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

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    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 directly to a website specific to that one genome. The individual sites include direct access to download sequence files, BLAST, search, view and navigate the genomic annotations.

  2. JGI Fungal Genomics Program

    E-Print Network [OSTI]

    Grigoriev, Igor V.

    2012-01-01

    JGI Fungal Genomics Program Igor V. Grigoriev 1 Lawrenceof California. JGI Fungal Genomics Program Contact: IgorJGI). Its key project, the Genomics Encyclopedia of Fungi,

  3. JGI Fungal Genomics Program

    E-Print Network [OSTI]

    Grigoriev, Igor V.

    2011-01-01

    View Supports functional genomics, user data deposition andJGI Fungal Genomics Program Igor V. Grigoriev 1 DOE Jointof California. JGI Fungal Genomics Program Contact: Igor

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

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    As of March 2008, The Joint Genome Institute has released 296 Prokaryotic microbial sites, with 216 in finished status.

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

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    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.

  6. DOE JGI Whole Genome Shotgun Sequencing, part 2

    ScienceCinema (OSTI)

    Miranda Harmon-Smith

    2010-09-01

    A Howard Hughes Medical Institute (HHMI) video production describing the Whole Genome Shotgun Sequencing process at the US Department of Energy's Joint Genome Institute (JGI).

  7. DOE JGI Whole Genome Shotgun Sequencing, part 1

    ScienceCinema (OSTI)

    Miranda Harmon-Smith

    2010-09-01

    A Howard Hughes Medical Institute (HHMI) video production describing the Whole Genome Shotgun Sequencing process at the US Department of Energy's Joint Genome Institute (JGI).

  8. DOE JGI Whole Genome Shotgun Sequencing, part 3

    ScienceCinema (OSTI)

    Miranda Harmon-Smith

    2010-09-01

    A Howard Hughes Medical Institute (HHMI) video production describing the Whole Genome Shotgun Sequencing process at the US Department of Energy's Joint Genome Institute (JGI).

  9. JGI Genomics and Bioinformatics for Undergraduate Educators Workshop

    Broader source: Energy.gov [DOE]

    The JGI will be holding the JGI Genomics and Bioinformatics for Undergraduate Educators Workshop in conjunction with the JGI User Meeting. The workshop will take place March 23-26, 2013 at the JGI.

  10. Diatom Genomics (2009 JGI User Meeting)

    ScienceCinema (OSTI)

    Ambrust, Ginger

    2011-04-25

    Ginger Armbrust from the University of Washington spoke about diatom genomics on March 26, 2009 at the DOE JGI User Meeting

  11. Genome Improvement at JGI-HAGSC

    SciTech Connect (OSTI)

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

    2012-03-03

    Since the completion of the sequencing of the human genome, the 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.

  12. Opening Remarks from the Joint Genome Institute and Argonne Lab High Performance Computing Workshop (2010 JGI/ANL HPC Workshop)

    ScienceCinema (OSTI)

    Rubin, Eddy

    2011-06-03

    DOE JGI Director Eddy Rubin gives opening remarks at the JGI/Argonne High Performance Computing (HPC) Workshop on January 25, 2010.

  13. Opening Remarks from the Joint Genome Institute and Argonne Lab High Performance Computing Workshop (2010 JGI/ANL HPC Workshop)

    SciTech Connect (OSTI)

    Rubin, Eddy

    2010-01-25

    DOE JGI Director Eddy Rubin gives opening remarks at the JGI/Argonne High Performance Computing (HPC) Workshop on January 25, 2010.

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

    SciTech Connect (OSTI)

    Hodges, Scott [University of California, Santa Barbara] [University of California, Santa Barbara

    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

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

    SciTech Connect (OSTI)

    Shuster, Stephen [Penn State University] [Penn State University

    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

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

    ScienceCinema (OSTI)

    Hodges, Scott [University of California, Santa Barbara

    2011-06-03

    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

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

    ScienceCinema (OSTI)

    Shuster, Stephen [Penn State University

    2011-06-03

    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

  18. Using Genomics to Dissect Seed Development (JGI Seventh Annual...

    Office of Scientific and Technical Information (OSTI)

    Using Genomics to Dissect Seed Development (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment Meeting) Citation Details In-Document Search Title: Using...

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

    ScienceCinema (OSTI)

    Moose, Steve

    2011-04-25

    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

  20. Computational Challenges for Microbial Genome and Metagenome Analysis (2010 JGI/ANL HPC Workshop)

    ScienceCinema (OSTI)

    Mavrommatis, Kostas

    2011-06-08

    Kostas Mavrommatis of the DOE JGI gives a presentation on "Computational Challenges for Microbial Genome & Metagenome Analysis" at the JGI/Argonne HPC Workshop on January 26, 2010.

  1. Joint Genome Institute (JGI)

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity ofkandz-cm11 Outreach Home Room NewsInformationJesse Bergkamp Graduate student Subtask 4Photo of John HrynJohnJoin

  2. Efficient Short-Read Assembly of Eukaryotic Genomes (2010 JGI/ANL HPC Workshop)

    ScienceCinema (OSTI)

    Chapman, Jarrod

    2011-06-03

    Jarrod Chapman of the DOE JGI gives a presentation on "Efficient Short-Read Assembly of Eukaryotic Genomes" at the JGI/Argonne HPC Workshop on January 25, 2010.

  3. Joint Genome Institute's Automation Approach and History

    SciTech Connect (OSTI)

    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.

  4. Rooted in Wonder: Joint Genome Institute Study Reveals Amazing...

    Broader source: Energy.gov (indexed) [DOE]

    underfoot essentials so easily overlooked. Recently, a team of researchers led by the Energy Department Office of Science's Joint Genome Institute (JGI) and the University of...

  5. Keynote Presentation: Genome Beat (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    ScienceCinema (OSTI)

    Zimmer, Carl [New York Times

    2013-01-22

    Carl Zimmer, a reporter for the New York Times, speaks on "The Genome Beat," the opening keynote presentation at the JGI User 7th Annual Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, Calif

  6. Keynote Presentation: Genome Beat (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    SciTech Connect (OSTI)

    Zimmer, Carl [New York Times] [New York Times

    2012-03-20

    Carl Zimmer, a reporter for the New York Times, speaks on "The Genome Beat," the opening keynote presentation at the JGI User 7th Annual Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, Calif

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

    ScienceCinema (OSTI)

    Tringe, Susannah [DOE JGI

    2013-01-22

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

  8. A Collection of Algal Genomes from the JGI (Conference) | SciTech...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Citation Details In-Document Search Title: A Collection of Algal Genomes from the JGI Algae, defined as photosynthetic eukaryotes other than plants, constitute a major component...

  9. Brian Giebel Subject: FW: Faculty positions in Plant Genomics and Pathway Engineering at the JGI

    E-Print Network [OSTI]

    Borenstein, Elhanan

    1 Brian Giebel Subject: FW: Faculty positions in Plant Genomics and Pathway Engineering at the JGI: Faculty positions in Plant Genomics and Pathway Engineering at the JGI To: Jay Shendure coming out in Science targeted at recruiting individuals in plant genomics and pathway engineering

  10. Association Genetics of Populus trichocarpa or Resequencing in Populus: Towards Genome Wide Association Genetics (2011 JGI User Meeting)

    ScienceCinema (OSTI)

    Tuskan, Gerry

    2011-06-03

    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. Gerry Tuskan of Oak Ridge National Laboratory on "Resequencing in Populus: Towards Genome Wide Association Genetics" at the 6th annual Genomics of Energy & Environment Meeting on March 23, 2011

  11. Association Genetics of Populus trichocarpa or Resequencing in Populus: Towards Genome Wide Association Genetics (2011 JGI User Meeting)

    SciTech Connect (OSTI)

    Tuskan, Gerry

    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. Gerry Tuskan of Oak Ridge National Laboratory on "Resequencing in Populus: Towards Genome Wide Association Genetics" at the 6th annual Genomics of Energy & Environment Meeting on March 23, 2011

  12. Closing Keynote Presentation on the Genomics of Energy and the Environment (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    SciTech Connect (OSTI)

    Benner, Stephen [Foundation for Applied Molecular Evolution, Westheimer Institute of Science and Technology] [Foundation for Applied Molecular Evolution, Westheimer Institute of Science and Technology

    2012-03-22

    Steve Benner, a distinguished chemist at the Foundation for Applied Molecular Evolution, Westheimer Institute of Science and Technology, provides the closing keynote address for the JGI 7th Annual Users Meeting: Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, California.

  13. Closing Keynote Presentation on the Genomics of Energy and the Environment (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    ScienceCinema (OSTI)

    Benner, Stephen [Foundation for Applied Molecular Evolution, Westheimer Institute of Science and Technology

    2013-01-22

    Steve Benner, a distinguished chemist at the Foundation for Applied Molecular Evolution, Westheimer Institute of Science and Technology, provides the closing keynote address for the JGI 7th Annual Users Meeting: Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, California.

  14. Using Genomics to Dissect Seed Development (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment Meeting)

    ScienceCinema (OSTI)

    Goldberg, Robert [UCLA

    2013-01-22

    Robert Goldberg of UCLA presents "Using Genomics to Dissect Seed Development" at the JGI 7th Annual Users Meeting: Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, California.

  15. Using Genomics to Dissect Seed Development (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment Meeting)

    SciTech Connect (OSTI)

    Goldberg, Robert [UCLA] [UCLA

    2012-03-21

    Robert Goldberg of UCLA presents "Using Genomics to Dissect Seed Development" at the JGI 7th Annual Users Meeting: Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, California.

  16. Genomic and Systems Biology Analyses of Social Behavior or Evolutionary Genomic Analyses of Insect Society: Eat, Drink, and Be Scary (2011 JGI User Meeting)

    SciTech Connect (OSTI)

    Robinson, Gene

    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. Gene Robinson of the University of Illinois on "Genomic and Systems Biology Analyses of Social Behavior" at the 6th Annual Genomics of Energy & Environment Meeting on March 23, 2011

  17. Genomic and Systems Biology Analyses of Social Behavior or Evolutionary Genomic Analyses of Insect Society: Eat, Drink, and Be Scary (2011 JGI User Meeting)

    ScienceCinema (OSTI)

    Robinson, Gene

    2011-06-03

    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. Gene Robinson of the University of Illinois on "Genomic and Systems Biology Analyses of Social Behavior" at the 6th Annual Genomics of Energy & Environment Meeting on March 23, 2011

  18. Annotation of Plant Genomes using RNA-seq Data (2010 JGI/ANL HPC Workshop)

    ScienceCinema (OSTI)

    Pellegrinni, Matteo [UCLA

    2011-06-08

    Matteo Pellegrini from University of California, Los Angeles gives a presentation on "Annotation of Plant Genomes using RNA-seq Data" at the JGI/Argonne HPC Workshop on January 25, 2010.

  19. Discovery of Genes and Genomes through Deep Metagenomic Sequencing of Cow Rumen (2010 JGI User Meeting)

    ScienceCinema (OSTI)

    Rubin, Eddy

    2011-04-25

    Director Eddy Rubin on "Discovery of Genes and Genomes through Deep Metagenomic Sequencing of Cow Rumen" on March 25, 2010 at the 5th Annual DOE JGI User Meeting

  20. From Fjords to Open Seas: Ecological Genomics of Expanding Oxygen Minimum Zones (2010 JGI User Meeting)

    ScienceCinema (OSTI)

    Hallam, Steven

    2011-04-26

    Steven Hallam of the University of British Columbia talks "From Fjords to Open Seas: Ecological Genomics of Expanding Oxygen Minimum Zones" on March 24, 2010 at the 5th Annual DOE JGI User Meeting

  1. Parallel Assembly of Large Genomes from Paired Short Reads (2010 JGI/ANL HPC Workshop)

    ScienceCinema (OSTI)

    Aluru, Srinivas [Iowa State University

    2011-06-08

    Srinivas Aluru from Iowa State University gives a presentation on "Parallel Assembly of Large Genomes from Paired Short Reads" at the JGI/Argonne HPC Workshop on January 25, 2010.

  2. 2013 Progress Report -- DOE Joint Genome Institute None 59 BASIC...

    Office of Scientific and Technical Information (OSTI)

    bit.lyJGI-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...

  3. Genomics and Systems Biology of Tuberculosis (2009 JGI User Meeting)

    ScienceCinema (OSTI)

    Galagan, James

    2011-04-25

    James Galagan from the Broad Institute spoke about the "Genomics and Systems Biology of TB" on March 26, 2009 during the 4th Annual User Meeting

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

    E-Print Network [OSTI]

    Grigoriev, Igor V.

    2014-01-01

    The Genome Portal of the Department of Energy Joint Genome 10.1093/nar/gkr947 The Genome Portal of the Department ofthe web. The JGI Genome Portal (http://genome.jgi.doe.gov)

  5. CyanoGEBA: A Better Understanding of Cynobacterial Diversity through Large-scale Genomics (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    SciTech Connect (OSTI)

    Shih, Patrick [Kerfeld Lab, UC Berkeley and JGI] [Kerfeld Lab, UC Berkeley and JGI

    2012-03-22

    Patrick Shih, representing both the University of California, Berkeley and JGI, gives a talk titled "CyanoGEBA: A Better Understanding of Cynobacterial Diversity through Large-scale Genomics" at the JGI 7th Annual Users Meeting: Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, California.

  6. CyanoGEBA: A Better Understanding of Cynobacterial Diversity through Large-scale Genomics (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    ScienceCinema (OSTI)

    Shih, Patrick [Kerfeld Lab, UC Berkeley and JGI

    2013-01-22

    Patrick Shih, representing both the University of California, Berkeley and JGI, gives a talk titled "CyanoGEBA: A Better Understanding of Cynobacterial Diversity through Large-scale Genomics" at the JGI 7th Annual Users Meeting: Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, California.

  7. Reprogramming Bacteria to Seek and Destroy Small Molecules (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    ScienceCinema (OSTI)

    Gallivan, Justin [Emory University

    2013-01-22

    Justin Gallivan, of Emory University presents a talk titled "Reprogramming Bacteria to Seek and Destroy Small Molecules" at the JGI User 7th Annual Genomics of Energy & Environment Meeting on March 21, 2012 in Walnut Creek, Calif

  8. Reprogramming Bacteria to Seek and Destroy Small Molecules (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    SciTech Connect (OSTI)

    Gallivan, Justin [Emory University] [Emory University

    2012-03-21

    Justin Gallivan, of Emory University presents a talk titled "Reprogramming Bacteria to Seek and Destroy Small Molecules" at the JGI User 7th Annual Genomics of Energy & Environment Meeting on March 21, 2012 in Walnut Creek, Calif

  9. Genomics on the Half Shell: So, What do Oysters Have to do with Energy? (2010 JGI User Meeting)

    ScienceCinema (OSTI)

    Hedgecock, Dennis

    2011-04-26

    Dennis Hedgecock from the University of Southern California answers the question, "Genomics on the Half Shell: So, What Do Oysters Have to Do with Energy?" on March 24, 2010 at the 5th Annual DOE JGI User Meeting

  10. DOE Joint Genome Institute 2008 Progress Report

    SciTech Connect (OSTI)

    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 dominated how sequencing was done in the last decade is being replaced by a variety of new processes and sequencing instruments. The JGI, with an increasing number of next-generation sequencers, whose throughput is 100- to 1,000-fold greater than the Sanger capillary-based sequencers, is increasingly focused in new directions on projects of scale and complexity not previously attempted. These new directions for the JGI come, in part, from the 2008 National Research Council report on the goals of the National Plant Genome Initiative as well as the 2007 National Research Council report on the New Science of Metagenomics. Both reports outline a crucial need for systematic large-scale surveys of the plant and microbial components of the biosphere as well as an increasing need for large-scale analysis capabilities to meet the challenge of converting sequence data into knowledge. The JGI is extensively discussed in both reports as vital to progress in these fields of major national interest. JGI's future plan for plants and microbes includes a systematic approach for investigation of these organisms at a scale requiring the special capabilities of the JGI to generate, manage, and analyze the datasets. JGI will generate and provide not only community access to these plant and microbial datasets, but also the tools for analyzing them. These activities will produce essential knowledge that will be needed if we are to be able to respond to the world's energy and environmental challenges. As the JGI Plant and Microbial programs advance, the JGI as a user facility is also evolving. The Institute has been highly successful in bending its technical and analytical skills to help users solve large complex problems of major importance, and that effort will continue unabated. The JGI will increasingly move from a central focus on 'one-off' user projects coming from small user communities to much larger scale projects driven by systematic and problem-focused approaches to selection of sequencing targets. Entire communities of scientists working in a particular field, such as feeds

  11. The DOE-JGI Standard Operating Procedure for the Annotations of the Microbial Genomes

    E-Print Network [OSTI]

    Mavromatis, Konstantinos

    2010-01-01

    1:63-67 DOI:10.4056/sigs.632 The DOE-JGI Standard OperatingtRNA-Scan, RNAmmer, Rfam, IMG-ER. The DOE-JGI MicrobialAnnotation Pipeline (DOE-JGI MAP) supports gene prediction

  12. Genome-Scale Discovery of Cell Wall Biosynthesis Genes in Populus (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    SciTech Connect (OSTI)

    Muchero, Wellington [Oak Ridge National Laboratory] [Oak Ridge National Laboratory

    2012-03-22

    Wellington Muchero from Oak Ridge National Laboratory gives a talk titled "Discovery of Cell Wall Biosynthesis Genes in Populus" at the JGI 7th Annual Users Meeting: Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, California.

  13. Genome-Scale Discovery of Cell Wall Biosynthesis Genes in Populus (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    ScienceCinema (OSTI)

    Muchero, Wellington [Oak Ridge National Laboratory

    2013-01-22

    Wellington Muchero from Oak Ridge National Laboratory gives a talk titled "Discovery of Cell Wall Biosynthesis Genes in Populus" at the JGI 7th Annual Users Meeting: Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, California.

  14. Fueling Future with Algal Genomics (Conference) | SciTech Connect

    Office of Scientific and Technical Information (OSTI)

    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...

  15. Building Communities: The Community Sequencing Program at JGI (2011 JGI User Meeting)

    SciTech Connect (OSTI)

    Bristow, Jim [DOE JGI Deputy Director] [DOE JGI Deputy Director

    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. DOE JGI Deputy Director Jim Bristow gives a presentation on the Community Sequencing Program at the 6th annual Genomics of Energy and Environment Meeting on March 23, 2011

  16. Building Communities: The Community Sequencing Program at JGI (2011 JGI User Meeting)

    ScienceCinema (OSTI)

    Bristow, Jim [DOE JGI Deputy Director

    2011-06-03

    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. DOE JGI Deputy Director Jim Bristow gives a presentation on the Community Sequencing Program at the 6th annual Genomics of Energy and Environment Meeting on March 23, 2011

  17. Accelerating Biofuel Feedstock Crop Improvement with Miscanthus Genomics (2014 DOE JGI Genomics of Energy & Environment Meeting)

    SciTech Connect (OSTI)

    Swaminathan, Kankshita [Energy Biosciences Institute

    2014-03-20

    Kankshita Swaminathan of the Energy Biosciences Institute speaks at the 9th Annual Genomics of Energy & Environment Meeting on March 20, 2014 in Walnut Creek, Calif.

  18. JGI Fungal Genomics Program (Technical Report) | SciTech Connect

    Office of Scientific and Technical Information (OSTI)

    agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts), and explores fungal diversity by means of genome sequencing and analysis....

  19. JGI Fungal Genomics Program Grigoriev, Igor V. 99; BIOFUELS;...

    Office of Scientific and Technical Information (OSTI)

    Its key project, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose...

  20. JGI Fungal Genomics Program (Technical Report) | SciTech Connect

    Office of Scientific and Technical Information (OSTI)

    Its key project, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose...

  1. Tapping the Molecular Potential of Microalgae to Produce Biomass (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    ScienceCinema (OSTI)

    Sayre, Richard [LANL

    2013-01-22

    Richard Sayre, from Los Alamos National Laboratory, presents a talk titled "Tapping the Molecular Potential of Microalgae to Produce Biomass" at the JGI 7th Annual Users Meeting: Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, California.

  2. Getting to the Root of Things: Spatiotemporal Regulatory Networks (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    ScienceCinema (OSTI)

    Brady, Siobhan [UC Davis

    2013-01-22

    Siobhan Brady from University of California, Davis, gives a talk titled "tGetting to the Root of things: Spatiotemporal Regulatory Networks" at the JGI 7th Annual Users Meeting: Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, California.

  3. Tapping the Molecular Potential of Microalgae to Produce Biomass (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    SciTech Connect (OSTI)

    Sayre, Richard [LANL] [LANL

    2012-03-22

    Richard Sayre, from Los Alamos National Laboratory, presents a talk titled "Tapping the Molecular Potential of Microalgae to Produce Biomass" at the JGI 7th Annual Users Meeting: Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, California.

  4. Getting to the Root of Things: Spatiotemporal Regulatory Networks (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    SciTech Connect (OSTI)

    Brady, Siobhan [UC Davis] [UC Davis

    2012-03-22

    Siobhan Brady from University of California, Davis, gives a talk titled "tGetting to the Root of things: Spatiotemporal Regulatory Networks" at the JGI 7th Annual Users Meeting: Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, California.

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

    ScienceCinema (OSTI)

    Chain, Patrick [DOE JGI at LANL

    2013-01-22

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

  6. 2012 U.S. Department of Energy: Joint Genome Institute: Progress Report

    SciTech Connect (OSTI)

    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.

  7. Synthetic Metagenomics: Converting digital information back to Biology (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

    SciTech Connect (OSTI)

    Deutsch, Sam [DOE Joint Genome Institute

    2013-03-01

    Sam Deutsch of the DOE JGI on "Synthetic Metagenomics: Converting digital information back to Biology" at the 8th Annual Genomics of Energy & Environment Meeting in Walnut Creek, Calif.

  8. Fueling Future with Algal Genomics Grigoriev, Igor 59 BASIC BIOLOGICAL

    Office of Scientific and Technical Information (OSTI)

    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...

  9. High Performance Computing and Genomics: Overview of the Issues (2010 JGI/ANL HPC Workshop)

    ScienceCinema (OSTI)

    Stevens, Rick [ANL

    2011-06-08

    Rick Stevens of Argonne National Laboratory presents an overview of the issues to be covered during the JGI/Argonne HPC Workshop on January 25, 2010.

  10. Genes and Genomics for Improving Energy Crops (Keynote Address - 2010 JGI User Meeting)

    ScienceCinema (OSTI)

    Pennell, Roger

    2011-04-28

    Roger Pennell, Vice President of Trait Development at Ceres, Inc., delivers a keynote address at the 5th Annual DOE JGI User Meeting on March 25, 2010

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

    SciTech Connect (OSTI)

    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.

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

    ScienceCinema (OSTI)

    Kyrpides, Nikos [DOE JGI

    2013-01-22

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

  13. An Inside Look at the JGI’s Sequencing Operation

    SciTech Connect (OSTI)

    Daum, Chris

    2010-06-02

    Chris Daum of the DOE Joint Genome Institute discusses how the DOE JGI's Production Sequencing group optimizes the sequencer pipelines and assesses quality on the Production line on June 2, 2010 at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM

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

    SciTech Connect (OSTI)

    Bermingham, Eldredge [STRI-Panama

    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.

  15. In Situ Expression of Acidic and Thermophilic Carbohydrate Active Enzymes by Filamentous Fungi (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    ScienceCinema (OSTI)

    Mosier, Annika [Stanford University

    2013-01-22

    Annika Mosier, graduate student from Stanford University presents a talk titled "In Situ Expression of Acidic and Thermophilic Carbohydrate Active Enzymes by Filamentous Fungi" at the JGI User 7th Annual Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, Calif

  16. Systems Biology Approaches to Dissecting Plant Cell Wall Biosynthesis Genes in Poplus (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    ScienceCinema (OSTI)

    Glass, N Louise [UC Berkeley

    2013-01-25

    N. Louise Glass from the University of California, Berkeley, presents a talk titled "Systems Biology Approaches to Dissecting Plant Cell Wall Biosynthesis Genes in Poplus" at the JGI 7th Annual Users Meeting: Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, California.

