Sequencing the Human Genome: Science, Ethics, and Public Policy.

    ERIC Educational Resources Information Center

    Cutter, Mary Ann G.; Drexler, Edward; McCullough, Laurence B.; McInerney, Joseph D.; Murray, Jeffrey C.; Rossiter, Belinda; Zola, John

    The human genome project started in 1989 with the collaboration of the National Institutes of Health (NIH) and the U.S. Department of Energy (DOE). This document aims to develop an understanding among students of the human genome project and relevant issues. Topics include the science and technology of the human genome project, and the ethical and…

  16. Plant Genome Duplication Database.

    PubMed

    Lee, Tae-Ho; Kim, Junah; Robertson, Jon S; Paterson, Andrew H

    2017-01-01

    Genome duplication, widespread in flowering plants, is a driving force in evolution. Genome alignments between/within genomes facilitate identification of homologous regions and individual genes to investigate evolutionary consequences of genome duplication. PGDD (the Plant Genome Duplication Database), a public web service database, provides intra- or interplant genome alignment information. At present, PGDD contains information for 47 plants whose genome sequences have been released. Here, we describe methods for identification and estimation of dates of genome duplication and speciation by functions of PGDD.The database is freely available at http://chibba.agtec.uga.edu/duplication/.

  17. Ensembl genomes 2016: more genomes, more complexity

    USDA-ARS?s Scientific Manuscript database

    Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the context of the Ensembl project (http://www.ensembl.org). Together, the two resources provide a consistent...

  18. Ensembl Genomes 2016: more genomes, more complexity.

    PubMed

    Kersey, Paul Julian; Allen, James E; Armean, Irina; Boddu, Sanjay; Bolt, Bruce J; Carvalho-Silva, Denise; Christensen, Mikkel; Davis, Paul; Falin, Lee J; Grabmueller, Christoph; Humphrey, Jay; Kerhornou, Arnaud; Khobova, Julia; Aranganathan, Naveen K; Langridge, Nicholas; Lowy, Ernesto; McDowall, Mark D; Maheswari, Uma; Nuhn, Michael; Ong, Chuang Kee; Overduin, Bert; Paulini, Michael; Pedro, Helder; Perry, Emily; Spudich, Giulietta; Tapanari, Electra; Walts, Brandon; Williams, Gareth; Tello-Ruiz, Marcela; Stein, Joshua; Wei, Sharon; Ware, Doreen; Bolser, Daniel M; Howe, Kevin L; Kulesha, Eugene; Lawson, Daniel; Maslen, Gareth; Staines, Daniel M

    2016-01-04

    Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the context of the Ensembl project (http://www.ensembl.org). Together, the two resources provide a consistent set of programmatic and interactive interfaces to a rich range of data including reference sequence, gene models, transcriptional data, genetic variation and comparative analysis. This paper provides an update to the previous publications about the resource, with a focus on recent developments. These include the development of new analyses and views to represent polyploid genomes (of which bread wheat is the primary exemplar); and the continued up-scaling of the resource, which now includes over 23 000 bacterial genomes, 400 fungal genomes and 100 protist genomes, in addition to 55 genomes from invertebrate metazoa and 39 genomes from plants. This dramatic increase in the number of included genomes is one part of a broader effort to automate the integration of archival data (genome sequence, but also associated RNA sequence data and variant calls) within the context of reference genomes and make it available through the Ensembl user interfaces.

  19. Ensembl Genomes 2016: more genomes, more complexity

    PubMed Central

    Kersey, Paul Julian; Allen, James E.; Armean, Irina; Boddu, Sanjay; Bolt, Bruce J.; Carvalho-Silva, Denise; Christensen, Mikkel; Davis, Paul; Falin, Lee J.; Grabmueller, Christoph; Humphrey, Jay; Kerhornou, Arnaud; Khobova, Julia; Aranganathan, Naveen K.; Langridge, Nicholas; Lowy, Ernesto; McDowall, Mark D.; Maheswari, Uma; Nuhn, Michael; Ong, Chuang Kee; Overduin, Bert; Paulini, Michael; Pedro, Helder; Perry, Emily; Spudich, Giulietta; Tapanari, Electra; Walts, Brandon; Williams, Gareth; Tello–Ruiz, Marcela; Stein, Joshua; Wei, Sharon; Ware, Doreen; Bolser, Daniel M.; Howe, Kevin L.; Kulesha, Eugene; Lawson, Daniel; Maslen, Gareth; Staines, Daniel M.

    2016-01-01

    Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the context of the Ensembl project (http://www.ensembl.org). Together, the two resources provide a consistent set of programmatic and interactive interfaces to a rich range of data including reference sequence, gene models, transcriptional data, genetic variation and comparative analysis. This paper provides an update to the previous publications about the resource, with a focus on recent developments. These include the development of new analyses and views to represent polyploid genomes (of which bread wheat is the primary exemplar); and the continued up-scaling of the resource, which now includes over 23 000 bacterial genomes, 400 fungal genomes and 100 protist genomes, in addition to 55 genomes from invertebrate metazoa and 39 genomes from plants. This dramatic increase in the number of included genomes is one part of a broader effort to automate the integration of archival data (genome sequence, but also associated RNA sequence data and variant calls) within the context of reference genomes and make it available through the Ensembl user interfaces. PMID:26578574

  20. The Precise - and Wild - Genomics Revolution: Genomics Provides Novel Treatments for Disease and Is Opening New Frontiers for Precision Medicine.

    PubMed

    Campbell, Sarah

    2016-01-01

    In the epic endeavor to sequence the human genome, it was as though the size of the equipment and amount of effort required were inversely proportional to the microscopic materials being parsed (Figure 1). "Imagine thousands of people, many laboratories … hundreds, hundreds, hundreds of these machines just to generate that first human genome sequence over a six to eight year period," says Dr. Eric Green, director of the National Human Genome Research Institute (NHGRI) at the National Institutes of Health (NIH) (Figure 2).

  1. Energy and institution size

    PubMed Central

    2017-01-01

    Why do institutions grow? Despite nearly a century of scientific effort, there remains little consensus on this topic. This paper offers a new approach that focuses on energy consumption. A systematic relation exists between institution size and energy consumption per capita: as energy consumption increases, institutions become larger. I hypothesize that this relation results from the interplay between technological scale and human biological limitations. I also show how a simple stochastic model can be used to link energy consumption with firm dynamics. PMID:28178339

  2. 10. international mouse genome conference

    SciTech Connect

    Meisler, M.H.

    1996-12-31

    Ten years after hosting the First International Mammalian Genome Conference in Paris in 1986, Dr. Jean-Louis Guenet presided over the Tenth Conference at the Pasteur Institute, October 7--10, 1996. The 1986 conference was a satellite to the Human Gene Mapping Workshop and had approximately 50 attendees. The 1996 meeting was attended by 300 scientists from around the world. In the interim, the number of mapped loci in the mouse increased from 1,000 to over 20,000. This report contains a listing of the program and its participants, and two articles that review the meeting and the role of the laboratory mouse in the Human Genome project. More than 200 papers were presented at the conference covering the following topics: International mouse chromosome committee meetings; Mutant generation and identification; Physical and genetic maps; New technology and resources; Chromatin structure and gene regulation; Rate and hamster genetic maps; Informatics and databases; and Quantitative trait analysis.

  3. Methods of Genomic Competency Integration in Practice

    PubMed Central

    Jenkins, Jean; Calzone, Kathleen A.; Caskey, Sarah; Culp, Stacey; Weiner, Marsha; Badzek, Laurie

    2015-01-01

    Purpose Genomics is increasingly relevant to health care, necessitating support for nurses to incorporate genomic competencies into practice. The primary aim of this project was to develop, implement, and evaluate a year-long genomic education intervention that trained, supported, and supervised institutional administrator and educator champion dyads to increase nursing capacity to integrate genomics through assessments of program satisfaction and institutional achieved outcomes. Design Longitudinal study of 23 Magnet Recognition Program® Hospitals (21 intervention, 2 controls) participating in a 1-year new competency integration effort aimed at increasing genomic nursing competency and overcoming barriers to genomics integration in practice. Methods Champion dyads underwent genomic training consisting of one in-person kick-off training meeting followed by monthly education webinars. Champion dyads designed institution-specific action plans detailing objectives, methods or strategies used to engage and educate nursing staff, timeline for implementation, and outcomes achieved. Action plans focused on a minimum of seven genomic priority areas: champion dyad personal development; practice assessment; policy content assessment; staff knowledge needs assessment; staff development; plans for integration; and anticipated obstacles and challenges. Action plans were updated quarterly, outlining progress made as well as inclusion of new methods or strategies. Progress was validated through virtual site visits with the champion dyads and chief nursing officers. Descriptive data were collected on all strategies or methods utilized, and timeline for achievement. Descriptive data were analyzed using content analysis. Findings The complexity of the competency content and the uniqueness of social systems and infrastructure resulted in a significant variation of champion dyad interventions. Conclusions Nursing champions can facilitate change in genomic nursing capacity through

  4. Critical Materials Institute

    ScienceCinema

    Alex King

    2016-07-12

    Ames Laboratory Director Alex King talks about the goals of the Critical Materials Institute in diversifying the supply of critical materials, developing substitute materials, developing tools and techniques for recycling critical materials, and forecasting materials needs to avoid future shortages.

  5. Minority Innovation Challenges Institute

    NASA Image and Video Library

    Do you want to learn more about how to compete in NASA’s technical challenges for both prestige and significant cash prizes? NASA’s Minority Innovation Challenges Institute trains and mentors mino...

  6. Institutionally based videoconferencing.

    PubMed

    Caudill, Robert Lee; Sager, Zachary

    2015-01-01

    The delivery of psychiatric care via video-teleconferencing (VTC) technology is thought to have reached a tipping point. As a medical speciality with relatively few material or technical requirements for service delivery, psychiatry has been one of the earliest to embrace the possibility of providing evaluations and treatment at a distance. Such technical infrastructure as is necessary can often be found in the institutions already in existence. It was natural therefore that institutionally based telepsychiatry would lay the foundation for the development of the field. In this article we review the history and development of institutional VTC in a wide variety of clinically supervised settings such as hospitals, outpatient clinics, and forensic settings. We cite evidence supporting institutionally sponsored use and expand on key takeaways for the development and expansion of videoconferencing in these settings. We also speculate on the future direction and development of psychiatric care provided by these arrangements.

  7. Critical Materials Institute

    SciTech Connect

    Alex King

    2013-01-09

    Ames Laboratory Director Alex King talks about the goals of the Critical Materials Institute in diversifying the supply of critical materials, developing substitute materials, developing tools and techniques for recycling critical materials, and forecasting materials needs to avoid future shortages.

  8. Institutional Transformation Model

    SciTech Connect

    2015-10-19

    Reducing the energy consumption of large institutions with dozens to hundreds of existing buildings while maintaining and improving existing infrastructure is a critical economic and environmental challenge. SNL's Institutional Transformation (IX) work integrates facilities and infrastructure sustainability technology capabilities and collaborative decision support modeling approaches to help facilities managers at Sandia National Laboratories (SNL) simulate different future energy reduction strategies and meet long term energy conservation goals.

  9. Great Lakes Energy Institute

    SciTech Connect

    Alexander, J. Iwan

    2012-11-18

    The vision of the Great Lakes Energy Institute is to enable the transition to advanced, sustainable energy generation, storage, distribution and utilization through coordinated research, development, and education. The Institute will place emphasis on translating leading edge research into next generation energy technology. The Institute’s research thrusts focus on coordinated research in decentralized power generation devices (e.g. fuel cells, wind turbines, solar photovoltaic devices), management of electrical power transmission and distribution, energy storage, and energy efficiency.

  10. National Cancer Institute Perspectives

    SciTech Connect

    Wong, Rosemary S.L. . E-mail: rw26f@nih.gov; Brechbiel, Martin W.

    2006-10-01

    The National Cancer Institute (NCI) Perspectives this year presented information on the systemic targeted radionuclide therapy (STaRT) research projects: (1) being investigated at the NCI's Intramural Center for Cancer Research; (2) funded by NCI's Radiation Research Program and other extramural programs; and (3) the appropriate National Institutes of Health/NCI funding mechanisms applicable to researchers for obtaining funds for STaRT projects.

  11. Funding Opportunity: Genomic Data Centers

    Cancer.gov

    Funding Opportunity CCG, Funding Opportunity Center for Cancer Genomics, CCG, Center for Cancer Genomics, CCG RFA, Center for cancer genomics rfa, genomic data analysis network, genomic data analysis network centers,

  12. Ontology for Genome Comparison and Genomic Rearrangements

    PubMed Central

    Flanagan, Keith; Stevens, Robert; Pocock, Matthew; Lee, Pete

    2004-01-01

    We present an ontology for describing genomes, genome comparisons, their evolution and biological function. This ontology will support the development of novel genome comparison algorithms and aid the community in discussing genomic evolution. It provides a framework for communication about comparative genomics, and a basis upon which further automated analysis can be built. The nomenclature defined by the ontology will foster clearer communication between biologists, and also standardize terms used by data publishers in the results of analysis programs. The overriding aim of this ontology is the facilitation of consistent annotation of genomes through computational methods, rather than human annotators. To this end, the ontology includes definitions that support computer analysis and automated transfer of annotations between genomes, rather than relying upon human mediation. PMID:18629137

  13. 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. © 2015 Hilton and Gersbach; Published by Cold Spring Harbor Laboratory Press.

  14. 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

  15. Implementing genomic medicine in the clinic: the future is here

    PubMed Central

    Manolio, Teri A.; Chisholm, Rex L.; Ozenberger, Brad; Roden, Dan M.; Williams, Marc S.; Wilson, Richard; Bick, David; Bottinger, Erwin P.; Brilliant, Murray H.; Eng, Charis; Frazer, Kelly A.; Korf, Bruce; Ledbetter, David H.; Lupski, James R.; Marsh, Clay; Mrazek, David; Murray, Michael F.; O'Donnell, Peter H.; Rader, Daniel J.; Relling, Mary V.; Shuldiner, Alan R.; Valle, David; Weinshilboum, Richard; Green, Eric D.; Ginsburg, Geoffrey S.

    2013-01-01

    Although the potential for genomics to contribute to clinical care has long been anticipated, the pace of defining the risks and benefits of incorporating genomic findings into medical practice has been relatively slow. Several institutions have recently begun genomic medicine programs, encountering many of the same obstacles and developing the same solutions, often independently. Recognizing that successful early experiences can inform subsequent efforts, the National Human Genome Research Institute brought together a number of these groups to describe their ongoing projects and challenges, identify common infrastructure and research needs, and outline an implementation framework for investigating and introducing similar programs elsewhere. Chief among the challenges were limited evidence and consensus on which genomic variants were medically relevant; lack of reimbursement for genomically driven interventions; and burden to patients and clinicians of assaying, reporting, intervening, and following up genomic findings. Key infrastructure needs included an openly accessible knowledge base capturing sequence variants and their phenotypic associations and a framework for defining and cataloging clinically actionable variants. Multiple institutions are actively engaged in using genomic information in clinical care. Much of this work is being done in isolation and would benefit from more structured collaboration and sharing of best practices. Genet Med 2013:15(4):258–267 PMID:23306799

  16. Breaking down institutional barriers: Undergraduate institutions

    SciTech Connect

    Morrison, C.

    1995-12-31

    This paper assesses the knowledge base on the undergraduate years, and the critical transition to graduate school or the workplace. The paper addresses the overarching issues associated with the institutional climate of undergraduate colleges and the transition on to the next step. What are the particular dynamics of retaining students in SM&E? How do these differ for various ethnic groups and by discipline? What has been the impact on minority students of curriculum reform and attempts to improve the quality of undergraduate instruction in the sciences and mathematics (especially among the gatekeeper courses)? Do present curriculum reforms and teaching practices reflect what is known about different learning styles of students from different ethnic backgrounds? What do we know about the attitudes and practices of college faculty in mentoring minority students in science and math courses? Has mentoring been a factor for change in campus climate? What do we know about higher education interventions, and why have these programs been more successful in engineering than in science? Can interventions change negative campus climates, or become a precipitating factor institutional change?

  17. Navigating yeast genome maintenance with functional genomics.

    PubMed

    Measday, Vivien; Stirling, Peter C

    2016-03-01

    Maintenance of genome integrity is a fundamental requirement of all organisms. To address this, organisms have evolved extremely faithful modes of replication, DNA repair and chromosome segregation to combat the deleterious effects of an unstable genome. Nonetheless, a small amount of genome instability is the driver of evolutionary change and adaptation, and thus a low level of instability is permitted in populations. While defects in genome maintenance almost invariably reduce fitness in the short term, they can create an environment where beneficial mutations are more likely to occur. The importance of this fact is clearest in the development of human cancer, where genome instability is a well-established enabling characteristic of carcinogenesis. This raises the crucial question: what are the cellular pathways that promote genome maintenance and what are their mechanisms? Work in model organisms, in particular the yeast Saccharomyces cerevisiae, has provided the global foundations of genome maintenance mechanisms in eukaryotes. The development of pioneering genomic tools inS. cerevisiae, such as the systematic creation of mutants in all nonessential and essential genes, has enabled whole-genome approaches to identifying genes with roles in genome maintenance. Here, we review the extensive whole-genome approaches taken in yeast, with an emphasis on functional genomic screens, to understand the genetic basis of genome instability, highlighting a range of genetic and cytological screening modalities. By revealing the biological pathways and processes regulating genome integrity, these analyses contribute to the systems-level map of the yeast cell and inform studies of human disease, especially cancer. © The Author 2015. Published by Oxford University Press. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  18. Culex genome is not just another genome for comparative genomics.

    PubMed

    Reddy, B P Niranjan; Labbé, Pierrick; Corbel, Vincent

    2012-03-30

    Formal publication of the Culex genome sequence has closed the human disease vector triangle by meeting the Anopheles gambiae and Aedes aegypti genome sequences. Compared to these other mosquitoes, Culex quinquefasciatus possesses many specific hallmark characteristics, and may thus provide different angles for research which ultimately leads to a practical solution for controlling the ever increasing burden of insect-vector-borne diseases around the globe. We argue the special importance of the cosmopolitan species- Culex genome sequence by invoking many interesting questions and the possible of potential of the Culex genome to answer those.

  19. Culex genome is not just another genome for comparative genomics

    PubMed Central

    2012-01-01

    Formal publication of the Culex genome sequence has closed the human disease vector triangle by meeting the Anopheles gambiae and Aedes aegypti genome sequences. Compared to these other mosquitoes, Culex quinquefasciatus possesses many specific hallmark characteristics, and may thus provide different angles for research which ultimately leads to a practical solution for controlling the ever increasing burden of insect-vector-borne diseases around the globe. We argue the special importance of the cosmopolitan species- Culex genome sequence by invoking many interesting questions and the possible of potential of the Culex genome to answer those. PMID:22463777

  20. GenomeFingerprinter: the genome fingerprint and the universal genome fingerprint analysis for systematic comparative genomics.

    PubMed

    Ai, Yuncan; Ai, Hannan; Meng, Fanmei; Zhao, Lei

    2013-01-01

    No attention has been paid on comparing a set of genome sequences crossing genetic components and biological categories with far divergence over large size range. We define it as the systematic comparative genomics and aim to develop the methodology. First, we create a method, GenomeFingerprinter, to unambiguously produce a set of three-dimensional coordinates from a sequence, followed by one three-dimensional plot and six two-dimensional trajectory projections, to illustrate the genome fingerprint of a given genome sequence. Second, we develop a set of concepts and tools, and thereby establish a method called the universal genome fingerprint analysis (UGFA). Particularly, we define the total genetic component configuration (TGCC) (including chromosome, plasmid, and phage) for describing a strain as a systematic unit, the universal genome fingerprint map (UGFM) of TGCC for differentiating strains as a universal system, and the systematic comparative genomics (SCG) for comparing a set of genomes crossing genetic components and biological categories. Third, we construct a method of quantitative analysis to compare two genomes by using the outcome dataset of genome fingerprint analysis. Specifically, we define the geometric center and its geometric mean for a given genome fingerprint map, followed by the Euclidean distance, the differentiate rate, and the weighted differentiate rate to quantitatively describe the difference between two genomes of comparison. Moreover, we demonstrate the applications through case studies on various genome sequences, giving tremendous insights into the critical issues in microbial genomics and taxonomy. We have created a method, GenomeFingerprinter, for rapidly computing, geometrically visualizing, intuitively comparing a set of genomes at genome fingerprint level, and hence established a method called the universal genome fingerprint analysis, as well as developed a method of quantitative analysis of the outcome dataset. These have set

  1. GenomeFingerprinter: The Genome Fingerprint and the Universal Genome Fingerprint Analysis for Systematic Comparative Genomics

    PubMed Central

    Ai, Yuncan; Ai, Hannan; Meng, Fanmei; Zhao, Lei

    2013-01-01

    Background No attention has been paid on comparing a set of genome sequences crossing genetic components and biological categories with far divergence over large size range. We define it as the systematic comparative genomics and aim to develop the methodology. Results First, we create a method, GenomeFingerprinter, to unambiguously produce a set of three-dimensional coordinates from a sequence, followed by one three-dimensional plot and six two-dimensional trajectory projections, to illustrate the genome fingerprint of a given genome sequence. Second, we develop a set of concepts and tools, and thereby establish a method called the universal genome fingerprint analysis (UGFA). Particularly, we define the total genetic component configuration (TGCC) (including chromosome, plasmid, and phage) for describing a strain as a systematic unit, the universal genome fingerprint map (UGFM) of TGCC for differentiating strains as a universal system, and the systematic comparative genomics (SCG) for comparing a set of genomes crossing genetic components and biological categories. Third, we construct a method of quantitative analysis to compare two genomes by using the outcome dataset of genome fingerprint analysis. Specifically, we define the geometric center and its geometric mean for a given genome fingerprint map, followed by the Euclidean distance, the differentiate rate, and the weighted differentiate rate to quantitatively describe the difference between two genomes of comparison. Moreover, we demonstrate the applications through case studies on various genome sequences, giving tremendous insights into the critical issues in microbial genomics and taxonomy. Conclusions We have created a method, GenomeFingerprinter, for rapidly computing, geometrically visualizing, intuitively comparing a set of genomes at genome fingerprint level, and hence established a method called the universal genome fingerprint analysis, as well as developed a method of quantitative analysis of the

  2. Exploring Other Genomes: Bacteria.

    ERIC Educational Resources Information Center

    Flannery, Maura C.

    2001-01-01

    Points out the importance of genomes other than the human genome project and provides information on the identified bacterial genomes Pseudomonas aeuroginosa, Leprosy, Cholera, Meningitis, Tuberculosis, Bubonic Plague, and plant pathogens. Considers the computer's use in genome studies. (Contains 14 references.) (YDS)

  3. Exploring Other Genomes: Bacteria.

    ERIC Educational Resources Information Center

    Flannery, Maura C.

    2001-01-01

    Points out the importance of genomes other than the human genome project and provides information on the identified bacterial genomes Pseudomonas aeuroginosa, Leprosy, Cholera, Meningitis, Tuberculosis, Bubonic Plague, and plant pathogens. Considers the computer's use in genome studies. (Contains 14 references.) (YDS)

  4. The complete genome sequence of a dog: a perspective.

    PubMed

    Lee, Soohyun; Kasif, Simon

    2006-06-01

    A complete, high-quality reference sequence of a dog genome was recently produced by a team of researchers led by the Broad Institute, achieving another major milestone in deciphering the genomic landscape of mammalian organisms. The genome sequence provides an indispensable resource for comparative analysis and novel insights into dog and human evolution and history. Together with the survey sequence of a poodle previously published in 2003, the two dog genome sequences allowed identification of more than 2.5 million single nucleotide polymorphisms within and between dog breeds, which can be used in evolutionary analysis, behavioral studies and disease gene mapping.(1)

  5. Complete genome sequence of Methanoculleus marisnigri type strain JR1

    SciTech Connect

    Anderson, Iain; Sieprawska-Lupa, Magdalena; Goltsman, Eugene; Lapidus, Alla L.; Copeland, A; Glavina Del Rio, Tijana; Tice, Hope; Dalin, Eileen; Barry, Kerrie; Saunders, Elizabeth H; Han, Cliff; Brettin, Tom; Detter, J. Chris; Bruce, David; Mikhailova, Natalia; Pitluck, Sam; Hauser, Loren John; Land, Miriam L; Lucas, Susan; Richardson, P M; Whitman, W. B.; Kyrpides, Nikos C

    2009-01-01

    Methanoculleus marisnigri Romesser et al. 1981 is a methanogen belonging to the order Methanomicrobiales within the archaeal phylum Euryarchaeota. The type strain, JR1, was isolated from anoxic sediments of the Black Sea. M. marisnigri is of phylogenetic interest because at the time the sequencing project began only one genome had previously been sequenced from the order Methanomicrobiales. We report here the complete genome sequence of M. marisnigri type strain JR1 and its annotation. This is part of a Joint Genome Institute 2006 Community Sequencing Program to sequence genomes of diverse Archaea.

  6. Complete genome sequence of Methanocorpusculum labreanum type strain Z

    SciTech Connect

    Anderson, Iain; Sieprawska-Lupa, Magdalena; Goltsman, Eugene; Lapidus, Alla L.; Copeland, A; Glavina Del Rio, Tijana; Tice, Hope; Dalin, Eileen; Barry, Kerrie; Pitluck, Sam; Hauser, Loren John; Land, Miriam L; Lucas, Susan; Richardson, P M; Whitman, W. B.; Kyrpides, Nikos C

    2009-01-01

    Methanocorpusculum labreanum is a methanogen belonging to the order Methanomicrobiales within the archaeal phylum Euryarchaeota. The type strain Z was isolated from surface sediments of Tar Pit Lake in the La Brea Tar Pits in Los Angeles, California. M. labreanum is of phylogenetic interest because at the time the sequencing project began only one genome had previously been sequenced from the order Methanomicrobiales. We report here the complete genome sequence of M. labreanum type strain Z and its annotation. This is part of a 2006 Joint Genome Institute Community Sequencing Program project to sequence genomes of diverse Archaea.

  7. Genome empowerment for the Puerto Rican parrot – Amazona vittata

    PubMed Central

    2012-01-01

    A unique community-funded project in Puerto Rico has launched whole-genome sequencing of the critically endangered Puerto Rican Parrot (Amazona vittata), with interpretation by genome bioinformaticians and students, and deposition into public online databases. This is the first article that focuses on the whole genome of a parrot species, one endemic to the USA and recently threatened with extinction. It provides invaluable conservation tools and a vivid example of hopeful prospects for future genome assessment of so many new species. It also demonstrates inventive ways for smaller institutions to contribute to a field largely considered the domain of large sequencing centers. PMID:23587407

  8. The human genome project and international health

    SciTech Connect

    Watson, J.D.; Cook-Deegan, R.M. )

    1990-06-27

    The human genome project is designed to provide common resources for the study of human genetics, and to assist biomedical researchers in their assault on disease. The main benefit will be to provide several kinds of maps of the human genome, and those of other organisms, to permit rapid isolation of genes for further study about DNA structure and function. This article describes genome research programs in developed and developing countries, and the international efforts that have contributed to genome research programs. For example, the large-scale collaborations to study Duchenne's muscular dystrophy, Huntington's disease, Alzheimer's disease, cystic fibrosis involve collaborators from many nations and families spread throughout the world. In the USA, the US Department of Energy was first to start a dedicated genome research program in 1987. Since then, another major government program has begun at the National Center for Human Genome Research of the National Institutes of Health. Italy, China, Australia, France, Canada, and Japan have genome research programs also.

  9. Exploiting the Genome

    DTIC Science & Technology

    1998-09-11

    complete human genome sequence . 14. SUBJECT TERMS 15. NUMBER OF PAGES 16. PRICE CODE 17. SECURITY CLASSIFICATION OF REPORT Unclassified 18. SECURITY...goal of the project is to ob- tain the complete sequence of the human genome by the year 2005. The genome contains approximately 3.3 Gb (billion base...and second, to consider possible roles for the DOE in the "post- genomic " era, following acquisition of the complete human genome

  10. The kangaroo genome

    PubMed Central

    Wakefield, Matthew J.; Graves, Jennifer A. Marshall

    2003-01-01

    The kangaroo genome is a rich and unique resource for comparative genomics. Marsupial genetics and cytology have made significant contributions to the understanding of gene function and evolution, and increasing the availability of kangaroo DNA sequence information would provide these benefits on a genomic scale. Here we summarize the contributions from cytogenetic and genetic studies of marsupials, describe the genomic resources currently available and those being developed, and explore the benefits of a kangaroo genome project. PMID:12612602

  11. Genome Maps, a new generation genome browser

    PubMed Central

    Medina, Ignacio; Salavert, Francisco; Sanchez, Rubén; de Maria, Alejandro; Alonso, Roberto; Escobar, Pablo; Bleda, Marta; Dopazo, Joaquín

    2013-01-01

    Genome browsers have gained importance as more genomes and related genomic information become available. However, the increase of information brought about by new generation sequencing technologies is, at the same time, causing a subtle but continuous decrease in the efficiency of conventional genome browsers. Here, we present Genome Maps, a genome browser that implements an innovative model of data transfer and management. The program uses highly efficient technologies from the new HTML5 standard, such as scalable vector graphics, that optimize workloads at both server and client sides and ensure future scalability. Thus, data management and representation are entirely carried out by the browser, without the need of any Java Applet, Flash or other plug-in technology installation. Relevant biological data on genes, transcripts, exons, regulatory features, single-nucleotide polymorphisms, karyotype and so forth, are imported from web services and are available as tracks. In addition, several DAS servers are already included in Genome Maps. As a novelty, this web-based genome browser allows the local upload of huge genomic data files (e.g. VCF or BAM) that can be dynamically visualized in real time at the client side, thus facilitating the management of medical data affected by privacy restrictions. Finally, Genome Maps can easily be integrated in any web application by including only a few lines of code. Genome Maps is an open source collaborative initiative available in the GitHub repository (https://github.com/compbio-bigdata-viz/genome-maps). Genome Maps is available at: http://www.genomemaps.org. PMID:23748955

  12. Genome Maps, a new generation genome browser.

    PubMed

    Medina, Ignacio; Salavert, Francisco; Sanchez, Rubén; de Maria, Alejandro; Alonso, Roberto; Escobar, Pablo; Bleda, Marta; Dopazo, Joaquín

    2013-07-01

    Genome browsers have gained importance as more genomes and related genomic information become available. However, the increase of information brought about by new generation sequencing technologies is, at the same time, causing a subtle but continuous decrease in the efficiency of conventional genome browsers. Here, we present Genome Maps, a genome browser that implements an innovative model of data transfer and management. The program uses highly efficient technologies from the new HTML5 standard, such as scalable vector graphics, that optimize workloads at both server and client sides and ensure future scalability. Thus, data management and representation are entirely carried out by the browser, without the need of any Java Applet, Flash or other plug-in technology installation. Relevant biological data on genes, transcripts, exons, regulatory features, single-nucleotide polymorphisms, karyotype and so forth, are imported from web services and are available as tracks. In addition, several DAS servers are already included in Genome Maps. As a novelty, this web-based genome browser allows the local upload of huge genomic data files (e.g. VCF or BAM) that can be dynamically visualized in real time at the client side, thus facilitating the management of medical data affected by privacy restrictions. Finally, Genome Maps can easily be integrated in any web application by including only a few lines of code. Genome Maps is an open source collaborative initiative available in the GitHub repository (https://github.com/compbio-bigdata-viz/genome-maps). Genome Maps is available at: http://www.genomemaps.org.

  13. Defining Genome Project Standards in a New Era of Sequencing (GSC8 Meeting)

    ScienceCinema

    Chain, Patrick [DOE JGI

    2016-07-12

    The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding "Research Coordination Network" from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego.

  14. Building international genomics collaboration for global health security

    DOE PAGES

    Cui, Helen H.; Erkkila, Tracy; Chain, Patrick S. G.; ...

    2015-12-07

    Genome science and technologies are transforming life sciences globally in many ways and becoming a highly desirable area for international collaboration to strengthen global health. The Genome Science Program at the Los Alamos National Laboratory is leveraging a long history of expertise in genomics research to assist multiple partner nations in advancing their genomics and bioinformatics capabilities. The capability development objectives focus on providing a molecular genomics-based scientific approach for pathogen detection, characterization, and biosurveillance applications. The general approaches include introduction of basic principles in genomics technologies, training on laboratory methodologies and bioinformatic analysis of resulting data, procurement, and installationmore » of next-generation sequencing instruments, establishing bioinformatics software capabilities, and exploring collaborative applications of the genomics capabilities in public health. Genome centers have been established with public health and research institutions in the Republic of Georgia, Kingdom of Jordan, Uganda, and Gabon; broader collaborations in genomics applications have also been developed with research institutions in many other countries.« less

  15. Institutional Policy and Its Abuses

    ERIC Educational Resources Information Center

    Bogue, E. G.; Riggs, R. O.

    1974-01-01

    Reviews the role of institutional policy, cites frequent abuses of institutional policy, and delineates several principles of policy management (development, communication, execution and evaluation). (Author/PG)

  16. The integrated microbial genomes (IMG) system in 2007: datacontent and analysis tool extensions

    SciTech Connect

    Markowitz, Victor M.; Szeto, Ernest; Palaniappan, Krishna; Grechkin, Yuri; Chu, Ken; Chen, I-Min A.; Dubchak, Inna; Anderson, Iain; Lykidis, Athanasios; Mavromatis, Konstantinos; Ivanova, Natalia N.; Kyrpides, Nikos C.

    2007-08-01

    The Integrated Microbial Genomes (IMG) system is a data management, analysis and annotation platform for all publicly available genomes. IMG contains both draft and complete JGI microbial genomes integrated with all other publicly available genomes from all three domains of life, together with a large number of plasmids and viruses. IMG provides tools and viewers for analyzing and annotating genomes, genes and functions, individually or in a comparative context. Since its first release in 2005, IMG's data content and analytical capabilities have been constantly expanded through quarterly releases. IMG is provided by the DOE-Joint Genome Institute (JGI) and is available from http://img.jgi.doe.gov.

  17. Cancer genomics object model: an object model for multiple functional genomics data for cancer research.

    PubMed

    Park, Yu Rang; Lee, Hye Won; Cho, Sung Bum; Kim, Ju Han

    2007-01-01

    The development of functional genomics including transcriptomics, proteomics and metabolomics allow us to monitor a large number of key cellular pathways simultaneously. Several technology-specific data models have been introduced for the representation of functional genomics experimental data, including the MicroArray Gene Expression-Object Model (MAGE-OM), the Proteomics Experiment Data Repository (PEDRo), and the Tissue MicroArray-Object Model (TMA-OM). Despite the increasing number of cancer studies using multiple functional genomics technologies, there is still no integrated data model for multiple functional genomics experimental and clinical data. We propose an object-oriented data model for cancer genomics research, Cancer Genomics Object Model (CaGe-OM). We reference four data models: Functional Genomic-Object Model, MAGE-OM, TMAOM and PEDRo. The clinical and histopathological information models are created by analyzing cancer management workflow and referencing the College of American Pathology Cancer Protocols and National Cancer Institute Common Data Elements. The CaGe-OM provides a comprehensive data model for integrated storage and analysis of clinical and multiple functional genomics data.

  18. The Commercialization of Genomic Research in Canada

    PubMed Central

    Joly, Yann; Caulfield, Timothy; Knoppers, Bartha M.; Harmsen, Eef; Pastinen, Tomi

    2010-01-01

    The commercialization of academic research has been promoted by North American policy makers for over 30 years as a means of increasing university financing and to ensure that promising research would eventually find its way to the marketplace. The following issues paper constitutes a reflection on the impact of the Canadian commercialization framework on academic research in the field of genomics. It was written following two workshops and two independent studies organized by academic groups in Quebec (Centre of Genomics and Policy) and Alberta (Health Law Institute). The full sets of recommendations are available upon request to the authors. PMID:22043221

  19. Modeling the costs of clinical decision support for genomic precision medicine

    PubMed Central

    Mathias, Patrick C.; Tarczy-Hornoch, Peter; Shirts, Brian H.

    2016-01-01

    Clinical decision support (CDS) within the electronic health record represents a promising mechanism to provide important genomic findings within clinical workflows. To better understand the current and possible future costs of genomic CDS, we leveraged our local CDS experience to assemble a simple model with inputs such as initial cost and numbers of patients, rules, and institutions. Our model assumed efficiencies of scale and allowed us to perform a one-way sensitivity analysis of the impact of each model input. The number of patients with genomic results per institution was the only single variable that could decrease the cost of CDS per useful alert below projected genomic sequencing costs. Because of the prohibitive upfront cost of sequencing large numbers of individuals, increasing the number of institutions using genomic CDS and improving the efficiency of sharing CDS infrastructure represent the most promising paths to making genomic CDS cost-effective. PMID:27570652

  20. 78 FR 56238 - Office of the Director, National Institutes of Health; Notice of Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-09-12

    ... HUMAN SERVICES National Institutes of Health Office of the Director, National Institutes of Health... of its working groups: the Brain Research through Advancing Innovative Neurotechnologies (BRAIN) working group and the HeLa Genome Data Access working group. The BRAIN working group presentation and...

  1. 78 FR 56904 - National Institute of Diabetes and Digestive and Kidney Diseases; Notice of Closed Meetings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-09-16

    ... HUMAN SERVICES National Institutes of Health National Institute of Diabetes and Digestive and Kidney... Kidney Diseases Special Emphasis Panel; PAR-12-265: NIDDK Ancillary Studies: Genomics of IBD. Date... and Kidney Diseases Special Emphasis Panel; DDK-D Member Conflict of Interest SEP. Date: November 1...

  2. Genomic Data and Annotation from the SEED

    DOE Data Explorer

    Fonstein, Michael; Kogan, Yakov; Osterman, Andrei; Overbeek, Ross; Vonstein, Veronika The Fellowship for Interpretation of Genomes (FIG)

    The SEED Project is a cooperative effort to annotate ever-expanding genomic data so researchers can conduct effective comparative analyses of genomes. Launched in 2003 by the Fellowship for Interpretation of Genomes (FIG), the project is one of several initiatives in ongoing development of data curation systems. SEED is designed to be used by scientists from numerous centers and with varied research objectives. As such, several institutions have since joined FIG in a consortium, including the University of Chicago, DOE’s Argonne National Laboratory (ANL), the University of Illinois at Urbana-Champaign, and others. As one example, ANL has used SEED to develop the National Microbial Pathogen Data Resource. Other agencies and institutions have used the project to discover genome components and clarify gene functions such as metabolism. SEED also has enabled researchers to conduct comparative analyses of closely related genomes and has supported derivation of stoichiometric models to understand metabolic processes. The SEED Project has been extended to support metagenomic samples and concomitant analytical tools. Moreover, the number of genomes being introduced into SEED is growing very rapidly. Building a framework to support this growth while providing highly accurate annotations is centrally important to SEED. The project’s subsystem-based annotation strategy has become the technological foundation for addressing these challenges.(copied from Appendix 7 of Systems Biology Knowledgebase for a New Era in Biology, A Genomics:GTL Report from the May 2008 Workshop, DOE/SC-0113, Grequrick, S; Fredrickson, J.K.; Stevens, R., Pub March 1, 2009.)

  3. Genetics-genomics competencies and nursing regulation.

    PubMed

    Kirk, Maggie; Calzone, Kathleen; Arimori, Naoko; Tonkin, Emma

    2011-06-01

    The aim of this article is to explore the interaction between the integration of genetics-genomics competencies into nursing curricula and regulatory standards. By taking a global perspective of activity in this field, we aim to develop a framework that can inform strategic planning in relation to international genetics-genomics and nursing education. We focus our exploration around a small-scale international survey on the progress, achievements, and critical success factors of 10 countries in relation to the integration of genetics-genomics into nursing education, with exemplars from three of those countries. Analysis of the data generated 10 themes, each with several subthemes that play a critical role in the development of genetics-genomics in nursing education and practice. The themes were organized into three overarching themes: nursing in genetics, genetics in nursing, and recognition and support. Genetics-genomics competence is not fully integrated into nursing education at an appropriate level in any country, nor was it reflected robustly in current standards for registration and licensure. Strong leadership from the specialist genetics community plays a critical role in defining genetics-genomics competence but the engagement of nursing professionals at senior levels in both government and regulatory institutions is essential if nurses are to be active participants in the innovations offered by genomic healthcare. Safe and effective nursing practice must incorporate the needs of those with, at risk for, or susceptible to genetic-genomic conditions, as well as those who might benefit from the application of genomic technologies in the diagnosis and management of common conditions such as cancer and heart disease. The scope of such practice can be articulated though competence statements. Professional regulation defines the standard of competence that practicing nurses should demonstrate at initial registration and licensure. No claim to original US

  4. Genomics of Extinct and Endangered Species (2011 JGI User Meeting)

    ScienceCinema

    Shuster, Stephen [Penn State University

    2016-07-12

    The U.S. Department of Energy Joint Genome Institute (JGI) invited scientists interested in the application of genomics to bioenergy and environmental issues, as well as all current and prospective users and collaborators, to attend the annual DOE JGI Genomics of Energy & Environment Meeting held March 22-24, 2011 in Walnut Creek, Calif. The emphasis of this meeting was on the genomics of renewable energy strategies, carbon cycling, environmental gene discovery, and engineering of fuel-producing organisms. The meeting features presentations by leading scientists advancing these topics. Stephen Shuster of Penn State University gives a presentation on "Genomics of Extinct and Endangered Species" at the 6th annual Genomics of Energy & Environment Meeting on March 23, 2011

  5. Genomics of Extinct and Endangered Species (2011 JGI User Meeting)

    SciTech Connect

    Shuster, Stephen

    2011-03-23

    The U.S. Department of Energy Joint Genome Institute (JGI) invited scientists interested in the application of genomics to bioenergy and environmental issues, as well as all current and prospective users and collaborators, to attend the annual DOE JGI Genomics of Energy & Environment Meeting held March 22-24, 2011 in Walnut Creek, Calif. The emphasis of this meeting was on the genomics of renewable energy strategies, carbon cycling, environmental gene discovery, and engineering of fuel-producing organisms. The meeting features presentations by leading scientists advancing these topics. Stephen Shuster of Penn State University gives a presentation on "Genomics of Extinct and Endangered Species" at the 6th annual Genomics of Energy & Environment Meeting on March 23, 2011

  6. Genomic Speciation and Adaptation in Aquilegia (2011 JGI User Meeting)

    SciTech Connect

    Hodges, Scott

    2011-03-23

    The U.S. Department of Energy Joint Genome Institute (JGI) invited scientists interested in the application of genomics to bioenergy and environmental issues, as well as all current and prospective users and collaborators, to attend the annual DOE JGI Genomics of Energy & Environment Meeting held March 22-24, 2011 in Walnut Creek, Calif. The emphasis of this meeting was on the genomics of renewable energy strategies, carbon cycling, environmental gene discovery, and engineering of fuel-producing organisms. The meeting features presentations by leading scientists advancing these topics. Scott Hodges of the University of California, Santa Barbara gives a presentation on "Genomic Speciation and Adaptation in Aquilegia" at the 6th annual Genomics of Energy & Environment Meeting on March 23, 2011

  7. Genomic Speciation and Adaptation in Aquilegia (2011 JGI User Meeting)

    ScienceCinema

    Hodges, Scott [University of California, Santa Barbara

    2016-07-12

    The U.S. Department of Energy Joint Genome Institute (JGI) invited scientists interested in the application of genomics to bioenergy and environmental issues, as well as all current and prospective users and collaborators, to attend the annual DOE JGI Genomics of Energy & Environment Meeting held March 22-24, 2011 in Walnut Creek, Calif. The emphasis of this meeting was on the genomics of renewable energy strategies, carbon cycling, environmental gene discovery, and engineering of fuel-producing organisms. The meeting features presentations by leading scientists advancing these topics. Scott Hodges of the University of California, Santa Barbara gives a presentation on "Genomic Speciation and Adaptation in Aquilegia" at the 6th annual Genomics of Energy & Environment Meeting on March 23, 2011