  17. In Situ Expression of Acidic and Thermophilic Carbohydrate Active Enzymes by Filamentous Fungi (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    SciTech Connect (OSTI)

    Mosier, Annika [Stanford University] [Stanford University

    2012-03-22

    Annika Mosier, graduate student from Stanford University presents a talk titled "In Situ Expression of Acidic and Thermophilic Carbohydrate Active Enzymes by Filamentous Fungi" at the JGI User 7th Annual Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, Calif

  18. Systems Biology Approaches to Dissecting Plant Cell Wall Biosynthesis Genes in Poplus (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    SciTech Connect (OSTI)

    Glass, N Louise [UC Berkeley] [UC Berkeley

    2012-03-22

    N. Louise Glass from the University of California, Berkeley, presents a talk titled "Systems Biology Approaches to Dissecting Plant Cell Wall Biosynthesis Genes in Poplus" at the JGI 7th Annual Users Meeting: Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, California.

  19. JGI Digital Scavenger Hunt

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    JGI Digital Scavenger Hunt JGI Digital Scavenger Hunt The NERSC webpages are a great resource for New and Old users, so this is the first stop on the JGI Digital Scavenger Hunt....

  20. Cassava Genomics: can genomic technology benefit smallholder farmers in Africa? (2014 DOE JGI Genomics of Energy & Environment Meeting)

    SciTech Connect (OSTI)

    Rounsley, Steve [University of Arizona

    2014-03-20

    Steve Rounsley of the University of Arizona speaks at the 9th Annual Genomics of Energy & Environment Meeting on March 20, 2014 in Walnut Creek, Calif.

  1. Metagenomic and Metaproteomic Analyses of Symbioses between Bacteria and Gutless Marine Worms (2014 DOE JGI Genomics of Energy & Environment Meeting)

    SciTech Connect (OSTI)

    Dubilier, Nicole

    2014-03-19

    Nicole Dubilier of the Max Planck Institute speaks at the 9th Annual Genomics of Energy & Environment Meeting on March 20, 2014 in Walnut Creek, Calif.

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

    SciTech Connect (OSTI)

    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.

  3. Designing Biological Systems for Sustainability and Programmed Environmental Interface (2011 JGI User Meeting)

    ScienceCinema (OSTI)

    Silver, Pam [Harvard University

    2011-06-03

    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. Pam Silver of Harvard University gives a presentation on "Designing Biological Systems for Sustainability and Programmed Environmental Interface" at the 6th annual Genomics of Energy & Environment Meeting on March 23, 2011

  4. Designing Biological Systems for Sustainability and Programmed Environmental Interface (2011 JGI User Meeting)

    SciTech Connect (OSTI)

    Silver, Pam [Harvard University] [Harvard University

    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. Pam Silver of Harvard University gives a presentation on "Designing Biological Systems for Sustainability and Programmed Environmental Interface" at the 6th annual Genomics of Energy & Environment Meeting on March 23, 2011

  5. The Gulf Oil Spill: Ecogenomics and Ecoresilience (Keynote - 2011 JGI User Meeting)

    SciTech Connect (OSTI)

    Hazen, Terry [LBNL] [LBNL

    2011-03-22

    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. Berkeley Lab microbial ecologist Terry Hazen delivers a keynote on "The Gulf Oil Spill: Ecogenomics and Ecoresilience" at the 6th Genomics of Energy & Environment Meeting on March 22, 2011.

  6. Spatially and Temporally Resolved Studies of the Human Microbiome (2011 JGI User Meeting)

    SciTech Connect (OSTI)

    Knight, Rob [University of Colorado] [University of Colorado

    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. Rob Knight of the University of Colorado gives a presentation on "Spatially and Temporally Resolved Studies of the Human Microbiome" at the 6th annual Genomics of Energy & Environment Meeting on March 23, 2011

  7. The Gulf Oil Spill: Ecogenomics and Ecoresilience (Keynote - 2011 JGI User Meeting)

    ScienceCinema (OSTI)

    Hazen, Terry [LBNL

    2011-06-03

    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. Berkeley Lab microbial ecologist Terry Hazen delivers a keynote on "The Gulf Oil Spill: Ecogenomics and Ecoresilience" at the 6th Genomics of Energy & Environment Meeting on March 22, 2011.

  8. Spatially and Temporally Resolved Studies of the Human Microbiome (2011 JGI User Meeting)

    ScienceCinema (OSTI)

    Knight, Rob [University of Colorado

    2011-06-03

    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. Rob Knight of the University of Colorado gives a presentation on "Spatially and Temporally Resolved Studies of the Human Microbiome" at the 6th annual Genomics of Energy & Environment Meeting on March 23, 2011

  9. Visualizing Assembling Everything (2010 JGI/ANL HPC Workshop)

    ScienceCinema (OSTI)

    Jaffe, David; Gnerre, Sante

    2011-06-08

    David Jaffe and Sante Gnerre of the Broad Institute give a presentation on "Visualizing assembling everything" at the JGI/Argonne HPC Workshop on January 25, 2010.

  10. Genomic Analysis of Adaptation and Speciation in Mimulus guttatus (2009 JGI User Meeting)

    ScienceCinema (OSTI)

    Willis, John

    2011-04-25

    John Willis of Duke University spoke about the "Genomic Analysis of Adaptation and Speciation in Mimulus guttatus" on March 26, 2009 at the 4th Annual User Meeting

  11. Genetic Control of Mosquitoes (2014 DOE JGI Genomics of Energy & Environment Meeting)

    SciTech Connect (OSTI)

    Matzen, Kelly

    2014-03-19

    Kelly Matzen of OXITEC speaks at the 9th Annual Genomics of Energy & Environment Meeting on March 20, 2014 in Walnut Creek, Calif.

  12. DOE Systems Biology Knowledgebase: KBase (2014 DOE JGI Genomics of Energy & Environment Meeting)

    SciTech Connect (OSTI)

    Arkin, Adam

    2014-03-20

    Adam Arkin from LBNL speaks at the 9th Annual Genomics of Energy & Environment Meeting on March 20, 2014 in Walnut Creek, Calif.

  13. Improving biofuel feedstocks by modifying xylan biosynthesis (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

    SciTech Connect (OSTI)

    Lau, Jane [JBEI

    2013-03-01

    Jane Lau of the Joint BioEnergy Institute on "Improving biofuel feedstocks by modifying xylan biosynthesis" at the 8th Annual Genomics of Energy & Environment Meeting on March 28, 2013 in Walnut Creek, Calif.

  14. 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 (OSTI)

    Schmutz, Jeremy [HudsonAlpha Institute

    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.

  15. DOE Systems Biology Knowledgebase (KBASE) (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    ScienceCinema (OSTI)

    Arkin, Adam [LBNL

    2013-01-15

    Adam Arkin from Berkeley Lab on the DOE Systems Biology Knowledgebase (KBASE) at the 7th Annual Genomics of Energy & Environment Meeting on March 21, 2012 in Walnut Creek, Calif

  16. DOE Systems Biology Knowledgebase (KBASE) (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    SciTech Connect (OSTI)

    Arkin, Adam [LBNL] [LBNL

    2012-03-21

    Adam Arkin from Berkeley Lab on the DOE Systems Biology Knowledgebase (KBASE) at the 7th Annual Genomics of Energy & Environment Meeting on March 21, 2012 in Walnut Creek, Calif

  17. 10-Year Strategic Vision: Forging the Future of the DOE JGI

    SciTech Connect (OSTI)

    2012-09-01

    Dramatic technological advances in genomics continue to transform modern biology. The DOE Joint Genome Institute (DOE JGI) has been at the leading edge of large-scale sequence-based science from its inception. Presently our ability to generate genomic data greatly outpaces our capacity to convert these data into biological insights. Bridging the gap between a sequenced genome and understanding of organism-scale functions is a significant unsolved problem in modern biology. Consequently, as the DOE JGI plans for its future, a major objective is to couple the generation of sequence data with the development of new large-scale experimental and computational capabilities to functionally annotate DNA sequences, thereby narrowing the gap between generation and interpretation of sequence data.

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

    ScienceCinema (OSTI)

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

    2013-01-22

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

  19. Entering the Era of Mega-genomics ( JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    SciTech Connect (OSTI)

    Schatz, Michael C [Cold Spring Harbor Laboratory] [Cold Spring Harbor Laboratory

    2012-03-21

    Michael Schatz from Cold Spring Harbor Laboratory on "Entering the Era of Mega-genomics" at the 7th Annual Genomics of Energy & Environment Meeting on March 21, 2012 in Walnut Creek, Calif.

  20. The Sunflower Genome and its Evolution (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    SciTech Connect (OSTI)

    Rieseberg, Loren [University of British Columbia] [University of British Columbia

    2012-03-21

    Loren Rieseberg from the University of British Columbia on "The Sunflower Genome and its Evolution" at the 7th Annual Genomics of Energy & Environment Meeting on March 21, 2012 in Walnut Creek, California.

  1. Entering the Era of Mega-genomics ( JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    ScienceCinema (OSTI)

    Schatz, Michael C [Cold Spring Harbor Laboratory

    2013-01-15

    Michael Schatz from Cold Spring Harbor Laboratory on "Entering the Era of Mega-genomics" at the 7th Annual Genomics of Energy & Environment Meeting on March 21, 2012 in Walnut Creek, Calif.

  2. The Sunflower Genome and its Evolution (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    ScienceCinema (OSTI)

    Rieseberg, Loren [University of British Columbia

    2013-01-15

    Loren Rieseberg from the University of British Columbia on "The Sunflower Genome and its Evolution" at the 7th Annual Genomics of Energy & Environment Meeting on March 21, 2012 in Walnut Creek, California.

  3. The US Department of Energy Joint Genome Institute Microbial Genome Program

    E-Print Network [OSTI]

    Lapidus, Alla

    2005-01-01

    Department of Energy Joint Genome Institute Microbial GenomeDepartment of Energy Joint Genome Institute Microbial Genome

  4. Using Genomics to Dissect Seed Development (JGI Seventh Annual User Meeting

    Office of Scientific and Technical Information (OSTI)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity of NaturalDukeWakefieldSulfateSciTechtail.Theory of rare Kaonfor Direct Measurement of2012: Genomics of Energy and Environment

  5. Using Genomics to Dissect Seed Development (JGI Seventh Annual User Meeting

    Office of Scientific and Technical Information (OSTI)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity of NaturalDukeWakefieldSulfateSciTechtail.Theory of rare Kaonfor Direct Measurement of2012: Genomics of Energy and

  6. The Turn-on of LCLS: the X-Ray Free Electron Laser at SLAC ( Keynote - 2011 JGI User Meeting)

    ScienceCinema (OSTI)

    Drell, Persis [SLAC Director

    2011-06-08

    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. SLAC National Laboratory Director Persis Drell gives a keynote talk on "The Turn-on of LCLS: the X-Ray Free-Electron Laser at SLAC" at the 6th Genomics of Energy & Environment Meeting on March 22, 2011

  7. Comparative Metagenomics of Gut and Ocean: Identification of Microbial Marker Genes for Complex Environmental Properties(2011 JGI User Meeting)

    ScienceCinema (OSTI)

    Bork, Peer

    2011-06-03

    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. Peer Bork of the European Molecular Biology Laboratory on "Comparative Metagenomics of Gut and Ocean: Identification of Microbial Marker Genes for Complex Environmental Properties" at the 6th annual Genomics of Energy & Environment Meeting on March 23, 2011

  8. Comparative Metagenomics of Gut and Ocean: Identification of Microbial Marker Genes for Complex Environmental Properties(2011 JGI User Meeting)

    SciTech Connect (OSTI)

    Bork, Peer

    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. Peer Bork of the European Molecular Biology Laboratory on "Comparative Metagenomics of Gut and Ocean: Identification of Microbial Marker Genes for Complex Environmental Properties" at the 6th annual Genomics of Energy & Environment Meeting on March 23, 2011

  9. Regulatory Networks Controlling Plant Cold Acclimation or Low Temperature Regulatory Networks Controlling Cold Acclimation in Arabidopsis (2011 JGI User Meeting)

    SciTech Connect (OSTI)

    Thomashow, Mike

    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. Mike Thomashow of Michigan State University gives a presentation on on "Low Temperature Regulatory Networks Controlling Cold Acclimation in Arabidopsis" at the 6th annual Genomics of Energy & Environment Meeting on March 23, 2011. «

  10. The Turn-on of LCLS: the X-Ray Free Electron Laser at SLAC ( Keynote - 2011 JGI User Meeting)

    SciTech Connect (OSTI)

    Drell, Persis [SLAC Director] [SLAC Director

    2011-03-22

    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. SLAC National Laboratory Director Persis Drell gives a keynote talk on "The Turn-on of LCLS: the X-Ray Free-Electron Laser at SLAC" at the 6th Genomics of Energy & Environment Meeting on March 22, 2011

  11. Regulatory Networks Controlling Plant Cold Acclimation or Low Temperature Regulatory Networks Controlling Cold Acclimation in Arabidopsis (2011 JGI User Meeting)

    ScienceCinema (OSTI)

    Thomashow, Mike

    2011-06-03

    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. Mike Thomashow of Michigan State University gives a presentation on on "Low Temperature Regulatory Networks Controlling Cold Acclimation in Arabidopsis" at the 6th annual Genomics of Energy & Environment Meeting on March 23, 2011. «

  12. Joint Genome Institute's Automation Approach and History

    E-Print Network [OSTI]

    Roberts, Simon

    2006-01-01

    Joint Genome Institute’s Automation Approach and Historythroughput environment; – automation does not necessarilyissues “Islands of Automation” – modular instruments with

  13. The Power of Teamwork: JGI Ergonomics Program

    E-Print Network [OSTI]

    Naca, Christine; Janowitz, Ira; Franaszek, Stephen; Turner, Ray; Lucas, Susan

    2007-01-01

    Power of Teamwork: JGI Ergonomics Program Christine Naca,Production Tasks • JGI Ergonomics Program • Ergo MethodologyDNA Sequence History of Ergonomics at JGI (May 2005-Current)

  14. Institute for Plant Genomics and Biotechnology GENOMICS AND BIOTECHNOLOGY

    E-Print Network [OSTI]

    Institute for Plant Genomics and Biotechnology GENOMICS AND BIOTECHNOLOGY A multidisciplinary organization, the Institute for Plant Genomics and Biotechnology is a composed of faculty members representing projects at the Institute for Plant Genomics and Biotechnology include the development of transgenic plants

  15. Sequencing Technologies and Computational pipelines at the JGI

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Sequencing Technologies and Computational pipelines at the JGI Sequencing Technologies and Computational pipelines at the JGI September 17, 2013 JGI logo 2 James Han, JGI...

  16. Host Genetic Control of the Microbiome in Humans and Maise or Relating Host Genetic Variation to the Microbiome (2011 JGI User Meeting)

    ScienceCinema (OSTI)

    Ley, Ruth [Cornell University

    2011-06-03

    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. Ruth Ley of Cornell University gives a presentation on "Relating Host Genetic Variation to the Microbiome" at the 6th annual Genomics of Energy & Environment Meeting on March 23, 2011.

  17. Host Genetic Control of the Microbiome in Humans and Maise or Relating Host Genetic Variation to the Microbiome (2011 JGI User Meeting)

    SciTech Connect (OSTI)

    Ley, Ruth [Cornell University] [Cornell University

    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. Ruth Ley of Cornell University gives a presentation on "Relating Host Genetic Variation to the Microbiome" at the 6th annual Genomics of Energy & Environment Meeting on March 23, 2011.

  18. Synthetic Biology for Advanced Fuels (Opening Keynote Address - 2010 JGI User Meeting)

    ScienceCinema (OSTI)

    Keasling, Jay

    2011-04-28

    Jay Keasling, CEO of the Joint BioEnergy Institute, delivers the opening keynote on March 24, 2010 at the 5th Annual DOE JGI User Meeting

  19. The JGI Metagenome Program (2009 JGI User Meeting)

    ScienceCinema (OSTI)

    Tringe, Susannah Green

    2011-04-25

    Susannah Tringe discussed the DOE JGI Metagenomic Program on March 25, 2009 at the 4th Annual User Meeting.

  20. OSCARS Extends JGI Network Capacity

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    appear part of JGI. The decision was quickly made and, despite being in the midst of acceptance testing, the Magellan team allocated 120 nodes to JGI. Working against a tight...

  1. Yangzhong Tang Functional Genomics Platform@ Whitehead Institute

    E-Print Network [OSTI]

    Sabatini, David M.

    Yangzhong Tang Functional Genomics Platform@ Whitehead Institute June 1st, 2015 Entering the CRISPR-Cas9 Era #12;Outline · The Human Genome o Basics and timeline o Exponential increase in genomic data o How to use the big data for biological discoveries · Functional Genomics · CRISPR-Cas systems o

  2. Development of High-Throughput Screens to Target SAM-I Riboswitches (2014 DOE JGI Genomics of Energy & Environment Meeting)

    SciTech Connect (OSTI)

    Hickey, Scott [UC Berkely

    2014-03-19

    Scott Hickey of the University of California Berkeley speaks at the 9th Annual Genomics of Energy & Environment Meeting on March 20, 2014 in Walnut Creek, Calif.

  3. Planning the Genome Institute's Future

    E-Print Network [OSTI]

    Botstein, David

    floors of a house, resting on a foundation of the Human Genome Project, with "Genomics to Society" on top planning that society will realize the scientific and public health benefits of the Human Genome Project. It has been a genome community tradi- tion since before there was a Human Genome Project, and NHGRI

  4. Understanding Historical Human Migration Patterns and Interbreeding (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    SciTech Connect (OSTI)

    Willerslev, Eske [University of Copenhagen] [University of Copenhagen

    2012-03-21

    Eske Willerslev from the University of Copenhagen on "Understanding Historical Human Migration Patterns and Interbreeding Using the Ancient Genomes of a Palaeo-Eskimo and an Aboriginal Australian" at the 7th Annual Genomics of Energy & Environment Meeting on March 21, 2012 in Walnut Creek, California.

  5. Understanding Historical Human Migration Patterns and Interbreeding (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    ScienceCinema (OSTI)

    Willerslev, Eske [University of Copenhagen

    2013-01-15

    Eske Willerslev from the University of Copenhagen on "Understanding Historical Human Migration Patterns and Interbreeding Using the Ancient Genomes of a Palaeo-Eskimo and an Aboriginal Australian" at the 7th Annual Genomics of Energy & Environment Meeting on March 21, 2012 in Walnut Creek, California.

  6. Strange Tails: Viral Discovery and Deep Sequencing (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

    SciTech Connect (OSTI)

    DeRisi, Joe

    2013-03-01

    Joe DeRisi of UC San Francisco on "Strange Tails: Viral discovery & deep sequencing" at the 8th Annual Genomics of Energy & Environment Meeting on March 27, 2013 in Walnut Creek, Calif.

  7. Ocean Viruses: Tiny entities with Global Impacts ( JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    ScienceCinema (OSTI)

    Sullivan, Matthew B [University of Arizona

    2013-01-15

    Matt Sullivan from the University of Arizona on "Ocean Viruses: Tiny Entities with Global Impacts" at the 7th Annual Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, Calif.

  8. Ocean Viruses: Tiny entities with Global Impacts ( JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    SciTech Connect (OSTI)

    Sullivan, Matthew B [University of Arizona] [University of Arizona

    2012-03-22

    Matt Sullivan from the University of Arizona on "Ocean Viruses: Tiny Entities with Global Impacts" at the 7th Annual Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, Calif.

  9. Part Mining for Synthetic Biology (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

    SciTech Connect (OSTI)

    Voigt, Chris [MIT

    2013-03-01

    Chris Voigt from MIT delivers the opening keynote on "Part Mining for Synthetic Biology" at the 8th Annual Genomics of Energy & Environment Meeting on March 26, 2013 in Walnut Creek, Calif.

  10. Synthetic Biology and Bioenergy: Helping the Good Guy and Stopping the Bad (2014 DOE JGI Genomics of Energy & Environment Meeting)

    SciTech Connect (OSTI)

    Mercedes-Roca, Maria [Zamorano Panamerican Agriculture School

    2014-03-19

    Maria Mercedes-Roca of the Zamorano Panamerican Agriculture School speaks at the 9th Annual Genomics of Energy & Environment Meeting on March 20, 2014 in Walnut Creek, Calif.

  11. Regulation of Flowering in Brachypodium distachyon (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

    SciTech Connect (OSTI)

    Amasino, Rick [University of Wisconsin

    2013-03-01

    Rick Amasino of the University of Wisconsin on "Regulation of Flowering in Brachypodium distachyon" at the 8th Annual Genomics of Energy & Environment Meeting on March 27, 2013 in Walnut Creek, Calif.

  12. PMI: Plant-Microbe Interfaces (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

    SciTech Connect (OSTI)

    Schadt, Christopher [ORNL

    2013-03-01

    Christopher Schadt of Oak Ridge National Laboratory on "Plant-Microbe Interactions" in the context of poplar trees at the 8th Annual Genomics of Energy & Environment Meeting on March 27, 2013 held in Walnut Creek, Calif.

  13. Joint Genome Institute (JGI) | U.S. DOE Office of Science (SC)

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantityBonneville Power Administration would likeUniverseIMPACT EVALUATIONIntroducingJobs Human ResourcesJohn@EnergySecurityUsing

  14. The JGI Mission and Programs (2009 JGI User Meeting)

    ScienceCinema (OSTI)

    Bristow, Jim

    2011-04-25

    Deputy Director of Programs Jim Bristow spoke about the DOE JGI's mission and programs at the 4th Annual User Meeting on March 25, 2009

  15. Casting Annotation as an Optimization Problem (2010 JGI/ANL HPC Workshop)

    SciTech Connect (OSTI)

    Overbeek, Ross

    2010-01-25

    Ross Overbeek of the Fellowship for Interpretation of Genomes gives a presentation on "Casting Annotation as an Optimization Problem" at the JGI/Argonne HPC Workshop on January 25, 2010.

  16. Casting Annotation as an Optimization Problem (2010 JGI/ANL HPC Workshop)

    ScienceCinema (OSTI)

    Overbeek, Ross

    2011-06-08

    Ross Overbeek of the Fellowship for Interpretation of Genomes gives a presentation on "Casting Annotation as an Optimization Problem" at the JGI/Argonne HPC Workshop on January 25, 2010.

  17. Illumina Production Sequencing at DOE Joint Genome Institute

    E-Print Network [OSTI]

    Tarver, Angela

    2014-01-01

    Production Sequencing at DOE Joint Genome Institute Angelathe US Department of Energy (DOE) Joint Genome Institute isthe Office of Science of the DOE under Contract Number DE-

  18. A GSC Global Genome Census (GSC8 Meeting)

    ScienceCinema (OSTI)

    Kyrpides, Nikos [DOE JGI

    2011-04-29

    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.

  19. The Genome of Selaginella: A Remnant of an Ancient Vascular Plant Lineage (JGI Seventh Annual User Meeting, 2012: Genomics of Energy and Environment)

    ScienceCinema (OSTI)

    Banks, Jody [Purdue University

    2013-01-22

    Jody Banks from Purdue University on "The Genome of Selaginella, a Remnant of an Ancient Vascular Plant Lineage" at the 7th Annual Genomics of Energy & Environment Meeting on March 21, 2012 in Walnut Creek, Calif.

  20. Genomic Analysis of Natural Variation for Seed and Plant Size in Maize ( JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    ScienceCinema (OSTI)

    Kaeppler, Shawn [University of Wisconsin, Madison

    2013-01-15

    Shawn Kaeppler from the University of Wisconsin-Madison on "Genomic Analysis of Biofuel Traits in Maize and Switchgrass" at the 7th Annual Genomics of Energy & Environment Meeting on March 21, 2012 in Walnut Creek, Calif

  1. The Genome of Selaginella: A Remnant of an Ancient Vascular Plant Lineage (JGI Seventh Annual User Meeting, 2012: Genomics of Energy and Environment)

    SciTech Connect (OSTI)

    Banks, Jody [Purdue University] [Purdue University

    2012-03-21

    Jody Banks from Purdue University on "The Genome of Selaginella, a Remnant of an Ancient Vascular Plant Lineage" at the 7th Annual Genomics of Energy & Environment Meeting on March 21, 2012 in Walnut Creek, Calif.

  2. The Challenges and Opportunities for Extending Plant Genomics to Climate (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

    SciTech Connect (OSTI)

    Weston, David [ORNL

    2013-03-01

    David Weston of Oak Ridge National Laboratory on "The challenges and opportunities for extending plant genomics to climate" at the 8th Annual Genomics of Energy & Environment Meeting on March 27, 2013 in Walnut Creek, Calif.

  3. Genomic Analysis of Natural Variation for Seed and Plant Size in Maize ( JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    SciTech Connect (OSTI)

    Kaeppler, Shawn [University of Wisconsin, Madison] [University of Wisconsin, Madison

    2012-03-21

    Shawn Kaeppler from the University of Wisconsin-Madison on "Genomic Analysis of Biofuel Traits in Maize and Switchgrass" at the 7th Annual Genomics of Energy & Environment Meeting on March 21, 2012 in Walnut Creek, Calif

  4. Uncovering Transcriptional Circuits in Arabidoposis by Functional Genomics (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

    SciTech Connect (OSTI)

    Pruneda-Paz, Jose [UC San Diego

    2013-03-01

    Jose Pruneda-Paz of UC San Diego on "Uncovering Transcriptional Circuits in Arabidopsis by Functional Genomics" at the 8th Annual Genomics of Energy & Environment Meeting in Walnut Creek, Calif.

  5. Whole Genome Sequencing of Rice Mutants to identify Genes Controlling Cell Wall Saccharification and Response to Biotic Stress (2014 DOE JGI Genomics of Energy & Environment Meeting)

    SciTech Connect (OSTI)

    Ronald, Pamela [UC Davis

    2014-03-20

    Pamela Ronald of the University of California Davis speaks at the 9th Annual Genomics of Energy & Environment Meeting on March 20, 2014 in Walnut Creek, Calif.

  6. Applications of Genome-based Science in Shaping Citrus Industries of the World (JGI Seventh Annual User Meeting, 2012: Genomics of Energy and Environment)

    ScienceCinema (OSTI)

    Gmitter Jr, Fred [University of Florida

    2013-01-15

    Fred Gmitter from the University of Florida on "Applications of Genome-based Science in Shaping the Future of the World's Citrus Industries" at the 7th Annual Genomics of Energy & Environment Meeting on March 21, 2012 in Walnut Creek, California.

  7. Omics in the Arctic: Genome-enabled Contributions to Carbon Cycle Research in High-Latitude Ecosystems (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    ScienceCinema (OSTI)

    Wullschleger, Stan [ORNL

    2013-01-22

    Stan Wullschleger of Oak Ridge National Laboratory on "Omics in the Arctic: Genome-enabled Contributions to Carbon Cycle Research in High-Latitude Ecosystems" on March 22, 2012 at the 7th Annual Genomics of Energy & Environment Meeting in Walnut Creek, California.

  8. Omics in the Arctic: Genome-enabled Contributions to Carbon Cycle Research in High-Latitude Ecosystems (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    SciTech Connect (OSTI)

    Wullschleger, Stan [ORNL] [ORNL

    2012-03-22

    Stan Wullschleger of Oak Ridge National Laboratory on "Omics in the Arctic: Genome-enabled Contributions to Carbon Cycle Research in High-Latitude Ecosystems" on March 22, 2012 at the 7th Annual Genomics of Energy & Environment Meeting in Walnut Creek, California.

  9. Applications of Genome-based Science in Shaping Citrus Industries of the World (JGI Seventh Annual User Meeting, 2012: Genomics of Energy and Environment)

    SciTech Connect (OSTI)

    Gmitter Jr, Fred [University of Florida

    2012-03-21

    Fred Gmitter from the University of Florida on "Applications of Genome-based Science in Shaping the Future of the World's Citrus Industries" at the 7th Annual Genomics of Energy & Environment Meeting on March 21, 2012 in Walnut Creek, California.

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

    ScienceCinema (OSTI)

    Chain, Patrick [DOE JGI

    2011-04-28

    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.

  11. JGI Digital Scavenger Hunt

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity ofkandz-cm11 Outreach Home Room NewsInformation CurrentHenryInhibitingInteractivePGASelectron tomography |J.Argonne DataJGI

  12. Soybean (2010 JGI User Meeting)

    ScienceCinema (OSTI)

    Stacey, Gary

    2011-04-26

    Gary Stacey, associate director of the National Center for Soybean Biotechnology at the University of Missouri, gives a talk simply titled "Soybean" on March 24, 2010 at the 5th Annual DOE JGI User Meeting

  13. is a Bioinformatics Scientist at the Institute for Genomic

    E-Print Network [OSTI]

    Salzberg, Steven

    Mihai Pop is a Bioinformatics Scientist at the Institute for Genomic Research. He earned his PhD in Computer Science from Johns Hopkins University in 2000. His research interests include genome assembly and comparative genomics. Adam Phillippy is a Bioinformatics Software Engineer at The Institute for Genomic

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

    ScienceCinema (OSTI)

    Sczyrba, Alex [DOE JGI

    2013-01-22

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

  15. INSTITUTE OF FUNCTIONAL GENOMICS Montpellier, Biomedical Campus Arnaud de Villeneuve

    E-Print Network [OSTI]

    van Tiggelen, Bart

    INSTITUTE OF FUNCTIONAL GENOMICS Montpellier, Biomedical Campus Arnaud de Villeneuve Seeking new group leaders The Institute of Functional Genomics (IGF) (www.igf.cnrs.fr), located in Montpellier of a wide range of state of the art facilities, including Genomics, Proteomics, medium throughput screening

  16. DOE Joint Genome Institute 2008 Progress Report

    E-Print Network [OSTI]

    Gilbert, David

    2009-01-01

    completion of the Human Genome Project, sequencing and itsimagined when the Human Genome Project first began. Accord-genes. Instead, the Human Genome Project found that hu- mans

  17. Next-Generation Genetics in Plants: Evolutionary Trade-off, Immunity and Speciation (2010 JGI User Meeting)

    ScienceCinema (OSTI)

    Wiegel, Detlef

    2011-04-25

    Detlef Wiegel from the Max Planck Institute for Developmental Biology on "Next-generation genetics in plants: Evolutionary tradeoffs, immunity and speciation" on March 25, 2010 at the 5th Annual DOE JGI User Meeting

  18. The Genomes and Metagenomes (GEM) Catalogue (first presentation) and The ISA-GCDML Workshop (second presentation) (GSC8 Meeting)

    ScienceCinema (OSTI)

    Field, Dawn [NERC Centre for Ecology and Hydrology]; Sansone, Susanna [EBI

    2011-04-29

    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. Dawn Field of the NERC Centre for Ecology & Hydrology briefly introduces the GEM Catalogue, followed by Susanna Sansone of the European Bioinformatics Institute who talks about the ISA-GCDML workshop at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, Calif. on Sept. 9, 2009.

  19. New Challenges of the Computation of Multiple Sequence Alignments in the High-Throughput Era (2010 JGI/ANL HPC Workshop)

    ScienceCinema (OSTI)

    Notredame, Cedric [Centre for Genomic Regulation

    2011-06-08

    Cedric Notredame from the Centre for Genomic Regulation gives a presentation on "New Challenges of the Computation of Multiple Sequence Alignments in the High-Throughput Era" at the JGI/Argonne HPC Workshop on January 26, 2010.

  20. Joint Genome Institute Progress Report 2002-2005

    SciTech Connect (OSTI)

    Gilbert, David

    2005-10-03

    Progress report covering activities at the DOE-Joint Genome Institute in Walnut Creek, California for the period 2002-2005.

  1. PLPA4380 Fungal Genetics and Genomics B. Gillian Turgeon

    E-Print Network [OSTI]

    Chen, Tsuhan

    PLPA4380 Fungal Genetics and Genomics B. Gillian Turgeon Spring 2016 Date Topic Wed Jan 27 Feb 22 Quiz Wed Feb 24 Sequenced fungal genomes: JGI Mycocosm tools Characteristics/ typical features/ comparative genomics/annotation Fri Feb 26 Sequenced fungal genomes: JGI Mycocosm tools Characteristics

  2. Ocean Viral Metagenomics (2010 JGI User Meeting)

    ScienceCinema (OSTI)

    Rohwer, Forest

    2011-04-26

    Forest Rohwer from San Diego State University talks about "Ocean Viral Metagenomics" on March 25, 2010 at the 5th Annual DOE JGI User Meeting

  3. Single Cell Isotope Probing via Raman Microspectroscopy: A New Way for Functional Analyses of Microbes in Environmental and Medical Samples (2014 DOE JGI Genomics of Energy & Environment Meeting)

    SciTech Connect (OSTI)

    Berry, David

    2014-03-20

    David Berry, University of Vienna, at the 9th Annual Genomics of Energy & Environment Meeting on March 20, 2014 in Walnut Creek, Calif.

  4. Multi-kb Illumina reads Reveal Significant Strain Variation and Rare Organisms in Aquifer (2014 DOE JGI Genomics of Energy & Environment Meeting)

    SciTech Connect (OSTI)

    Sharon, Itai [UC Berkely

    2014-03-20

    Itai Sharon from the University of California at Berkely speaks at the 9th Annual Genomics of Energy & Environment Meeting on March 20, 2014 in Walnut Creek, Calif.

  5. Creating a Multi-functional Library of Grass Transcription Factors for the Energy Crop Model System Brachypodium Distachyon (2014 DOE JGI Genomics of Energy & Environment Meeting)

    SciTech Connect (OSTI)

    Coomey, Joshua [University of Massashusetts Amherst

    2014-03-20

    Joshua Coomey of the University of Massachusetts Amherst, speaks at the 9th Annual Genomics of Energy & Environment Meeting on March 20, 2014 in Walnut Creek, Calif.

  6. Genomics Encyclopedia of Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB): a resource for microsymbiont genomes (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

    SciTech Connect (OSTI)

    Reeve, Wayne [Murdoch University

    2013-03-01

    Wayne Reeve of Murdoch University on "Genomics Encyclopedia of Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB): a resource for microsymbiont genomes" at the 8th Annual Genomics of Energy & Environment Meeting on March 27, 2013 in Walnut Creek, Calif.

  7. Genome Rearrangement and Planning Institute of Information Systems

    E-Print Network [OSTI]

    Erdem, Esra

    Genome Rearrangement and Planning Esra Erdem Institute of Information Systems Vienna University Avenue, Toronto, Canada e.tillier@utoronto.ca Abstract The genome rearrangement problem is to find the most eco­ nomical explanation for observed differences between the gene orders of two genomes

  8. Natural variation in Brachypodium disctachyon: Deep Sequencing of Highly Diverse Natural Accessions (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

    SciTech Connect (OSTI)

    Gordon, Sean

    2013-03-01

    Sean Gordon of the USDA on "Natural variation in Brachypodium disctachyon: Deep Sequencing of Highly Diverse Natural Accessions" at the 8th Annual Genomics of Energy & Environment Meeting on March 27, 2013 in Walnut Creek, Calif.

  9. Biodiversity Monitoring Using NGS Approaches on Unusual Substrates (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

    SciTech Connect (OSTI)

    Gilbert, Tom

    2013-03-01

    Tom Gilbert of the Natural History Museum of Denmark on "Biodiversity monitoring using NGS approaches on unusual substrates" at the 8th Annual Genomics of Energy & Environment Meeting in Walnut Creek, Calif.

  10. Evolutionary Perspectives on Diversity of Lignocellulose Decay Mechanisms in Basidionycetes (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    ScienceCinema (OSTI)

    Hibbett, David [Clark University

    2013-01-15

    David Hibbett from Clark University on "Evolutionary Perspectives on Diversity of Lignocellulose Decay Mechanisms in Basidiomycetes" at the 7th Annual Genomics of Energy & Environment Meeting on March 21, 2012 in Walnut Creek, California.

  11. Assembly-driven metagenomics of a hypersaline microbial ecosystem (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

    SciTech Connect (OSTI)

    Allen, Eric [Scripps and UCSD

    2013-03-01

    Eric Allen of Scripps and UC San Diego on "Assembly-driven metagenomics of a hypersaline microbial ecosystem" at the 8th Annual Genomics of Energy & Environment Meeting on March 27, 2013 in Walnut Creek, Calif.

  12. TARA OCEANS: A Global Analysis of Oceanic Plankton Ecosystems (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

    SciTech Connect (OSTI)

    Karsenti, Eric [EMBL Heidelberg

    2013-03-01

    Eric Karsenti of EMBL delivers the closing keynote on "TARA OCEANS: A Global Analysis of Oceanic Plankton Ecosystems" at the 8th Annual Genomics of Energy & Environment Meeting on March 28, 2013 in Walnut Creek, Calif.

  13. Metabolic Engineering of Clostridium thermocellum for Biofuel Production (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

    SciTech Connect (OSTI)

    Guess, Adam [ORNL

    2013-03-01

    Adam Guss of Oak Ridge National Lab on "Metabolic engineering of Clostridium thermocellum for biofuel production" at the 8th Annual Genomics of Energy & Environment Meeting on March 28, 2013 in Walnut Creek, Calif.

  14. Evolutionary Perspectives on Diversity of Lignocellulose Decay Mechanisms in Basidionycetes (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    SciTech Connect (OSTI)

    Hibbett, David [Clark University] [Clark University

    2012-03-21

    David Hibbett from Clark University on "Evolutionary Perspectives on Diversity of Lignocellulose Decay Mechanisms in Basidiomycetes" at the 7th Annual Genomics of Energy & Environment Meeting on March 21, 2012 in Walnut Creek, California.

  15. Delineating Molecular Interaction Mechanisms in an In Vitro Microbial-Plant Community (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

    SciTech Connect (OSTI)

    Larsen, Peter [Argonne

    2013-03-01

    Peter Larsen of Argonne National Lab on "Delineating molecular interaction mechanisms in an in vitro microbial-plant community" at the 8th Annual Genomics of Energy & Environment Meeting in Walnut Creek, Calif.

  16. Succession of Phylogeny and Function During Plant Litter Decomposition (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

    SciTech Connect (OSTI)

    Brodie, Eoin [Berkeley Lab

    2013-03-01

    Eoin Brodie of Berkeley Lab on "Succession of phylogeny and function during plant litter decomposition" at the 8th Annual Genomics of Energy & Environment Meeting on March 27, 2013 in Walnut Creek, Calif.

  17. Modulation of Root Microbiome Community Assembly by the Plant Immune Response (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

    SciTech Connect (OSTI)

    Lebeis, Sarah [University of North Carolina

    2013-03-01

    Sarah Lebeis of University of North Carolina on "Modulation of root microbiome community assembly by the plant immune response" at the 8th Annual Genomics of Energy & Environment Meeting on March 28, 2013 in Walnut Creek, Calif.

  18. Network as Discovery Instrument: A Quick-Start Guide (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

    SciTech Connect (OSTI)

    Bell, Gregory [Berkeley Lab

    2013-03-01

    Gregory Bell of Berkeley Lab on "Network as discovery instrument: a Quick-Start Guide" at the 8th Annual Genomics of Energy & Environment Meeting in Walnut Creek, Calif.

  19. Genetic Regulation of Grass Biomass Accumulation and Biological Conversion Quality (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

    SciTech Connect (OSTI)

    Hazen, Sam [University of Massachusetts

    2013-03-01

    Sam Hazen of the University of Massachusetts on "Genetic Regulation of Grass Biomass Accumulation and Biological Conversion Quality" at the 8th Annual Genomics of Energy & Environment Meeting on March 27, 2013 in Walnut Creek, Calif.

  20. Fungal Genomics Program Grigoriev, Igor 59 BASIC BIOLOGICAL SCIENCES...

    Office of Scientific and Technical Information (OSTI)

    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...

  1. Fungal Genomics Program (Conference) | SciTech Connect

    Office of Scientific and Technical Information (OSTI)

    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...

  2. DOE Joint Genome Institute 2008 Progress Report

    E-Print Network [OSTI]

    Gilbert, David

    2009-01-01

    proteins for biofuel production. Trends in Mi- crobiology,could help improve biofuel production. Diatom Genome Helpsa key target. Current biofuel production meth- ods, such as

  3. New Metadata Organizer Streamlines JGI Data Management

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Scientific Computing Day December 5, 2013 | Tags: Joint Genome Institute, NERSC, Storage Systems Group Contact: Kathy Kincade, +1 510 495 2124, kkincade@lbl.gov A new centralized...

  4. Genomics at the Ontario Institute for Cancer Research

    SciTech Connect (OSTI)

    Ali, Johar

    2010-06-02

    Johar Ali of the Ontario Institute for Cancer Research discusses genomics and next-gen applications at the OICR on June 2, 2010 at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM

  5. Complete Genome Sequence of the Thermophilic Bacterium Exiguobacterium sp. AT1b

    SciTech Connect (OSTI)

    Vishnivetskaya, T. [University of Tennessee, Knoxville (UTK); Lucas, Susan [U.S. Department of Energy, Joint Genome Institute; Copeland, A [U.S. Department of Energy, Joint Genome Institute; Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute; Glavina Del Rio, Tijana [U.S. Department of Energy, Joint Genome Institute; Dalin, Eileen [U.S. Department of Energy, Joint Genome Institute; Tice, Hope [U.S. Department of Energy, Joint Genome Institute; Bruce, David [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Saunders, Elizabeth H [Los Alamos National Laboratory (LANL); Brettin, Thomas S [ORNL; Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Han, Cliff [Los Alamos National Laboratory (LANL); Larimer, Frank W [ORNL; Land, Miriam L [ORNL; Hauser, Loren John [ORNL; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute; Ovchinnikova, Galina [U.S. Department of Energy, Joint Genome Institute; Kathariou, Sophia [North Carolina State University; Ramaley, Robert F. [University of Nebraska Medical Center; Rodrigues, Debora F. [University of Houston, Houston; Hendrix, Christie [Yellowstone National Park; Richardson, Paul [U.S. Department of Energy, Joint Genome Institute; Tiedje, James M. [Michigan State University, East Lansing

    2011-01-01

    Here we present the genome of strain Exiguobacterium sp. AT1b, a thermophilic member of the genus Exiguobacterium whose representatives were isolated from various environments along a thermal and physico-chemical gradient. This genome was sequenced to be a comparative resource for study of thermal adaptation with a psychroactive representative of the genus, Exiguobacterium sibiricum strain 255-15, that was previously sequenced by the U.S. Department of Energy's (DOE) Joint Genome Institute (JGI) (http://genome.ornl.gov/microbial/exig/).

  6. Complete Genome Sequence of the Thermophilic Bacterium Exiguobacterium sp. AT1b

    SciTech Connect (OSTI)

    Vishnivetskaya, T. [University of Tennessee, Knoxville (UTK); Lucas, Susan [U.S. Department of Energy, Joint Genome Institute; Copeland, A [U.S. Department of Energy, Joint Genome Institute; Lapidus, Alla L [ORNL; Glavina Del Rio, Tijana [U.S. Department of Energy, Joint Genome Institute; Dalin, Eileen [U.S. Department of Energy, Joint Genome Institute; Tice, Hope [U.S. Department of Energy, Joint Genome Institute; Bruce, David [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Saunders, Elizabeth H [Los Alamos National Laboratory (LANL); Brettin, Tom [Los Alamos National Laboratory (LANL); Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Han, Cliff [Los Alamos National Laboratory (LANL); Larimer, Frank W [ORNL; Land, Miriam L [ORNL; Hauser, Loren John [ORNL; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute; Ovchinnikova, Galina [U.S. Department of Energy, Joint Genome Institute; Kathariou, Sophia [North Carolina State University; Ramaley, Robert F. [University of Nebraska Medical Center; Rodrigues, Debora F. [University of Houston, Houston; Hendrix, Christie [Yellowstone National Park; Richardson, Paul [U.S. Department of Energy, Joint Genome Institute; Tiedje, James M. [Michigan State University, East Lansing

    2011-01-01

    Here we present the genome of strain Exiguobacterium sp. AT1b, a thermophilic member of the genus Exiguobacterium whose representatives were isolated from various environments along a thermal and physicochemical gradient. This genome was sequenced to be a comparative resource for the study of thermal adaptation with a psychroactive representative of the genus, Exiguobacterium sibiricum strain 255-15, that was previously sequenced by the U.S. Department of Energy s (DOE s) Joint Genome Institute (JGI) (http://genome.ornl.gov/microbial/exig/).

  7. Competitiveness of Second Generation Biofuel Feedstocks: Role of Technology and Policy (2010 JGI User Meeting)

    SciTech Connect (OSTI)

    Khanna, Madhu

    2010-03-26

    Madhu Khanna from the University of Illinois at Urbana-Champaign and the Energy Biosciences Institute on "Competitiveness of Second Generation Biofuel Feedstocks: Role of Technology and Policy" on March 25, 2010 at the 5th Annual DOE JGI User Meeting

  8. Competitiveness of Second Generation Biofuel Feedstocks: Role of Technology and Policy (2010 JGI User Meeting)

    ScienceCinema (OSTI)

    Khanna, Madhu

    2011-04-26

    Madhu Khanna from the University of Illinois at Urbana-Champaign and the Energy Biosciences Institute on "Competitiveness of Second Generation Biofuel Feedstocks: Role of Technology and Policy" on March 25, 2010 at the 5th Annual DOE JGI User Meeting

  9. The Promise and Challenge of Producing Biofuel Feedstocks: An Ecological Perspective (2010 JGI User Meeting)

    ScienceCinema (OSTI)

    DeLucia, Evan

    2011-04-26

    Evan DeLucia of the University of Illinois at Urbana-Champaign and the Energy Biosciences Institute talks about "The Promise and Challenge of Producing Biofuel Feedstocks: An Ecological Perspective" on March 25, 2010 at the 5th Annual DOE JGI User Meeting

  10. Acceleration Architectures for Bioinformatics (2010 JGI/ANL HPC Workshop)

    ScienceCinema (OSTI)

    Gokhale, Maya

    2011-06-08

    Maya Gokhale of the Lawrence Livermore National Laboratory presents at the JGI/Argonne HPC Workshop on January 26, 2010

  11. JGI's Carbon Cycling Studies on Restored Marshes

    SciTech Connect (OSTI)

    Tringe, Susannah; Theroux, Susanna

    2015-06-02

    DOE Joint Genome Institute Metagenome Program Head, Susannah Tringe, and postdoc, Susie Theroux, discuss the lessons to be learned from studying the microbial diversity of marshes that have been converted to other uses, and are now being restored, as well as the potential impacts on the global carbon cycle.

  12. Phytozome: a Tool for Green Plant Comparative Genomics

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    Phytozome is a joint project of the Department of Energy's Joint Genome Institute and the Center for Integrative Genomics to facilitate comparative genomic studies amongst green plants. Clusters of orthologous and paralogous genes that represent the modern descendents of ancestral gene sets are constructed at key phylogenetic nodes. These clusters allow easy access to clade specific orthology/paralogy relationships as well as clade specific genes and gene expansions. As of release v4.0, Phytozome provides access to nine sequenced and annotated green plant genomes, eight of which have been clustered into gene families at six evolutionarily significant nodes. Where possible, each gene has been annotated with PFAM, KOG, KEGG, and PANTHER assignments, and publicly available annotations from RefSeq, UniProt, TAIR, JGI are hyper-linked and searchable. [Copied from the Overview at http://www.phytozome.net/Phytozome_info.php

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

    ScienceCinema (OSTI)

    Pop, Mihai [University of Maryland

    2013-01-22

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

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

    ScienceCinema (OSTI)

    Quake, Steve [University of Stanford

    2013-01-22

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

  15. Standards in Genomic Science: An Open-Access Journal of the Genomic Standards Consortium (GSC8 Meeting)

    ScienceCinema (OSTI)

    Garrity, George

    2011-06-03

    George Garrity of Michigan State University talks about the GSC's open-access journal SIGS at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, Calif. on Sept. 9, 2009.