  8. A blueprint for genomic nursing science.

    PubMed

    Calzone, Kathleen A; Jenkins, Jean; Bakos, Alexis D; Cashion, Ann K; Donaldson, Nancy; Feero, W Gregory; Feetham, Suzanne; Grady, Patricia A; Hinshaw, Ada Sue; Knebel, Ann R; Robinson, Nellie; Ropka, Mary E; Seibert, Diane; Stevens, Kathleen R; Tully, Lois A; Webb, Jo Ann

    2013-03-01

    This article reports on recommendations arising from an invitational workshop series held at the National Institutes of Health for the purposes of identifying critical genomics problems important to the health of the public that can be addressed through nursing science. The overall purpose of the Genomic Nursing State of the Science Initiative is to establish a nursing research blueprint based on gaps in the evidence and expert evaluation of the current state of the science and through public comment. A Genomic Nursing State of the Science Advisory Panel was convened in 2012 to develop the nursing research blueprint. The Advisory Panel, which met via two webinars and two in-person meetings, considered existing evidence from evidence reviews, testimony from key stakeholder groups, presentations from experts in research synthesis, and public comment. The genomic nursing science blueprint arising from the Genomic Nursing State of Science Advisory Panel focuses on biologic plausibility studies as well as interventions likely to improve a variety of outcomes (e.g., clinical, economic, environmental). It also includes all care settings and diverse populations. The focus is on (a) the client, defined as person, family, community, or population; (b) the context, targeting informatics support systems, capacity building, education, and environmental influences; and (c) cross-cutting themes. It was agreed that building capacity to measure the impact of nursing actions on costs, quality, and outcomes of patient care is a strategic and scientific priority if findings are to be synthesized and aggregated to inform practice and policy. The genomic nursing science blueprint provides the framework for furthering genomic nursing science to improve health outcomes. This blueprint is an independent recommendation of the Advisory Panel with input from the public and is not a policy statement of the National Institutes of Health or the federal government. This genomic nursing science

  9. A Blueprint for Genomic Nursing Science

    PubMed Central

    Calzone, Kathleen A.; Jenkins, Jean; Bakos, Alexis D.; Cashion, Ann; Donaldson, Nancy; Feero, Greg; Feetham, Suzanne; Grady, Patricia A.; Hinshaw, Ada Sue; Knebel, Ann R.; Robinson, Nellie; Ropka, Mary E.; Seibert, Diane; Stevens, Kathleen R.; Tully, Lois A.; Webb, Jo Ann

    2012-01-01

    Purpose This article reports on recommendations arising from an invitational workshop series held at the National Institutes of Health for the purposes of identifying critical genomics problems important to the health of the public that can be addressed through nursing science. The overall purpose of the Genomic Nursing State of the Science Initiative is to establish a nursing research blueprint based on gaps in the evidence and expert evaluation of the current state of the science and through public comment. Organizing Constructs A Genomic Nursing State of the Science Advisory Panel was convened in 2012 to develop the nursing research blueprint. The Advisory Panel, which met via two webinars and two in-person meetings, considered existing evidence from evidence reviews, testimony from key stakeholder groups, presentations from experts in research synthesis, and public comment. Findings The genomic nursing science blueprint arising from the Genomic Nursing State of Science Advisory Panel focuses on biologic plausibility studies as well as interventions likely to improve a variety of outcomes (e.g., clinical, economic, environmental). It also includes all care settings and diverse populations. The focus is on (a) the client, defined as person, family, community, or population; (b) the context, targeting informatics support systems, capacity building, education, and environmental influences; and (c) cross-cutting themes. It was agreed that building capacity to measure the impact of nursing actions on costs, quality, and outcomes of patient care is a strategic and scientific priority if findings are to be synthesized and aggregated to inform practice and policy. Conclusions The genomic nursing science blueprint provides the framework for furthering genomic nursing science to improve health outcomes. This blueprint is an independent recommendation of the Advisory Panel with input from the public and is not a policy statement of the National Institutes of Health or the

  10. Plant genomics: an overview.

    PubMed

    Campos-de Quiroz, Hugo

    2002-01-01

    Recent technological advancements have substantially expanded our ability to analyze and understand plant genomes and to reduce the gap existing between genotype and phenotype. The fast evolving field of genomics allows scientists to analyze thousand of genes in parallel, to understand the genetic architecture of plant genomes and also to isolate the genes responsible for mutations. Furthermore, whole genomes can now be sequenced. This review addresses these issues and also discusses ways to extract biological meaning from DNA data. Although genomic issuesare addressed from a plant perspective, this review provides insights into the genomic analyses of other organisms.

  11. The Institutes of Nations

    ERIC Educational Resources Information Center

    Barnett, Franklyn M.

    1972-01-01

    During the past ten years, the Institutes have presented a series of living and learning summer sessions in an outdoor setting among the redwoods near San Francisco. Young people from 16 to 20 have participated in the cross cultural studies, some involving foreign scholars studying in the United States. (Author)

  12. Planning for Institutional Effectiveness.

    ERIC Educational Resources Information Center

    Wright, Frank W., Comp.; Garthwaite, Elloyse M., Comp.

    Drawing from the experiences of Delgado Community College (DCC) in Louisiana, this manual offers guidance on choosing and implementing an institutional planning system. Section 1 offers introductory comments on planning, educators' reluctance to embrace the management systems of the private sector, and the growing recognition of the importance of…

  13. Institutional Research, July 1976.

    ERIC Educational Resources Information Center

    South Oklahoma City Junior Coll., OK.

    Ten of the eleven research monographs which embody the major institutional research thrust of South Oklahoma City Junior College (SOCJC) during 1975 are presented in this compilation. The first study considers the American College Testing Program scores of students entering SOCJC in Fall 1975 in relation to college choice, student characteristics,…

  14. Institute Born of Gratitude.

    ERIC Educational Resources Information Center

    McLellan, Vin

    1980-01-01

    The Wang Institute of Graduate Studies plans to offer a master's degree in software engineering. The development of an academic program to produce superior, technically qualified managers for the computer industry's software production is discussed. (Journal availability: Datamation, 666 Fifth Ave., New York, NY 10103.) (MLW)

  15. Honors and Institutional Transformation

    ERIC Educational Resources Information Center

    Ransdell, Gary A.

    2015-01-01

    Honors colleges and programs often evolve in response to a mandate from boards of regents or trustees. Such mandates can lead to new or accelerated change within the institution, change that in many cases is linked to and represented by honors. Such has been the case at Western Kentucky University (WKU), where the honors program has played a key…

  16. Summer Youth Forestry Institute

    ERIC Educational Resources Information Center

    Roesch, Gabrielle E.; Neuffer, Tamara; Zobrist, Kevin

    2013-01-01

    The Summer Youth Forestry Institute (SYFI) was developed to inspire youth through experiential learning opportunities and early work experience in the field of natural resources. Declining enrollments in forestry and other natural resource careers has made it necessary to actively engage youth and provide them with exposure to careers in these…

  17. Model Reading Institute.

    ERIC Educational Resources Information Center

    Dworkin, Nancy; Dworkin, Yehoash

    The 1978 Summer Reading Institute, which served 58 Washington, D.C., elementary school children, is described in this paper. Major characteristics of the program model are first identified, along with elements that were added to the model in the preplanning stage. Numerous aspects of the program are then described, including the make-up of the…

  18. Defense Language Institute.

    ERIC Educational Resources Information Center

    Defense Language Inst., Washington, DC.

    Discussed in this Defense Language Institute (DLI) brochure are its intensive language programs' history, and its four schools, which are located in Monterey, California, Washington, D.C., Lackland Air Force Base, and Fort Bliss, Texas. Proficiency levels determined by the DLI and utilization of the audiolingual method are also described.…

  19. A Contested Institutional Culture

    ERIC Educational Resources Information Center

    Morin, Stephanie A.

    2010-01-01

    The College of William and Mary (Williamsburg, Virginia) found itself at a crossroads in 2005. Their long-popular president Timothy J. Sullivan was retiring after 13 years at the helm of the world's second oldest institution of higher education (Petkofsky, 2004). Long known as a bastion of conservatism, William and Mary could now change their…

  20. An Institute for Inquiry

    ERIC Educational Resources Information Center

    Kelly, Janet; Weis, R. Stephen

    2005-01-01

    This article discusses professional development that offers practical tips for elementary teachers to implement in their classrooms right away. The programs at the Institute of Math, Science, and Technology Education at Texas Christian University at Fort Worth, Texas, offer a professional development model. In this successful collaborative, formed…

  1. Instituting the Greater Good

    ERIC Educational Resources Information Center

    Matthews, Frank

    2011-01-01

    Teachers, higher education administrators and financial planners are well acquainted with the work of TIAA-CREF. The insurance and investment company has been a central player in teacher retirement and financial planning for nearly a century. Twelve years ago, the organization spawned the TIAA-CREF Institute, a research-focused arm that brings…

  2. Institution-Sponsored Internships.

    ERIC Educational Resources Information Center

    Ard, Anne K.

    1994-01-01

    Colleges can use institutionally-sponsored internships, in-house opportunities to participate in the daily activities of leadership, to let employees learn the culture of leadership and interact with staff currently in such positions. Administrative internships at Pennsylvania State University, Eastern Illinois University, and Arizona State…

  3. Implementing Sustainable Institutional Practices

    ERIC Educational Resources Information Center

    Shepard, Joseph; Johnson, Lewis

    2009-01-01

    Recent research has found that few institutions of higher education implemented the necessary strategies to make their campuses sustainable (Thompson and Green 2005). Ironically, universities are the segment of society with the most access to the intellectual capital needed to provide sound sustainable practices and measurements. Having top…

  4. Leadership in Educational Institutions

    ERIC Educational Resources Information Center

    Sunko, Esmeralda

    2012-01-01

    Many questions concerning quality of functioning and effectiveness are connected with the management of education as a professional field in educational organizations. The role of educational leadership in an educational organization raises many questions related to legislative regulations of activities, issues of institutional placement,…

  5. A Contested Institutional Culture

    ERIC Educational Resources Information Center

    Morin, Stephanie A.

    2010-01-01

    The College of William and Mary (Williamsburg, Virginia) found itself at a crossroads in 2005. Their long-popular president Timothy J. Sullivan was retiring after 13 years at the helm of the world's second oldest institution of higher education (Petkofsky, 2004). Long known as a bastion of conservatism, William and Mary could now change their…

  6. Institutional Effectiveness Resource Manual.

    ERIC Educational Resources Information Center

    Cannon, Delinda T.; And Others

    This resource manual was produced to assist the South Carolina Technical College System's efforts to improve institutional effectiveness and accountability. The first two sections of the manual provide a brief foreword, a description of state initiatives for research and academic excellence in South Carolina, the text of state legislation…

  7. Implementing Sustainable Institutional Practices

    ERIC Educational Resources Information Center

    Shepard, Joseph; Johnson, Lewis

    2009-01-01

    Recent research has found that few institutions of higher education implemented the necessary strategies to make their campuses sustainable (Thompson and Green 2005). Ironically, universities are the segment of society with the most access to the intellectual capital needed to provide sound sustainable practices and measurements. Having top…

  8. The Francis Crick Institute.

    PubMed

    Peters, Keith; Smith, Jim

    2017-04-01

    The Francis Crick Institute Laboratory, opened in 2016, is supported by the Medical Research Council, Cancer Research UK, the Wellcome Trust, and University College London, King's College London and Imperial College London. The emphasis on research training and early independence of gifted scientists in a multidisciplinary environment provides unique opportunities for UK medical science, including clinical and translational research.

  9. Institutional Research Bulletin, 1993.

    ERIC Educational Resources Information Center

    Abou-Sayf, Frank, Ed.

    1993-01-01

    The "Institutional Research Bulletin" is a collection of research summaries relating to Kapi'olani Community College (KCC) in Hawaii. Highlights from the 1993 volume (September-December) include: (1) the number of students in art classes and programs increased from 1988-1992; (2) the results of a survey about how health students find out…

  10. The Gesell Institute Responds.

    ERIC Educational Resources Information Center

    Young Children, 1987

    1987-01-01

    Responding to Dr. Meisels' article concerning the uses and abuses of the Gesell readiness tests, the Gesell Institute of Child development maintains that the Gesell series of assessments are used by schools to gain a fuller developmental understanding of the child and have been predictive of school success. (BB)

  11. Institute Born of Gratitude.

    ERIC Educational Resources Information Center

    McLellan, Vin

    1980-01-01

    The Wang Institute of Graduate Studies plans to offer a master's degree in software engineering. The development of an academic program to produce superior, technically qualified managers for the computer industry's software production is discussed. (Journal availability: Datamation, 666 Fifth Ave., New York, NY 10103.) (MLW)

  12. Personnel Management Institutes, 1975.

    ERIC Educational Resources Information Center

    Hinman, Stanley B., Jr., Comp.

    This publication is a compilation of five papers presented at the 1975 Personnel Management Institutes held by the New York State School Boards Association. Although the meeting was intended to provide useful information about personnel matters specifically for school board members and school administrators from New York, much of the content of…

  13. Personnel Management Institutes 1974.

    ERIC Educational Resources Information Center

    Hinman, Stanley B., Jr.

    This report is a compilation of presentations made at the Personnel Management Institutes held by the New York State School Boards Association in the fall of 1974. Included are the following six presentations: "New Laws Affecting School Boards and School Administration," by Bernard T. McGivern; "How to Prepare for Tenure Hearings,…

  14. Managing Institutional Image.

    ERIC Educational Resources Information Center

    Melchiori, Gerlinda S.

    1990-01-01

    A managerial process for enhancing the image and public reputation of a higher education institution is outlined. It consists of five stages: market research; data analysis and market positioning; communication of results and recommendations to the administration; development of a global image program; and impact evaluation. (MSE)

  15. Summer Youth Forestry Institute

    ERIC Educational Resources Information Center

    Roesch, Gabrielle E.; Neuffer, Tamara; Zobrist, Kevin

    2013-01-01

    The Summer Youth Forestry Institute (SYFI) was developed to inspire youth through experiential learning opportunities and early work experience in the field of natural resources. Declining enrollments in forestry and other natural resource careers has made it necessary to actively engage youth and provide them with exposure to careers in these…

  16. Telecommunications Management: Institutional Imperative.

    ERIC Educational Resources Information Center

    Creutz, Alan

    1986-01-01

    An overview of the management and planning issues that confront higher education institutions in the area of telecommunications is provided. The focus is on management issues such as coordination, cost control, functionality, flexibility, and relationship between telecommunications and management information systems. (Author/MLW)

  17. Instituting the Greater Good

    ERIC Educational Resources Information Center

    Matthews, Frank

    2011-01-01

    Teachers, higher education administrators and financial planners are well acquainted with the work of TIAA-CREF. The insurance and investment company has been a central player in teacher retirement and financial planning for nearly a century. Twelve years ago, the organization spawned the TIAA-CREF Institute, a research-focused arm that brings…

  18. Oprelvekin. Genetics Institute.

    PubMed

    Sitaraman, S V; Gewirtz, A T

    2001-10-01

    Genetics Institute has developed and launched oprelvekin (rhIL-11; Neumega), a recombinant form of human IL-11. In November 1997, the FDA cleared oprelvekin for the prevention of severe thrombocytopenia and the reduction of the need for platelet transfusions following myelosuppressive chemotherapy in susceptible patients with non-myeloid malignancies 12703021. The product was launched at the end of 1997 [312556]. By December 1999, phase III trials for Crohn's disease (CD) were underway [363007]. Genetics Institute had commenced a 150-patient phase II trial for mild-to-moderate CD and mucositis and the company planned to file regulatory procedures for the indication of CD in 1999 [271210]. An oral formulation for this indication has been developed. Oprelvekin is also undergoing phase I clinical trials for colitis [396157], phase II clinical trials for rheumatoid arthritis [413835] and clinical trials for psoriasis [299644]. In March 1997, Wyeth-Ayerst became the licensee for Europe, Africa, Latin America and Asia (with the exception of Japan). Genetics Institute holds marketing rights for North America [239273]. In Japan, oprelvekin is being developed by Genetics Institute and Yamanouchi; phase III trials have commenced [295049] and were ongoing in May 2001 [411763]. In April 1996, analysts at Yamaichi estimated launch in 2001 and maximum annual sales of over yen 10 billion [215896]. In January 1998, Morgan Stanley Dean Witter predicted Yamanouchi's share of sales to be yen 1 billion in 2001, rising to yen 2 billion in 2002 [315458]. Sales of oprelvekin were US $34 million for Genetics institute in fiscal 2000 while, in July 2001, Credit Suisse First Boston estimated that this figure will be US $30 million and US $34 million in 2001 and 2002, respectively [416883].

  19. National Space Biomedical Research Institute

    NASA Technical Reports Server (NTRS)

    2004-01-01

    This report outlines the National Space Biomedical Research Institute's (NSBRI) activities during FY 2004, the Institute's seventh year. It is prepared in accordance with Cooperative Agreement NCC 9-58 between NASA's Lyndon B. Johnson Space Center (JSC) and the Institute's lead institution, Baylor College of Medicine.

  20. Assessment and 2-Year Institutions.

    ERIC Educational Resources Information Center

    Bradley, Jama L.; And Others

    1994-01-01

    Describes a national study of the current availability and use of commercially and institutionally developed educational assessment instruments. Indicates that two-year institutions reported less activity than four-year institutions in assessing the major fields of study but that 77% of all two-year institutions assessed basic skills. (MAB)

  1. Are Schools and Colleges Institutions?

    ERIC Educational Resources Information Center

    Glatter, Ron

    2015-01-01

    This paper asks whether schools and colleges should be regarded as institutions as well as organizations, and if so what are the implications. Different conceptions of "institution" are examined including an attempt to distinguish "institution" from "organization". It is suggested that institutions are committed to a…

  2. Endogenous and costly institutional deterrence

    Treesearch

    David C. Kingsley; Thomas C. Brown

    2014-01-01

    Modern economies rely on central-authority institutions to regulate individual behaviour. Despite the importance of such institutions little is known about their formation within groups. In a public good experiment, groups selected the level of deterrence implemented by the institution, knowing that the administrative costs of the institution rose with the level of...

  3. Integrating sequence, evolution and functional genomics in regulatory genomics

    PubMed Central

    Vingron, Martin; Brazma, Alvis; Coulson, Richard; van Helden, Jacques; Manke, Thomas; Palin, Kimmo; Sand, Olivier; Ukkonen, Esko

    2009-01-01

    With genome analysis expanding from the study of genes to the study of gene regulation, 'regulatory genomics' utilizes sequence information, evolution and functional genomics measurements to unravel how regulatory information is encoded in the genome. PMID:19226437

  4. Genomic Data Commons | Office of Cancer Genomics

    Cancer.gov

    The NCI’s Center for Cancer Genomics launches the Genomic Data Commons (GDC), a unified data sharing platform for the cancer research community. The mission of the GDC is to enable data sharing across the entire cancer research community, to ultimately support precision medicine in oncology.

  5. WGE: a CRISPR database for genome engineering

    PubMed Central

    Hodgkins, Alex; Farne, Anna; Perera, Sajith; Grego, Tiago; Parry-Smith, David J.; Skarnes, William C.; Iyer, Vivek

    2015-01-01

    Summary: The rapid development of CRISPR-Cas9 mediated genome editing techniques has given rise to a number of online and stand-alone tools to find and score CRISPR sites for whole genomes. Here we describe the Wellcome Trust Sanger Institute Genome Editing database (WGE), which uses novel methods to compute, visualize and select optimal CRISPR sites in a genome browser environment. The WGE database currently stores single and paired CRISPR sites and pre-calculated off-target information for CRISPRs located in the mouse and human exomes. Scoring and display of off-target sites is simple, and intuitive, and filters can be applied to identify high-quality CRISPR sites rapidly. WGE also provides a tool for the design and display of gene targeting vectors in the same genome browser, along with gene models, protein translation and variation tracks. WGE is open, extensible and can be set up to compute and present CRISPR sites for any genome. Availability and implementation: The WGE database is freely available at www.sanger.ac.uk/htgt/wge Contact: vvi@sanger.ac.uk or skarnes@sanger.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25979474

  6. Genomic Data Commons launches

    Cancer.gov

    The Genomic Data Commons (GDC), a unified data system that promotes sharing of genomic and clinical data between researchers, launched today with a visit from Vice President Joe Biden to the operations center at the University of Chicago.

  7. GENOMICS AND ENVIRONMENTAL RESEARCH

    EPA Science Inventory

    The impact of recently developed and emerging genomics technologies on environmental sciences has significant implications for human and ecological risk assessment issues. The linkage of data generated from genomics, transcriptomics, proteomics, metabalomics, and ecology can be ...

  8. GENOMICS AND ENVIRONMENTAL RESEARCH

    EPA Science Inventory

    The impact of recently developed and emerging genomics technologies on environmental sciences has significant implications for human and ecological risk assessment issues. The linkage of data generated from genomics, transcriptomics, proteomics, metabalomics, and ecology can be ...

  9. Connecting Genomic Alterations to Cancer Biology with Proteomics: The NCI Clinical Proteomic Tumor Analysis Consortium

    SciTech Connect

    Ellis, Matthew; Gillette, Michael; Carr, Steven A.; Paulovich, Amanda G.; Smith, Richard D.; Rodland, Karin D.; Townsend, Reid; Kinsinger, Christopher; Mesri, Mehdi; Rodriguez, Henry; Liebler, Daniel

    2013-10-03

    The National Cancer Institute (NCI) Clinical Proteomic Tumor Analysis Consortium is applying the latest generation of proteomic technologies to genomically annotated tumors from The Cancer Genome Atlas (TCGA) program, a joint initiative of the NCI and the National Human Genome Research Institute. By providing a fully integrated accounting of DNA, RNA, and protein abnormalities in individual tumors, these datasets will illuminate the complex relationship between genomic abnormalities and cancer phenotypes, thus producing biologic insights as well as a wave of novel candidate biomarkers and therapeutic targets amenable to verifi cation using targeted mass spectrometry methods.