  16. FACILITIES and EQUIPMENT DESCRIPTION The UCR Institute for Integrative Genome Biology

    E-Print Network [OSTI]

    Lyubomirsky, Ilya

    1 FACILITIES and EQUIPMENT DESCRIPTION The UCR Institute for Integrative Genome Biology interdisciplinary, four-story Genomics Building in 2009 to accommodate over 200 faculty members, graduate students one roof who use modern genetic tools, genomics and bioinformatics to help address basic and applied

  17. Metabolic Noise, Vestigial Metabolites or the Raw Material of Ecological Adaptation? Opportunitistic Enzymes, Catalytic Promiscuity and the Evolution of chemodiversity in Nature (2010 JGI User Meeting)

    ScienceCinema (OSTI)

    Noel, Joseph

    2011-04-25

    Joseph Noel from the Salk Institute on "Metabolic Noise, Vestigial Metabolites or the Raw Material of Ecological Adaptation? Enzymes, Catalytic Promiscuity and the Evolution of Chemodiversity in Nature" on March 26, 2010 at the 5th Annual DOE JGI User Meeting

  18. Institute of Functional Genomics, University of Regensburg, Regensburg, Germany. Present address: Center for Systems Biology, Harvard Medical School, Boston, MA.

    E-Print Network [OSTI]

    Rosenberg, Noah

    1 Institute of Functional Genomics, University of Regensburg, Regensburg, Germany. 2 Present, Food and Environment, The Hebrew University of Jeru- salem, Rehovot, Israel. 7 Department of Genetics

  19. Patterns of Nitrogen Utilization in Deep-Sea Syntrophic Consortia (2010 JGI User Meeting)

    ScienceCinema (OSTI)

    Wiegel, Detlef

    2011-04-26

    Victoria Orphan from Caltech discusses "Patterns of nitrogen utilization in deep-sea syntrophic consortia" on March 25, 2010 at the 5th Annual DOE JGI User Meeting

  20. High Performance Computational Biology: A Distributed computing Perspective (2010 JGI/ANL HPC Workshop)

    ScienceCinema (OSTI)

    Konerding, David [Google, Inc

    2011-06-08

    David Konerding from Google, Inc. gives a presentation on "High Performance Computational Biology: A Distributed Computing Perspective" at the JGI/Argonne HPC Workshop on January 26, 2010.

  1. Solving Problems with Sequences (Closing Keynote Address - 2010 JGI User Meeting)

    ScienceCinema (OSTI)

    Colwell, Rita

    2011-04-28

    Rita Colwell, recipient of the 2010 Stockholm Water Prize, delivers the closing keynote at the 5th Annual DOE JGI User Meeting on March 26, 2010

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

    ScienceCinema (OSTI)

    Simpson, Jared [Wellcome Trust Sanger Institute

    2013-01-22

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

  3. Casting a Wider Net: Distributed Resources for Metagenomics (2010 JGI/ANL HPC Workshop)

    SciTech Connect (OSTI)

    Meyer, Folker [ANL] [ANL

    2010-01-26

    Folker Meyer from Argonne National Lab gives a presentation on "Casting a Wider Net: Distributed Resources for Metagenomics" at the JGI/Argonne HPC Workshop on January 26, 2010.

  4. High Performance Computing for Sequence Analysis (2010 JGI/ANL HPC Workshop)

    ScienceCinema (OSTI)

    Oehmen, Chris [PNNL

    2011-06-08

    Chris Oehmen of the Pacific Northwest National Laboratory gives a presentation on "High Performance Computing for Sequence Analysis" at the JGI/Argonne HPC Workshop on January 25, 2010.

  5. Next-Gen Annotation Based on Transcriptomics (2010 JGI/ANL HPC Workshop)

    ScienceCinema (OSTI)

    Cottingham, Bob [ORNL

    2011-06-08

    Bob Cottingham of the Oak Ridge National Laboratory gives a presentation on "Next-Gen Annotation based on Transcriptomics" at the JGI/Argonne HPC Workshop on January 25, 2010.

  6. Rapid Evolutionary Placement of Short Sequence Reads (2010 JGI/ANL HPC Workshop)

    ScienceCinema (OSTI)

    Stamatakis, Alexis [Technical University of Munich

    2011-06-08

    Alexis Stamatakis of the Technical University of Munich gives a presentation on "Rapid Evolutionary Placement of Short Sequence Reads" at the JGI/Argonne HPC Workshop on January 26, 2010.

  7. High Performance Computing for Sequence Analysis (2010 JGI/ANL HPC Workshop)

    SciTech Connect (OSTI)

    Oehmen, Chris [PNNL] [PNNL

    2010-01-25

    Chris Oehmen of the Pacific Northwest National Laboratory gives a presentation on "High Performance Computing for Sequence Analysis" at the JGI/Argonne HPC Workshop on January 25, 2010.

  8. Casting a Wider Net: Distributed Resources for Metagenomics (2010 JGI/ANL HPC Workshop)

    ScienceCinema (OSTI)

    Meyer, Folker [ANL

    2011-06-08

    Folker Meyer from Argonne National Lab gives a presentation on "Casting a Wider Net: Distributed Resources for Metagenomics" at the JGI/Argonne HPC Workshop on January 26, 2010.

  9. Genomics, Gene Expression and Other Studies in Soybean Rust

    E-Print Network [OSTI]

    Posada-Buitrago, Martha Lucia

    2005-01-01

    Joint Genome Institute Genomics, Gene Expression and otherRust Martha Lucía Posada-Buitrago Ph.D Genomics DivisionEvolutionary Genomics DOE- Joint Genome Institute Lawrence

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

    SciTech Connect (OSTI)

    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.

  11. TITLE AUTHORS SUBJECT SUBJECT RELATED DESCRIPTION PUBLISHER AVAILABILI...

    Office of Scientific and Technical Information (OSTI)

    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...

  12. Challenges in Whole-Genome Annotation of Pyrosequenced Eukaryotic Genomes

    SciTech Connect (OSTI)

    Kuo, Alan; Grigoriev, Igor

    2009-04-17

    Pyrosequencing technologies such as 454/Roche and Solexa/Illumina vastly lower the cost of nucleotide sequencing compared to the traditional Sanger method, and thus promise to greatly expand the number of sequenced eukaryotic genomes. However, the new technologies also bring new challenges such as shorter reads and new kinds and higher rates of sequencing errors, which complicate genome assembly and gene prediction. At JGI we are deploying 454 technology for the sequencing and assembly of ever-larger eukaryotic genomes. Here we describe our first whole-genome annotation of a purely 454-sequenced fungal genome that is larger than a yeast (>30 Mbp). The pezizomycotine (filamentous ascomycote) Aspergillus carbonarius belongs to the Aspergillus section Nigri species complex, members of which are significant as platforms for bioenergy and bioindustrial technology, as members of soil microbial communities and players in the global carbon cycle, and as agricultural toxigens. Application of a modified version of the standard JGI Annotation Pipeline has so far predicted ~;;10k genes. ~;;12percent of these preliminary annotations suffer a potential frameshift error, which is somewhat higher than the ~;;9percent rate in the Sanger-sequenced and conventionally assembled and annotated genome of fellow Aspergillus section Nigri member A. niger. Also,>90percent of A. niger genes have potential homologs in the A. carbonarius preliminary annotation. Weconclude, and with further annotation and comparative analysis expect to confirm, that 454 sequencing strategies provide a promising substrate for annotation of modestly sized eukaryotic genomes. We will also present results of annotation of a number of other pyrosequenced fungal genomes of bioenergy interest.

  13. Visualizing Distributed Data with BigWig and BigBed at UCSC (2010 JGI/ANL HPC Workshop)

    ScienceCinema (OSTI)

    Kent, Jim [UCSC

    2011-06-08

    Jim Kent from University of California, Santa Cruz presents on "Visualizing Distributed Data with BigWig and BigBed at UCSC" at the JGI/Argonne HPC Workshop on January 26, 2010.

  14. Three Non-Technical Challenges in the Development of Biomass-based Energy (2010 JGI User Meeting)

    ScienceCinema (OSTI)

    Savage, Steve

    2011-04-25

    Steve Savage from Cirrus Partners on "Three Non-Technical Challenges in the Development of Biomass-based Energy" on March 25, 2010 at the 5th Annual DOE JGI User Meeting

  15. Wood-Producing Sunflower? Mining Genetic Diversity in Desert-Dwelling Wild Species (2010 JGI User Meeting)

    SciTech Connect (OSTI)

    Knapp, Steve

    2010-03-25

    Steve Knapp from Monsanto on "Wood-Producing Sunflower? Mining Genetic Diversity in Desert-Dwelling Wild Species" on March 25, 2010 at the 5th Annual DOE JGI User Meeting

  16. Wood-Producing Sunflower? Mining Genetic Diversity in Desert-Dwelling Wild Species (2010 JGI User Meeting)

    ScienceCinema (OSTI)

    Knapp, Steve

    2011-04-26

    Steve Knapp from Monsanto on "Wood-Producing Sunflower? Mining Genetic Diversity in Desert-Dwelling Wild Species" on March 25, 2010 at the 5th Annual DOE JGI User Meeting

  17. Kjiersten Fagnan Appointed NERSC/JGI Engagement Lead

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    systems to assemble and perform comparative analysis for genomes from plant, fungal, microbial and metagenome communities. In her new role, Fagnan will coordinate NERSC...

  18. GenePRIMP: A GENE PRediction IMprovement Pipeline for Prokaryotic genomes

    SciTech Connect (OSTI)

    Pati, Amrita; Ivanova, Natalia N.; Mikhailova, Natalia; Ovchinnikova, Galina; Hooper, Sean D.; Lykidis, Athanasios; Kyrpides, Nikos C.

    2010-04-01

    We present 'gene prediction improvement pipeline' (GenePRIMP; http://geneprimp.jgi-psf.org/), a computational process that performs evidence-based evaluation of gene models in prokaryotic genomes and reports anomalies including inconsistent start sites, missed genes and split genes. We found that manual curation of gene models using the anomaly reports generated by GenePRIMP improved their quality, and demonstrate the applicability of GenePRIMP in improving finishing quality and comparing different genome-sequencing and annotation technologies.

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

    E-Print Network [OSTI]

    Daum, Christopher

    2011-01-01

    Sequencing and QC Analysis Pipelines at the DOE Joint GenomeSequencing and QC Analysis Pipelines at the DOE Joint GenomeGenome Analyzer and HiSeq pipeline has been established.

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

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    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.

  1. A Collection of Algal Genomes from the JGI Kuo, Alan; Grigoriev...

    Office of Scientific and Technical Information (OSTI)

    chains as primary producers. Algae play profound roles in the carbon cycle, can impose health and economic costs through toxic blooms, and are candidate sources for bio-fuels; all...

  2. A Collection of Algal Genomes from the JGI (Conference) | SciTech...

    Office of Scientific and Technical Information (OSTI)

    chains as primary producers. Algae play profound roles in the carbon cycle, can impose health and economic costs through toxic blooms, and are candidate sources for bio-fuels; all...

  3. Genomics Dan Rokhsar, DOE JGI/LBNL & UC Berkeley NERSC User Meeting

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantityBonneville Power Administration would likeUniverse (Journalvivo Low-Dose Low LET Ionizing Radiation Exposure: Pathwaysfor

  4. Overview of IMG Challenges (MICW - Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    ScienceCinema (OSTI)

    Markowitz, Victor [JGI

    2013-01-22

    DOE JGI's Victor Markowitz gives an overview of IMG challenges at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

  5. FUNCTIONAL GENOMICS Program of Study

    E-Print Network [OSTI]

    Thomas, Andrew

    FUNCTIONAL GENOMICS Program of Study Research Areas Students Applying Correspondence Graduate Genomics. Students receive training in the biological, physical and computational sciences through of primary institutional affiliation. The Functional Genomics program is administered through the Graduate

  6. The Future of Microbial Genomics

    SciTech Connect (OSTI)

    Kyrpides, Nikos [Genome Biology group at the DOE Joint Genome Institute

    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

  7. Comparative genomics reveals evidence of marine adaptation in Salinispora species.

    E-Print Network [OSTI]

    Penn, Kevin; Jensen, Paul R

    2012-01-01

    in microbial nutrient utilization and energy transduction.Energy Joint Genome Institute website (http://genome. ornl.gov/microbial/

  8. The Integrated Microbial Genomes (IMG) System: An Expanding Comparative Analysis Resource

    SciTech Connect (OSTI)

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

    2009-09-13

    The integrated microbial genomes (IMG) system serves as a community resource for comparative analysis of publicly available genomes in a comprehensive integrated context. IMG contains both draft and complete microbial genomes integrated with 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 reviewing the annotations of genes and genomes in a comparative context. Since its first release in 2005, IMG's data content and analytical capabilities have been constantly expanded through regular releases. Several companion IMG systems have been set up in order to serve domain specific needs, such as expert review of genome annotations. IMG is available at jgi.doe.gov>.

  9. Environmental Genomics Reveals a Single-Species Ecosystem Deep Earth

    E-Print Network [OSTI]

    Arkin, Adam P.

    2014-01-01

    Environmental Genomics Reveals a Single-Species EcosystemTechnology Program, DOE Joint Genomics Institute, Berkeley,and Environmental Research, Genomics:GTL program through

  10. Incorporating Genomics and Bioinformatics across the Life Sciences Curriculum

    SciTech Connect (OSTI)

    Ditty, Jayna L.; Kvaal, Christopher A.; Goodner, Brad; Freyermuth, Sharyn K.; Bailey, Cheryl; Britton, Robert A.; Gordon, Stuart G.; Heinhorst, Sabine; Reed, Kelynne; Xu, Zhaohui; Sanders-Lorenz, Erin R.; Axen, Seth; Kim, Edwin; Johns, Mitrick; Scott, Kathleen; Kerfeld, Cheryl A.

    2011-08-01

    Undergraduate life sciences education needs an overhaul, as clearly described in the National Research Council of the National Academies publication BIO 2010: Transforming Undergraduate Education for Future Research Biologists. Among BIO 2010's top recommendations is the need to involve students in working with real data and tools that reflect the nature of life sciences research in the 21st century. Education research studies support the importance of utilizing primary literature, designing and implementing experiments, and analyzing results in the context of a bona fide scientific question in cultivating the analytical skills necessary to become a scientist. Incorporating these basic scientific methodologies in undergraduate education leads to increased undergraduate and post-graduate retention in the sciences. Toward this end, many undergraduate teaching organizations offer training and suggestions for faculty to update and improve their teaching approaches to help students learn as scientists, through design and discovery (e.g., Council of Undergraduate Research [www.cur.org] and Project Kaleidoscope [www.pkal.org]). With the advent of genome sequencing and bioinformatics, many scientists now formulate biological questions and interpret research results in the context of genomic information. Just as the use of bioinformatic tools and databases changed the way scientists investigate problems, it must change how scientists teach to create new opportunities for students to gain experiences reflecting the influence of genomics, proteomics, and bioinformatics on modern life sciences research. Educators have responded by incorporating bioinformatics into diverse life science curricula. While these published exercises in, and guidelines for, bioinformatics curricula are helpful and inspirational, faculty new to the area of bioinformatics inevitably need training in the theoretical underpinnings of the algorithms. Moreover, effectively integrating bioinformatics into courses or independent research projects requires infrastructure for organizing and assessing student work. Here, we present a new platform for faculty to keep current with the rapidly changing field of bioinformatics, the Integrated Microbial Genomes Annotation Collaboration Toolkit (IMG-ACT). It was developed by instructors from both research-intensive and predominately undergraduate institutions in collaboration with the Department of Energy-Joint Genome Institute (DOE-JGI) as a means to innovate and update undergraduate education and faculty development. The IMG-ACT program provides a cadre of tools, including access to a clearinghouse of genome sequences, bioinformatics databases, data storage, instructor course management, and student notebooks for organizing the results of their bioinformatic investigations. In the process, IMG-ACT makes it feasible to provide undergraduate research opportunities to a greater number and diversity of students, in contrast to the traditional mentor-to-student apprenticeship model for undergraduate research, which can be too expensive and time-consuming to provide for every undergraduate. The IMG-ACT serves as the hub for the network of faculty and students that use the system for microbial genome analysis. Open access of the IMG-ACT infrastructure to participating schools ensures that all types of higher education institutions can utilize it. With the infrastructure in place, faculty can focus their efforts on the pedagogy of bioinformatics, involvement of students in research, and use of this tool for their own research agenda. What the original faculty members of the IMG-ACT development team present here is an overview of how the IMG-ACT program has affected our development in terms of teaching and research with the hopes that it will inspire more faculty to get involved.

  11. TITLE AUTHORS SUBJECT SUBJECT RELATED DESCRIPTION PUBLISHER AVAILABILI...

    Office of Scientific and Technical Information (OSTI)

    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...

  12. "Title","Creator/Author","Publication Date","OSTI Identifier...

    Office of Scientific and Technical Information (OSTI)

    bit.lyJGI-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...

  13. Fuzzy Genome Sequence Assembly for Single and Environmental Genomes

    E-Print Network [OSTI]

    Nicolescu, Monica

    and to the first genome sequence as- sembly, Bacteriophage X174 [38]. In 1990 the Human Genome Project in 2003, two years before its projected date. #12;2 Sara Nasser, et al In 1993 The Institute for Genome advancements in technology that lead the to complete sequencing of the Human Genome and the H. influenzae

  14. 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 [Office of Scientific and Technical Information (OSTI)]

    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.

  15. EUKARYOTIC CELL, Feb. 2005, p. 230241 Vol. 4, No. 2 1535-9778/05/$08.00 0 doi:10.1128/EC.4.2.230241.2005

    E-Print Network [OSTI]

    encoded in the Chlamydomonas genome. A comprehensive description of Chlamydomonas im- munophilins thus appears desirable. With the recent release by the Joint Genome Institute (JGI) of a draft nuclear genome sequence, Chlamydomonas has fully entered the genomics era (16). Among the primary goals of genomics

  16. Environmental genomics reveals a single species ecosystem deep within the Earth

    E-Print Network [OSTI]

    Chivian, Dylan

    2008-01-01

    Environmental genomics reveals a single species ecosystemMaterial for Environmental genomics reveals a single speciesTechnology Program, DOE Joint Genomics Institute, Berkeley,

  17. Gene Calling Standards (GSC8 Meeting)

    ScienceCinema (OSTI)

    Kyrpides, Nikos [Genome Biology Program, DOE JGI

    2011-04-28

    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 gene calling standards at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, Calif. on Sept. 10, 2009.

  18. Methods in comparative genomics: genome correspondence, gene identification and motif discovery

    E-Print Network [OSTI]

    Kellis, Manolis

    1 Methods in comparative genomics: genome correspondence, gene identification and motif discovery@mit.edu, nickp@genome.wi.mit.edu, bwb@genome.wi.mit.edu, bab@mit.edu, lander@wi.mit.edu (1) MIT/Whitehead Institute Center for Genome Research, 320 Charles St., Cambridge MA 02139 (2) MIT Computer Science

  19. Division ORPS Points of Contact Division Point-of-Contact Phone Ext.

    E-Print Network [OSTI]

    Technologies Ron Scholtz 495-8137 Facilities Eugene Tucker Jim Dahlgard (backup) 6985 6647 Genomics - JGI

  20. In the International Year of Soils, EMSL Researchers Dig Deep...

    Office of Science (SC) Website

    Berkeley National Laboratory, to enable scientists to leverage opportunities in genomics research at JGI and molecular characterization at EMSL at the same time. The JGI-EMSL...

  1. Hindawi Publishing Corporation Comparative and Functional Genomics

    E-Print Network [OSTI]

    Newcastle upon Tyne, University of

    Hindawi Publishing Corporation Comparative and Functional Genomics Volume 2007, Article ID 47304, 7 pages doi:10.1155/2007/47304 Meeting Report eGenomics: Cataloguing Our Complete Genome Collection III, Michigan State University, East Lansing, MI 48824, USA 3 The Institute for Genomic Research, 9712 Medical

  2. SHORT REVIEW Ecological genomics: understanding gene and

    E-Print Network [OSTI]

    Herman, Mike

    SHORT REVIEW Ecological genomics: understanding gene and genome function in the natural environment MC Ungerer, LC Johnson and MA Herman Division of Biology, Ecological Genomics Institute, Kansas State University, Manhattan, KS, USA The field of ecological genomics seeks to understand the genetic mechanisms

  3. Defining Genome Project Standards in a New Era of Sequencing

    SciTech Connect (OSTI)

    Chain, Patrick [DOE-JGI

    2009-05-27

    Patrick Chain of the DOE Joint Genome Institute gives a talk on behalf of the International Genome Sequencing Standards Consortium on the need for intermediate genome classifications between "draft" and "finished"

  4. Standards and the INSDC: Submission of MIGS, MIMS, MIENS (GSC8 Meeting)

    ScienceCinema (OSTI)

    Mizrachi, Ilene [NCBI

    2011-04-29

    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. Ilene Mizrachi of the NCBI talks about submission of MIGS/MIMS/MIENS information at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, Calif. on Sept. 9, 2009.

  5. The Biocurator Society (GSC8 Meeting)

    ScienceCinema (OSTI)

    Gaudet, Pascal [Northwestern University

    2011-04-28

    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. Pascal Gaudet of Northwestern University talks about "The Biocurator Society" at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, Calif. on Sept. 11, 2009

  6. Annotations in Refseq (GSC8 Meeting)

    ScienceCinema (OSTI)

    Tatusova, Tatiana

    2011-04-28

    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. Tatiana Tatusova of NCBI discusses "Annotations in Refseq" at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, Calif. on Sept. 10, 2009.

  7. Oceanic Communities in a Changing Planet - The Tara Oceans Project (GSC8 Meeting)

    ScienceCinema (OSTI)

    Raes, Jeroen [University of Brussels

    2011-04-28

    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. Jeroen Raes of the University of Brussels discusses the Tara-Oceans expedition at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, Calif. on Sept. 9, 2009

  8. Terragenome: International Soil Metagenome Sequencing Consortium (GSC8 Meeting)

    ScienceCinema (OSTI)

    Jansson, Janet [LBNL

    2011-04-29

    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. Janet Jansson of the Lawrence Berkeley National Laboratory discusses the Terragenome Initiative at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, Calif. on Sept. 9, 2009

  9. Systems Biology Knowledgebase (GSC8 Meeting)

    ScienceCinema (OSTI)

    Cottingham, Robert W [ORNL

    2011-04-29

    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. Robert W. Cottingham of Oak Ridge National Laboratory discusses the DOE KnowledgeBase at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, Calif. on Sept. 9, 2009.

  10. Towards a Consensus Annotation System (GSC8 Meeting)

    ScienceCinema (OSTI)

    White, Owen [University of Maryland

    2011-04-28

    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. "Comparing Annotations: Towards Consensus Annotation" at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, Calif. on Sept. 10, 2009

  11. THE CAMPAIGN FOR UC SANTA CRUZ THE GENOMICS

    E-Print Network [OSTI]

    California at Santa Cruz, University of

    THE CAMPAIGN FOR UC SANTA CRUZ THE GENOMICS INSTITUTE #12;OVERVIEW The UC Santa Cruz Genomics Institute provides the framework for the next great leap in the science of genomics. ensured it would genomic science and speed the benefits of discoveries that improve and save lives. Cancer, autoimmune

  12. THE CAMPAIGN FOR UC SANTA CRUZ THE GENOMICS

    E-Print Network [OSTI]

    California at Santa Cruz, University of

    THE CAMPAIGN FOR UC SANTA CRUZ THE GENOMICS INSTITUTE #12;T he promise of genomics to revolutionize. We imagine a future in which genomic data is a tool for fighting diseases--from childhood cancer Genome Project to today's effort to create international protocols for sharing and interpreting genomic

  13. The Genome of Deep-Sea Vent Chemolithoautotroph Thiomicrospira...

    Office of Scientific and Technical Information (OSTI)

    Tampa Woods Hole Oceanographic Institution (WHOI), Woods Hole, MA ORNL U.S. Department of Energy, Joint Genome Institute University of Missouri, Columbia Richard Stockton College...

  14. Genome Snapshot: a new resource at the Saccharomyces Genome Database (SGD) presenting

    E-Print Network [OSTI]

    Botstein, David

    Genome Snapshot: a new resource at the Saccharomyces Genome Database (SGD) presenting an overview of the Saccharomyces cerevisiae genome Jodi E. Hirschman, Rama Balakrishnan, Karen R. Christie, Maria C. Costanzo, 5-Sigler Institute for Integrative Genomics, Carl Icahn Laboratory, Princeton University, Washington Road, Princeton

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

    ScienceCinema (OSTI)

    Mavrommatis, Kostas [JGI

    2013-01-22

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

  16. Finding Fingerprints of Selection in Poplar Genomes

    ScienceCinema (OSTI)

    Tuskan, Gerald

    2014-10-28

    Jerry Tuskan of Oak Ridge National Laboratory and the DOE JGI talks about poplar trees as models for selective adaptation to an environment. This video complements a study published ahead online August 24, 2014 in Nature Genetics.

  17. Leading Edge Bacterial Genomics and Pathogen Evolution

    E-Print Network [OSTI]

    Mekalanos, John

    Leading Edge Review Bacterial Genomics and Pathogen Evolution David M. Raskin,1 Rekha Seshadri,2 Medical School, Boston, MA 02115, USA 2 The Institute for Genomic Research, 9712 Medical Center Drive.02.002 The availability of hundreds of bacterial genome sequences has altered the study of bacte- rial pathogenesis

  18. Flash Updates of GSC projects (GSC8 Meeting)

    ScienceCinema (OSTI)

    Glockner, Frank Oliver; Markowitz, Victor; Kyrpides, Nikos; Meyer, Folker; Amaral-Zettler, Linda; Cole, James

    2011-04-29

    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. In quick succession Frank Oliver Glockner (MPI-Bremen), Victor Markowitz (LBNL), Nikos Kyripides (JGI), Folker Meyer (ANL), Linda Amaral-Zettler (Marine Biology Lab), and James Cole (Michigan State University) provide updates on a number of topics related to GSC projects at the Genomic Standards Consortium 8th meeting at the DOE JGI in Walnut Creek, Calif. on Sept. 9, 2009.

  19. JGI Case Study (NERSC-BER Workshop, Sep 11 2012).pptx

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantityBonneville Power Administration would likeUniverseIMPACT EVALUATIONIntroducing theActivation byIs aItem NotJ.NOONC 1Institute

  20. Sequencing the fungal tree Terrestrial ecosystems host a complex array of interacting

    E-Print Network [OSTI]

    Hibbett, David S.

    of interacting communities, with thousands of species of animals, plants, fungi and bacteria. In soils, this complex web of life is responsible for the cycling of carbon (C), for water and nutrients, for soil, the US Department of Energy Joint Genome Institute (JGI) launched the Fungal Genomics Program (FGP

  1. JIBS | Joint Institute for Biological Sciences | ORNL

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    joint institute is located close to ORNL's Laboratory for Comparative and Functional Genomics, other biomolecular sciences research laboratories, and the Environmental Sciences...

  2. Discovering Geometric Patterns in Genomic Data Wenxuan Gao

    E-Print Network [OSTI]

    Grossman, Robert

    Discovering Geometric Patterns in Genomic Data Wenxuan Gao Department of Computer Science University of Illinois at Chicago wgao5@uic.edu Christopher Brown Institute for Genomics & Systems Biology caseybrown@uchicago.edu Robert L. Grossman Institute for Genomics & Systems Biology robert.grossman @uchicago

  3. Prescreening Illumina Data Results in High-Quality Genome Polishing

    SciTech Connect (OSTI)

    Han, Cliff [DOE Joint Genome Institute at Los Alamos National Laboratory

    2009-05-28

    Cliff Han of the DOE Joint Genome Institute at Los Alamos National Laboratory, talks about modifying their bacterial genome sequencing process to accommodate new sequencing technologies at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM

  4. Genome duplications (polyploidy) / ancientGenome duplications (polyploidy) / ancient genome duplications (genome duplications (paleopolyploidypaleopolyploidy))

    E-Print Network [OSTI]

    Utrecht, Universiteit

    Genome duplications (polyploidy) / ancientGenome duplications (polyploidy) / ancient genome duplications (genome duplications (paleopolyploidypaleopolyploidy)) Mechanism? e.g. a diploid cell undergoes;Paramecium genome duplicationsParamecium genome duplications #12;Comparison of two scaffolds originating from

  5. Functional genomics as a window on radiation stress signaling Sally A Amundson*,1

    E-Print Network [OSTI]

    Functional genomics as a window on radiation stress signaling Sally A Amundson*,1 , Michael Bittner 20892, USA; 2 National Human Genome Research Institute, National Institutes of Health, Bethesda, MD before the completion of the human genome draft sequence, a number of techniques for genomic expression

  6. Molluscan Evolutionary Genomics

    E-Print Network [OSTI]

    Simison, W. Brian

    2010-01-01

    59179 Molluscan Evolutionary Genomics W. Brian Simison andBoore Molluscan Evolutionary Genomics W. Brian Simison andL. Boore Evolutionary Genomics Department, DOE Joint Genome

  7. de novo Metagenomic Assembly (Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    ScienceCinema (OSTI)

    Koren, Sergey [University of Maryland

    2013-01-22

    University of Maryland's Sergey Koren on "denovo Metagenomic Assembly" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

  8. Insular Organization of Gene Space in Grass Genomes Andrea Gottlieb1.

    E-Print Network [OSTI]

    Müller, Hans-Georg

    Insular Organization of Gene Space in Grass Genomes Andrea Gottlieb1. , Hans-Georg Mu¨ ller1 States of America, 2 Institute of Plant Breeding, Genetics and Genomics (Department of Crop and Soil Venter Institute, Rockville, Maryland, United States of America, 6 Institute for Genome Sciences

  9. Genome Engineering

    SciTech Connect (OSTI)

    Voytas, Dan [University of Minnesota

    2014-03-20

    Dan Voytas, University of Minnesota, at the 9th Annual Genomics of Energy & Environment Meeting on March 20, 2014 in Walnut Creek, Calif

  10. Gerber-JGI

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    a standard Linux configuration, or need up to 48 GB of memory on a node. Dedicated to HPC Cloud Computing research 4,480 compute cores 560 compute nodes Two quad-core Intel Nehalem...

  11. Rob Egan JGI

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantityBonneville Power Administration wouldMassR&D100NationalquestionnairesDrought-induced forestNovember 2012)Parallelized

  12. Gerber-JGI

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantityBonneville Power Administration would likeUniverse (Journalvivo Low-Dose Low LETUseful Links Useful Links: TheGerard* HPC -NERSC

  13. Reference-Free Comparative Genomics of 174 Chloroplasts

    E-Print Network [OSTI]

    Reference-Free Comparative Genomics of 174 Chloroplasts Chai-Shian Kua1,2 , Jue Ruan3 , John's Republic of China, 3 The CAS Key Laboratory of Genome Science and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, People's Republic of China, 4 Department of Biological

  14. Potential of metabolomics as a functional genomics tool

    E-Print Network [OSTI]

    Wurtele, Eve Syrkin

    Potential of metabolomics as a functional genomics tool Raoul J. Bino1,2,3 , Robert D. Hall2 3 Centre for BioSystems Genomics, POB 98, 6700 AB Wageningen, The Netherlands 4 Max-Planck Institute Australian Centre for Plant Functional Genomics, School of Botany, University of Melbourne, Victoria 3010

  15. Fungal Genomics Program

    E-Print Network [OSTI]

    Grigoriev, Igor

    2012-01-01

    strains Comparative genomics and transcriptomics of xyloseFungal Genomics Program Igor Grigoriev 1 * (complex communities Fungal Genomics Program Igor Grigoriev

  16. First anniversary gift for Critical Material Institute? Inventions...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    teamwork by our researchers and their support staff." The institute even won a nod from the White House as it celebrated the third anniversary of the Materials Genome...

  17. Selecting Genomes for Reconstruction of Ancestral Genomes

    E-Print Network [OSTI]

    Zhang, Louxin

    Selecting Genomes for Reconstruction of Ancestral Genomes Guoliang Li1 , Jian Ma2 , and Louxin. It is often impossible to sequence all descendent genomes to reconstruct an ancestral genome. In addition, more genomes do not neces- sarily give a higher accuracy for the reconstruction of ancestral character

  18. An initial strategy for the systematic identification of functional elements in the human genome by

    E-Print Network [OSTI]

    Miller, Webb

    An initial strategy for the systematic identification of functional elements in the human genome*§ , Eric S. Lander , James C. Mullikin*§ **, and Michele Clamp ** *Genome Technology Branch and §NISC, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892; Broad

  19. Comparative Microbial Genomics group CenterforBiologicalSequenceanalysisDepartmentofSystemsBiology,TechnicalUniversityofDenmark

    E-Print Network [OSTI]

    Ussery, David W.

    Comparative Microbial Genomics group CenterforBiologicalSequenceanalysisDepartmentofSystemsBiology,TechnicalUniversityofDenmark Burkholderia Pan-genomics Dave Ussery Max Planck Institut fur Terrestrial Microbiology Marburg, Germany 26 May, 2008 - or - What can we learn from more than 50 sequenced genomes? #12;Comparative Microbial Genomics

  20. Building on a Decade of Accomplishments Report of the 2010 Blue Ribbon Panel on Genomics

    E-Print Network [OSTI]

    Levin, Judith G.

    Building on a Decade of Accomplishments Report of the 2010 Blue Ribbon Panel on Genomics Division of Microbiology and Infectious Diseases, Genomics Programs National Institute of Allergy and Infectious Diseases Blue Ribbon Panel on Genomics Division of Microbiology and Infectious Diseases, Genomics Programs

  1. Enhancing a Genome Database Using the XSB Tabled Logic Programming System

    E-Print Network [OSTI]

    Davulcu, Hasan

    goal of the Human Genome Project 1] is to construct detailed physical maps of the human genome Research at the Whitehead Institute in MIT is engaged in several large-scale genome mapping projectsEnhancing a Genome Database Using the XSB Tabled Logic Programming System Hasan Davulcu I

  2. MIENS Minimum Information about an ENvironmental Sequence and The GSC's Not-for-Profit (GSC8 Meeting)

    ScienceCinema (OSTI)

    Yilmaz, Pelin [Max Planck Institute - Bremen]; Kolker, Eugene [Seattle Childrens Hospital

    2011-04-29

    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 held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. Pelin Yilmaz of the Max Planck Institute-Bremen talks about the MIENS specification and Eugene Kolker of Seattle Children's Hospital discusses the GSC's non-for-profit at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, Calif. on Sept. 9, 2009

  3. Joint Genome Institute's Automation Approach and History

    E-Print Network [OSTI]

    Roberts, Simon

    2006-01-01

    DOE & NIH present their joint HGP plan to Congress. The 15-staff from LLNL & LBNL. 2000 HGP leaders & President Clintonof the 21st century. ” 2003 HGP completed and published.

  4. DOE Joint Genome Institute 2008 Progress Report

    E-Print Network [OSTI]

    Gilbert, David

    2009-01-01

    and Outreach Safety and Ergonomics Appendices Appendix A:QA, Instrumenta- tion, Ergonomics, Informatics) in the pastReport 2008 safety and ergonomics Safety is a core value of

  5. DOE Joint Genome Institute 2008 Progress Report

    E-Print Network [OSTI]

    Gilbert, David

    2009-01-01

    digestion, could produce biogas—primarily methane and carbongasoline per day. When biogas is cleaned of its particulates

  6. DOE Joint Genome Institute 2008 Progress Report

    E-Print Network [OSTI]

    Gilbert, David

    2009-01-01

    ries Oak Ri a ato nt o DO me e DOE l labor amos, onAlph ar tio teg ac ana hem dP or B DOE m ogeoc ides in tional achesmanufacturer, or otherwise, does not necessarily constitute

  7. DOE Joint Genome Institute 2008 Progress Report

    E-Print Network [OSTI]

    Gilbert, David

    2009-01-01

    an emerging feed- stock for biodiesel production. Soybean iscenters on its use in biodiesel, a renewable alternativefor more than 80% of biodiesel production. The soybean

  8. Today, DOE's Joint Genome Institute (a

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantityBonneville Power AdministrationRobust,Field-effectWorking With U.S.Week DayDr.Theories81 to 1990Be PreseRted1 6/1/2011 6.2

  9. RNAi-Assisted Genome Evolution in Saccharomyces cerevisiae for Complex Phenotype Engineering

    E-Print Network [OSTI]

    Zhao, Huimin

    RNAi-Assisted Genome Evolution in Saccharomyces cerevisiae for Complex Phenotype Engineering Tong Si, Yunzi Luo, Zehua Bao, and Huimin Zhao*,,,§ Department of Chemical and Biomolecular Engineering, Department of Biochemistry, § Departments of Chemistry and Bioengineering, Institute for Genomic Biology

  10. Genomics and the human genome project: implications for psychiatry

    E-Print Network [OSTI]

    Kelsoe, J R

    2004-01-01

    300 Genomics and the Human Genome Project: implications forpast decade the Human Genome Project has made extraordinaryto each other. The Human Genome Project has approached human

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

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    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.

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

    ScienceCinema (OSTI)

    Canon, Shane [LBNL

    2013-01-22

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

  13. Submitting MIGS, MIMS, MIENS Information to EMBL and Standards and the Sequencing Pipelines of the Gordon and Betty Moore Foundation (GSC8 Meeting)

    ScienceCinema (OSTI)

    Vaughan, Bob [EMBL]; Kaye, Jon [Gordon and Betty Moore Foundation

    2011-04-29

    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. Bob Vaughan of EMBL on submitting MIGS/MIMS/MIENS information to EMBL-EBI's system, followed by a brief talk from Jon Kaye of the Gordon and Betty Moore Foundation on standards and the foundation's sequencing pipelines at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, Calif. on Sept. 9, 2009

  14. The Human Microbiome Project (HMP) and the Data Analysis and Coordination Center (DAAC) portal to the HMP (GSC8 Meeting)

    ScienceCinema (OSTI)

    Weinstock, George [Washington University School of Medicine]; Wortman, Jennifer [University of Maryland School of Medicine

    2011-04-29

    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. George Weinstock from Washington University School of Medicine talks about the Human Microbiome Project (HMP) followed briefly by Jennifer Wortman from the University of Maryland School of Medicine on the Data Analysis and Coordination Center (DACC) portal to the HMP at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, Calif. on Sept. 9, 2009.

  15. A New Arm of the GSC: the RCN4GSC and Curation of MIGS-compliant Data (GSC8 Meeting)

    ScienceCinema (OSTI)

    Field, Dawn [NERC]; Sterk, Peter [NERC

    2011-04-29

    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. Dawn Field of the NERC Centre for Ecology and Hydrology briefly describes RCN4GSC and Peter Sterk of the NERC Centre for Ecology and Hydrology follows with a talk on curation of MIGS-compliant data at the Genomic Standards Consortium 8th meeting at the DOE JGI in Walnut Creek, Calif. on Sept. 9, 2009.

  16. The Human Microbiome Project (HMP) and the Data Analysis and Coordination Center (DAAC) portal to the HMP (GSC8 Meeting)

    SciTech Connect (OSTI)

    Weinstock, George; Wortman, Jennifer

    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. George Weinstock from Washington University School of Medicine talks about the Human Microbiome Project (HMP) followed briefly by Jennifer Wortman from the University of Maryland School of Medicine on the Data Analysis and Coordination Center (DACC) portal to the HMP at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, Calif. on Sept. 9, 2009.

  17. The Encyclopedia of Systems Biology and OMICS (first presentation) and The ISA Infrastructure for Multi-omics Data (second presentation) (GSC8 Meeting)

    SciTech Connect (OSTI)

    Kolker, Eugene; Sansone, Susanna

    2011-09-11

    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. Eugene Kolker from Seattle Children's Hospital briefly discusses "The Encyclopedia of Systems Biology and OMICS," followed by Susanna Sansone from the EBI on "The ISA Infrastructure for multi-omics data" at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, Calif. on Sept. 11, 2009.

  18. The Encyclopedia of Systems Biology and OMICS (first presentation) and The ISA Infrastructure for Multi-omics Data (second presentation) (GSC8 Meeting)

    ScienceCinema (OSTI)

    Kolker, Eugene [Seattle Children's Hospital]; Sansone, Susanna [EBI

    2011-04-28

    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. Eugene Kolker from Seattle Children's Hospital briefly discusses "The Encyclopedia of Systems Biology and OMICS," followed by Susanna Sansone from the EBI on "The ISA Infrastructure for multi-omics data" at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, Calif. on Sept. 11, 2009.

  19. GOLD: The Genomes Online Database

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    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

    (Specialized Interface)

  20. The Human Genome From human genome to other

    E-Print Network [OSTI]

    Linial, Michal

    The Human Genome Project From human genome to other genomes and to gene function June 2000 From genome to health Structural Genomics initiative #12;What is the Human Genome Project? · U.S. govt that arise from genome research #12;The Human Genome Project Project began in 1990 as a $3 billion, 15-year

  1. 388 nature genetics volume 22 august 1999 A YAC-based physical map of the mouse genome

    E-Print Network [OSTI]

    Boguski, Mark S.

    goals of the Human Genome Project1. Here we report the results of a project at the Whitehead Institute of approximately 92% of the mouse genome. We also report the results of a project at the MRC UK Mouse Genome Centre assembling a physical map of the human genome3. The STSs used for screening came from several sources: simple

  2. Genomics and Systems Biology

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Genomics and Systems Biology LANL leads the world in computational finishing of microbial genomes Read caption + In 2013, Los Alamos scientist Richard Sayre and his team...

  3. Genome patent fight erupts

    SciTech Connect (OSTI)

    Roberts, L.

    1991-10-11

    At a Congressional briefing while describing a new project to sequence partially every gene active in the human brain, it was made known that the National Institutes of Health was planning to file patent applications on 1,000 of these sequences a month. The scheme has engendered a firestorm of criticism from genome scientists and project officials alike. The critics argue that these sequences probably can't be patented in the first place - and even if they can, they shouldn't be. The plan would undercut patent protection for those who labor long and hard at the real task of elucidating the function of the proteins encoded by the genes, thereby driving industry away from developing inventions based on that work.

  4. Whole Genome Sequencing of Individual Bacterial Cells from the Ocean

    SciTech Connect (OSTI)

    Malmstrom, Rex [DOE Joint Genome Institute

    2010-06-04

    Rex Malmstrom of the DOE Joint Genome Institute discusses single-cell sequencing of Prochlorococcus on June 4, 2010 at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM

  5. The Comparative Genomics of Salinispora and the Distribution and Abundance of Secondary Metabolite Genes in Marine Plankton

    E-Print Network [OSTI]

    Penn, Kevin Matthew

    2012-01-01

    in microbial nutrient utilization and energy transduction.Energy Joint Genome Institute website (genome.ornl.gov/microbial/microbial loop was coined to describe the major role microbes have in the transformation of matter and energy

  6. The comparative genomics of salinispora and the distribution and abundance of secondary metabolite genes in marine plankton

    E-Print Network [OSTI]

    Penn, Kevin Matthew

    2012-01-01

    in microbial nutrient utilization and energy transduction.Energy Joint Genome Institute website (genome.ornl.gov/microbial/microbial loop was coined to describe the major role microbes have in the transformation of matter and energy

  7. Operations capability improvement of a molecular biology laboratory in a high throughput genome sequencing center

    E-Print Network [OSTI]

    Vokoun, Matthew R. (Matthew Richard)

    2005-01-01

    The Broad Institute is a research collaboration of MIT, Harvard University and affiliated hospitals, and the Whitehead Institute for Biomedical Research. Its scientific mission is to "(1) create tools for genomic medicine ...

  8. Personal Genomics, Personalized Medicine,

    E-Print Network [OSTI]

    Napp, Nils

    /Science Translational Medicine panel discussion; MLA 2012 #12;Timeline: Human Genome Sequence HSLS, U.Pitt 1995 2014 2000 2003 2007 2007 2010 Human Genome Draft Sequence Complete Human Reference Genome Individual Human of a free living organism: Haemophilus Influenzae #12;Personal Genome Project HSLS, U.Pitt #12;Why get

  9. Financial Institutions

    Broader source: Energy.gov [DOE]

    A lending program begins with a financial institution that procures the funds they lend from a number of other sources.

  10. Comparative Genomics of Transcriptional Control in the Human Malaria Parasite Plasmodium falciparum

    E-Print Network [OSTI]

    Arnold, Jonathan

    Comparative Genomics of Transcriptional Control in the Human Malaria Parasite Plasmodium falciparum Richard M.R. Coulson,1,3 Neil Hall,2 and Christos A. Ouzounis1 1 Computational Genomics Group10 1SD, United Kingdom; 2 The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus

  11. Improved Yield and Diverse Finished Bacterial Genomes using Pacific Biosciences RS II SMRT Sequencing

    E-Print Network [OSTI]

    Weber, David J.

    Improved Yield and Diverse Finished Bacterial Genomes using Pacific Biosciences RS II SMRT-Cruz, Alvaro Godinez, Luke J. Tallon Institute for Genome Sciences, University of Maryland School of Medicine, effective, and highly accurate platform for generation of complete microbial genome sequences. As early

  12. Corrigendum Corrigendum to ddApplications of DNA tiling arrays for whole-genome

    E-Print Network [OSTI]

    Jacobsen, Steve

    Corrigendum Corrigendum to ddApplications of DNA tiling arrays for whole-genome analysisTT [Genomics 85 (2005) 1­15] Todd C. Mocklera , Simon Chanc , Ambika Sundaresana,b , Huaming Chenb , Steven E Jolla, CA 92037, USA b Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla

  13. A Tournament Approach to the Detection of Multiple Associations in Genome-wide Studies

    E-Print Network [OSTI]

    Chen, Jiahua

    A Tournament Approach to the Detection of Multiple Associations in Genome-wide Studies of Waterloo 3 Genome Institute of Singapore Correspondence Author: Zehua Chen Department of Statistics@nus.edu.sg 1 #12;Abstract Genome-wide association studies become feasible and promising with the availability

  14. The evolution of modularity in genome architecture John W. Pepper 1

    E-Print Network [OSTI]

    Nehaniv, Chrystopher

    The evolution of modularity in genome architecture John W. Pepper 1 1 Santa Fe Institute, Santa Fe phenomenon is modularity in genome architecture, in which genes with epistatic effects are co­ localized of genome modularity were investigated using a computational model, in which a population of individuals

  15. Whole-genome Comparative Annotation and Regulatory Motif Discovery in Multiple Yeast Species

    E-Print Network [OSTI]

    Kellis, Manolis

    Whole-genome Comparative Annotation and Regulatory Motif Discovery in Multiple Yeast Species@mit.edu, nickp@genome.wi.mit.edu, birren@wi.mit.edu, bab@mit.edu, lander@wi.mit.edu (1) MIT/Whitehead Institute Center for Genome Research, 320 Charles St., Cambridge MA 02139 (2) MIT Lab for Computer Science, 200

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

    SciTech Connect (OSTI)

    Elkins, James G [ORNL; Hamilton-Brehm, Scott [ORNL; Walston Davenport, Karen [Los Alamos National Laboratory (LANL); Land, Miriam L [ORNL; Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Tapia, Roxanne [Los Alamos National Laboratory (LANL); Meincke, Linda [Los Alamos National Laboratory (LANL); Detter, J C [U.S. Department of Energy, Joint Genome Institute; Bruce, David [Los Alamos National Laboratory (LANL); Han, Cliff [Los Alamos National Laboratory (LANL); Cottingham, Robert W [ORNL

    2013-01-01

    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.

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

    ScienceCinema (OSTI)

    Rokhsar, Daniel

    2011-04-28

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

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

    ScienceCinema (OSTI)

    Stepanauskas, Ramunas [Bigelow Laboratory

    2013-01-22

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

  19. 10. international mouse genome conference

    SciTech Connect (OSTI)

    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.

  20. Genomics and the human genome project: implications for psychiatry

    E-Print Network [OSTI]

    Kelsoe, J R

    2004-01-01

    and psychosis: a convergent functional genomics approach.Physiology & Genomics, 4, 83–91. O LIPHANT , A. , B ARKER ,2004), 16(4), 294–300 Genomics and the Human Genome Project:

  1. Comparative genomic workflow

    E-Print Network [OSTI]

    Rajapakse, Jagath

    his article describes a workflow for identifying conserved patterns in noncoding regions of vertebrate genomes, with an intention of investigating possible functions of the conserved regions. The annotations of genomes are ...