  10. 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.

  11. National Plant Genome Initiative

    DTIC Science & Technology

    2005-01-01

    JAN 2005 2. REPORT TYPE 3. DATES COVERED 00-00-2005 to 00-00-2005 4. TITLE AND SUBTITLE National Plant Genome Initiative. Progress Report 5a...refl ected in future Administration budgets. Cover Photo: National Plant Genome Initiative Progress Report January 2005 National Science and...Technology Council Committee on Science Interagency Working Group on Plant Genomes [Blank Page] Interagency Working Group on Plant Genomes Committee on

  12. GENESIS: genome evolution scenarios.

    PubMed

    Gog, Simon; Bader, Martin; Ohlebusch, Enno

    2008-03-01

    We implemented a software tool called GENESIS for three different genome rearrangement problems: Sorting a unichromosomal genome by weighted reversals and transpositions (SwRT), sorting a multichromosomal genome by reversals, translocations, fusions and fissions (SRTl), and sorting a multichromosomal genome by weighted reversals, translocations, fusions, fissions and transpositions (SwRTTl). Source code can be obtained by the authors, or use the web interface http://www.uni-ulm.de/in/theo/research/genesis.html.

  13. Whole-genome patenting.

    PubMed

    O'Malley, Maureen A; Bostanci, Adam; Calvert, Jane

    2005-06-01

    Gene patenting is now a familiar commercial practice, but there is little awareness that several patents claim ownership of the complete genome sequence of a prokaryote or virus. When these patents are analysed and compared to those for other biological entities, it becomes clear that genome patents seek to exploit the genome as an information base and are part of a broader shift towards intangible intellectual property in genomics.

  14. 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.

  15. The human genome project

    SciTech Connect

    Yager, T.D.; Zewert, T.E.; Hood, L.E. )

    1994-04-01

    The Human Genome Project (HGP) is a coordinated worldwide effort to precisely map the human genome and the genomes of selected model organisms. The first explicit proposal for this project dates from 1985 although its foundations (both conceptual and technological) can be traced back many years in genetics, molecular biology, and biotechnology. The HGP has matured rapidly and is producing results of great significance.

  16. 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.

  17. Transportation Institutional Plan

    SciTech Connect

    Not Available

    1986-08-01

    This Institutional Plan is divided into three chapters. Chapter 1 provides background information, discusses the purposes of the Plan and the policy guidance for establishing the transportation system, and describes the projected system and the plans for its integrated development. Chapter 2 discusses the major participants who must interact to build the system. Chapter 3 suggests mechanisms for interaction that will foster wide participation in program planning and implementation and provides a framework for managing and resolving the issues related to development and operation of the transportation system. A list of acronyms and a glossary are included for the reader's convenience. Also included in this Plan are four appendices. Of particular importance is Appendix A, which includes detailed discussion of specific transportation issues. Appendices B, C, and D provide supporting material to assist the reader in understanding the roles of the involved institutions.

  18. Institute for Mechanical Engineering

    NASA Astrophysics Data System (ADS)

    The Institute of Mechanical Engineering has the objectives of supporting in Canada the following activities: improvement of vehicles, propulsion systems, and transportation-related facilities and services; improvements in the design and operation of maritime engineering works; protection of the environment; enhancement of energy flexibility; advancement of firms engaged in manufacturing and resource extraction; and related programs of other government departments and agencies. In 1990-91 the Institute, which had changed its name that year from the Division of Mechanical Engineering, consolidated its research activities from nine laboratories to six programs. Activities in these six programs are described: Advanced Manufacturing Technology, Coastal Zone Engineering, Cold Regions Engineering, Combustion and Fluids Engineering, Ground Transportation Technology, and Machinery and Engine Technology.

  19. Institutions and poverty.

    PubMed

    Tebaldi, Edinaldo; Mohan, Ramesh

    2010-01-01

    This study utilises eight alternative measures of institutions and the instrumental variable method to examine the impacts of institutions on poverty. The estimates show that an economy with a robust system to control corruption, an effective government, and a stable political system will create the conditions to promote economic growth, minimise income distribution conflicts, and reduce poverty. Corruption, ineffective governments, and political instability will not only hurt income levels through market inefficiencies, but also escalate poverty incidence via increased income inequality. The results also imply that the quality of the regulatory system, rule of law, voice and accountability, and expropriation risk are inversely related to poverty but their effect on poverty is via average income rather than income distribution.

  20. The Townes Laser Institute

    NASA Astrophysics Data System (ADS)

    Richardson, Martin

    2009-06-01

    The State of Florida has recently established a new center of excellence in advanced core laser technologies, associated with the College of Optics & Photonics. This center, dedicated in 2007 in tribute to the pioneering work of Charles Townes, whose insight lead to the development of the maser and the laser, will invest in next generation laser technologies for applications to medicine, advanced manufacturing and defense. It joins the cluster of photonics-related centers at UCF, adding a focused national center for the education and training of scientists and engineers in laser technology. This paper describes the mission and objectives of the Townes Institute, the educational and training programs it is creating, its current investments and opportunities, and the future institutional and industrial partnerships and global reach it hopes to create.

  1. 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.

  2. ChloroMitoCU: Codon patterns across organelle genomes for functional genomics and evolutionary applications.

    PubMed

    Sablok, Gaurav; Chen, Ting-Wen; Lee, Chi-Ching; Yang, Chi; Gan, Ruei-Chi; Wegrzyn, Jill L; Porta, Nicola L; Nayak, Kinshuk C; Huang, Po-Jung; Varotto, Claudio; Tang, Petrus

    2017-06-01

    Organelle genomes are widely thought to have arisen from reduction events involving cyanobacterial and archaeal genomes, in the case of chloroplasts, or α-proteobacterial genomes, in the case of mitochondria. Heterogeneity in base composition and codon preference has long been the subject of investigation of topics ranging from phylogenetic distortion to the design of overexpression cassettes for transgenic expression. From the overexpression point of view, it is critical to systematically analyze the codon usage patterns of the organelle genomes. In light of the importance of codon usage patterns in the development of hyper-expression organelle transgenics, we present ChloroMitoCU, the first-ever curated, web-based reference catalog of the codon usage patterns in organelle genomes. ChloroMitoCU contains the pre-compiled codon usage patterns of 328 chloroplast genomes (29,960 CDS) and 3,502 mitochondrial genomes (49,066 CDS), enabling genome-wide exploration and comparative analysis of codon usage patterns across species. ChloroMitoCU allows the phylogenetic comparison of codon usage patterns across organelle genomes, the prediction of codon usage patterns based on user-submitted transcripts or assembled organelle genes, and comparative analysis with the pre-compiled patterns across species of interest. ChloroMitoCU can increase our understanding of the biased patterns of codon usage in organelle genomes across multiple clades. ChloroMitoCU can be accessed at: http://chloromitocu.cgu.edu.tw/. © The Author 2017. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

  3. [Academies Institute Andalucia].

    PubMed

    Piédrola Angulo, Gonzalo

    2012-01-01

    Academies Institute of Andalusia is the only corporation in the State grouping twenty seven Spanish Academies and Royal Academies of an autonomous region, with a total of 760 Academicians. This paper sets out as conceived, their roles and relationships with other national corporations, as well as the primary mission to maintain and strengthen fraternal relations, culture, research and collaboration between the Andalusian Academy, showing academic representation whole of them.

  4. The genomic psychiatry cohort: partners in discovery.

    PubMed

    Pato, Michele T; Sobell, Janet L; Medeiros, Helena; Abbott, Colony; Sklar, Brooke M; Buckley, Peter F; Bromet, Evelyn J; Escamilla, Michael A; Fanous, Ayman H; Lehrer, Douglas S; Macciardi, Fabio; Malaspina, Dolores; McCarroll, Steve A; Marder, Stephen R; Moran, Jennifer; Morley, Christopher P; Nicolini, Humberto; Perkins, Diana O; Purcell, Shaun M; Rapaport, Mark H; Sklar, Pamela; Smoller, Jordan W; Knowles, James A; Pato, Carlos N

    2013-06-01

    The Genomic Psychiatry Cohort (GPC) is a longitudinal resource designed to provide the necessary population-based sample for large-scale genomic studies, studies focusing on Research Domain Criteria (RDoC) and/or other alternate phenotype constructs, clinical and interventional studies, nested case-control studies, long-term disease course studies, and genomic variant-to-phenotype studies. We provide and will continue to encourage access to the GPC as an international resource. DNA and other biological samples and diagnostic data are available through the National Institute of Mental Health (NIMH) Repository. After appropriate review and approval by an advisory board, investigators are able to collaborate in, propose, and co-lead studies involving cohort participants. Copyright © 2013 Wiley Periodicals, Inc.

  5. Comparative genomics of Lactobacillus

    PubMed Central

    Kant, Ravi; Blom, Jochen; Palva, Airi; Siezen, Roland J.; de Vos, Willem M.

    2011-01-01

    Summary The genus Lactobacillus includes a diverse group of bacteria consisting of many species that are associated with fermentations of plants, meat or milk. In addition, various lactobacilli are natural inhabitants of the intestinal tract of humans and other animals. Finally, several Lactobacillus strains are marketed as probiotics as their consumption can confer a health benefit to host. Presently, 154 Lactobacillus species are known and a growing fraction of these are subject to draft genome sequencing. However, complete genome sequences are needed to provide a platform for detailed genomic comparisons. Therefore, we selected a total of 20 genomes of various Lactobacillus strains for which complete genomic sequences have been reported. These genomes had sizes varying from 1.8 to 3.3 Mb and other characteristic features, such as G+C content that ranged from 33% to 51%. The Lactobacillus pan genome was found to consist of approximately 14 000 protein‐encoding genes while all 20 genomes shared a total of 383 sets of orthologous genes that defined the Lactobacillus core genome (LCG). Based on advanced phylogeny of the proteins encoded by this LCG, we grouped the 20 strains into three main groups and defined core group genes present in all genomes of a single group, signature group genes shared in all genomes of one group but absent in all other Lactobacillus genomes, and Group‐specific ORFans present in core group genes of one group and absent in all other complete genomes. The latter are of specific value in defining the different groups of genomes. The study provides a platform for present individual comparisons as well as future analysis of new Lactobacillus genomes. PMID:21375712

  6. A genome blogger manifesto.

    PubMed

    Corpas, Manuel

    2012-10-26

    Cheap prices for genomic testing have revolutionized consumers' access to personal genomics. Exploration of personal genomes poses significant challenges for customers wishing to learn beyond provider customer reports. A vibrant community has spontaneously appeared blogging experiences and data as a way to learn about their personal genomes. No set of values has publicly been described to date encapsulating ideals and code of conduct for this community. Here I present a first attempt to address this vacuum based on my own personal experiences as genome blogger.

  7. Chromium and Genomic Stability

    PubMed Central

    Wise, Sandra S.; Wise, John Pierce

    2014-01-01

    Many metals serve as micronutrients which protect against genomic instability. Chromium is most abundant in its trivalent and hexavalent forms. Trivalent chromium has historically been considered an essential element, though recent data indicate that while it can have pharmacological effects and value, it is not essential. There are no data indicating that trivalent chromium promotes genomic stability and, instead may promote genomic instability. Hexavalent chromium is widely accepted as highly toxic and carcinogenic with no nutritional value. Recent data indicate that it causes genomic instability and also has no role in promoting genomic stability. PMID:22192535

  8. The Genomic Medicine Game.

    PubMed

    Tran, Elvis; de Andrés-Galiana, Enrique J; Benitez, Sonia; Martin-Sanchez, Fernando; Lopez-Campos, Guillermo H

    2016-01-01

    With advancements in genomics technology, health care has been improving and new paradigms of medicine such as genomic medicine have evolved. The education of clinicians, researchers and students to face the challenges posed by these new approaches, however, has been often lagging behind. From this the Genomic Medicine Game, an educational tool, was created for the purpose of conceptualizing the key components of Genomic Medicine. A number of phenotype-genotype associations were found through a literature review, which was used to be a base for the concepts the Genomic Medicine Game would focus on. Built in Java, the game was successfully tested with promising results.

  9. The Bluejay genome browser.

    PubMed

    Soh, Jung; Gordon, Paul M K; Sensen, Christoph W

    2012-03-01

    The Bluejay genome browser is a stand-alone visualization tool for the multi-scale viewing of annotated genomes and other genomic elements. Bluejay allows users to customize display features to suit their needs, and produces publication-quality graphics. Bluejay provides a multitude of ways to interrelate biological data at the genome scale. Users can load gene expression data into a genome display for expression visualization in context. Multiple genomes can be compared concurrently, including time series expression data, based on Gene Ontology labels. External, context-sensitive biological Web Services are linked to the displayed genomic elements ad hoc for in-depth genomic data analysis and interpretation. Users can mark multiple points of interest in a genome by creating waypoints, and exploit them for easy navigation of single or multiple genomes. Using this comprehensive visual environment, users can study a gene not just in relation to its genome, but also its transcriptome and evolutionary origins. Written in Java, Bluejay is platform-independent and is freely available from http://bluejay.ucalgary.ca.

  10. Microbial genomic taxonomy

    PubMed Central

    2013-01-01

    A need for a genomic species definition is emerging from several independent studies worldwide. In this commentary paper, we discuss recent studies on the genomic taxonomy of diverse microbial groups and a unified species definition based on genomics. Accordingly, strains from the same microbial species share >95% Average Amino Acid Identity (AAI) and Average Nucleotide Identity (ANI), >95% identity based on multiple alignment genes, <10 in Karlin genomic signature, and > 70% in silico Genome-to-Genome Hybridization similarity (GGDH). Species of the same genus will form monophyletic groups on the basis of 16S rRNA gene sequences, Multilocus Sequence Analysis (MLSA) and supertree analysis. In addition to the established requirements for species descriptions, we propose that new taxa descriptions should also include at least a draft genome sequence of the type strain in order to obtain a clear outlook on the genomic landscape of the novel microbe. The application of the new genomic species definition put forward here will allow researchers to use genome sequences to define simultaneously coherent phenotypic and genomic groups. PMID:24365132

  11. UCSC genome browser tutorial.

    PubMed

    Zweig, Ann S; Karolchik, Donna; Kuhn, Robert M; Haussler, David; Kent, W James

    2008-08-01

    The University of California Santa Cruz (UCSC) Genome Bioinformatics website consists of a suite of free, open-source, on-line tools that can be used to browse, analyze, and query genomic data. These tools are available to anyone who has an Internet browser and an interest in genomics. The website provides a quick and easy-to-use visual display of genomic data. It places annotation tracks beneath genome coordinate positions, allowing rapid visual correlation of different types of information. Many of the annotation tracks are submitted by scientists worldwide; the others are computed by the UCSC Genome Bioinformatics group from publicly available sequence data. It also allows users to upload and display their own experimental results or annotation sets by creating a custom track. The suite of tools, downloadable data files, and links to documentation and other information can be found at http://genome.ucsc.edu/.

  12. Bacterial Genome Instability

    PubMed Central

    Darmon, Elise

    2014-01-01

    SUMMARY Bacterial genomes are remarkably stable from one generation to the next but are plastic on an evolutionary time scale, substantially shaped by horizontal gene transfer, genome rearrangement, and the activities of mobile DNA elements. This implies the existence of a delicate balance between the maintenance of genome stability and the tolerance of genome instability. In this review, we describe the specialized genetic elements and the endogenous processes that contribute to genome instability. We then discuss the consequences of genome instability at the physiological level, where cells have harnessed instability to mediate phase and antigenic variation, and at the evolutionary level, where horizontal gene transfer has played an important role. Indeed, this ability to share DNA sequences has played a major part in the evolution of life on Earth. The evolutionary plasticity of bacterial genomes, coupled with the vast numbers of bacteria on the planet, substantially limits our ability to control disease. PMID:24600039

  13. Whole-genome alignment.

    PubMed

    Dewey, Colin N

    2012-01-01

    Whole-genome alignment (WGA) is the prediction of evolutionary relationships at the nucleotide level between two or more genomes. It combines aspects of both colinear sequence alignment and gene orthology prediction, and is typically more challenging to address than either of these tasks due to the size and complexity of whole genomes. Despite the difficulty of this problem, numerous methods have been developed for its solution because WGAs are valuable for genome-wide analyses, such as phylogenetic inference, genome annotation, and function prediction. In this chapter, we discuss the meaning and significance of WGA and present an overview of the methods that address it. We also examine the problem of evaluating whole-genome aligners and offer a set of methodological challenges that need to be tackled in order to make the most effective use of our rapidly growing databases of whole genomes.

  14. Genomic Sequencing in Cancer

    PubMed Central

    Tuna, Musaffe; Amos, Christopher I.

    2013-01-01

    Genomic sequencing has provided critical insights into the etiology of both simple and complex diseases. The enormous reductions in cost for whole genome sequencing have allowed this technology to gain increasing use. Whole genome analysis has impacted research of complex diseases including cancer by allowing the systematic analysis of entire genomes in a single experiment, thereby facilitating the discovery of somatic and germline mutations, and identification of the function and impact of the insertions, deletions, and structural rearrangements, including translocations and inversions, in novel disease genes. Whole-genome sequencing can be used to provide the most comprehensive characterization of the cancer genome, the complexity of which we are only beginning to understand. Hence in this review, we focus on whole-genome sequencing in cancer. PMID:23178448

  15. Institutional Churn: Institutional Change in United Kingdom Higher Education

    ERIC Educational Resources Information Center

    Tight, Malcolm

    2013-01-01

    This article considers how higher education institutions change over time, using the United Kingdom system as an exemplar, and focusing on the 15-year period between 1994/95 and 2009/10. While there are many aspects of institutional change worthy of study, the focus here is on how institutions appear to others. Thus, the article examines the…

  16. Institutional Repositories: The Experience of Master's and Baccalaureate Institutions

    ERIC Educational Resources Information Center

    Markey, Karen; St. Jean, Beth; Soo, Young Rieh; Yakel, Elizabeth; Kim, Jihyun

    2008-01-01

    In 2006, MIRACLE Project investigators censused library directors at all U.S. academic institutions about their activities planning, pilot testing, and implementing the institutional repositories on their campuses. Out of 446 respondents, 289 (64.8 percent) were from master's and baccalaureate institutions (M&BIs) where few operational…

  17. Institutional Repositories in Indian Universities and Research Institutes: A Study

    ERIC Educational Resources Information Center

    Krishnamurthy, M.; Kemparaju, T. D.

    2011-01-01

    Purpose: The purpose of this paper is to report on a study of the institutional repositories (IRs) in use in Indian universities and research institutes. Design/methodology/approach: Repositories in various institutions in India were accessed and described in a standardised way. Findings: The 20 repositories studied covered collections of diverse…

  18. Institutional Repositories at Small Institutions in America: Some Current Trends

    ERIC Educational Resources Information Center

    Nykanen, Melissa

    2011-01-01

    The research reported in this article was undertaken to determine the level of implementation of institutional repositories (IRs) at small institutions enrolling fewer than 10,000 students. The study analyzed quantitative and qualitative data from IRs at a number of small institutions with the aim of observing relevant patterns and trends that may…

  19. International Security Institutions, Domestic Politics, and Institutional Legitimacy

    ERIC Educational Resources Information Center

    Chapman, Terrence L.

    2007-01-01

    Scholars have devoted considerable attention to the informational role of international institutions. However, several questions about the informational aspects of institutional behavior remain underexplored: What determines how audiences respond to institutional decisions? Through what channels does information provision affect foreign policy? To…

  20. Institutional Repositories in Indian Universities and Research Institutes: A Study

    ERIC Educational Resources Information Center

    Krishnamurthy, M.; Kemparaju, T. D.

    2011-01-01

    Purpose: The purpose of this paper is to report on a study of the institutional repositories (IRs) in use in Indian universities and research institutes. Design/methodology/approach: Repositories in various institutions in India were accessed and described in a standardised way. Findings: The 20 repositories studied covered collections of diverse…

  1. Enabling responsible public genomics.

    PubMed

    Conley, John M; Doerr, Adam K; Vorhaus, Daniel B

    2010-01-01

    As scientific understandings of genetics advance, researchers require increasingly rich datasets that combine genomic data from large numbers of individuals with medical and other personal information. Linking individuals' genetic data and personal information precludes anonymity and produces medically significant information--a result not contemplated by the established legal and ethical conventions governing human genomic research. To pursue the next generation of human genomic research and commerce in a responsible fashion, scientists, lawyers, and regulators must address substantial new issues, including researchers' duties with respect to clinically significant data, the challenges to privacy presented by genomic data, the boundary between genomic research and commerce, and the practice of medicine. This Article presents a new model for understanding and addressing these new challenges--a "public genomics" premised on the idea that ethically, legally, and socially responsible genomics research requires openness, not privacy, as its organizing principle. Responsible public genomics combines the data contributed by informed and fully consenting information altruists and the research potential of rich datasets in a genomic commons that is freely and globally available. This Article examines the risks and benefits of this public genomics model in the context of an ambitious genetic research project currently under way--the Personal Genome Project. This Article also (i) demonstrates that large-scale genomic projects are desirable, (ii) evaluates the risks and challenges presented by public genomics research, and (iii) determines that the current legal and regulatory regimes restrict beneficial and responsible scientific inquiry while failing to adequately protect participants. The Article concludes by proposing a modified normative and legal framework that embraces and enables a future of responsible public genomics.