  2. JGI Lab Ergo Products Catalog

    E-Print Network [OSTI]

    Alexandre, Melanie

    2010-01-01

    35 Page 1 of 35 Laboratory Ergonomics Product Arm Supports/Page 2 of 35 Laboratory Ergonomics Product Features/OptionsPage 3 of 35 Laboratory Ergonomics Product SoftEdge Corners

  3. JGI Lab Ergo Products Catalog

    E-Print Network [OSTI]

    Alexandre, Melanie

    2010-01-01

    Yes New Tech Vortex 50mL conical tube vertical adapter w/Yes Location New Tech Vortex 50mL conical tube horizontalModified Products Vortex 50mL conical tube horizontal

  4. JGI Lab Ergo Products Catalog

    E-Print Network [OSTI]

    Alexandre, Melanie

    2010-01-01

    bending neck awkwardly Yes New Tech Page 5 of 35 Laboratorygrip. Yes Demo Room and New Tech Amco Swing-A-Way 711BK1200 µl pipettors). Yes New Tech Vistalab Ovation Manual and

  5. JGI Lab Ergo Products Catalog

    E-Print Network [OSTI]

    Alexandre, Melanie

    2010-01-01

    Low-temperature thermoplastic pellets mold together quicklymicrowave oven. The thermoplastic will stick to most porous

  6. JGI Lab Ergo Products Catalog

    E-Print Network [OSTI]

    Alexandre, Melanie

    2010-01-01

    fluids and airborne pathogens Infection control "antimicrobial" prevents mold, mildew and bacterial growth Light weight, easy to clean.

  7. OSCARS Extends JGI Network Capacity

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantityBonneville Power Administration wouldMass map shinesSolarNewsusceptometer underIRossybelle PeralesORNOperations OfficeOSCARS

  8. JGI Compute User Training Series

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity ofkandz-cm11 Outreach Home Room NewsInformation CurrentHenryInhibitingInteractivePGASelectron tomography |J.Argonne Data

  9. The human genome project

    SciTech Connect (OSTI)

    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.

  10. Advances in Whole Genome

    E-Print Network [OSTI]

    Ciocan-Fontanine, Ionut

    Advances in Whole Genome Sequencing IMA Public Lecture: Tuesday, May 6, 2003, 7:30 p.m. Moos Tower sequenced genome, the virus Lambda at 50,000 nucleotides, was sequenced via the shotgun method by Sanger that this approach could not be applied to genomes over 100,000 nucleotides long, so a long period followed where

  11. "Title","Creator/Author","Publication Date","OSTI Identifier...

    Office of Scientific and Technical Information (OSTI)

    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...

  12. TITLE AUTHORS SUBJECT SUBJECT RELATED DESCRIPTION PUBLISHER AVAILABILI...

    Office of Scientific and Technical Information (OSTI)

    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...

  13. Bioinformatics Computing Consultant Position Available

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    exploit advanced computing platforms. JGI provides production sequencing and genomics for the Department of Energy. These activities are critical to the DOE missions in...

  14. TITLE AUTHORS SUBJECT SUBJECT RELATED DESCRIPTION PUBLISHER AVAILABILI...

    Office of Scientific and Technical Information (OSTI)

    JGI Its key project the Genomics Encyclopedia of Fungi targets fungi related to plant health symbionts pathogens and biocontrol agents and biorefinery processes cellulose...

  15. Scaling MG-RAST to Terabases (MICW - Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    ScienceCinema (OSTI)

    Desai, Narayan [ANL

    2013-01-22

    Argonne National Lab's Narayan Desai on "Scaling MG-RAST to Terabases" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

  16. A Collaborative Ecosystem Model for Metagenomics Data Preservation (MICW - Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    ScienceCinema (OSTI)

    Cochrane, Guy [EMBL-EBI

    2013-01-22

    EMBL-EBI's Guy Cochrane on "A Collaborative Ecosystem Model for Metagenomics Data Preservation" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

  17. Meta-IDBA: A de novo Assembler for Metagenomic Data (Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    ScienceCinema (OSTI)

    Chin, Francis [University of Hong Kong

    2013-01-22

    University of Hong Kong's Francis Chin on "Meta-­?IDBA: A de novo Assembler for Metagenomic Data" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

  18. Metagenome Data Integration, Data Storage, and Retrieval (MICW - Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    ScienceCinema (OSTI)

    White, Owen [University of Maryland

    2013-01-22

    University of Maryland's Owen White on "Metagenome Data Integration, Data Storage and Retrieval" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

  19. Marriage or Civil Unions for Single Cells and Metagenomics (Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    ScienceCinema (OSTI)

    Rusch, Doug [J. Craig Venter Institute

    2013-01-22

    JCVI's Doug Rusch on "Marriage or Civil Unions for Single Cells and Metagenomes" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

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

    ScienceCinema (OSTI)

    Dehal, Paramvir [LBNL

    2013-01-22

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

  1. Wetlands, Microbes, and the Carbon Cycle: Behind the Scenes @ Berkeley Lab

    SciTech Connect (OSTI)

    Tringe, Susannah

    2012-01-01

    Susannah Tringe, who leads the Metagenome Program at the Department of Energy's Joint Genome Institute (JGI), a collaboration in which Berkeley Lab plays a leading role, takes us behind the scenes to show how DNA from unknown wild microbes is extracted and analyzed to see what role they play in the carbon cycle. Tringe collects samples of microbial communities living in the wetland muck of the Sacramento-San Joaquin River Delta, organisms that can determine how these wetlands store or release carbon.

  2. Wetlands, Microbes, and the Carbon Cycle: Behind the Scenes @ Berkeley Lab

    ScienceCinema (OSTI)

    Tringe, Susannah

    2013-05-29

    Susannah Tringe, who leads the Metagenome Program at the Department of Energy's Joint Genome Institute (JGI), a collaboration in which Berkeley Lab plays a leading role, takes us behind the scenes to show how DNA from unknown wild microbes is extracted and analyzed to see what role they play in the carbon cycle. Tringe collects samples of microbial communities living in the wetland muck of the Sacramento-San Joaquin River Delta, organisms that can determine how these wetlands store or release carbon.

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

    SciTech Connect (OSTI)

    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.

  4. Dynamic Genomes of Eukaryotes and the Maintenance of Genomic Integrity

    E-Print Network [OSTI]

    Katz, Laura

    Dynamic Genomes of Eukaryotes and the Maintenance of Genomic Integrity Eukaryotes specify a genome to be inherited stably, enabling dynamic rearrangements and amplifications of other genomic elements Laura Wegener Parfrey and Laura A. Katz M any biologists assume that eu- karyotic genomes are transmit- ted stably

  5. Phylogenetic Inference Using Whole Genomes

    E-Print Network [OSTI]

    Phylogenetic Inference Using Whole Genomes Bruce Rannala1 and Ziheng Yang2 1 Genome Center.yang@ucl.ac.uk Annu. Rev. Genomics Hum. Genet. 2008. 9:217­31 First published online as a Review in Advance on June 3, 2008 The Annual Review of Genomics and Human Genetics is online at genom.annualreviews.org This article

  6. Webinar: Materials Genome Initative

    Broader source: Energy.gov [DOE]

    Audio recording and text version of the Fuel Cell Technologies Office webinar titled "Materials Genome Initiative," originally presented on December 2, 2014.

  7. Genomics and Systems Biology

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    and structural genomics, and applications for such work cover diverse fields such as energy, agriculture, and environmental cleanup. Get Expertise Babetta Marrone Biofuels...

  8. Genomics Division Home

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    to the most primitive soil microbe represent a watershed opportunity for biology. The Genomics Division is taking advantage of this wealth of new information. While it is well...

  9. Genome Science/Technologies

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    primary focus is to develop technologies to obtain near complete genomes from single cells for the purposes of improved taxonomic identification and determining metabolic...

  10. Complete genome sequence of Ferroglobus placidus AEDII12DO

    SciTech Connect (OSTI)

    Anderson, Iain [U.S. Department of Energy, Joint Genome Institute; Risso, Carla [University of Massachusetts, Amherst; Holmes, Dawn [University of Massachusetts, Amherst; Lucas, Susan [U.S. Department of Energy, Joint Genome Institute; Copeland, A [U.S. Department of Energy, Joint Genome Institute; Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute; Cheng, Jan-Fang [U.S. Department of Energy, Joint Genome Institute; Bruce, David [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Saunders, Elizabeth H [Los Alamos National Laboratory (LANL); Brettin, Thomas S [ORNL; Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Han, Cliff [Los Alamos National Laboratory (LANL); Tapia, Roxanne [Los Alamos National Laboratory (LANL); Larimer, Frank W [ORNL; Land, Miriam L [ORNL; Hauser, Loren John [ORNL; Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute; Lovley, Derek [University of Massachusetts, Amherst; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute; Ivanova, N [U.S. Department of Energy, Joint Genome Institute

    2011-01-01

    Ferroglobus placidus belongs to the order Archaeoglobales within the archaeal phylum Euryar- chaeota. Strain AEDII12DO is the type strain of the species and was isolated from a shallow marine hydrothermal system at Vulcano, Italy. It is a hyperthermophilic, anaerobic chemoli- thoautotroph, but it can also use a variety of aromatic compounds as electron donors. Here we describe the features of this organism together with the complete genome sequence and anno- tation. The 2,196,266 bp genome with its 2,567 protein-coding and 55 RNA genes was se- quenced as part of a DOE Joint Genome Institute Laboratory Sequencing Program (LSP) project.

  11. Nicole Gurtler Genomics and Medicine

    E-Print Network [OSTI]

    Brutlag, Doug

    Gurtler 1 Nicole Gurtler Genomics and Medicine Final Paper Genomics and Multiple Sclerosis The recent breakthroughs in genomics have contributed greatly to the advancement of multiple sclerosis than previously maintenance-oriented treatments. What is Multiple Sclerosis? "Multiple sclerosis (MS

  12. Enhancer Identification through Comparative Genomics

    E-Print Network [OSTI]

    Visel, Axel; Bristow, James; Pennacchio, Len A.

    2006-01-01

    through Comparative Genomics Axel Visel, James Bristow andWalnut Creek, CA 94598 USA. Genomics Division, MS 84-171,Len A. Pennacchio, Genomics Division, One Cyclotron Road, MS

  13. Ginny Scholtes Genomics and Medicine

    E-Print Network [OSTI]

    Brutlag, Doug

    Ginny Scholtes Genomics and Medicine Professor Douglas Brutlag December 2, 2010 How Hard Could It Be? The Integration of Personal Genomics into Medical Practice Personal genomics carries incredible potential to revolutionize the way

  14. Evolutionary Genomics of Salmonella enterica Subspecies

    E-Print Network [OSTI]

    2013-01-01

    M. 2013. Evolutionary genomics of Salmonella entericaEvolutionary Genomics of Salmonella enterica Subspecies

  15. Evolutionary Genomics of Salmonella enterica Subspecies

    E-Print Network [OSTI]

    2013-01-01

    Evolutionary genomics of Salmonella enterica subspecies.Evolutionary Genomics of Salmonella enterica Subspecies

  16. IMG/M: A data management and analysis system for metagenomes

    SciTech Connect (OSTI)

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

    2007-08-01

    IMG/M is a data management and analysis system for microbial community genomes (metagenomes) hosted at the Joint Genome Institute (JGI). IMG/M consists of metagenome data integrated with isolate microbial genomes from the Integrated Microbial Genomes (IMG) system. IMG/M provides IMG's comparative data analysis tools extended to handle metagenome data, together with metagenome-specific analysis tools. IMG/M is available at http://img.jgi.doe.gov/m. Studies of the collective genomes (also known as metagenomes) of environmental microbial communities (also known as microbiomes) are expected to lead to advances in environmental cleanup, agriculture, industrial processes, alternative energy production, and human health (1). Metagenomes of specific microbiome samples are sequenced by organizations worldwide, such as the Department of Energy's (DOE) Joint Genome Institute (JGI), the Venter Institute and the Washington University in St. Louis using different sequencing strategies, technology platforms, and annotation procedures. According to the Genomes OnLine Database, about 28 metagenome studies have been published to date, with over 60 other projects ongoing and more in the process of being launched (2). The Department of Energy's (DOE) Joint Genome Institute (JGI) is one of the major contributors of metagenome sequence data, currently sequencing more than 50% of the reported metagenome projects worldwide. Due to the higher complexity, inherent incompleteness, and lower quality of metagenome sequence data, traditional assembly, gene prediction, and annotation methods do not perform on these datasets as well as they do on isolate microbial genome sequences (3, 4). In spite of these limitations, metagenome data are amenable to a variety of analyses, as illustrated by several recent studies (5-10). Metagenome data analysis is usually set up in the context of reference isolate genomes and considers the questions of composition and functional or metabolic potential of individual microbiomes, as well as differences between microbiome samples. Such analysis relies on efficient management of genome and metagenome data collected from multiple sources, while taking into account the iterative nature of sequence data generation and processing. IMG/M aims at providing support for comparative metagenome analysis in the integrated context of microbial genome and metagenome data generated with diverse sequencing technology platforms and data processing methods.

  17. SciTech Connect: genomics

    Office of Scientific and Technical Information (OSTI)

    genomics Find + Advanced Search Term Search Semantic Search Advanced Search All Fields: genomics Semantic Semantic Term Title: Full Text: Bibliographic Data: Creator Author:...

  18. Genome Project Standards in a New Era of Sequencing

    SciTech Connect (OSTI)

    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 quality of the genome sequence, based on our collective understanding of the different technologies, available assemblers, and the varied efforts to improve upon drafted genomes. Due to the increasingly rapid pace of genomics we avoided the use of rigid numerical thresholds in our definitions to take into account the types of products achieved by any combination of technology, chemistry, assembler, or improvement/finishing process.

  19. An assessment of health educators' likelihood of adopting genomic competencies for the public health workforce 

    E-Print Network [OSTI]

    Chen, Lei-Shih

    2009-05-15

    , the National Institutes of Health (NIH) announced the completion of the Human Genome Project (HGP). The project represents a milestone in human history, as advanced genomic technologies/information can offer insight into specific diseases and may help.... Certainly, genomics is going to have a profound impact on the public health practice of the future?? 10 Yet in the wake of its completion, the HGP also raised new and non-trivial public health issues. These include, but are not restricted to...

  20. Comparative genomics of the core and accessory genomes of 48 Sinorhizobium strains comprising five genospecies

    E-Print Network [OSTI]

    2013-01-01

    annotation and comparative genomics. Database (Oxford) 2009,et al. : Comparative genomics of the core and accessoryComparative genomics of the core and accessory genomes of 48

  1. Update on Genomic Studies of Algae Paths toward Algal Genomics

    E-Print Network [OSTI]

    Update on Genomic Studies of Algae Paths toward Algal Genomics Arthur R. Grossman* The Carnegie the expression of genes. In this introductory manuscript, I discuss select algae and how genomics is impacting our understanding of these organisms. Four algae for which near-full genome information has become

  2. Update on Genomic Studies of Algae Paths toward Algal Genomics

    E-Print Network [OSTI]

    Update on Genomic Studies of Algae Paths toward Algal Genomics Arthur R. Grossman* The Carnegie of genomic information that is being used to help researchers understand the gene content of organisms, how the expression of genes. In this introductory manuscript, I discuss select algae and how genomics is impacting

  3. Comparative and Functional Genomics Comp Funct Genom 2003; 4: 3136.

    E-Print Network [OSTI]

    Allen, John F.

    Comparative and Functional Genomics Comp Funct Genom 2003; 4: 31­36. Published online in Wiley and mitochondria contain genomes John F. Allen* Plant Biochemistry, Center for Chemistry and Chemical Engineering that the nucleotide sequences of mitochondrial and chloroplast genomes would provide the answer has proved unfounded

  4. Unraveling the 3D genome: genomics tools for multiscale exploration

    E-Print Network [OSTI]

    Straight, Aaron

    Unraveling the 3D genome: genomics tools for multiscale exploration Viviana I. Risca and William J genome and the roles it may play in regulating transcription. Here we review core methods and new tools-scale chromosomal domains, and discuss the emerging pic- ture of the 3D genome that these tools have revealed. Blind

  5. COMPUTATIONAL GENOMICS: MAPPING, COMPARISON, AND ANNOTATION OF GENOMES

    E-Print Network [OSTI]

    address key issues in the different stages of genome research: planning of a genome sequencing project areas: (1) In relation to the early stages of a genome project, we address physical mapping, and we structure and sequence analysis of orthologous human and mouse genomic regions, and develop ROSETTA

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

    ScienceCinema (OSTI)

    Weinstock, George [Washington University

    2013-03-22

    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.

  7. The genomic impact of 100 million years of social evolution in seven

    E-Print Network [OSTI]

    Alvarez, Nadir

    The genomic impact of 100 million years of social evolution in seven ant species Ju¨ rgen Gadau1, Switzerland Vital-IT Group, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland, School in terms of both their geographic distribution and species number. The publi- cation of seven ant genomes

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

    ScienceCinema (OSTI)

    Sakakibara, Yasumbumi [Keio University

    2013-01-22

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

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

    ScienceCinema (OSTI)

    Hugenholtz, Phil [University of Queensland

    2013-01-22

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

  10. Using Soir Lucene for Large-Scale Metagenomics Data Retrieval and Analysis (MICW - Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    ScienceCinema (OSTI)

    Goll, Johannes [JCVI

    2013-01-22

    JCVI's Johannes Goll on "Using Solr/Lucene for Large-Scale Metagenomics Data Retrieval and Analysis" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

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

    ScienceCinema (OSTI)

    Li, Weizhong [San Diego Supercomputer Center

    2013-01-22

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

  12. The Center for integrative genomics

    E-Print Network [OSTI]

    Kaessmann, Henrik

    The Center for integrative genomics Report 2005­2006 #12;Presentation Director's message 4 Scientific advisory committee 6 Organigram of the CIG 7 research The structure and function of genomes and their evolution alexandrereymond ­ Genome structure and expression 10 henrikKaessmann ­ Evolutionary genomics 12

  13. Human Genome Program

    SciTech Connect (OSTI)

    Not Available

    1993-01-01

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

  14. Hidden Breakpoints in Genome Alignments

    E-Print Network [OSTI]

    Spang, Rainer

    in Genome Alignments #12;11 Simulated evolution Hidden Breakpoints in Genome Alignments 400 alignments in Genome Alignments #12;13 Simulated evolution Hidden Breakpoints in Genome Alignments 400 alignments genome Sum-of-Pairs: d(A,B) + d(A,C) + d(B,C) argmin {d(A,M) + d(B,M) + d(C,M)} M A C #12;16 Hidden

  15. Advanced Studies Institute

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Engineering Institute Advanced Studies Institute Contact Institute Director Charles Farrar (505) 663-5330 Email UCSD EI Director Michael Todd (858) 534-5951 Professional Staff...

  16. Nucleomorph genomes: structure, function, origin and evolution

    E-Print Network [OSTI]

    Archibald, John

    Nucleomorph genomes: structure, function, origin and evolution John M. Archibald Summary and four genomes--two nuclear genomes, an endosymbiont- derived plastid genome and a mitochondrial genome derived from the host cell. Like mitochondrial and plastid genomes, the genome of the endosymbiont nucleus

  17. Genomic library construction

    DOE Patents [OSTI]

    Church, George M. (Brookline, MA); Zhang, Kun (San Diego, CA)

    2011-07-26

    Compositions and methods for amplifying nucleic acid sequences from a single cell are provided. Compositions and methods for constructing a genomic library from a single cell are also provided.

  18. Genomic definition of species

    SciTech Connect (OSTI)

    Crkvenjakov, R.; Drmanac, R.

    1991-07-01

    The subject of this paper is the definition of species based on the assumption that genome is the fundamental level for the origin and maintenance of biological diversity. For this view to be logically consistent it is necessary to assume the existence and operation of the new law which we call genome law. For this reason the genome law is included in the explanation of species phenomenon presented here even if its precise formulation and elaboration are left for the future. The intellectual underpinnings of this definition can be traced to Goldschmidt. We wish to explore some philosophical aspects of the definition of species in terms of the genome. The point of proposing the definition on these grounds is that any real advance in evolutionary theory has to be correct in both its philosophy and its science.

  19. Genome Engineering with TAL Effector Nucleases

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Genome Engineering with TAL Effector Nucleases Genome Engineering with TAL Effector Nucleases Print Tuesday, 24 April 2012 09:48 Genome engineering (GE), an emerging discipline in...

  20. Fueling the Future with Fungal Genomics

    E-Print Network [OSTI]

    Grigoriev, Igor V.

    2011-01-01

    JW. 2010. China's fungal genomics initiative: a whitepaper.and Saccharomycotina. BMC Genomics. 8, 325. Bailly J,Harnessing ectomycorrhizal genomics for ecological insights.

  1. VISTA - computational tools for comparative genomics

    E-Print Network [OSTI]

    Frazer, Kelly A.; Pachter, Lior; Poliakov, Alexander; Rubin, Edward M.; Dubchak, Inna

    2004-01-01

    tools for comparative genomics Kelly A. Frazer 1 , LiorBerkeley, CA, 94720 Genomics Division, Lawrence Berkeleymultiple comparative genomics tools and provides users with

  2. Bioinformatics and Genomics Degree Requirements Booklet

    E-Print Network [OSTI]

    dePamphilis, Claude

    Bioinformatics and Genomics Degree Requirements Booklet Fall 2011 #12;- -2 Contents Course Bioinformatics and Genomics Curriculum ------------------------------------------------------ 8 General--------------------------------------------------------------------- 14 #12;- -3 Bioinformatics and Genomics Option (BG

  3. Bioinformatics and Genomics Degree Requirements Booklet

    E-Print Network [OSTI]

    dePamphilis, Claude

    Bioinformatics and Genomics Degree Requirements Booklet Fall 2010 #12;Contents Course Requirements Bioinformatics and Genomics Curriculum -------------------------------------------------------8 General #12;Bioinformatics and Genomics Option (BG

  4. Department of Energy Joint Genome Institute, Walnut Creek, CA...

    Office of Scientific and Technical Information (OSTI)

    plant roots is a ubiquitous mutualism that plays key roles in plant nutrition, soil health, and carbon cycling. The symbiosis evolved repeatedly and independently as multiple...

  5. Critical Materials Institute uses the Materials Genome approach to

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantityBonneville Power Administration would like submit theCovalent Bonding in Actinide SandwichCray era Craycourse-inventory

  6. Final Technical Report of Institute for Environmental Genomics of

    Office of Scientific and Technical Information (OSTI)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity of NaturalDukeWakefield MunicipalTechnical Report:Speeding accessby aLED Street Lighting FINAL TECHNICALNumericalFinal

  7. 2013 Progress Report -- DOE Joint Genome Institute (Program Document) |

    Office of Scientific and Technical Information (OSTI)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity of NaturalDukeWakefield Municipal GasAdministrationTechnicalTechnicalScience.gov App Findin

  8. U.S. Department of Energy Joint Genome Institute

    Office of Scientific and Technical Information (OSTI)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity of NaturalDukeWakefield MunicipalTechnicalInformation FederatedInformationTITLE:Connectsubchitted manuscript

  9. Rooted in Wonder: Joint Genome Institute Study Reveals Amazing World

    Energy Savers [EERE]

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Home Page on Google Bookmark EERE: Alternative Fuels Data Center Home Page on DeliciousMathematicsEnergyInterestedReplacement-2-A WholesaleRetrofitElectrical Equipment

  10. Introduction to Using NERSC for the Joint Genome Institute

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity ofkandz-cm11 Outreach Home Room NewsInformation CurrentHenryInhibitingInteractivePGAS and Hybrid IntroScientific I/O Show All

  11. Comparative and Functional Genomics Comp Funct Genom 2003; 4: 239245.

    E-Print Network [OSTI]

    Wurtele, Eve Syrkin

    Biology, Iowa State University, Ames IA 50011, USA 2Bioinformatics and Computational Biology Program, Iowa Encyclopedia of Genes and Genomes [9] (KEGG) (http://www.genome.ad.jp/ kegg) provide molecular networks based

  12. Computational genomics : mapping, comparison, and annotation of genomes

    E-Print Network [OSTI]

    Batzoglou, Serafim

    2000-01-01

    The field of genomics provides many challenges to computer scientists and mathematicians. The area of computational genomics has been expanding recently, and the timely application of computer science in this field is ...

  13. Sequencing of Seven Haloarchaeal Genomes Reveals Patterns of Genomic Flux

    E-Print Network [OSTI]

    Hammerton, James

    Sequencing of Seven Haloarchaeal Genomes Reveals Patterns of Genomic Flux Erin A. Lynch1 , Morgan G. Eisen1,3,12,13 *, Marc T. Facciotti1,3,14 * 1 Microbiology Graduate Group, University of California We report the sequencing of seven genomes from two haloarchaeal genera, Haloferax and Haloarcula

  14. Mammalian comparative genomics and epigenomics

    E-Print Network [OSTI]

    Mikkelsen, Tarjei Sigurd, 1978-

    2009-01-01

    The human genome sequence can be thought of as an instruction manual for our species, written and rewritten over more than a billion of years of evolution. Taking a complete inventory of our genome, dissecting its genes ...

  15. Next-generation nematode genomes 

    E-Print Network [OSTI]

    Kumar, Sujai

    2013-06-29

    The first metazoan to be sequenced was a nematode (Caenorhabditis elegans), and understanding the genome of this model organism has led to many insights about all animals. Although eleven nematode genomes have been ...

  16. Genomics and Systems Biology

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity ofkandz-cm11 Outreach Home Room NewsInformation Current HABFESOpportunities NuclearlongGeneral Tables The GeneralGenomeGenomics

  17. Comparative Genomics of Mycobacterium Tuberculosis

    E-Print Network [OSTI]

    Brutlag, Doug

    Comparative Genomics of Mycobacterium Tuberculosis #12;My Questions · What is TB ­ What in the literature. · Emphasize that genomics techniques are not limited to hereditary diseases. #12;Methods · Deciphering the biology of Mycobacterium Tuberculosis from the complete genome sequence, Stuart Cole et al

  18. SHORT REVIEW Butterfly genomics eclosing

    E-Print Network [OSTI]

    Beldade, Patrícia

    SHORT REVIEW Butterfly genomics eclosing P Beldade1 , WO McMillan2 and A Papanicolaou3 1 Section to an explosion of genomic data and the emergence of new research avenues. Evolutionary and ecological functional genomics, with its focus on the genes that affect ecological success and adaptation in natural populations

  19. TOKYO INSTITUTE OF TECHNOLOGY

    E-Print Network [OSTI]

    TOKYO INSTITUTE OF TECHNOLOGY 2005 TOKYO INSTITUTE OF TECHNOLOGY 152-8550 2 12 1 E3-3 2005 8 TEL. 03 5734 2975 URL. http://www.titech.ac.jp/ PROFILE #12;TOKYO INSTITUTE OF TECHNOLOGY 0201 CONTENTS 03 06 06 08 09 10 15 17 25 31 33 37 41 0201 #12;TOKYO INSTITUTE OF TECHNOLOGY TOKYO INSTITUTE

  20. National Institutes of Health Current National Institute

    E-Print Network [OSTI]

    Rau, Don C.

    Library of Medicine John E. Fogarty International Center for Advanced Study in National Center National Institute of Nursing Research National Library of Medicine John E. Fogarty International CenterNational Institutes of Health Current National Institute of Arthritis and Musculoskeletal and Skin

  1. Environmental Change Institute Environmental Change Institute

    E-Print Network [OSTI]

    Oxford, University of

    Environmental Change Institute 2012/13 eci Environmental Change Institute #12;ii Environmental 06 Educating environmental leaders 08 Centre for interdisciplinary doctoral training 10 A thriving, Dumfriesshire (ECI) #12;1 The Environmental Change Institute has 21 years' experience in helping governments

  2. Genome Medicine 2009, 11

    E-Print Network [OSTI]

    Dehene, Frank

    Genome Medicine 2009, 11::88 Correspondence BBrriiddggiinngg tthhee ggaapp bbeettwweeeenn Care Medicine and CRISMA laboratory, University of Pittsburgh School of Medicine, Scaife 602, 3550 Biotechnology Center, University of Torino, Via Nizza 52, I, 10126 Torino, Italy; 10Institutionen för Medicin

  3. Coral Reef Genomics: Developing tools for functional genomics of coral symbiosis

    E-Print Network [OSTI]

    Schwarz, Jodi; Brokstein, Peter; Manohar, Chitra; Coffroth, Mary Alice; Szmant, Alina; Medina, Monica

    2008-01-01

    Coral Reef Genomics: Developing toolsfor functional genomics of coral symbiosis Jodi SCHWARZ 1 ,symbiosis functional genomics cDNA microarray ABSTRACT

  4. Navigating protected genomics data with UCSC Genome Browser in a Box.

    E-Print Network [OSTI]

    2014-01-01

    H. et al. (2013) Integrative Genomics Viewer (IGV):High-performance genomics data visualization andbrowsers for comparative genomics. Bioinformatics. In press.

  5. A Taste of Algal Genomes from the Joint Genome Institute (Conference...

    Office of Scientific and Technical Information (OSTI)

    from the National Technical Information Service, Springfield, VA at www.ntis.gov. Algae play profound roles in aquatic food chains and the carbon cycle, can impose health and...

  6. A Taste of Algal Genomes from the Joint Genome Institute Kuo...

    Office of Scientific and Technical Information (OSTI)

    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,...

  7. A Taste of Algal Genomes from the Joint Genome Institute (Conference...

    Office of Scientific and Technical Information (OSTI)

    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,...

  8. Computational methods and analyses in comparative genomics and epigenomics

    E-Print Network [OSTI]

    Peng, Qian

    2012-01-01

    promise of comparative genomics in mammals. Science, 286,homology relationships. Genomics, Dehal, P. and Boore, J.to plant comparative genomics. Genome Research, 13(5), 999–

  9. Salt Stress in Desulfovibrio vulgaris Hildenborough: An integrated genomics approach

    E-Print Network [OSTI]

    Mukhopadhyay, Aindrila

    2010-01-01

    2002. Integrating cancer genomics and proteomics in theWeb site for comparative genomics. Genome Res 15:1015-22.Hildenborough: An integrated genomics approach. Aindrila

  10. Petroleum Institute Scholarly Publications

    E-Print Network [OSTI]

    Abu Dhabi The Petroleum Institute Scholarly Publications 2010 #12;#12;The Petroleum Institute Belhaj Petroleum Engineering Sadoon Morad Petroleum Geosciences Sivakumar Sivasubramaniam College of Arts departments within the Petroleum Institute. Names in bold show Petroleum Institute faculty who are attached

  11. POSTDOCTORAL POSITION IN BIOINFORMATICS AND EVOLUTIONARY GENOMICS: Next generation sequencing and analysis of complex polyploid genomes

    E-Print Network [OSTI]

    Rennes, Université de

    POSTDOCTORAL POSITION IN BIOINFORMATICS AND EVOLUTIONARY GENOMICS: Next generation sequencing and analysis of complex polyploid genomes The research group Genome Evolution and Speciation (Team) to work on the analysis of genome and transcriptome sequence data (generated using 454 Roche

  12. Population genomics: Whole-genome analysis of polymorphism and divergence in Drosophila simulans

    E-Print Network [OSTI]

    2007-01-01

    PLoS BIOLOGY Population Genomics: Whole-Genome Analysis ofwww.plosbiology.org Population Genomics of D. simulans Table11 | e310 Population Genomics of D. simulans Table S15. GO

  13. GIS: a web-based genomics information system for efficiently manipulating and accessing genome physical maps 

    E-Print Network [OSTI]

    Chen, Huaming

    2000-01-01

    Biological science has entered the genome era. Global genome integrative physical and genetic mapping promises to revolutionize modern genomics research. To facilitate manipulation and applications of the results from genomics research, many...

  14. A Novel Approach for Comparative Genomics

    E-Print Network [OSTI]

    Paris-Sud XI, Université de

    A Novel Approach for Comparative Genomics & Annotation Transfer Alban MANCHERON Raluca URICARU Eric is genome comparison good for?" Genome comparison is crucial for genome annotation, regulatory motifs identification, and vaccine design aims at finding genomic regions either specific to or in one

  15. Genome: Unlocking Life's Code for Teachers of

    E-Print Network [OSTI]

    Miller, Scott

    GENOME CODE LIFE'S UNLOCKING Genome: Unlocking Life's Code Educator's Guide for Teachers of Grades Glossary 30 Other Resources 32 What the Exhibit Offers Genomics--the study of the entire genome. It is important that students understand what genomics is and what it teaches us about ourselves and the rest

  16. Original article Neisseria Base: a comparative genomics

    E-Print Network [OSTI]

    Jordan, King

    Original article Neisseria Base: a comparative genomics database for Neisseria meningitidis Lee S, septicemia and in some cases pneumonia. Genomic studies hold great promise for N. meningitidis research genomics database and genome browser that houses and displays publicly available N. meningitidis genomes

  17. GenomeView: a next-generation genome browser Thomas Abeel1,2,3,

    E-Print Network [OSTI]

    Gent, Universiteit

    of NGS is the re-sequencing of genomes, such as the 1000 human genomes project (http://www .1000genomes.org/) or the 1001 Arabidopsis genome project (http://www.1001genomes.org/). Genome (re)sequencing is importantGenomeView: a next-generation genome browser Thomas Abeel1,2,3, *, Thomas Van Parys1,2 , Yvan Saeys

  18. Diverse Lifestyles and Strategies of Plant Pathogenesis Encoded in the Genomes of Eighteen Doethideomycetes Fungi

    SciTech Connect (OSTI)

    Ohm, Robin A.; Feau, Nicolas; Henrissat, Bernard; Schoch, Conrad L.; Horwitz, Benjamin A.; Barry, Kerrie W.; Condon, Bradford J.; Copeland, Alex C.; Dhillon, Braham; Glaser, Fabien; Hesse, Cedar N.; Kosti, Idit; LaButti, Kurt; Lindquist, Erika A.; Lucas, Susan; Salamov, Asaf A.; Bradshaw, Rosie E.; Ciuffetti, Lynda; Hamelin, Richard C.; Kema, Gert H. J.; Lawrence, Christopher; Scott, James A.; Spatafora, Joseph W.; Turgeon, B. Gillian; de Wit, Pierre J. G. M.; Zhong, Shaobin; Goodwin, Stephen B.; Grigoriev, Igor V.

    2012-03-13

    The class of Dothideomycetes is one of the largest and most diverse groups of fungi. Many are plant pathogens and pose a serious threat to agricultural crops grown for biofuel, food or feed. Most Dothideomycetes have only a single host and related species can have very diverse host plants. Eighteen genomes of Dothideomycetes have currently been sequenced by the Joint Genome Institute and other sequencing centers. Here we describe the results of comparative analyses of the fungi in this group.

  19. Editorial: The Human Genome Project

    E-Print Network [OSTI]

    Crawford, Michael H.; Baer, A.S.; Hall, R.; Omenn, G.S.; Thomson, G.J.; Wilson, A.C.

    1990-08-01

    iv / Editorial: The Human Genome Project Dear readers, The last few decades have seen a number of exciting developments in genetics. First, Watson and Crick broke the genetic code; since then, tech-nologic and methodologic breakthroughs have... permitted the study and direct manipulation of our DNA. Now there is an international ground swell to map and sequence the human genome. The Bush administration had originally requested $128 million in last year's budget for the Human Genome Project. However...

  20. Genomic Sciences | Clean Energy | ORNL

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    to clean energy and environmental applications. Multidisciplinary genomic science research and communication resources at ORNL include the following: Plant Systems Biology...

  1. Complete genome sequence of Hirschia baltica type strain (IFAM 1418T)

    SciTech Connect (OSTI)

    Chertkov, Olga [Los Alamos National Laboratory (LANL); Brown, Pamela J.B. [Indiana University; Kysela, David T. [Indiana University; De Pedro, Miguel A. [Universidad Autonoma de Madrid, Madrid; Lucas, Susan [U.S. Department of Energy, Joint Genome Institute; Copeland, A [U.S. Department of Energy, Joint Genome Institute; Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute; Glavina Del Rio, Tijana [U.S. Department of Energy, Joint Genome Institute; Tice, Hope [U.S. Department of Energy, Joint Genome Institute; Bruce, David [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Han, Cliff [Los Alamos National Laboratory (LANL); Larimer, Frank W [ORNL; Chang, Yun-Juan [ORNL; Jeffries, Cynthia [Oak Ridge National Laboratory (ORNL); Land, Miriam L [ORNL; Hauser, Loren John [ORNL; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Ovchinnikova, Galina [U.S. Department of Energy, Joint Genome Institute; Tindall, Brian [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Goker, Markus [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Klenk, Hans-Peter [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Brun, Yves V. [Indiana University

    2011-01-01

    The family Hyphomonadaceae within the Alphaproteobacteria is largely comprised of bacte- ria isolated from marine environments with striking morphologies and an unusual mode of cell growth. Here, we report the complete genome sequence Hirschia baltica, which is only the second a member of the Hyphomonadaceae with a published genome sequence. H. bal- tica is of special interest because it has a dimorphic life cycle and is a stalked, budding bacte- rium. The 3,455,622 bp long chromosome and 84,492 bp plasmid with a total of 3,222 pro- tein-coding and 44 RNA genes were sequenced as part of the DOE Joint Genome Institute Program CSP 2008.

  2. Tissue sampling and standards for vertebrate genomics

    E-Print Network [OSTI]

    2012-01-01

    and standards for vertebrate genomics. GigaScience 2012 1:8.transition to conservation genomics. TIG 2010, 26:177–187.Siemens DH: Ecological genomics––changing perspectives on

  3. Evolutionary Genomics of Salmonella enterica Subspecies

    E-Print Network [OSTI]

    2013-01-01

    M. 2002. Evolutionary genomics of Salmonella: genesubsystems technology. BMC Genomics 9:75. 23. Ochman H,Salmonella enterica. BMC Genomics 12:425. PubMed. 29. Falush

  4. Trichoderma: the genomics of opportunistic success

    E-Print Network [OSTI]

    Druzhinina, Irina S.

    2011-01-01

    of a fungal prey. BMC Genomics 10, 567 (2009). This studythe TrichoEST functional genomics approach. Curr. Genet. 51,in Hypocrea jecorina. BMC Genomics. 9, 430 (2008) Mukherjee,

  5. INSTITUTIONAL MEMBERS CURRENT SCIENCE ASSOCIATION

    E-Print Network [OSTI]

    Giri, Ranjit K.

    , Guwahati 40. Indian Institute of Technology, Hyderabad 41. Indian Institute of Technology, Indore 42

  6. Human Genome: DOE Origins

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantityBonneville Power Administration would likeUniverse (JournalvivoHigh energyHighlandWorkshop-SummerHow is theHughHumanHuman Genome

  7. Human Genome Program Image Gallery (from genomics.energy.gov)

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    This collection contains approximately 240 images from the genome programs of DOE's Office of Science. The images are divided into galleries related to biofuels research, systems biology, and basic genomics. Each image has a title, a basic citation, and a credit or source. Most of the images are original graphics created by the Genome Management Information System (GMIS). GMIS images are recognizable by their credit line. Permission to use these graphics is not needed, but please credit the U.S. Department of Energy Genome Programs and provide the website http://genomics.energy.gov. Other images were provided by third parties and not created by the U.S. Department of Energy. Users must contact the person listed in the credit line before using those images. The high-resolution images can be downloaded.

  8. Comparative Genome Structure, Secondary Metabolite, and Effector...

    Office of Scientific and Technical Information (OSTI)

    Genome Structure, Secondary Metabolite, and Effector Coding Capacity across Cochliobolus Pathogens Citation Details In-Document Search Title: Comparative Genome Structure,...

  9. Implications of structural genomics target selection strategies...

    Office of Scientific and Technical Information (OSTI)

    Implications of structural genomics target selection strategies: Pfam5000, whole genome, and random approaches Citation Details In-Document Search Title: Implications of structural...

  10. Corey Clemons Genomics and Medicine

    E-Print Network [OSTI]

    Brutlag, Doug

    the Human Genome Project was completed. The goal of the HGP was to sequence the entire human genome in order to the private sector.i One unintended consequence of the HGP is that it actually challenged previously held with previously misunderstood conditions and ailments. Some practical uses of the HGP are the development

  11. Weizmann Institute 76100 Rehovot,

    E-Print Network [OSTI]

    Prior, Yehiam

    , Weizmann Institute 2006 - Alternative Energy Research Initiative (WIS), Steering Committee 2006 - Dean by the international diamond processing community, and sold hundreds of machines world wide. 1988 - 1990 Bell Foundation Israel Diamond Institute MAGNET program (LESHED, diode pumped lasers consortium) Minerva

  12. OIL & GAS INSTITUTE Introduction

    E-Print Network [OSTI]

    Strathclyde, University of

    OIL & GAS INSTITUTE CONTENTS Introduction Asset Integrity Underpinning Capabilities 2 4 4 6 8 9 10 COMPETITIVENESS UNIVERSITY of STRATHCLYDE OIL & GAS INSTITUTE OIL & GAS EXPERTISE AND PARTNERSHIPS #12;1 The launch of the Strathclyde Oil & Gas Institute represents an important step forward for the University

  13. The National Cancer Institute,

    E-Print Network [OSTI]

    The National Cancer Institute, International Cancer Information Center Bldg. 82, Rm 123 Bethesda, MD 20892 The National Cancer Institute (NCI) is part of the Federal Government. NCI coordinates the government's cancer research program. It is the largest of the 17 biomedical research institutes and centers

  14. Gene Action and Cellular Function in Parasitic Protozoa Genomics and post-genomics in parasitology: genome babble or

    E-Print Network [OSTI]

    Schnaufer, Achim

    Gene Action and Cellular Function in Parasitic Protozoa Genomics and post-genomics in parasitology: genome babble or a real opportunity? K. Gull1 School of Biological Sciences, University of Manchester, 2.205 Stopford Building, Oxford Road, Manchester M13 9PT, U.K. Abstract The genome projects represent one

  15. Hope or Hype? What is Next for Biofuels? (LBNL Science at the Theater)

    ScienceCinema (OSTI)

    Keasling, Jay; Bristow, Jim; Tringe, Susannah Green

    2011-04-28

    Science at the Theater: From the sun to your gas tank: A new breed of biofuels may help solve the global energy challenge and reduce the impact of fossil fuels on global warming. KTVU Channel 2 health and science editor John Fowler will moderate a panel of Lawrence Berkeley National Laboratory scientists who are developing ways to convert the solar energy stored in plants into liquid fuels. Jay Keasling is one of the foremost authorities in the ?eld of synthetic biology. He is applying this research toward the production of advanced carbon-neutral biofuels that can replace gasoline on a gallon-for-gallon basis. Keasling is Berkeley Labs Acting Deputy Director and the Chief Executive Of?cer of the U.S. Department of Energys Joint BioEnergy Institute. Jim Bristow is deputy director of programs for the U.S. Department of Energy Joint Genome Institute (JGI), a national user facility in Walnut Creek, CA. He developed and implemented JGIs Community Sequencing Program, which provides large-scale DNA sequencing and analysis to advance genomics related to bioenergy and environmental characterization and cleanup. Susanna Green Tringe is a computational biologist with the U.S. Department of Energy Joint Genome Institute (JGI). She helped pioneer the ?eld of metagenomics, a new strategy for isolating, sequencing, and characterizing DNA extracted directly from environmental samples, such as the contents of the termite gut, which yielded enzymes responsible for breakdown of wood into fuel.

  16. Genome Biology 2004, 5:R56 commentreviewsreportsdepositedresearchrefereedresearchinteractionsinformation

    E-Print Network [OSTI]

    . Although various genomic datasets are rele-vant to this issue, each dataset provides relatively weak

  17. A Million Cancer Genome Warehouse David Haussler

    E-Print Network [OSTI]

    McAuliffe, Jon

    Warehouse Regional Warehouses Design and Cost to Build and Operate a Million Cancer Genome Warehouse CAPEX

  18. Doug Brutlag 2015 Genomics, Bioinformatics & Medicine

    E-Print Network [OSTI]

    Brutlag, Doug

    in -Amylase Gene Tandem Repeat Arrays Sharp, Cheng & Eichler, Annu. Rev. Genomics Hum. Genet. 2006. 7

  19. A Statistical Framework for Spatial Comparative Genomics

    E-Print Network [OSTI]

    A Statistical Framework for Spatial Comparative Genomics Rose Hoberman May 2007 CMU-CS-07, or the U.S. Government. #12;Keywords: spatial comparative genomics, comparative genomics, gene clusters, max-gap clusters, gene teams, whole genome duplication, paralogons, synteny, ortholog detection #12

  20. Genomic Aspects of Research Involving Polyploid Plants

    SciTech Connect (OSTI)

    Yang, Xiaohan [ORNL; Ye, Chuyu [ORNL; Tschaplinski, Timothy J [ORNL; Wullschleger, Stan D [ORNL; Tuskan, Gerald A [ORNL

    2011-01-01

    Almost all extant plant species have spontaneously doubled their genomes at least once in their evolutionary histories, resulting in polyploidy which provided a rich genomic resource for evolutionary processes. Moreover, superior polyploid clones have been created during the process of crop domestication. Polyploid plants generated by evolutionary processes and/or crop domestication have been the intentional or serendipitous focus of research dealing with the dynamics and consequences of genome evolution. One of the new trends in genomics research is to create synthetic polyploid plants which provide materials for studying the initial genomic changes/responses immediately after polyploid formation. Polyploid plants are also used in functional genomics research to study gene expression in a complex genomic background. In this review, we summarize the recent progress in genomics research involving ancient, young, and synthetic polyploid plants, with a focus on genome size evolution, genomics diversity, genomic rearrangement, genetic and epigenetic changes in duplicated genes, gene discovery, and comparative genomics. Implications on plant sciences including evolution, functional genomics, and plant breeding are presented. It is anticipated that polyploids will be a regular subject of genomics research in the foreseeable future as the rapid advances in DNA sequencing technology create unprecedented opportunities for discovering and monitoring genomic and transcriptomic changes in polyploid plants. The fast accumulation of knowledge on polyploid formation, maintenance, and divergence at whole-genome and subgenome levels will not only help plant biologists understand how plants have evolved and diversified, but also assist plant breeders in designing new strategies for crop improvement.

  1. Genomics and ornithology Scott V. Edwards

    E-Print Network [OSTI]

    Edwards, Scott

    REVIEW Genomics and ornithology Scott V. Edwards Received: 23 September 2007 / Accepted: 27 Genomics is revolutionizing ornithology in the same ways it is reinvigorating other biological disciplines. In this review, I will highlight applications of genomics and genomics technologies to the study of the ecology

  2. Shotgun coverage of human genome computing

    E-Print Network [OSTI]

    Eddy, Sean

    take about 1.5 million pages. The Human Genome Project would not be possible if our revolution were-author collection of chapters on the various uses of computing in the Human Genome Project. Peculiarly absent fromShotgun coverage of human genome computing Human Genome Computing, Second Edition edited by Martin

  3. Doug Brutlag 2015 Sequencing the Human Genome

    E-Print Network [OSTI]

    Brutlag, Doug

    Project: Should we do it? · Service, R. F. (2001). The human genome: Objection #1: big biology is bad://www.elec-intro.com/m13-cloning #12;© Doug Brutlag 2015 Public Human Genome Project Strategy Published in Nature 15 The Human Genome Project: How should we do it? · Weber, J. L., & Myers, E. W. (1997). Human whole-genome

  4. Assignment of Orthologous Genes via Genome Rearrangement

    E-Print Network [OSTI]

    Lonardi, Stefano

    Assignment of Orthologous Genes via Genome Rearrangement Xin Chen, Jie Zheng, Zheng Fu, Peng Nan of genomes is a fundamental and challenging problem in comparative genomics. Existing methods that assign sequence similarity and evolutionary events at a genome level, where orthologous genes are assumed

  5. Pseudo Boolean Programming for Partially Ordered Genomes

    E-Print Network [OSTI]

    Fertin, Guillaume

    Pseudo Boolean Programming for Partially Ordered Genomes Sébastien Angibaud1 , Guillaume Fertin1.Angibaud,Guillaume.Fertin}@univ-nantes.fr, thevenin@lri.fr, vialette@univ-mlv.fr Abstract. Comparing genomes of different species is a crucial problem in comparative genomics. Different measures have been proposed to com- pare two genomes: number of common

  6. Extreme Genomics By Scouring the Genomes of 50 HIV-Resistant People, Study

    E-Print Network [OSTI]

    Dolbow, John

    Extreme Genomics By Scouring the Genomes of 50 HIV-Resistant People, Study Takes Aim at Rare Gene Genome Variation, and his colleagues think that the complete genome sequences of those fortunate few against the viral strain that usually infects humans. That's because the CCR5 protein is Extreme Genomics

  7. Chapter 14: Genome Assembly and Annotation Process Annotation of other genomes

    E-Print Network [OSTI]

    Levin, Judith G.