  2. The Genomes On Line Database (GOLD) v.2: a monitor of genome projects worldwide.

    PubMed

    Liolios, Konstantinos; Tavernarakis, Nektarios; Hugenholtz, Philip; Kyrpides, Nikos C

    2006-01-01

    The Genomes On Line Database (GOLD) is a web resource for comprehensive access to information regarding complete and ongoing genome sequencing projects worldwide. The database currently incorporates information on over 1500 sequencing projects, of which 294 have been completed and the data deposited in the public databases. GOLD v.2 has been expanded to provide information related to organism properties such as phenotype, ecotype and disease. Furthermore, project relevance and availability information is now included. GOLD is available at http://www.genomesonline.org. It is also mirrored at the Institute of Molecular Biology and Biotechnology, Crete, Greece at http://gold.imbb.forth.gr/

  3. Institute for Sustainable Energy

    SciTech Connect

    Agrawal, Ajay

    2016-03-28

    Alternate fuels offer unique challenges and opportunities as energy source for power generation, vehicular transportation, and industrial applications. Institute for Sustainable Energy (ISE) at UA conducts innovative research to utilize the complex mix of domestically-produced alternate fuels to achieve low-emissions, high energy-efficiency, and fuel-flexibility. ISE also provides educational and advancement opportunities to students and researchers in the energy field. Basic research probing the physics and chemistry of alternative fuels has generated practical concepts investigated in a burner and engine test platforms.

  4. Spaceborne Photonics Institute

    NASA Technical Reports Server (NTRS)

    Venable, D. D.; Farrukh, U. O.; Han, K. S.; Hwang, I. H.; Jalufka, N. W.; Lowe, C. W.; Tabibi, B. M.; Lee, C. J.; Lyons, D.; Maclin, A.

    1994-01-01

    This report describes in chronological detail the development of the Spaceborne Photonics Institute as a sustained research effort at Hampton University in the area of optical physics. This provided the research expertise to initiate a PhD program in Physics. Research was carried out in the areas of: (1) modelling of spaceborne solid state laser systems; (2) amplified spontaneous emission in solar pumped iodine lasers; (3) closely simulated AM0 CW solar pumped iodine laser and repeatedly short pulsed iodine laser oscillator; (4) a materials spectroscopy and growth program; and (5) laser induced fluorescence and atomic and molecular spectroscopy.

  5. Osteopathic postdoctoral training institutions.

    PubMed

    Schmit, Steven F

    2008-03-01

    The Osteopathic Postdoctoral Training Institution (OPTI) program was established by the American Osteopathic Association (AOA) in 1995 as a support and accreditation structure for osteopathic graduate medical education. Since 1999, all AOA-approved postdoctoral training programs are required to take place in OPTIs. In a continuing effort to further define standards for quality and to promote program development, the AOA's 2007 Annual OPTI Workshop focused on recommended changes to the OPTI standards document. In addition, an OPTI Inspectors Workshop was held in January 2008 to increase interrater reliability in determining whether individual OPTIs have met specific criteria.

  6. Whole-exome/genome sequencing and genomics.

    PubMed

    Grody, Wayne W; Thompson, Barry H; Hudgins, Louanne

    2013-12-01

    As medical genetics has progressed from a descriptive entity to one focused on the functional relationship between genes and clinical disorders, emphasis has been placed on genomics. Genomics, a subelement of genetics, is the study of the genome, the sum total of all the genes of an organism. The human genome, which is contained in the 23 pairs of nuclear chromosomes and in the mitochondrial DNA of each cell, comprises >6 billion nucleotides of genetic code. There are some 23,000 protein-coding genes, a surprisingly small fraction of the total genetic material, with the remainder composed of noncoding DNA, regulatory sequences, and introns. The Human Genome Project, launched in 1990, produced a draft of the genome in 2001 and then a finished sequence in 2003, on the 50th anniversary of the initial publication of Watson and Crick's paper on the double-helical structure of DNA. Since then, this mass of genetic information has been translated at an ever-increasing pace into useable knowledge applicable to clinical medicine. The recent advent of massively parallel DNA sequencing (also known as shotgun, high-throughput, and next-generation sequencing) has brought whole-genome analysis into the clinic for the first time, and most of the current applications are directed at children with congenital conditions that are undiagnosable by using standard genetic tests for single-gene disorders. Thus, pediatricians must become familiar with this technology, what it can and cannot offer, and its technical and ethical challenges. Here, we address the concepts of human genomic analysis and its clinical applicability for primary care providers.

  7. Differentiation of Higher Education Institutions.

    ERIC Educational Resources Information Center

    Cazenave, P.; Lapointe, S.

    1983-01-01

    Historical and political influences in the trend toward diversification in French universities are traced. Related issues discussed include institutional versus governmental preferences, institutional functions (curriculum, vocational training, research), and implications for the quality and democratization of higher education. (MSE)

  8. Institutional Research with "Smart Machines."

    ERIC Educational Resources Information Center

    Mason, Thomas R.

    1985-01-01

    Artificial intelligence programing for computers is advancing rapidly. The translation of databases into an institutional research knowledge base is explored, including the heuristic knowledge of institutional research experience. (Author/MLW)

  9. HeteroGenome: database of genome periodicity

    PubMed Central

    Chaley, Maria; Kutyrkin, Vladimir; Tulbasheva, Gayane; Teplukhina, Elena; Nazipova, Nafisa

    2014-01-01

    We present the first release of the HeteroGenome database collecting latent periodicity regions in genomes. Tandem repeats and highly divergent tandem repeats along with the regions of a new type of periodicity, known as profile periodicity, have been collected for the genomes of Saccharomyces cerevisiae, Arabidopsis thaliana, Caenorhabditis elegans and Drosophila melanogaster. We obtained data with the aid of a spectral-statistical approach to search for reliable latent periodicity regions (with periods up to 2000 bp) in DNA sequences. The original two-level mode of data presentation (a broad view of the region of latent periodicity and a second level indicating conservative fragments of its structure) was further developed to enable us to obtain the estimate, without redundancy, that latent periodicity regions make up ∼10% of the analyzed genomes. Analysis of the quantitative and qualitative content of located periodicity regions on all chromosomes of the analyzed organisms revealed dominant characteristic types of periodicity in the genomes. The pattern of density distribution of latent periodicity regions on chromosome unambiguously characterizes each chromosome in genome. Database URL: http://www.jcbi.ru/lp_baze/ PMID:24857969

  10. Complete genome sequence of Staphylothermus hellenicus P8T

    SciTech Connect

    Anderson, Iain; Wirth, Reinhard; Lucas, Susan; Copeland, A; Lapidus, Alla L.; Cheng, Jan-Fang; Goodwin, Lynne A.; Pitluck, Sam; Davenport, Karen W.; Detter, J. Chris; Han, Cliff; Tapia, Roxanne; Land, Miriam L; Hauser, Loren John; Pati, Amrita; Mikhailova, Natalia; Woyke, Tanja; Klenk, Hans-Peter; Kyrpides, Nikos C; Ivanova, N

    2011-01-01

    Staphylothermus hellenicus belongs to the order Desulfurococcales within the archaeal phy- lum Crenarchaeota. Strain P8T is the type strain of the species and was isolated from a shal- low hydrothermal vent system at Palaeochori Bay, Milos, Greece. It is a hyperthermophilic, anaerobic heterotroph. Here we describe the features of this organism together with the com- plete genome sequence and annotation. The 1,580,347 bp genome with its 1,668 protein- coding and 48 RNA genes was sequenced as part of a DOE Joint Genome Institute (JGI) La- boratory Sequencing Program (LSP) project.

  11. Developing a platform for genomic medicine in Mexico.

    PubMed

    Jimenez-Sanchez, Gerardo

    2003-04-11

    Mexico is preparing to develop a genomic medicine program focused on national health problems. Modern Mexicans result from an admixture of more than 65 native Indian groups with Spaniards, leading to a unique genetic makeup and a characteristic set of disease susceptibilities. Since 1999, more than 100 experts from different fields have joined efforts with government, academia, and industry to identify priorities and goals for genomic medicine in Mexico. The plan includes establishment of an Institute of Genomic Medicine with strong intramural and extramural programs. This project is expected to ease the social and financial burden of health problems in Mexico.

  12. Linking cancer genome to proteome: NCI's investment into proteogenomics.

    PubMed

    Rivers, Robert C; Kinsinger, Christopher; Boja, Emily S; Hiltke, Tara; Mesri, Mehdi; Rodriguez, Henry

    2014-12-01

    Advances in both targeted and unbiased MS-based proteomics are now at a mature stage for comprehensively and reproducibly characterizing a large part of the cancer proteome. These developments combined with the extensive genomic characterization of several cancer types by large-scale initiatives such as the International Cancer Genome Consortium and Cancer Genome Atlas Project have paved the way for proteogenomic analysis of omics datasets and integration methods. The advances serve as the basis for the National Cancer Institute's Clinical Proteomic Tumor Analysis Consortium and this article highlights its current work and future steps in the area of proteogenomics.

  13. Tackling the Triple-Threat Genome of Miscanthus x giganteus (2010 JGI User Meeting)

    SciTech Connect

    Moose, Steve

    2010-03-25

    Steve Moose from the University of Illinois at Urbana-Champaign and the Energy Biosciences Institute on "Tackling the Triple-Threat Genome of Miscanthus x giganteus" on March 25, 2010 at the 5th Annual DOE JGI User Meeting

  14. Tackling the Triple-Threat Genome of Miscanthus x giganteus (2010 JGI User Meeting)

    ScienceCinema

    Moose, Steve

    2016-07-12

    Steve Moose from the University of Illinois at Urbana-Champaign and the Energy Biosciences Institute on "Tackling the Triple-Threat Genome of Miscanthus x giganteus" on March 25, 2010 at the 5th Annual DOE JGI User Meeting

  15. Fulfilling the Promise of a Sequenced Human Genome – Part I

    SciTech Connect

    Green, Eric

    2009-05-27

    Eric Green, scientific director of the National Human Genome Research Institute (NHGRI), gives the opening keynote speech at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM on May 27, 2009. Part 1 of 2

  16. Fulfilling the Promise of a Sequenced Human Genome – Part II

    SciTech Connect

    Green, Eric

    2009-05-27

    Eric Green, scientific director of the National Human Genome Research Institute (NHGRI), gives the opening keynote speech at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM on May 27, 2009. Part 2 of 2

  17. The Laccaria and Tuber Genomes Reveal Unique Signatures of Mycorrhizal Symbiosis Evolution (2010 JGI User Meeting)

    SciTech Connect

    Knapp, Steve

    2010-03-24

    Francis Martin from the French agricultural research institute INRA talks on how "The Laccaria and Tuber genomes reveal unique signatures of mycorrhizal symbiosis evolution" on March 24, 2010 at the 5th Annual DOE JGI User Meeting

  18. Draft Transportation Institutional Plan

    SciTech Connect

    Not Available

    1985-09-01

    The Department of Energy recognizes that the success of its program to develop and implement a national system for nuclear waste management and disposal depends on broad-based public understanding and acceptance. While each program element has its particular sensitivity, the transportation of the waste may potentially affect the greatest number of people, and accordingly is highly visible and potentially issue-laden. Therefore, the Office of Civilian Radioactive Waste Management has developed this Transportation Institutional Plan to lay the foundation for interaction among all interested parties for the purpose of identifying and resolving issues of concern. The Plan is divided into four chapters. Chapter 1 provides bachground information and discusses the purpose of the Plan and the policy guidance for establishing the transportation system. Chapter 2 introduces the major participants who must interact to build both the system itself and the consensus philosophy that is essential for effective operations. Chapter 3 suggests mechanisms for interaction that will ensure wide participation in program planning and implementation. And, finally, Chapter 4 suggests a framework for managing and resolving the issues related to development and operation of the transportation system. A list of acronyms and a glossary are included for the reader's convenience. The Plan's appendices provide supporting material to assist the reader in understanding the roles of the involved institutions. 4 figs., 1 tab.

  19. [Antipsychotics in geriatric institutions].

    PubMed

    Szulik, Judith

    2007-01-01

    The present paper approaches the use of antipsychotics in elder people in general, and particularly in geriatric institutions. During the last few years, prescription of antipsychotics in geriatric institutions increased, especially because of the availability of the atypicals, and their use was extended beyond the indications these drugs had been approved for. In dementia they are suggested for treatment of behavioral symptoms, despite having been approved only for cases of aggressiveness and risk of damage. There is a common tendency of perpetuating antipsychotic medication in elder people, with its consequent collateral effects as well. Few years ago, the increase of both risk of cerebrovascular events and of mortality in dementia patients treated with atypical agents was noticed. This generated controversy regarding their use in those kind of patients. Diverse factors associated to caregivers affect the decision of prescribing an antipsychotic in elder people. Non-pharmacological interventions are the first choice when treating behavioral symptoms; pharmacological interventions must take place with the lowest doses possible, with limited durations.

  20. National Space Biomedical Research Institute

    NASA Technical Reports Server (NTRS)

    2003-01-01

    This report outlines the activities of the National Space Biomedical Research Institute (NSBRI) during FY 2003, the sixth year of the NSBRI's programs. It is prepared in accordance with Cooperative Agreement NCC 9-58 between NASA's Lyndon B. Johnson Space Center (JSC) and the Institute's lead institution, Baylor College of Medicine.

  1. A Profile of TAFE Institutes

    ERIC Educational Resources Information Center

    National Centre for Vocational Education Research (NCVER), 2006

    2006-01-01

    This report presents a profile of Australian technical and further education (TAFE) institutes for the 2003 calendar year. The project was undertaken to illustrate the extent of variation in the sector. The report also provides data on TAFE institutes that can be used by the institutes for planning, performance monitoring and marketing purposes.…

  2. Career Development in Institutional Research.

    ERIC Educational Resources Information Center

    Johnson, Mark D.

    1982-01-01

    The background, skills, and views of 20 distinguished professionals were surveyed to provide information about career development in institutional research and to provide ideas about program development. The respondents were members of the Association for Institutional Research and they included seven institutional researchers and planners, three…

  3. Institutional Effectiveness and Student Success.

    ERIC Educational Resources Information Center

    Kreider, Paul E.; And Others

    Since the early 1980's, the primary institutional mission of Mount Hood Community College (MHCC) in Gresham, Oregon, has been identified as student success. Toward that end, the college has instituted an ongoing systematic review of instructional program improvement and implemented institutional strategic planning directly linked to budget…

  4. Improving Institutional Report Card Indicators

    ERIC Educational Resources Information Center

    McGowan, Veronica

    2016-01-01

    Institutional report cards are increasingly being used by higher educational institutions to present academic outcomes to external audiences of prospective students and parents, as well as program and institutional evaluators. While some prospective students are served by national transparency measures most users mine information from the…

  5. MIPS: a database for protein sequences and complete genomes.

    PubMed Central

    Mewes, H W; Hani, J; Pfeiffer, F; Frishman, D

    1998-01-01

    The MIPS group [Munich Information Center for Protein Sequences of the German National Center for Environment and Health (GSF)] at the Max-Planck-Institute for Biochemistry, Martinsried near Munich, Germany, is involved in a number of data collection activities, including a comprehensive database of the yeast genome, a database reflecting the progress in sequencing the Arabidopsis thaliana genome, the systematic analysis of other small genomes and the collection of protein sequence data within the framework of the PIR-International Protein Sequence Database (described elsewhere in this volume). Through its WWW server (http://www.mips.biochem.mpg.de ) MIPS provides access to a variety of generic databases, including a database of protein families as well as automatically generated data by the systematic application of sequence analysis algorithms. The yeast genome sequence and its related information was also compiled on CD-ROM to provide dynamic interactive access to the 16 chromosomes of the first eukaryotic genome unraveled. PMID:9399795

  6. Genome editing: intellectual property and product development in plant biotechnology.

    PubMed

    Schinkel, Helga; Schillberg, Stefan

    2016-07-01

    Genome editing is a revolutionary technology in molecular biology. While scientists are fascinated with the unlimited possibilities provided by directed and controlled changes in DNA in eukaryotes and have eagerly adopted such tools for their own experiments, an understanding of the intellectual property (IP) implications involved in bringing genome editing-derived products to market is often lacking. Due to the ingenuity of genome editing, the time between new product conception and its actual existence can be relatively short; therefore knowledge about IP of the various genome editing methods is relevant. This point must be regarded in a national framework as patents are instituted nationally. Therefore, when designing scientific work that could lead to a product, it is worthwhile to consider the different methods used for genome editing not only for their scientific merits but also for their compatibility with a speedy and reliable launch into the desired market.

  7. Meeting Report from the Genomic Standards Consortium (GSC) Workshop 8

    PubMed Central

    Kyrpides, Nikos; Field, Dawn; Sterk, Peter; Kottmann, Renzo; Glöckner, Frank Oliver; Hirschman, Lynette; Garrity, George M.; Cochrane, Guy; Wooley, John

    2010-01-01

    This report summarizes the proceedings of the 8th meeting of the Genomic Standards Consortium held at the Department of Energy Joint Genome Institute in Walnut Creek, CA, USA on September 9-11, 2009. This three-day workshop marked the maturing of Genomic Standards Consortium from an informal gathering of researchers interested in developing standards in the field of genomic and metagenomics to an established community with a defined governance mechanism, its own open access journal, and a family of established standards for describing genomes, metagenomes and marker studies (i.e. ribosomal RNA gene surveys). There will be increased efforts within the GSC to reach out to the wider scientific community via a range of new projects. Further information about the GSC and its activities can be found at http://gensc.org/. PMID:21304696

  8. Genomic medicine in Mexico: initial steps and the road ahead.

    PubMed

    Jimenez-Sanchez, Gerardo; Silva-Zolezzi, Irma; Hidalgo, Alfredo; March, Santiago

    2008-08-01

    Mexico faces important demographic and epidemiological transitions with significant implications to patterns of disease, disability, and death. On the one hand, there are problems of underdevelopment and, on the other, the emerging challenges of the chronic and degenerative diseases of the industrialized world. For these diseases, prevention becomes a key strategy for alleviating a major burden to the economy and health of the Mexican population. Genomic medicine has become a priority to the Mexican government as a means of finding new strategies to tackle common diseases. In 2000, strategic planning for genomic medicine began, from a feasibility study and a multi-institutional consortium effort, to the creation of a National Institute of Genomic Medicine by the Mexican congress in 2004. Current research programs in genomic medicine in Mexico include the construction of a haplotype map of the Mexican population, several genome-wide association studies for common diseases, such as diabetes, obesity, cardiovascular disease, and cancer, as well as translational medicine projects that include biomarkers discovery for several kinds of cancer, pharmacogenomics, and nutrigenomics. Although this strategy has been successful, there are challenges that still need to be addressed, including increased investment in science and technology to stimulate a more vigorous and competitive research environment, development of more effective basic and clinical research synergies, recruitment and training of more human resources in genomic medicine, developing mechanisms to stimulate translational research, and developing a more modern regulatory framework to ensure that genomic medicine will successfully contribute to improve healthcare in the Mexican population.

  9. Phytozome: a comparative platform for green plant genomics.

    PubMed

    Goodstein, David M; Shu, Shengqiang; Howson, Russell; Neupane, Rochak; Hayes, Richard D; Fazo, Joni; Mitros, Therese; Dirks, William; Hellsten, Uffe; Putnam, Nicholas; Rokhsar, Daniel S

    2012-01-01

    The number of sequenced plant genomes and associated genomic resources is growing rapidly with the advent of both an increased focus on plant genomics from funding agencies, and the application of inexpensive next generation sequencing. To interact with this increasing body of data, we have developed Phytozome (http://www.phytozome.net), a comparative hub for plant genome and gene family data and analysis. Phytozome provides a view of the evolutionary history of every plant gene at the level of sequence, gene structure, gene family and genome organization, while at the same time providing access to the sequences and functional annotations of a growing number (currently 25) of complete plant genomes, including all the land plants and selected algae sequenced at the Joint Genome Institute, as well as selected species sequenced elsewhere. Through a comprehensive plant genome database and web portal, these data and analyses are available to the broader plant science research community, providing powerful comparative genomics tools that help to link model systems with other plants of economic and ecological importance.

  10. Beyond Base Pairs to Bedside: A Population Perspective on How Genomics Can Improve Health

    PubMed Central

    Gwinn, Marta; Bowen, M. Scott; Dotson, W. David

    2012-01-01

    A decade after the sequencing of the human genome, the National Human Genome Research Institute announced a strategic plan for genomic medicine. It calls for evaluating the structure and biology of genomes, understanding the biology of disease, advancing the science of medicine, and improving the effectiveness of health care. Fulfilling the promise of genomics urgently requires a population perspective to complement the bench-to-bedside model of translation. A population approach should assess the contribution of genomics to health in the context of social and environmental determinants of disease; evaluate genomic applications that may improve health care; design strategies for integrating genomics into practice; address ethical, legal, and social issues; and measure the population health impact of new technologies. PMID:22095352

  11. CPTAC Proteomics Data on UCSC Genome Browser | Office of Cancer Clinical Proteomics Research

    Cancer.gov

    The National Cancer Institute's Clinical Proteomic Tumor Analysis Consortium scientists are working together with the University of California, Santa Cruz (UCSC) Genomics Institute to provide public access to cancer proteomics data via the UCSC Genome Browser. This effort extends accessibility of the CPTAC data to more researchers and provides an additional level of analysis to assist the cancer biology community.

  12. State of cat genomics.

    PubMed

    O'Brien, Stephen J; Johnson, Warren; Driscoll, Carlos; Pontius, Joan; Pecon-Slattery, Jill; Menotti-Raymond, Marilyn

    2008-06-01

    Our knowledge of cat family biology was recently expanded to include a genomics perspective with the completion of a draft whole genome sequence of an Abyssinian cat. The utility of the new genome information has been demonstrated by applications ranging from disease gene discovery and comparative genomics to species conservation. Patterns of genomic organization among cats and inbred domestic cat breeds have illuminated our view of domestication, revealing linkage disequilibrium tracks consequent of breed formation, defining chromosome exchanges that punctuated major lineages of mammals and suggesting ancestral continental migration events that led to 37 modern species of Felidae. We review these recent advances here. As the genome resources develop, the cat is poised to make a major contribution to many areas in genetics and biology.

  13. Genomics of oral bacteria.

    PubMed

    Duncan, Margaret J

    2003-01-01

    Advances in bacterial genetics came with the discovery of the genetic code, followed by the development of recombinant DNA technologies. Now the field is undergoing a new revolution because of investigators' ability to sequence and assemble complete bacterial genomes. Over 200 genome projects have been completed or are in progress, and the oral microbiology research community has benefited through projects for oral bacteria and their non-oral-pathogen relatives. This review describes features of several oral bacterial genomes, and emphasizes the themes of species relationships, comparative genomics, and lateral gene transfer. Genomics is having a broad impact on basic research in microbial pathogenesis, and will lead to new approaches in clinical research and therapeutics. The oral microbiota is a unique community especially suited for new challenges to sequence the metagenomes of microbial consortia, and the genomes of uncultivable bacteria.

  14. The European Bioinformatics Institute's data resources

    PubMed Central

    Brooksbank, Catherine; Camon, Evelyn; Harris, Midori A.; Magrane, Michele; Martin, Maria Jesus; Mulder, Nicola; O'Donovan, Claire; Parkinson, Helen; Tuli, Mary Ann; Apweiler, Rolf; Birney, Ewan; Brazma, Alvis; Henrick, Kim; Lopez, Rodrigo; Stoesser, Guenter; Stoehr, Peter; Cameron, Graham

    2003-01-01

    As the amount of biological data grows, so does the need for biologists to store and access this information in central repositories in a free and unambiguous manner. The European Bioinformatics Institute (EBI) hosts six core databases, which store information on DNA sequences (EMBL-Bank), protein sequences (SWISS-PROT and TrEMBL), protein structure (MSD), whole genomes (Ensembl) and gene expression (ArrayExpress). But just as a cell would be useless if it couldn't transcribe DNA or translate RNA, our resources would be compromised if each existed in isolation. We have therefore developed a range of tools that not only facilitate the deposition and retrieval of biological information, but also allow users to carry out searches that reflect the interconnectedness of biological information. The EBI's databases and tools are all available on our website at www.ebi.ac.uk. PMID:12519944

  15. Querying genomic databases

    SciTech Connect

    Baehr, A.; Hagstrom, R.; Joerg, D.; Overbeek, R.

    1991-09-01

    A natural-language interface has been developed that retrieves genomic information by using a simple subset of English. The interface spares the biologist from the task of learning database-specific query languages and computer programming. Currently, the interface deals with the E. coli genome. It can, however, be readily extended and shows promise as a means of easy access to other sequenced genomic databases as well.

  16. The genome sequence of sweet cherry (Prunus avium) for use in genomics-assisted breeding.

    PubMed

    Shirasawa, Kenta; Isuzugawa, Kanji; Ikenaga, Mitsunobu; Saito, Yutaro; Yamamoto, Toshiya; Hirakawa, Hideki; Isobe, Sachiko

    2017-05-25

    We determined the genome sequence of sweet cherry (Prunus avium) using next-generation sequencing technology. The total length of the assembled sequences was 272.4 Mb, consisting of 10,148 scaffold sequences with an N50 length of 219.6 kb. The sequences covered 77.8% of the 352.9 Mb sweet cherry genome, as estimated by k-mer analysis, and included >96.0% of the core eukaryotic genes. We predicted 43,349 complete and partial protein-encoding genes. A high-density consensus map with 2,382 loci was constructed using double-digest restriction site-associated DNA sequencing. Comparing the genetic maps of sweet cherry and peach revealed high synteny between the two genomes; thus the scaffolds were integrated into pseudomolecules using map- and synteny-based strategies. Whole-genome resequencing of six modern cultivars found 1,016,866 SNPs and 162,402 insertions/deletions, out of which 0.7% were deleterious. The sequence variants, as well as simple sequence repeats, can be used as DNA markers. The genomic information helps us to identify agronomically important genes and will accelerate genetic studies and breeding programs for sweet cherries. Further information on the genomic sequences and DNA markers is available in DBcherry (http://cherry.kazusa.or.jp (8 May 2017, date last accessed)). © The Author 2017. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

  17. Institutional analysis for energy policy

    SciTech Connect

    Morris, F.A.; Cole, R.J.

    1980-07-01

    This report summarizes principles, techniques, and other information for doing institutional analyses in the area of energy policy. The report was prepared to support DOE's Regional Issues Identification and Assessment (RIIA) program. RIIA identifies environmental, health, safety, socioeconomic, and institutional issues that could accompany hypothetical future scenarios for energy consumption and production on a regional basis. Chapter 1 provides some theoretical grounding in institutional analysis. Chapter 2 provides information on constructing institutional maps of the processes for bringing on line energy technologies and facilities contemplated in RIIA scenarios. Chapter 3 assesses the institutional constraints, opportunities, and impacts that affect whether these technologies and facilities would in fact be developed. Chapters 4 and 5 show how institutional analysis can support use of exercises such as RIIA in planning institutional change and making energy policy choices.

  18. Cyclotron Institute Upgrade Project

    SciTech Connect

    Clark, Henry; Yennello, Sherry; Tribble, Robert

    2014-08-26

    The Cyclotron Institute at Texas A&M University has upgraded its accelerator facilities to extend research capabilities with both stable and radioactive beams. The upgrade is divided into three major tasks: (1) re-commission the K-150 (88”) cyclotron, couple it to existing beam lines to provide intense stable beams into the K-500 experimental areas and use it as a driver to produce radioactive beams; (2) develop light ion and heavy ion guides for stopping radioactive ions created with the K-150 beams; and (3) transport 1+ ions from the ion guides into a charge-breeding electron-cyclotron-resonance ion source (CB-ECR) to produce highly-charged radioactive ions for acceleration in the K-500 cyclotron. When completed, the upgraded facility will provide high-quality re-accelerated secondary beams in a unique energy range in the world.

  19. The Karst Waters Institute

    NASA Astrophysics Data System (ADS)

    The Karst Waters Institute (KWI) is a U.S. research organization that was formed to combine the skills of academic, governmental, and private sector specialists to solve existing karst water problems and anticipate future problems. KWI has been incorporated as a not-for-profit corporation in West Virginia to provide the human expertise and database needed to assist the nation in the preservation and utilization of its water resources. KWI plans to develop a core of resident and visiting scientists from across the nation and overseas, technicians, support staff, and graduate students. Its mission is to conduct research to improve our understanding of karst phenomena, to develop techniques to prevent environmental problems from occurring in karst areas, to assist in rectifying existing environmental problems, and to provide education and training for professionals and the general public on the risks and benefits of karst areas.

  20. Institutional Profile: Golden Helix Institute of Biomedical Research: interdisciplinary research and educational activities in pharmacogenomics and personalized medicine.

    PubMed

    Mitropoulos, Konstantinos; Innocenti, Federico; van Schaik, Ron H; Lezhava, Alexander; Tzimas, Giannis; Kollia, Panagoula; Macek, Milan; Fortina, Paolo; Patrinos, George P

    2012-03-01

    The Golden Helix Institute of Biomedical Research is an international nonprofit scientific organization with interdisciplinary research and educational activities in the field of genome medicine in Europe, Asia and Latin America. These activities are supervised by an international scientific advisory council, consisting of world leaders in the field of genomics and translational medicine. Research activities include the regional coordination of the Pharmacogenomics for Every Nation Initiative in Europe, in an effort to integrate pharmacogenomics in developing countries, the development of several national/ethnic genetic databases and related web services and the critical assessment of the impact of genetics and genomic medicine on society in various countries. Educational activities also include the organization of the Golden Helix Symposia(®), which are high-profile scientific research symposia in the field of personalized medicine and the Golden Helix Pharmacogenomics Days, an international educational activity focused on pharmacogenomics, as part of its international pharmacogenomics education and outreach efforts.

  1. Genomes by design

    PubMed Central

    Haimovich, Adrian D.; Muir, Paul; Isaacs, Farren J.

    2016-01-01

    Next-generation DNA sequencing has revealed the complete genome sequences of numerous organisms, establishing a fundamental and growing understanding of genetic variation and phenotypic diversity. Engineering at the gene, network and whole-genome scale aims to introduce targeted genetic changes both to explore emergent phenotypes and to introduce new functionalities. Expansion of these approaches into massively parallel platforms establishes the ability to generate targeted genome modifications, elucidating causal links between genotype and phenotype, as well as the ability to design and reprogramme organisms. In this Review, we explore techniques and applications in genome engineering, outlining key advances and defining challenges. PMID:26260262

  2. Genomics of Clostridium tetani.

    PubMed

    Brüggemann, Holger; Brzuszkiewicz, Elzbieta; Chapeton-Montes, Diana; Plourde, Lucile; Speck, Denis; Popoff, Michel R

    2015-05-01

    Genomic information about Clostridium tetani, the causative agent of the tetanus disease, is scarce. The genome of strain E88, a strain used in vaccine production, was sequenced about 10 years ago. One additional genome (strain 12124569) has recently been released. Here we report three new genomes of C. tetani and describe major differences among all five C. tetani genomes. They all harbor tetanus-toxin-encoding plasmids that contain highly conserved genes for TeNT (tetanus toxin), TetR (transcriptional regulator of TeNT) and ColT (collagenase), but substantially differ in other plasmid regions. The chromosomes share a large core genome that contains about 85% of all genes of a given chromosome. The non-core chromosome comprises mainly prophage-like genomic regions and genes encoding environmental interaction and defense functions (e.g. surface proteins, restriction-modification systems, toxin-antitoxin systems, CRISPR/Cas systems) and other fitness functions (e.g. transport systems, metabolic activities). This new genome information will help to assess the level of genome plasticity of the species C. tetani and provide the basis for detailed comparative studies.

  3. Filarial and Wolbachia genomics

    PubMed Central

    SCOTT, A. L.; GHEDIN, E.; NUTMAN, T. B.; McREYNOLDS, L. A.; POOLE, C. B.; SLATKO, B. E.; FOSTER, J. M.

    2012-01-01

    SUMMARY Filarial nematode parasites, the causative agents for a spectrum of acute and chronic diseases including lymphatic filariasis and river blindness, threaten the well-being and livelihood of hundreds of millions of people in the developing regions of the world. The 2007 publication on a draft assembly of the 95-Mb genome of the human filarial parasite Brugia malayi – representing the first helminth parasite genome to be sequenced – has been followed in rapid succession by projects that have resulted in the genome sequencing of six additional filarial species, seven nonfilarial nematode parasites of animals and nearly 30 plant parasitic and free-living species. Parallel to the genomic sequencing, transcriptomic and proteomic projects have facilitated genome annotation, expanded our understanding of stage-associated gene expression and provided a first look at the role of epigenetic regulation of filarial genomes through microRNAs. The expansion in filarial genomics will also provide a significant enrichment in our knowledge of the diversity and variability in the genomes of the endosymbiotic bacterium Wolbachia leading to a better understanding of the genetic principles that govern filarial–Wolbachia mutualism. The goal here is to provide an overview of the trends and advances in filarial and Wolbachia genomics. PMID:22098559

  4. Fungal Genomics Program

    SciTech Connect

    Grigoriev, Igor

    2012-03-12

    The JGI Fungal Genomics Program aims to scale up sequencing and analysis of fungal genomes to explore the diversity of fungi important for energy and the environment, and to promote functional studies on a system level. Combining new sequencing technologies and comparative genomics tools, JGI is now leading the world in fungal genome sequencing and analysis. Over 120 sequenced fungal genomes with analytical tools are available via MycoCosm (www.jgi.doe.gov/fungi), a web-portal for fungal biologists. Our model of interacting with user communities, unique among other sequencing centers, helps organize these communities, improves genome annotation and analysis work, and facilitates new larger-scale genomic projects. This resulted in 20 high-profile papers published in 2011 alone and contributing to the Genomics Encyclopedia of Fungi, which targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts). Our next grand challenges include larger scale exploration of fungal diversity (1000 fungal genomes), developing molecular tools for DOE-relevant model organisms, and analysis of complex systems and metagenomes.

  5. Between Two Fern Genomes

    PubMed Central

    2014-01-01

    Ferns are the only major lineage of vascular plants not represented by a sequenced nuclear genome. This lack of genome sequence information significantly impedes our ability to understand and reconstruct genome evolution not only in ferns, but across all land plants. Azolla and Ceratopteris are ideal and complementary candidates to be the first ferns to have their nuclear genomes sequenced. They differ dramatically in genome size, life history, and habit, and thus represent the immense diversity of extant ferns. Together, this pair of genomes will facilitate myriad large-scale comparative analyses across ferns and all land plants. Here we review the unique biological characteristics of ferns and describe a number of outstanding questions in plant biology that will benefit from the addition of ferns to the set of taxa with sequenced nuclear genomes. We explain why the fern clade is pivotal for understanding genome evolution across land plants, and we provide a rationale for how knowledge of fern genomes will enable progress in research beyond the ferns themselves. PMID:25324969

  6. [Landscape and ecological genomics].

    PubMed

    Tetushkin, E Ia

    2013-10-01

    Landscape genomics is the modern version of landscape genetics, a discipline that arose approximately 10 years ago as a combination of population genetics, landscape ecology, and spatial statistics. It studies the effects of environmental variables on gene flow and other microevolutionary processes that determine genetic connectivity and variations in populations. In contrast to population genetics, it operates at the level of individual specimens rather than at the level of population samples. Another important difference between landscape genetics and genomics and population genetics is that, in the former, the analysis of gene flow and local adaptations takes quantitative account of landforms and features of the matrix, i.e., hostile spaces that separate species habitats. Landscape genomics is a part of population ecogenomics, which, along with community genomics, is a major part of ecological genomics. One of the principal purposes of landscape genomics is the identification and differentiation of various genome-wide and locus-specific effects. The approaches and computation tools developed for combined analysis of genomic and landscape variables make it possible to detect adaptation-related genome fragments, which facilitates the planning of conservation efforts and the prediction of species' fate in response to expected changes in the environment.

  7. Between two fern genomes.

    PubMed

    Sessa, Emily B; Banks, Jo Ann; Barker, Michael S; Der, Joshua P; Duffy, Aaron M; Graham, Sean W; Hasebe, Mitsuyasu; Langdale, Jane; Li, Fay-Wei; Marchant, D Blaine; Pryer, Kathleen M; Rothfels, Carl J; Roux, Stanley J; Salmi, Mari L; Sigel, Erin M; Soltis, Douglas E; Soltis, Pamela S; Stevenson, Dennis W; Wolf, Paul G

    2014-01-01

    Ferns are the only major lineage of vascular plants not represented by a sequenced nuclear genome. This lack of genome sequence information significantly impedes our ability to understand and reconstruct genome evolution not only in ferns, but across all land plants. Azolla and Ceratopteris are ideal and complementary candidates to be the first ferns to have their nuclear genomes sequenced. They differ dramatically in genome size, life history, and habit, and thus represent the immense diversity of extant ferns. Together, this pair of genomes will facilitate myriad large-scale comparative analyses across ferns and all land plants. Here we review the unique biological characteristics of ferns and describe a number of outstanding questions in plant biology that will benefit from the addition of ferns to the set of taxa with sequenced nuclear genomes. We explain why the fern clade is pivotal for understanding genome evolution across land plants, and we provide a rationale for how knowledge of fern genomes will enable progress in research beyond the ferns themselves.

  8. Towards the Perfect Genome Sequence (Opening Keynote) ( 7th Annual SFAF Meeting, 2012)

    ScienceCinema

    Weinstock, George [Washington University

    2016-07-12

    George Weinstock, associate director at the Genome Institute at Washington University, delivered the opening keynote "Towards the Perfect Genome Sequence" at the 2012 Sequencing, Finishing, Analysis in the Future Meeting held June 5-7, 2012 in Santa Fe, New Mexico.

  9. Towards the Perfect Genome Sequence (Opening Keynote) ( 7th Annual SFAF Meeting, 2012)

    SciTech Connect

    Weinstock, George

    2012-06-01

    George Weinstock, associate director at the Genome Institute at Washington University, delivered the opening keynote "Towards the Perfect Genome Sequence" at the 2012 Sequencing, Finishing, Analysis in the Future Meeting held June 5-7, 2012 in Santa Fe, New Mexico.

  10. Complete genome sequence of "Thioalkalivibrio sulfidophilus" HL-EbGr7.

    PubMed

    Muyzer, Gerard; Sorokin, Dimitry Yu; Mavromatis, Konstantinos; Lapidus, Alla; Clum, Alicia; Ivanova, Natalia; Pati, Amrita; d'Haeseleer, Patrick; Woyke, Tanja; Kyrpides, Nikos C

    2011-02-14

    "Thioalkalivibrio sulfidophilus" HL-EbGr7 is an obligately chemolithoautotrophic, haloalkaliphilic sulfur-oxidizing bacterium (SOB) belonging to the Gammaproteobacteria. The strain was found to predominate a full-scale bioreactor, removing sulfide from biogas. Here we report the complete genome sequence of strain HL-EbGr7 and its annotation. The genome was sequenced within the Joint Genome Institute Community Sequencing Program, because of its relevance to the sustainable removal of sulfide from bio- and industrial waste gases.

  11. Complete Genome Sequence of the Thermophilic, Piezophilic, Heterotrophic Bacterium Marinitoga piezophila KA3

    SciTech Connect

    Lucas, Susan; Han, James; Lapidus, Alla L.; Cheng, Jan-Fang; Goodwin, Lynne A.; Pitluck, Sam; Peters, Lin; Mikhailova, Natalia; Teshima, Hazuki; Detter, J. Chris; Han, Cliff; Tapia, Roxanne; Land, Miriam L; Hauser, Loren John; Kyrpides, Nikos C; Ivanova, N; Pagani, Ioanna; Vannier, Pauline; Oger, Phil; Bartlett, Douglas; Noll, Kenneth M; Woyke, Tanja; Jebbar, Mohamed

    2012-01-01

    Marinitoga piezophila KA3 is a thermophilic, anaerobic, chemoorganotrophic, sulfur-reducing bacterium isolated from the Grandbonum deep-sea hydrothermal vent site at the East Pacific Rise (13 degrees N, 2,630-m depth). The genome of M. piezophila KA3 comprises a 2,231,407-bp circular chromosome and a 13,386-bp circular plasmid. This genome was sequenced within Department of Energy Joint Genome Institute CSP 2010.

  12. Home - The Cancer Genome Atlas - Cancer Genome - TCGA

    Cancer.gov

    The Cancer Genome Atlas (TCGA) is a comprehensive and coordinated effort to accelerate our understanding of the molecular basis of cancer through the application of genome analysis technologies, including large-scale genome sequencing.

  13. Teacher Enhancement Institute

    NASA Technical Reports Server (NTRS)

    Marshall-Bradley, Tina

    1994-01-01

    During the 1980's, a period of intense concern over educational quality in the United States, few indicators of U.S. student achievement garnered the interest of policy makers and pundits as successfully as the results of international testing in mathematics and science. This concern was so great that as a part of the Goals 2000 initiative, President George Bush indicated that 'By the year 2000, U.S. students should be first in the world in mathematics and science.' The Clinton Administration is placing a major emphasis, not only on rigorous academic standards and creating a new system for assessing students' progress, but also including professional development as a major focus. The argument being that teachers need more sustained, intensive training to prepare them to teach to higher standards. Executive order 12821 mandates that national laboratories 'assist in the mathematics and science education of our Nation's students, teachers, parents and the public by establishing programs at their agency to provide for training elementary and secondary school teachers to improve their knowledge of mathematics and science'. These and other issues led to the development of ideas for a project that addresses the need for excellence in mathematics, science and technology instruction. In response to these initiatives the NASA/LaRC Teacher Enhancement Institute was proposed. The TEI incorporated systemic reform perspectives, enhanced content knowledge for teachers, and teacher preparation. Emphasis was also placed on recruiting those educators who teach in impoverished urban school districts with at-risk student populations who have been traditionally under represented in science, mathematics, technology and engineering. Participants in the Teacher Enhancement Institute were 37 teachers from grades K-8, teaching in Region 2 in the state of Virginia, as well as 2 preservice teachers from Norfolk State University and one teacher from Dublin, Virginia, where a Science

  14. NEWS: Institute news

    NASA Astrophysics Data System (ADS)

    2000-03-01

    Recognition for teachers The Institute of Physics has continued its programme of recognition for inspiring teachers with nine Teachers Awards in 2000, one at primary level and eight at secondary. The quality and quantity of nominations for secondary awards was very encouraging, especially those nominations made by students, but the number of nominations for teachers in the primary sector was disappointing. The award winners are: Teacher of Primary Science Graham Tomlinson, Cockermouth School, Cumbria Gill Stafford, Greens Norton Church of England Primary School, Towcester, Northants Teachers of Physics (Secondary) John Allen, All Hallows High School, Penwortham, Preston Tim Gamble, Lings Upper School, Northampton Denise Gault, Dalriada School, Ballymoney, Co Antrim Ian Lovat, Ampleforth College, North Yorkshire David Smith, Highgate School, North London Clive Thomas, Newcastle Emlyn Comprehensive School Graham Tomlinson, Cockermouth School, Cumbria Mark Travis, Cape Cornwall School, St Just, Cornwall If you know a teacher in a local primary school who is doing an exceptional job in motivating youngsters and colleagues in the teaching and learning of science, why not consider nominating them for an award? Further details can be obtained from the Institute's Education Department (Steven Chapman) by post or e-mail (schools.education@iop.org .) Annual Congress More details are now available on the various activities at this event taking place on 27 - 30 March 2000 at the Brighton Conference Centre. Among those organized by the Education Department are general science and technology hands-on activities for pupils aged 10 to 12 and more specific physics activities on Static Electricity for older students: * A series of short talks with hands-on demonstrations of music and musical instruments given by musicians, manufacturers and physicists. * A chance for students in years 9 to 13 to experience music making from the professionals' perspective. Mornings, 28 to 30 March

  15. Privacy-preserving GWAS analysis on federated genomic datasets

    PubMed Central

    2015-01-01

    Background The biomedical community benefits from the increasing availability of genomic data to support meaningful scientific research, e.g., Genome-Wide Association Studies (GWAS). However, high quality GWAS usually requires a large amount of samples, which can grow beyond the capability of a single institution. Federated genomic data analysis holds the promise of enabling cross-institution collaboration for effective GWAS, but it raises concerns about patient privacy and medical information confidentiality (as data are being exchanged across institutional boundaries), which becomes an inhibiting factor for the practical use. Methods We present a privacy-preserving GWAS framework on federated genomic datasets. Our method is to layer the GWAS computations on top of secure multi-party computation (MPC) systems. This approach allows two parties in a distributed system to mutually perform secure GWAS computations, but without exposing their private data outside. Results We demonstrate our technique by implementing a framework for minor allele frequency counting and χ2 statistics calculation, one of typical computations used in GWAS. For efficient prototyping, we use a state-of-the-art MPC framework, i.e., Portable Circuit Format (PCF) [1]. Our experimental results show promise in realizing both efficient and secure cross-institution GWAS computations. PMID:26733045

  16. Meeting Report: Incorporating Genomics Research into Undergraduate Curricula

    ERIC Educational Resources Information Center

    Dyer, Betsey Dexter; LeBlanc, Mark D.

    2002-01-01

    In the first of two National Science Foundation (NSF)-funded workshops, 30 professors of biology and computer science from 18 institutions met at Wheaton College in Norton, Massachusetts, on June 6-7, 2002, to share ideas on how to incorporate genomics research into undergraduate curricula. The participants included nine pairs or trios of…

  17. Legume genomics: where we have been, where are we going?

    USDA-ARS?s Scientific Manuscript database

    With the recognition in 2000 that several multi-institutional projects focusing on legume genomics were becoming a reality, the legume research community advocated for organization of an international meeting to address fundamental and applied aspects of legume genetic research. The purposes delinea...

  18. The California Hazards Institute

    NASA Astrophysics Data System (ADS)

    Rundle, J. B.; Kellogg, L. H.; Turcotte, D. L.

    2006-12-01

    California's abundant resources are linked with its natural hazards. Earthquakes, landslides, wildfires, floods, tsunamis, volcanic eruptions, severe storms, fires, and droughts afflict the state regularly. These events have the potential to become great disasters, like the San Francisco earthquake and fire of 1906, that overwhelm the capacity of society to respond. At such times, the fabric of civic life is frayed, political leadership is tested, economic losses can dwarf available resources, and full recovery can take decades. A patchwork of Federal, state and local programs are in place to address individual hazards, but California lacks effective coordination to forecast, prevent, prepare for, mitigate, respond to, and recover from, the harmful effects of natural disasters. Moreover, we do not know enough about the frequency, size, time, or locations where they may strike, nor about how the natural environment and man-made structures would respond. As California's population grows and becomes more interdependent, even moderate events have the potential to trigger catastrophes. Natural hazards need not become natural disasters if they are addressed proactively and effectively, rather than reactively. The University of California, with 10 campuses distributed across the state, has world-class faculty and students engaged in research and education in all fields of direct relevance to hazards. For that reason, the UC can become a world leader in anticipating and managing natural hazards in order to prevent loss of life and property and degradation of environmental quality. The University of California, Office of the President, has therefore established a new system-wide Multicampus Research Project, the California Hazards Institute (CHI), as a mechanism to research innovative, effective solutions for California. The CHI will build on the rich intellectual capital and expertise of the Golden State to provide the best available science, knowledge and tools for

  19. Phanerochaete chrysosporium genomics

    Treesearch

    Luis F. Larrondo; Rafael Vicuna; Dan Cullen

    2005-01-01

    A high quality draft genome sequence has been generated for the lignocellulose-degrading basidiomycete Phanerochaete chrysosporium (Martinez et al. 2004). Analysis of the genome in the context of previously established genetics and physiology is presented. Transposable elements and their potential relationship to genes involved in lignin degradation are systematically...

  20. Unlocking the bovine genome

    USDA-ARS?s Scientific Manuscript database

    The draft genome sequence of cattle (Bos taurus) has now been analyzed by the Bovine Genome Sequencing and Analysis Consortium and the Bovine HapMap Consortium, which together represent an extensive collaboration involving more than 300 scientists from 25 different countries. ...

  1. Genomics for Weed Science

    USDA-ARS?s Scientific Manuscript database

    Numerous genomic-based studies have provided insight to the physiological and evolutionary processes involved in developmental and environmental processes of model plants such as arabidopsis and rice. However, far fewer efforts have been attempted to use genomic resources to study physiological and ...

  2. The cybernetic genome

    NASA Astrophysics Data System (ADS)

    Ben-Jacob, Eshel

    We propose a new picture of the genome as an adaptive cybernetic unit with self-awareness. We further propose that under colonial stress bacteria employ genetic communication which leads to the emergence of creative genomic web or “global brain”.

  3. Genetics and Genomics

    USDA-ARS?s Scientific Manuscript database

    Good progress is being made on genetics and genomics of sugar beet, however it is in process and the tools are now being generated and some results are being analyzed. The GABI BeetSeq project released a first draft of the sugar beet genome of KWS2320, a dihaploid (see http://bvseq.molgen.mpg.de/Gen...

  4. Breeding-assisted genomics.

    PubMed

    Poland, Jesse

    2015-04-01

    The revolution of inexpensive sequencing has ushered in an unprecedented age of genomics. The promise of using this technology to accelerate plant breeding is being realized with a vision of genomics-assisted breeding that will lead to rapid genetic gain for expensive and difficult traits. The reality is now that robust phenotypic data is an increasing limiting resource to complement the current wealth of genomic information. While genomics has been hailed as the discipline to fundamentally change the scope of plant breeding, a more symbiotic relationship is likely to emerge. In the context of developing and evaluating large populations needed for functional genomics, none excel in this area more than plant breeders. While genetic studies have long relied on dedicated, well-structured populations, the resources dedicated to these populations in the context of readily available, inexpensive genotyping is making this philosophy less tractable relative to directly focusing functional genomics on material in breeding programs. Through shifting effort for basic genomic studies from dedicated structured populations, to capturing the entire scope of genetic determinants in breeding lines, we can move towards not only furthering our understanding of functional genomics in plants, but also rapidly improving crops for increased food security, availability and nutrition. Copyright © 2015 Elsevier Ltd. All rights reserved.

  5. Genomics of Disease

    USDA-ARS?s Scientific Manuscript database

    This edited book represents the 23rd symposium in the Stadler Genetics Symposia series, and the general theme of this conference was "The Genomics of Disease." The 24 national and international speakers were invited to discuss their world-class research into the advances that genomics has made on c...

  6. Institutional Review Boards

    PubMed Central

    2015-01-01

    Institutional review boards (IRBs) or research ethics committees provide a core protection for human research participants through advance and periodic independent review of the ethical acceptability of proposals for human research. IRBs were codified in US regulation just over three decades ago and are widely required by law or regulation in jurisdictions globally. Since the inception of IRBs, the research landscape has grown and evolved, as has the system of IRB review and oversight. Evidence of inconsistencies in IRB review and in application of federal regulations has fueled dissatisfaction with the IRB system. Some complain that IRB review is time-consuming and burdensome without clear evidence of effectiveness at protecting human subjects. Multiple proposals have been offered to reform or update the current IRB system, and many alternative models are currently being tried. Current focus on centralizing and sharing reviews requires more attention and evidence. Proposed changes to the US federal regulations may bring more changes. Data and resourcefulness are needed to further develop and test review and oversight models that provide adequate and respectful protections of participant rights and welfare and that are appropriate, efficient, and adaptable for current and future research. PMID:26042632

  7. Integrative Bioengineering Institute

    SciTech Connect

    Eddington, David; Magin,L,Richard; Hetling, John; Cho, Michael

    2009-01-09

    Microfabrication enables many exciting experimental possibilities for medicine and biology that are not attainable through traditional methods. However, in order for microfabricated devices to have an impact they must not only provide a robust solution to a current unmet need, but also be simple enough to seamlessly integrate into standard protocols. Broad dissemination of bioMEMS has been stymied by the common aim of replacing established and well accepted protocols with equally or more complex devices, methods, or materials. The marriage of a complex, difficult to fabricate bioMEMS device with a highly variable biological system is rarely successful. Instead, the design philosophy of my lab aims to leverage a beneficial microscale phenomena (e.g. fast diffusion at the microscale) within a bioMEMS device and adapt to established methods (e.g. multiwell plate cell culture) and demonstrate a new paradigm for the field (adapt instead of replace). In order for the field of bioMEMS to mature beyond novel proof-of-concept demonstrations, researchers must focus on developing systems leveraging these phenomena and integrating into standard labs, which have largely been ignored. Towards this aim, the Integrative Bioengineering Institute has been established.

  8. Coburning in institutional incinerators

    SciTech Connect

    Green, A.; Prine, G.; Yost, R.; Green, B.; Williams, D.; Schwartz, J.; Wagner, J.; Clauson, D.; Proctor, B.; Feinberg, A.

    1987-01-01

    Our program, initiated in 1980, originally sought to replace imported oil by coburning coal and natural gas in oil designed boilers. Success came in 1986 with the co-combustion of coal water slurries (CWS) and natural gas (G) in a 20 MMBtu/hr watertube oil designed boiler. We achieved stable flames over broad load levels, good boiler efficiencies, low emissions, benign ash and--by increasing the G/CWS ratio--full power rating. Our biomass-waste co-combustion experiments will utilize a two chamber ram fed incinerator. Advanced analytical techniques will be used to measure available energy and stack emissions from various waste-biomass-fossil fuel combinations. Heating values, H/C ratios, percent moisture, emissions, prices and tipping fees are discussed. Locally grown annual dry biomass yields of napiergrass and leucaena, energetically equivalent to 30-50 barrels of oil per acre, are reported. Abundant local sources of waste biomass are identified. Together community waste and cultivated and waste biomass constitute a substantial source of renewable energy of use in forested and agricultural regions. Modular waste to energy systems are available in the 10-100 ton per day range. With aggressive recycling and hazardous waste reduction measures and good combustion management and emission controls, emissions should be maintained at low levels. The results from our system, a small modular waste-biomass to energy system, should be applicable to many institutions and small communities. 41 refs., 8 figs., 4 tabs.

  9. Microbial Genomes Multiply

    NASA Technical Reports Server (NTRS)

    Doolittle, Russell F.

    2002-01-01

    The publication of the first complete sequence of a bacterial genome in 1995 was a signal event, underscored by the fact that the article has been cited more than 2,100 times during the intervening seven years. It was a marvelous technical achievement, made possible by automatic DNA-sequencing machines. The feat is the more impressive in that complete genome sequencing has now been adopted in many different laboratories around the world. Four years ago in these columns I examined the situation after a dozen microbial genomes had been completed. Now, with upwards of 60 microbial genome sequences determined and twice that many in progress, it seems reasonable to assess just what is being learned. Are new concepts emerging about how cells work? Have there been practical benefits in the fields of medicine and agriculture? Is it feasible to determine the genomic sequence of every bacterial species on Earth? The answers to these questions maybe Yes, Perhaps, and No, respectively.

  10. The UCSC Genome Browser

    PubMed Central

    Karolchik, Donna; Hinrichs, Angie S.; Kent, W. James

    2011-01-01

    The University of California Santa Cruz (UCSC) Genome Browser is a popular Web-based tool for quickly displaying a requested portion of a genome at any scale, accompanied by a series of aligned annotation “tracks.” The annotations generated by the UCSC Genome Bioinformatics Group and external collaborators include gene predictions, mRNA and expressed sequence tag alignments, simple nucleotide polymorphisms, expression and regulatory data, phenotype and variation data, and pairwise and multiple-species comparative genomics data. All information relevant to a region is presented in one window, facilitating biological analysis and interpretation. The database tables underlying the Genome Browser tracks can be viewed, downloaded, and manipulated using another Web-based application, the UCSC Table Browser. Users can upload personal datasets in a wide variety of formats as custom annotation tracks in both browsers for research or educational purposes. PMID:21975940

  11. Microbial Genomes Multiply

    NASA Technical Reports Server (NTRS)

    Doolittle, Russell F.

    2002-01-01

    The publication of the first complete sequence of a bacterial genome in 1995 was a signal event, underscored by the fact that the article has been cited more than 2,100 times during the intervening seven years. It was a marvelous technical achievement, made possible by automatic DNA-sequencing machines. The feat is the more impressive in that complete genome sequencing has now been adopted in many different laboratories around the world. Four years ago in these columns I examined the situation after a dozen microbial genomes had been completed. Now, with upwards of 60 microbial genome sequences determined and twice that many in progress, it seems reasonable to assess just what is being learned. Are new concepts emerging about how cells work? Have there been practical benefits in the fields of medicine and agriculture? Is it feasible to determine the genomic sequence of every bacterial species on Earth? The answers to these questions maybe Yes, Perhaps, and No, respectively.

  12. Comparative genomics of nematodes.

    PubMed

    Mitreva, Makedonka; Blaxter, Mark L; Bird, David M; McCarter, James P

    2005-10-01

    Recent transcriptome and genome projects have dramatically expanded the biological data available across the phylum Nematoda. Here we summarize analyses of these sequences, which have revealed multiple unexpected results. Despite a uniform body plan, nematodes are more diverse at the molecular level than was previously recognized, with many species- and group-specific novel genes. In the genus Caenorhabditis, changes in chromosome arrangement, particularly local inversions, are also rapid, with breakpoints occurring at 50-fold the rate in vertebrates. Tylenchid plant parasitic nematode genomes contain several genes closely related to genes in bacteria, implicating horizontal gene transfer events in the origins of plant parasitism. Functional genomics techniques are also moving from Caenorhabditis elegans to application throughout the phylum. Soon, eight more draft nematode genome sequences will be available. This unique resource will underpin both molecular understanding of these most abundant metazoan organisms and aid in the examination of the dynamics of genome evolution in animals.

  13. Global Implementation of Genomic Medicine: We Are Not Alone

    PubMed Central

    Manolio, Teri A.; Abramowicz, Marc; Al-Mulla, Fahd; Anderson, Warwick; Balling, Rudi; Berger, Adam C.; Bleyl, Steven; Chakravarti, Aravinda; Chantratita, Wasun; Chisholm, Rex L.; Dissanayake, Vajira H. W.; Dunn, Michael; Dzau, Victor J.; Han, Bok-Ghee; Hubbard, Tim; Kolbe, Anne; Korf, Bruce; Kubo, Michiaki; Lasko, Paul; Leego, Erkki; Mahasirimongkol, Surakameth; Majumdar, Partha P.; Matthijs, Gert; McLeod, Howard L.; Metspalu, Andres; Meulien, Pierre; Miyano, Satoru; Naparstek, Yaakov; O’Rourke, P. Pearl; Patrinos, George P.; Rehm, Heidi L.; Relling, Mary V.; Rennert, Gad; Rodriguez, Laura Lyman; Roden, Dan M.; Shuldiner, Alan R.; Sinha, Sukdev; Tan, Patrick; Ulfendahl, Mats; Ward, Robyn; Williams, Marc S.; Wong, John E.L.; Green, Eric D.; Ginsburg, Geoffrey S.

    2016-01-01

    Advances in high-throughput genomic technologies coupled with a growing number of genomic results potentially useful in clinical care have led to ground-breaking genomic medicine implementation programs in various nations. Many of these innovative programs capitalize on unique local capabilities arising from the structure of their health care systems or their cultural or political milieu, as well as from unusual burdens of disease or risk alleles. Many such programs are being conducted in relative isolation and might benefit from sharing of approaches and lessons learned in other nations. The National Human Genome Research Institute recently brought together 25 of these groups from around the world to describe and compare projects, examine the current state of implementation and desired near-term capabilities, and identify opportunities for collaboration to promote the responsible implementation of genomic medicine. The wide variety of nascent programs in diverse settings demonstrates that implementation of genomic medicine is expanding globally in varied and highly innovative ways. Opportunities for collaboration abound in the areas of evidence generation, health information technology, education, workforce development, pharmacogenomics, and policy and regulatory issues. Several international organizations that are already facilitating effective research collaborations should engage to ensure implementation proceeds collaboratively without potentially wasteful duplication. Efforts to coalesce these groups around concrete but compelling signature projects, such as global eradication of genetically-mediated drug reactions or developing a truly global genomic variant data resource across a wide number of ethnicities, would accelerate appropriate implementation of genomics to improve clinical care world-wide. PMID:26041702

  14. Psychology's dilemma: an institutional neurosis?

    PubMed

    Katzko, Michael W

    2004-12-01

    The term psychology refers both to an institutional discipline and to a subject matter. Henriques, in his article "Psychology Defined" (this issue) , emphasizes the second reference, and its focus can be sharpened by taking into account the first reference. On the one hand, epistemic progress in science is a dynamic process, which, as often as not, cuts across institutional divisions. However, on the other hand there are some problems of disunity that solely concern the institution. That the latter falls within the scope of the Tree of Knowledge is illustrated in how Henriques' "Justification Hypothesis" sheds light on the nature of institutional disunity.

  15. Multi-Species Genome Comparison Sheds New Light on Evolutionary Processes, Cancer Mutations

    ERIC Educational Resources Information Center

    Journal of College Science Teaching, 2005

    2005-01-01

    An international team that includes researchers from the National Human Genome Research Institute (NHGRI), part of the National Institutes of Health (NIH), has discovered that mammalian chromosomes have evolved by breaking at specific sites rather than randomly as long thought--and that many of the breakage hot spots are also involved in human…

  16. Multi-Species Genome Comparison Sheds New Light on Evolutionary Processes, Cancer Mutations

    ERIC Educational Resources Information Center

    Journal of College Science Teaching, 2005

    2005-01-01

    An international team that includes researchers from the National Human Genome Research Institute (NHGRI), part of the National Institutes of Health (NIH), has discovered that mammalian chromosomes have evolved by breaking at specific sites rather than randomly as long thought--and that many of the breakage hot spots are also involved in human…

  17. NEWS: Institute news

    NASA Astrophysics Data System (ADS)

    2000-07-01

    When Mary took up her appointment in the Institute's Education Department in June 1997, she indicated that she wished to return to teaching in two or three years. We have just heard that in September she will be joining the staff of the Science Department at Camden Girls' School, London. Mary's departure from the Institute is a great loss to the Department, where she has worked tirelessly, and with great imagination, to support those who teach physics at all secondary levels - and at primary level too when the opportunity presented itself. She has made tremendous contributions to the careers side of the Department's work, supporting careers events, providing informal training for others willing to do the same, helping to develop new careers materials and identifying people whom the Institute could use as role models or as the subject of case studies in print or electronic publications. Mary has been equally happy and willing to support pupils, students and teachers, and has been a wonderful role model herself, coming from an industrial research background, training for teaching after a career break and willing and able to teach biology, chemistry and design technology as well as physics. Mary has also written and edited Phases virtually single-handed. We are delighted to hear that Mary will continue to support the department's work as one of its teacher `volunteers'. Ilya Eigenbrot We are pleased to report that Ilya Eigenbrot, who will be known to some through his work at the Royal Institution and his appearances at the Christmas Lectures in a technical support role, has agreed to give the IOP Schools (touring) Lecture next year. The subject will be Lasers and this will follow nicely on to Zbig's lecture this year. Resources (print) Physics on Course The tenth issue of the Institute's popular guide to higher education, Physics on Course 2001, will be published early in July and distributed to all schools and colleges in the United Kingdom and the Republic of

  18. Education in Young Offender Institutions and Secure Youth Care Institutions

    ERIC Educational Resources Information Center

    Smeets, Ed

    2014-01-01

    The main goal of this study was to gain a better insight into efforts made to provide optimum education to juveniles in young offender institutions and in secure youth care institutions, and into barriers with which educators are confronted in this process. Results show that for a substantial number of juveniles insufficient information is…

  19. Education in Young Offender Institutions and Secure Youth Care Institutions

    ERIC Educational Resources Information Center

    Smeets, Ed

    2014-01-01

    The main goal of this study was to gain a better insight into efforts made to provide optimum education to juveniles in young offender institutions and in secure youth care institutions, and into barriers with which educators are confronted in this process. Results show that for a substantial number of juveniles insufficient information is…

  20. Accredited Postsecondary Institutions and Programs. Including Institutions Holding Preaccredited Status.

    ERIC Educational Resources Information Center

    Ross, Leslie, W.; Green, Yvonne W.

    This is the fifth edition of a list of postsecondary educational institutions and programs that are accredited by, or that have preaccredited status awarded by, the regional and national accrediting agencies formally recognized by the Secretary of Education. In addition to the lists of postsecondary specialized and vocational institutions and…

  1. Validation of rice genome sequence by optical mapping

    PubMed Central

    Zhou, Shiguo; Bechner, Michael C; Place, Michael; Churas, Chris P; Pape, Louise; Leong, Sally A; Runnheim, Rod; Forrest, Dan K; Goldstein, Steve; Livny, Miron; Schwartz, David C

    2007-01-01

    Background Rice feeds much of the world, and possesses the simplest genome analyzed to date within the grass family, making it an economically relevant model system for other cereal crops. Although the rice genome is sequenced, validation and gap closing efforts require purely independent means for accurate finishing of sequence build data. Results To facilitate ongoing sequencing finishing and validation efforts, we have constructed a whole-genome SwaI optical restriction map of the rice genome. The physical map consists of 14 contigs, covering 12 chromosomes, with a total genome size of 382.17 Mb; this value is about 11% smaller than original estimates. 9 of the 14 optical map contigs are without gaps, covering chromosomes 1, 2, 3, 4, 5, 7, 8 10, and 12 in their entirety – including centromeres and telomeres. Alignments between optical and in silico restriction maps constructed from IRGSP (International Rice Genome Sequencing Project) and TIGR (The Institute for Genomic Research) genome sequence sources are comprehensive and informative, evidenced by map coverage across virtually all published gaps, discovery of new ones, and characterization of sequence misassemblies; all totalling ~14 Mb. Furthermore, since optical maps are ordered restriction maps, identified discordances are pinpointed on a reliable physical scaffold providing an independent resource for closure of gaps and rectification of misassemblies. Conclusion Analysis of sequence and optical mapping data effectively validates genome sequence assemblies constructed from large, repeat-rich genomes. Given this conclusion we envision new applications of such single molecule analysis that will merge advantages offered by high-resolution optical maps with inexpensive, but short sequence reads generated by emerging sequencing platforms. Lastly, map construction techniques presented here points the way to new types of comparative genome analysis that would focus on discernment of structural differences

  2. Evolution of Genome Architecture

    PubMed Central

    Koonin, Eugene V.

    2012-01-01

    Charles Darwin believed that all traits of organisms have been honed to near perfection by natural selection. The empirical basis underlying Darwin’s conclusions consisted of numerous observations made by him and other naturalists on the exquisite adaptations of animals and plants to their natural habitats and on the impressive results of artificial selection. Darwin fully appreciated the importance of heredity but was unaware of the nature and, in fact, the very existence of genomes. A century and a half after the publication of the “Origin”, we have the opportunity to draw conclusions from the comparisons of hundreds of genome sequences from all walks of life. These comparisons suggest that the dominant mode of genome evolution is quite different from that of the phenotypic evolution. The genomes of vertebrates, those purported paragons of biological perfection, turned out to be veritable junkyards of selfish genetic elements where only a small fraction of the genetic material is dedicated to encoding biologically relevant information. In sharp contrast, genomes of microbes and viruses are incomparably more compact, with most of the genetic material assigned to distinct biological functions. However, even in these genomes, the specific genome organization (gene order) is poorly conserved. The results of comparative genomics lead to the conclusion that the genome architecture is not a straightforward result of continuous adaptation but rather is determined by the balance between the selection pressure, that is itself dependent on the effective population size and mutation rate, the level of recombination, and the activity of selfish elements. Although genes and, in many cases, multigene regions of genomes possess elaborate architectures that ensure regulation of expression, these arrangements are evolutionarily volatile and typically change substantially even on short evolutionary scales when gene sequences diverge minimally. Thus, the observed genome

  3. Comparison of the genomic sequence of the microminipig, a novel breed of swine, with the genomic database for conventional pig.

    PubMed

    Miura, Naoki; Kucho, Ken-Ichi; Noguchi, Michiko; Miyoshi, Noriaki; Uchiumi, Toshiki; Kawaguchi, Hiroaki; Tanimoto, Akihide

    2014-01-01

    The microminipig, which weighs less than 10 kg at an early stage of maturity, has been reported as a potential experimental model animal. Its extremely small size and other distinct characteristics suggest the possibility of a number of differences between the genome of the microminipig and that of conventional pigs. In this study, we analyzed the genomes of two healthy microminipigs using a next-generation sequencer SOLiD™ system. We then compared the obtained genomic sequences with a genomic database for the domestic pig (Sus scrofa). The mapping coverage of sequenced tag from the microminipig to conventional pig genomic sequences was greater than 96% and we detected no clear, substantial genomic variance from these data. The results may indicate that the distinct characteristics of the microminipig derive from small-scale alterations in the genome, such as Single Nucleotide Polymorphisms or translational modifications, rather than large-scale deletion or insertion polymorphisms. Further investigation of the entire genomic sequence of the microminipig with methods enabling deeper coverage is required to elucidate the genetic basis of its distinct phenotypic traits. Copyright © 2014 International Institute of Anticancer Research (Dr. John G. Delinassios), All rights reserved.

  4. 34 CFR 686.4 - Institutional participation.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... institution and who submitted a SAR with an official EFC to the institution, or for whom the institution... who, during the award year, submitted a SAR with an official EFC to the institution or for whom it...

  5. 34 CFR 686.4 - Institutional participation.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... institution and who submitted a SAR with an official EFC to the institution, or for whom the institution... who, during the award year, submitted a SAR with an official EFC to the institution or for whom it...

  6. Genome Project Standards in a New Era of Sequencing

    SciTech Connect

    GSC Consortia; HMP Jumpstart Consortia; Chain, P. S. G.; Grafham, D. V.; Fulton, R. S.; FitzGerald, M. G.; Hostetler, J.; Muzny, D.; Detter, J. C.; Ali, J.; Birren, B.; Bruce, D. C.; Buhay, C.; Cole, J. R.; Ding, Y.; Dugan, S.; Field, D.; Garrity, G. M.; Gibbs, R.; Graves, T.; Han, C. S.; Harrison, S. H.; Highlander, S.; Hugenholtz, P.; Khouri, H. M.; Kodira, C. D.; Kolker, E.; Kyrpides, N. C.; Lang, D.; Lapidus, A.; Malfatti, S. A.; Markowitz, V.; Metha, T.; Nelson, K. E.; Parkhill, J.; Pitluck, S.; Qin, X.; Read, T. D.; Schmutz, J.; Sozhamannan, S.; Strausberg, R.; Sutton, G.; Thomson, N. R.; Tiedje, J. M.; Weinstock, G.; Wollam, A.

    2009-06-01

    For over a decade, genome 43 sequences have adhered to only two standards that are relied on for purposes of sequence analysis by interested third parties (1, 2). However, ongoing developments in revolutionary sequencing technologies have resulted in a redefinition of traditional whole genome sequencing that requires a careful reevaluation of such standards. With commercially available 454 pyrosequencing (followed by Illumina, SOLiD, and now Helicos), there has been an explosion of genomes sequenced under the moniker 'draft', however these can be very poor quality genomes (due to inherent errors in the sequencing technologies, and the inability of assembly programs to fully address these errors). Further, one can only infer that such draft genomes may be of poor quality by navigating through the databases to find the number and type of reads deposited in sequence trace repositories (and not all genomes have this available), or to identify the number of contigs or genome fragments deposited to the database. The difficulty in assessing the quality of such deposited genomes has created some havoc for genome analysis pipelines and contributed to many wasted hours of (mis)interpretation. These same novel sequencing technologies have also brought an exponential leap in raw sequencing capability, and at greatly reduced prices that have further skewed the time- and cost-ratios of draft data generation versus the painstaking process of improving and finishing a genome. The resulting effect is an ever-widening gap between drafted and finished genomes that only promises to continue (Figure 1), hence there is an urgent need to distinguish good and poor datasets. The sequencing institutes in the authorship, along with the NIH's Human Microbiome Project Jumpstart Consortium (3), strongly believe that a new set of standards is required for genome sequences. The following represents a set of six community-defined categories of genome sequence standards that better reflect the

  7. Predicting discovery rates of genomic features.

    PubMed

    Gravel, Simon

    2014-06-01

    Successful sequencing experiments require judicious sample selection. However, this selection must often be performed on the basis of limited preliminary data. Predicting the statistical properties of the final sample based on preliminary data can be challenging, because numerous uncertain model assumptions may be involved. Here, we ask whether we can predict "omics" variation across many samples by sequencing only a fraction of them. In the infinite-genome limit, we find that a pilot study sequencing 5% of a population is sufficient to predict the number of genetic variants in the entire population within 6% of the correct value, using an estimator agnostic to demography, selection, or population structure. To reach similar accuracy in a finite genome with millions of polymorphisms, the pilot study would require ∼15% of the population. We present computationally efficient jackknife and linear programming methods that exhibit substantially less bias than the state of the art when applied to simulated data and subsampled 1000 Genomes Project data. Extrapolating based on the National Heart, Lung, and Blood Institute Exome Sequencing Project data, we predict that 7.2% of sites in the capture region would be variable in a sample of 50,000 African Americans and 8.8% in a European sample of equal size. Finally, we show how the linear programming method can also predict discovery rates of various genomic features, such as the number of transcription factor binding sites across different cell types.

  8. Role of genomics in eliminating health disparities

    PubMed Central

    Kashyap, Meghana V; Nolan, Michael; Sprouse, Marc; Chakraborty, Ranajit; Cross, Deanna; Roby, Rhonda; Vishwanatha, Jamboor K

    2015-01-01

    The Texas Center for Health Disparities, a National Institute on Minority Health and Health Disparities Center of Excellence, presents an annual conference to discuss prevention, awareness education, and ongoing research about health disparities both in Texas and among the national population. The 2014 Annual Texas Conference on Health Disparities brought together experts in research, patient care, and community outreach on the “Role of Genomics in Eliminating Health Disparities.” Rapid advances in genomics and pharmacogenomics are leading the field of medicine to use genetics and genetic risk to build personalized or individualized medicine strategies. We are at a critical juncture of ensuring such rapid advances benefit diverse populations. Relatively few forums have been organized around the theme of the role of genomics in eliminating health disparities. The conference consisted of three sessions addressing “Gene-Environment Interactions and Health Disparities,” “Personalized Medicine and Elimination of Health Disparities,” and “Ethics and Public Policy in the Genomic Era.” This article summarizes the basic science, clinical correlates, and public health data presented by the speakers. PMID:26435701

  9. Biomartr: genomic data retrieval with R.

    PubMed

    Drost, Hajk-Georg; Paszkowski, Jerzy

    2017-04-15

    Retrieval and reproducible functional annotation of genomic data are crucial in biology. However, the current poor usability and transparency of retrieval methods hinders reproducibility. Here we present an open source R package, biomartr , which provides a comprehensive easy-to-use framework for automating data retrieval and functional annotation for meta-genomic approaches. The functions of biomartr achieve a high degree of clarity, transparency and reproducibility of analyses. The biomartr package implements straightforward functions for bulk retrieval of all genomic data or data for selected genomes, proteomes, coding sequences and annotation files present in databases hosted by the National Center for Biotechnology Information (NCBI) and European Bioinformatics Institute (EMBL-EBI). In addition, biomartr communicates with the BioMart database for functional annotation of retrieved sequences. Comprehensive documentation of biomartr functions and five tutorial vignettes provide step-by-step instructions on how to use the package in a reproducible manner. The open source biomartr package is available at https://github.com/HajkD/biomartr and https://cran.r-project.org/web/packages/biomartr/index.html . hgd23@cam.ac.uk. Supplementary data are available at Bioinformatics online.

  10. The banana genome hub.

    PubMed

    Droc, Gaëtan; Larivière, Delphine; Guignon, Valentin; Yahiaoui, Nabila; This, Dominique; Garsmeur, Olivier; Dereeper, Alexis; Hamelin, Chantal; Argout, Xavier; Dufayard, Jean-François; Lengelle, Juliette; Baurens, Franc-Christophe; Cenci, Alberto; Pitollat, Bertrand; D'Hont, Angélique; Ruiz, Manuel; Rouard, Mathieu; Bocs, Stéphanie

    2013-01-01

    Banana is one of the world's favorite fruits and one of the most important crops for developing countries. The banana reference genome sequence (Musa acuminata) was recently released. Given the taxonomic position of Musa, the completed genomic sequence has particular comparative value to provide fresh insights about the evolution of the monocotyledons. The study of the banana genome has been enhanced by a number of tools and resources that allows harnessing its sequence. First, we set up essential tools such as a Community Annotation System, phylogenomics resources and metabolic pathways. Then, to support post-genomic efforts, we improved banana existing systems (e.g. web front end, query builder), we integrated available Musa data into generic systems (e.g. markers and genetic maps, synteny blocks), we have made interoperable with the banana hub, other existing systems containing Musa data (e.g. transcriptomics, rice reference genome, workflow manager) and finally, we generated new results from sequence analyses (e.g. SNP and polymorphism analysis). Several uses cases illustrate how the Banana Genome Hub can be used to study gene families. Overall, with this collaborative effort, we discuss the importance of the interoperability toward data integration between existing information systems. Database URL: http://banana-genome.cirad.fr/

  11. The Banana Genome Hub

    PubMed Central

    Droc, Gaëtan; Larivière, Delphine; Guignon, Valentin; Yahiaoui, Nabila; This, Dominique; Garsmeur, Olivier; Dereeper, Alexis; Hamelin, Chantal; Argout, Xavier; Dufayard, Jean-François; Lengelle, Juliette; Baurens, Franc-Christophe; Cenci, Alberto; Pitollat, Bertrand; D’Hont, Angélique; Ruiz, Manuel; Rouard, Mathieu; Bocs, Stéphanie

    2013-01-01

    Banana is one of the world’s favorite fruits and one of the most important crops for developing countries. The banana reference genome sequence (Musa acuminata) was recently released. Given the taxonomic position of Musa, the completed genomic sequence has particular comparative value to provide fresh insights about the evolution of the monocotyledons. The study of the banana genome has been enhanced by a number of tools and resources that allows harnessing its sequence. First, we set up essential tools such as a Community Annotation System, phylogenomics resources and metabolic pathways. Then, to support post-genomic efforts, we improved banana existing systems (e.g. web front end, query builder), we integrated available Musa data into generic systems (e.g. markers and genetic maps, synteny blocks), we have made interoperable with the banana hub, other existing systems containing Musa data (e.g. transcriptomics, rice reference genome, workflow manager) and finally, we generated new results from sequence analyses (e.g. SNP and polymorphism analysis). Several uses cases illustrate how the Banana Genome Hub can be used to study gene families. Overall, with this collaborative effort, we discuss the importance of the interoperability toward data integration between existing information systems. Database URL: http://banana-genome.cirad.fr/ PMID:23707967

  12. Genomic Insights into Bifidobacteria

    PubMed Central

    Lee, Ju-Hoon; O'Sullivan, Daniel J.

    2010-01-01

    Summary: Since the discovery in 1899 of bifidobacteria as numerically dominant microbes in the feces of breast-fed infants, there have been numerous studies addressing their role in modulating gut microflora as well as their other potential health benefits. Because of this, they are frequently incorporated into foods as probiotic cultures. An understanding of their full interactions with intestinal microbes and the host is needed to scientifically validate any health benefits they may afford. Recently, the genome sequences of nine strains representing four species of Bifidobacterium became available. A comparative genome analysis of these genomes reveals a likely efficient capacity to adapt to their habitats, with B. longum subsp. infantis exhibiting more genomic potential to utilize human milk oligosaccharides, consistent with its habitat in the infant gut. Conversely, B. longum subsp. longum exhibits a higher genomic potential for utilization of plant-derived complex carbohydrates and polyols, consistent with its habitat in an adult gut. An intriguing observation is the loss of much of this genome potential when strains are adapted to pure culture environments, as highlighted by the genomes of B. animalis subsp. lactis strains, which exhibit the least potential for a gut habitat and are believed to have evolved from the B. animalis species during adaptation to dairy fermentation environments. PMID:20805404

  13. NCBI viral genomes resource.

    PubMed

    Brister, J Rodney; Ako-Adjei, Danso; Bao, Yiming; Blinkova, Olga

    2015-01-01

    Recent technological innovations have ignited an explosion in virus genome sequencing that promises to fundamentally alter our understanding of viral biology and profoundly impact public health policy. Yet, any potential benefits from the billowing cloud of next generation sequence data hinge upon well implemented reference resources that facilitate the identification of sequences, aid in the assembly of sequence reads and provide reference annotation sources. The NCBI Viral Genomes Resource is a reference resource designed to bring order to this sequence shockwave and improve usability of viral sequence data. The resource can be accessed at http://www.ncbi.nlm.nih.gov/genome/viruses/ and catalogs all publicly available virus genome sequences and curates reference genome sequences. As the number of genome sequences has grown, so too have the difficulties in annotating and maintaining reference sequences. The rapid expansion of the viral sequence universe has forced a recalibration of the data model to better provide extant sequence representation and enhanced reference sequence products to serve the needs of the various viral communities. This, in turn, has placed increased emphasis on leveraging the knowledge of individual scientific communities to identify important viral sequences and develop well annotated reference virus genome sets. Published by Oxford University Press on behalf of Nucleic Acids Research 2014. This work is written by US Government employees and is in the public domain in the US.

  14. NCBI Viral Genomes Resource

    PubMed Central

    Brister, J. Rodney; Ako-adjei, Danso; Bao, Yiming; Blinkova, Olga

    2015-01-01

    Recent technological innovations have ignited an explosion in virus genome sequencing that promises to fundamentally alter our understanding of viral biology and profoundly impact public health policy. Yet, any potential benefits from the billowing cloud of next generation sequence data hinge upon well implemented reference resources that facilitate the identification of sequences, aid in the assembly of sequence reads and provide reference annotation sources. The NCBI Viral Genomes Resource is a reference resource designed to bring order to this sequence shockwave and improve usability of viral sequence data. The resource can be accessed at http://www.ncbi.nlm.nih.gov/genome/viruses/ and catalogs all publicly available virus genome sequences and curates reference genome sequences. As the number of genome sequences has grown, so too have the difficulties in annotating and maintaining reference sequences. The rapid expansion of the viral sequence universe has forced a recalibration of the data model to better provide extant sequence representation and enhanced reference sequence products to serve the needs of the various viral communities. This, in turn, has placed increased emphasis on leveraging the knowledge of individual scientific communities to identify important viral sequences and develop well annotated reference virus genome sets. PMID:25428358

  15. Report of the 13(th) Genomic Standards Consortium Meeting, Shenzhen, China, March 4-7, 2012.

    PubMed

    Gilbert, Jack A; Bao, Yiming; Wang, Hui; Sansone, Susanna-Assunta; Edmunds, Scott C; Morrison, Norman; Meyer, Folker; Schriml, Lynn M; Davies, Neil; Sterk, Peter; Wilkening, Jared; Garrity, George M; Field, Dawn; Robbins, Robert; Smith, Daniel P; Mizrachi, Ilene; Moreau, Corrie

    2012-05-25

    This report details the outcome of the 13(th) Meeting of the Genomic Standards Consortium. The three-day conference was held at the Kingkey Palace Hotel, Shenzhen, China, on March 5-7, 2012, and was hosted by the Beijing Genomics Institute. The meeting, titled From Genomes to Interactions to Communities to Models, highlighted the role of data standards associated with genomic, metagenomic, and amplicon sequence data and the contextual information associated with the sample. To this end the meeting focused on genomic projects for animals, plants, fungi, and viruses; metagenomic studies in host-microbe interactions; and the dynamics of microbial communities. In addition, the meeting hosted a Genomic Observatories Network session, a Genomic Standards Consortium biodiversity working group session, and a Microbiology of the Built Environment session sponsored by the Alfred P. Sloan Foundation.

  16. Report of the 13th Genomic Standards Consortium Meeting, Shenzhen, China, March 4–7, 2012.

    PubMed Central

    Bao, Yiming; Wang, Hui; Sansone, Susanna-Assunta; Edmunds, Scott C.; Morrison, Norman; Meyer, Folker; Schriml, Lynn M.; Davies, Neil; Sterk, Peter; Wilkening, Jared; Garrity, George M.; Field, Dawn; Robbins, Robert; Smith, Daniel P.; Mizrachi, Ilene; Moreau, Corrie

    2012-01-01

    This report details the outcome of the 13th Meeting of the Genomic Standards Consortium. The three-day conference was held at the Kingkey Palace Hotel, Shenzhen, China, on March 5–7, 2012, and was hosted by the Beijing Genomics Institute. The meeting, titled From Genomes to Interactions to Communities to Models, highlighted the role of data standards associated with genomic, metagenomic, and amplicon sequence data and the contextual information associated with the sample. To this end the meeting focused on genomic projects for animals, plants, fungi, and viruses; metagenomic studies in host-microbe interactions; and the dynamics of microbial communities. In addition, the meeting hosted a Genomic Observatories Network session, a Genomic Standards Consortium biodiversity working group session, and a Microbiology of the Built Environment session sponsored by the Alfred P. Sloan Foundation. PMID:22768370

  17. Ensembl comparative genomics resources

    PubMed Central

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

    2016-01-01

    Evolution provides the unifying framework with which to understand biology. The coherent investigation of genic and genomic data often requires comparative genomics analyses based on whole-genome alignments, sets of homologous genes and other relevant datasets in order to evaluate and answer evolutionary-related questions. However, the complexity and computational requirements of producing such data are substantial: this has led to only a small number of reference resources that are used for most comparative analyses. The Ensembl comparative genomics resources are one such reference set that facilitates comprehensive and reproducible analysis of chordate genome data. Ensembl computes pairwise and multiple whole-genome alignments from which large-scale synteny, per-base conservation scores and constrained elements are obtained. Gene alignments are used to define Ensembl Protein Families, GeneTrees and homologies for both protein-coding and non-coding RNA genes. These resources are updated frequently and have a consistent informatics infrastructure and data presentation across all supported species. Specialized web-based visualizations are also available including synteny displays, collapsible gene tree plots, a gene family locator and different alignment views. The Ensembl comparative genomics infrastructure is extensively reused for the analysis of non-vertebrate species by other projects including Ensembl Genomes and Gramene and much of the information here is relevant to these projects. The consistency of the annotation across species and the focus on vertebrates makes Ensembl an ideal system to perform and support vertebrate comparative genomic analyses. We use robust software and pipelines to produce reference comparative data and make it freely available. Database URL: http://www.ensembl.org. PMID:26896847

  18. Toward 959 nematode genomes

    PubMed Central

    Kumar, Sujai; Koutsovoulos, Georgios; Kaur, Gaganjot; Blaxter, Mark

    2012-01-01

    The sequencing of the complete genome of the nematode Caenorhabditis elegans was a landmark achievement and ushered in a new era of whole-organism, systems analyses of the biology of this powerful model organism. The success of the C. elegans genome sequencing project also inspired communities working on other organisms to approach genome sequencing of their species. The phylum Nematoda is rich and diverse and of interest to a wide range of research fields from basic biology through ecology and parasitic disease. For all these communities, it is now clear that access to genome scale data will be key to advancing understanding, and in the case of parasites, developing new ways to control or cure diseases. The advent of second-generation sequencing technologies, improvements in computing algorithms and infrastructure and growth in bioinformatics and genomics literacy is making the addition of genome sequencing to the research goals of any nematode research program a less daunting prospect. To inspire, promote and coordinate genomic sequencing across the diversity of the phylum, we have launched a community wiki and the 959 Nematode Genomes initiative (www.nematodegenomes.org/). Just as the deciphering of the developmental lineage of the 959 cells of the adult hermaphrodite C. elegans was the gateway to broad advances in biomedical science, we hope that a nematode phylogeny with (at least) 959 sequenced species will underpin further advances in understanding the origins of parasitism, the dynamics of genomic change and the adaptations that have made Nematoda one of the most successful animal phyla. PMID:24058822

  19. 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. © The Author(s) 2016. Published by Oxford University Press.

  20. Library Media Institute for Paraprofessionals.

    ERIC Educational Resources Information Center

    Baird, Lucille

    A training institute was held by the School of Education at Eastern New Mexico University to increase the library and audiovisual media skills of elementary school library media aides in this sparsely populated area, where many school media technicians have little or no college training. The institute was designed to increase competencies of…