    Chapter 14: Genome Assembly and Annotation Process Paul Kitts Summary Box 1 Annotation of other genomes NCBI may assemble a genome prior to annotation, add annotations to a genome assembled elsewhere, or simply process an annotated genome to produce RefSeqs and maps for display in Map Viewer (Chapter 20

  8. The Genome Database Organism-centered listing of available genomic sequence records and projects

    E-Print Network [OSTI]

    Levin, Judith G.

    The Genome Database Organism-centered listing of available genomic sequence records and projects http://www.ncbi.nlm.nih.gov/genome National Center for Biotechnology Information · National Library | NCBI Genome | Last Update August 19, 2013 Contact: info@ncbi.nlm.nih.gov Scope Since 2011, the Genome

  9. Genomics and vertebrate adaptive radiation: a celebration of the first cichlid genome

    E-Print Network [OSTI]

    Renn, Susan C.P.

    Genomics and vertebrate adaptive radiation: a celebration of the first cichlid genome C. Darrin ``Genomics and Vertebrate Adaptive Radiation: A Celebration of the First Cichlid Genome'' was held the central topic was the genomics of adaptive radiation in cichlid fishes, the symposium integrated speakers

  10. Growth Temperature and Genome Size in Bacteria Are Negatively Correlated, Suggesting Genomic Streamlining

    E-Print Network [OSTI]

    Wagner, Andreas

    Growth Temperature and Genome Size in Bacteria Are Negatively Correlated, Suggesting Genomic.wagner@ieu.uzh.ch; nsabath@gmail.com. Accepted: March 25, 2013 Abstract Prokaryotic genomes are small and compact. Either this feature is caused by neutral evolution or by natural selection favoring small genomes--genome streamlining

  11. Human genome. 1993 Program report

    SciTech Connect (OSTI)

    Not Available

    1994-03-01

    The purpose of this report is to update the Human Genome 1991-92 Program Report and provide new information on the DOE genome program to researchers, program managers, other government agencies, and the interested public. This FY 1993 supplement includes abstracts of 60 new or renewed projects and listings of 112 continuing and 28 completed projects. These two reports, taken together, present the most complete published view of the DOE Human Genome Program through FY 1993. Research is progressing rapidly toward 15-year goals of mapping and sequencing the DNA of each of the 24 different human chromosomes.

  12. Indian Institute of Technology Bombay INDIAN INSTITUTE OF TECHNOLOGY BOMBAY

    E-Print Network [OSTI]

    Narayanan, H.

    Indian Institute of Technology Bombay INDIAN INSTITUTE OF TECHNOLOGY BOMBAY INVITATION Description of work Estimated cost (1) (2) (3) 1 Construction of Institutional/Residential buildings, external development, HVAC, Elevators etc. for Indian Institute of Technology Bombay, at the campus

  13. Institutional Research & Development Reports | National Nuclear...

    National Nuclear Security Administration (NNSA)

    Advanced Simulation and Computing and Institutional R&D Programs Institutional Research & Development Institutional Research & Development Reports Institutional Research &...

  14. Determine Institutional Change Sustainability Goals | Department...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Institutional Change Determine Institutional Change Sustainability Goals Determine Institutional Change Sustainability Goals Institutional Change Continuous Improvement Cycle...

  15. Institutional Change for Sustainability Contacts | Department...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Institutional Change Institutional Change for Sustainability Contacts Institutional Change for Sustainability Contacts For more information about institutional change for...

  16. Synthetic Genomics: Options for Governance

    E-Print Network [OSTI]

    Garfinkel, Michele

    2007-10-17

    Gene and genome synthesis, that is, constructing long stretches of DNA from constituent chemicals, provides scientists with new and unparalleled capabilities both for understanding biology and for using it for beneficial ...

  17. UNCLASSIFIED Institute for Materials ...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Antonia Antoniou Georgia Institute of Technology, Atlanta, Georgia Mechanical Behavior of Hierarchical Nanoporous Metals Thursday, August 27, 2015 1:30 - 2:30pm MSL Auditorium...

  18. Edison Electric Institute Update

    Broader source: Energy.gov [DOE]

    Presentation—given at the Fall 2011 Federal Utility Partnership Working Group (FUPWG) meeting—discusses the Edison Electric Institute (EEI) and the current electricity landscape.

  19. UNCLASSIFIED Institute for Materials ...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Gabriel Aeppli Head of the Synchrotron and Nanotechnology Department Paul Scherrer Institute, Switzerland Accelerator-based Light Sources for the Future Wednesday, August 12, 2015...

  20. UNCLASSIFIED Institute for Materials ...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Dr. Jol Mesot Director, Paul Scherrer Institute, Switzerland Probing Excitations in Strongly Correlated Electron Systems: Recent Highlights Obtained at the Large-Scale Facilities...

  1. UNCLASSIFIED Institute for Materials ...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Head of the Synchrotron and Nanotechnology Department Paul Scherrer Institute, Switzerland Accelerator-based Light Sources for the Future Wednesday, August 12, 2015 2:00 to...

  2. Genomic neighbourhood and the regulation of gene expression Genomic neighbourhood and transcriptional regulation

    E-Print Network [OSTI]

    Babu, M. Madan

    Genomic neighbourhood and the regulation of gene expression Genomic neighbourhood and transcriptional regulation Subhajyoti De and M. Madan Babu MRC Laboratory of Molecular Biology, Hills Road..................................................................................................................................................................................1 2. Genomic neighbourhood and its influence on gene regulation

  3. Implications of structural genomics target selection strategies: Pfam5000, whole genome, and random approaches

    E-Print Network [OSTI]

    Chandonia, John-Marc; Brenner, Steven E.

    2004-01-01

    SK, Bonanno JB. Structural genomics. Methods Biochem AnalMizuguchi K. Structural genomics: an overview. Prog BiophysSE. A tour of structural genomics. Nat Rev Genet 2001;2(10):

  4. Amplification of Genomic DNA from Single Cells using Multiple Displacement Amplification

    SciTech Connect (OSTI)

    Lasken, Roger [J. Craig Venter Institute

    2010-06-04

    Roger Lasken of the J. Craig Venter Institute discusses the combined use of single cell genomics and metagenomics as well as methods for single-cell sequencing on June 4, 2010 at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM

  5. Genome Analysis Serial Analysis of Gene Expression Study of a Hybrid

    E-Print Network [OSTI]

    Kansas, University of

    for Functional Genomics, Evanston Northwestern Healthcare Research Institute, Northwestern University, Evanston our initial functional analyses on a subset of the data that are supported by full-length c crops for human consumption, providing staple food for more than one-half of the world's population

  6. Complete Genome Sequence of Le Blanc Virus, a Third Caenorhabditis Nematode-Infecting Virus

    E-Print Network [OSTI]

    Wang, David

    Complete Genome Sequence of Le Blanc Virus, a Third Caenorhabditis Nematode-Infecting Virus Carl J,a and Institute of Biology of the Ecole Normale Supérieure (IBENS), Paris, Franceb Orsay virus and Santeuil virus, the first known viruses capable of naturally infecting the nematodes Caenorhabditis elegans

  7. Glass Sponges and Bilaterian Animals Share Derived Mitochondrial Genomic Features: A Common Ancestry or Parallel Evolution?

    E-Print Network [OSTI]

    Lavrov, Dennis V.

    Glass Sponges and Bilaterian Animals Share Derived Mitochondrial Genomic Features: A Common Oceanographic Institution, Fort Pierce, Florida Glass sponges (Hexactinellida) are a group of deep-water benthic glass sponges and bilaterian animals, including an Arg / Ser change in the genetic code

  8. Ecological Genomics of Nematode Community Interactions: Model and Non-model Approaches

    E-Print Network [OSTI]

    Herman, Mike

    Science Board in the United States issued a report that stated: Human activities are transforming. Abbreviations GO Gene ontology TD50 Time to death for 50% of a population M.A. Herman Ecological Genomics Institute, Kansas State University, 266 Chalmers Hall, Manhattan, KS, USA; Division of Biology, Kansas State

  9. Comparative genomics reveals diversity among xanthomonads infecting tomato and pepper

    E-Print Network [OSTI]

    2011-01-01

    Potnis et al. : Comparative genomics reveals diversity amongtomato and pepper. BMC Genomics Submit your next manuscriptpv. syringae Potnis et al. BMC Genomics 2011, 12:146 http://

  10. Genomics of emerging infectious disease: A PLoS collection.

    E-Print Network [OSTI]

    Eisen, Jonathan A; MacCallum, Catriona J

    2009-01-01

    Origins and evolutionary genomics of the 2009 swine-originan Infectious Diseases Genomics Project predict and preventRavel J (2009) The role of genomics in the identification,

  11. Incorporating Genomics and Bioinformatics across the Life Sciences Curriculum

    E-Print Network [OSTI]

    Ditty, Jayna L.

    2012-01-01

    Page Incorporating Genomics and Bioinformatics across the2007) Discovering Genomics, Proteomics, and Bioinformatics,2003) Public access for teaching genomics, proteomics, and

  12. TOPSAN: a collaborative annotation environment for structural genomics.

    E-Print Network [OSTI]

    Weekes, Dana; Krishna, S; Bakolitsa, Constantina; Wilson, Ian A; Godzik, Adam; Wooley, John

    2010-01-01

    environment for structural genomics Dana Weekes 1† , S Srihigh-throughput structural genomics centers, despite theirbeing determined by structural genomics centers and high-

  13. MicrobesOnline: an integrated portal for comparative functional genomics

    E-Print Network [OSTI]

    Joachimiak, Marcin P.

    2014-01-01

    comparative functional genomics Marcin P. Joachimiak 1,2 ,for comparative functional genomics of bacteria and archaea.publicly avail- able functional genomics data from published

  14. Validation in Genomics: CpG Island Methylation Revisited

    E-Print Network [OSTI]

    Segal, Mark R

    2006-01-01

    analysis. In: Functional Genomics: Methods and Protocols, M.Segal: Validation in Genomics: CpG Island Methylationpackage and applications to genomics. Bioinformatics and

  15. Dissection of Plant Defense Mechanisms Using Chemical and Molecular Genomics

    E-Print Network [OSTI]

    Rodriguez-Salus, Melinda Sue

    2012-01-01

    of auxins by a chemical genomics approach." Journal ofadvances in chemical genomics." Current Medicinal Chemistrymolecular and chemical genomics." Phytopathology 97(7): S58-

  16. Microbes Online: an integrated portal for comparative functional genomics

    E-Print Network [OSTI]

    Arkin, Adam P.

    2014-01-01

    comparative functional genomics of bacteria, archaea, fungifor comparative functional genomics Paramvir S. Dehal 1,2* (and Environmental Research, Genomics:GTL program through

  17. The Human Genome Project and its Social Implications

    E-Print Network [OSTI]

    Meyer, Paul B

    1990-01-01

    The Human Genome Project and its Social Implications By Paulit is about the Human Genome Project. In a sense this isheredity. The Human Genome Project is concerned essentially

  18. Genome-scale reconstruction and analysis of eukaryotic metabolic networks

    E-Print Network [OSTI]

    Hurlen, Natalie Christine

    2006-01-01

    803. Leja, D. , Human Genome Project Timeline, 38-72.jpg,p. Illustration of Human Genome Project Timeline. Varki,Human Genome Project. ..

  19. Complete genome sequence of Allochromatium vinosum DSM 180T

    SciTech Connect (OSTI)

    Weissgerber, Thomas [Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany; Zigann, Renate [Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany; Bruce, David [Los Alamos National Laboratory (LANL); Chang, Yun-Juan [ORNL; Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Han, Cliff [Los Alamos National Laboratory (LANL); Hauser, Loren John [ORNL; Jeffries, Cynthia [Oak Ridge National Laboratory (ORNL); Land, Miriam L [ORNL; Munk, Christine [U.S. Department of Energy, Joint Genome Institute; Tapia, Roxanne [Los Alamos National Laboratory (LANL); Dahl, Christiane [Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany

    2011-01-01

    Allochromatium vinosum formerly Chromatium vinosum is a mesophilic purple sulfur bacte- rium belonging to the family Chromatiaceae in the bacterial class Gammaproteobacteria. The genus Allochromatium contains currently five species. All members were isolated from fresh- water, brackish water or marine habitats and are predominately obligate phototrophs. Here we describe the features of the organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of a member of the Chromatiaceae within the purple sulfur bacteria thriving in globally occurring habitats. The 3,669,074 bp ge- nome with its 3,302 protein-coding and 64 RNA genes was sequenced within the Joint Ge- nome Institute Community Sequencing Program.

  20. Universittsarchiv Mainz Physiologisches Institut

    E-Print Network [OSTI]

    ;Vorwort II Vorwort Das Physiologische Institut wurde 1946 mit der Berufung von Prof. Hans Schriever (1898-1979) einge- richtet. Der 1898 in Düsseldorf geborene Schriever promovierte 1921 in Bonn zum Dr. med. und 1922 wurde er 1939 zum ordentlichen Professor ernannt. Prof. Schriever leitete das Mainzer Institut bis zu

  1. Microbial Dark Matter & Beyond

    SciTech Connect (OSTI)

    Rubin, Eddy [DOE JGI Director

    2014-03-19

    Eddy Rubin, DOE JGI Director, at the 9th Annual Genomics of Energy & Environment Meeting on March 19, 2014 in Walnut Creek, Calif. The talk is related to a study published in the journal Science

  2. Addressing the Omics Data Explosion: a Comprehensive Reference Genome Representation and the Democratization of Comparative Genomics and Immunogenomics

    E-Print Network [OSTI]

    Nguyen, Ngan Kim

    2014-01-01

    Hubs: Web Accessible Browsers for Compar- ative Genomics 3.1Comparative Genomics Analyses . . . . . . . . . . . . . .browsers for comparative genomics” B.1 E. coli KO11FL 162099

  3. TOKYO INSTITUTE OF TECHNOLOGY TOKYO INSTITUTE OF TECHNOLOGY TOKYO INSTITUTE OF TECHNOLOGY

    E-Print Network [OSTI]

    #12;06 06 TOKYO INSTITUTE OF TECHNOLOGY 0201 CONTENTS 03 08 09 10 15 17 25 31 33 37 41 0201 08 23 TokyoTech #12;TOKYO INSTITUTE OF TECHNOLOGY TOKYO INSTITUTE OF TECHNOLOGY 0403 20 1 5 11 #12;TOKYO INSTITUTE OF TECHNOLOGY TOKYO INSTITUTE OF TECHNOLOGY 0605 4 3 2 5 5 4 3 #12;TOKYO INSTITUTE OF TECHNOLOGY

  4. The mouse genome informatics and the mouse genome database

    SciTech Connect (OSTI)

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

    1994-09-01

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

  5. Trichoderma: the genomics of opportunistic success

    E-Print Network [OSTI]

    Druzhinina, Irina S.

    2011-01-01

    Applied Biochemistry, Institute of Chemical Engineering 5and Applied Biochemistry, Institute of Chemical Engineering

  6. Towards a standards-compliant genomic and metagenomic publication record

    SciTech Connect (OSTI)

    Fenner, Marsha W; Garrity, George M.; Field, Dawn; Kyrpides, Nikos; Hirschman, Lynette; San-sone, Susanna-Assunta; Anguiloi, Samuel; Cole, James R.; Glockner, Frank Oliver; Kolker, Eugene; Kowaluchuk, George; Moran, Mary Ann; Ussery, Dave; White, Owen

    2008-04-01

    Increasingly we are aware as a community of the growing need to manage the avalanche of genomic and metagenomic data, in addition to related data types like ribosomal RNA and barcode sequences, in a way that tightly integrates contextual data with traditional literature in a machine-readable way. It is for this reason that the Genomic Standards Consortium (GSC) formed in 2005. Here we suggest that we move beyond the development of standards and tackle standards-compliance and improved data capture at the level of the scientific publication. We are supported in this goal by the fact that the scientific community is in the midst of a publishing revolution. This revolution is marked by a growing shift away from a traditional dichotomy between 'journal articles' and 'database entries' and an increasing adoption of hybrid models of collecting and disseminating scientific information. With respect to genomes and metagenomes and related data types, we feel the scientific community would be best served by the immediate launch of a central repository of short, highly structured 'Genome Notes' that must be standards-compliant. This could be done in the context of an existing journal, but we also suggest the more radical solution of launching a new journal. Such a journal could be designed to cater to a wide range of standards-related content types that are not currently centralized in the published literature. It could also support the demand for centralizing aspects of the 'gray literature' (documents developed by institutions or communities) such as the call by the GSCl for a central repository of Standard Operating Procedures describing the genomic annotation pipelines of the major sequencing centers. We argue that such an 'eJournal', published under the Open Access paradigm by the GSC, could be an attractive publishing forum for a broader range of standardization initiatives within, and beyond, the GSC and thereby fill an unoccupied yet increasingly important niche within the current research landscape.

  7. Expanding genomics of mycorrhizal symbiosis

    SciTech Connect (OSTI)

    Kuo, Alan; Kohler, Annegret; Martin, Francis M.; Grigoriev, Igor V.

    2014-11-04

    The mycorrhizal symbiosis between soil fungi and plant roots is a ubiquitous mutualism that plays key roles in plant nutrition, soil health, and carbon cycling. The symbiosis evolved repeatedly and independently as multiple morphotypes [e.g., arbuscular mycorrhizae (AM), ectomycorrhizal (ECM)] in multiple fungal clades (e.g., phyla Glomeromycota, Ascomycota, Basidiomycota). The accessibility and cultivability of many mycorrhizal partners make them ideal models for symbiosis studies. Alongside molecular, physiological, and ecological investigations, sequencing led to the first three mycorrhizal fungal genomes, representing two morphotypes and three phyla. The genome of the ECM basidiomycete Laccaria bicolor showed that the mycorrhizal lifestyle can evolve through loss of plant cell wall-degrading enzymes (PCWDEs) and expansion of lineage-specific gene families such as short secreted protein (SSP) effectors. The genome of the ECM ascomycete Tuber melanosporum showed that the ECM type can evolve without expansion of families as in Laccaria, and thus a different set of symbiosis genes. The genome of the AM glomeromycete Rhizophagus irregularis showed that despite enormous phylogenetic distance and morphological difference from the other two fungi, symbiosis can involve similar solutions as symbiosis-induced SSPs and loss of PCWDEs. The three genomes provide a solid base for addressing fundamental questions about the nature and role of a vital mutualism.

  8. ; Evolution of genes and genomes on the Drosophila phylogeny

    E-Print Network [OSTI]

    Kellis, Manolis

    ARTICLES ; Evolution of genes and genomes on the Drosophila phylogeny Drosophila 12 Genomes Consortium* Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome

  9. MEETING: Chlamydomonas Annotation Jamboree - October 2003

    SciTech Connect (OSTI)

    Grossman, Arthur R

    2007-04-13

    Shotgun sequencing of the nuclear genome of Chlamydomonas reinhardtii (Chlamydomonas throughout) was performed at an approximate 10X coverage by JGI. Roughly half of the genome is now contained on 26 scaffolds, all of which are at least 1.6 Mb, and the coverage of the genome is ~95%. There are now over 200,000 cDNA sequence reads that we have generated as part of the Chlamydomonas genome project (Grossman, 2003; Shrager et al., 2003; Grossman et al. 2007; Merchant et al., 2007); other sequences have also been generated by the Kasuza sequence group (Asamizu et al., 1999; Asamizu et al., 2000) or individual laboratories that have focused on specific genes. Shrager et al. (2003) placed the reads into distinct contigs (an assemblage of reads with overlapping nucleotide sequences), and contigs that group together as part of the same genes have been designated ACEs (assembly of contigs generated from EST information). All of the reads have also been mapped to the Chlamydomonas nuclear genome and the cDNAs and their corresponding genomic sequences have been reassembled, and the resulting assemblage is called an ACEG (an Assembly of contiguous EST sequences supported by genomic sequence) (Jain et al., 2007). Most of the unique genes or ACEGs are also represented by gene models that have been generated by the Joint Genome Institute (JGI, Walnut Creek, CA). These gene models have been placed onto the DNA scaffolds and are presented as a track on the Chlamydomonas genome browser associated with the genome portal (http://genome.jgi-psf.org/Chlre3/Chlre3.home.html). Ultimately, the meeting grant awarded by DOE has helped enormously in the development of an annotation pipeline (a set of guidelines used in the annotation of genes) and resulted in high quality annotation of over 4,000 genes; the annotators were from both Europe and the USA. Some of the people who led the annotation initiative were Arthur Grossman, Olivier Vallon, and Sabeeha Merchant (with many individual annotators from Europe and the USA). Olivier Vallon has been most active in continued input of annotation information.

  10. Enhancer Identification through Comparative Genomics

    SciTech Connect (OSTI)

    Visel, Axel; Bristow, James; Pennacchio, Len A.

    2006-10-01

    With the availability of genomic sequence from numerousvertebrates, a paradigm shift has occurred in the identification ofdistant-acting gene regulatory elements. In contrast to traditionalgene-centric studies in which investigators randomly scanned genomicfragments that flank genes of interest in functional assays, the modernapproach begins electronically with publicly available comparativesequence datasets that provide investigators with prioritized lists ofputative functional sequences based on their evolutionary conservation.However, although a large number of tools and resources are nowavailable, application of comparative genomic approaches remains far fromtrivial. In particular, it requires users to dynamically consider thespecies and methods for comparison depending on the specific biologicalquestion under investigation. While there is currently no single generalrule to this end, it is clear that when applied appropriately,comparative genomic approaches exponentially increase our power ingenerating biological hypotheses for subsequent experimentaltesting.

  11. The Genome of the Epsilonproteobacterial Chemolithoautotroph Sulfurimonas dentrificans

    E-Print Network [OSTI]

    Sievert, Stefan M.; USF Genomics Class

    2008-01-01

    10 , Jörg Simon 11 , and the USF Genomics Class 2, ? Biologyof coverage at the Production Genomics Facility of the Joint

  12. SRF Institute | Jefferson Lab

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Lab Jefferson Lab's SRF Institute designs, manufactures, assembles and tests SRF technology, such as these niobium cavities, for facilities worldwide. A D D I T I O N A L...

  13. Massachusetts Institute of Technology

    E-Print Network [OSTI]

    ChemE Massachusetts Institute of Technology Department of Chemical Engineering Undergraduate technology, chemical engineers play a role in almost every industry and they collaborate with all types, creating and improving pharmaceuticals, fuels, polymers, plastics, cosmetics, cereals and more." Klavs

  14. Petroleum Institute Scholarly Publications

    E-Print Network [OSTI]

    Abu Dhabi The Petroleum Institute Scholarly Publications 2009 #12 Mechanical Engineering HHaaddii BBeellhhaajj Petroleum Engineering SSaaddoooonn MMoorraadd Petroleum LLaannggiillllee Advanced University Placement Editors' notes: Names in bold in citations indicate Petroleum

  15. Critical Materials Institute

    ScienceCinema (OSTI)

    Alex King

    2013-06-05

    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.

  16. INSTITUTE COLLOQUIA AND SEMINARS

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    2-March 31, 2003 2002 April 2 Dr. Bency John, Cyclotron Institute, Texas A&M University Isoscalar Giant Resonances in 12 C April 9 Professor J. Rapaport, Ohio University, Athens,...

  17. Human Genome Education Program

    SciTech Connect (OSTI)

    Richard Myers; Lane Conn

    2000-05-01

    The funds from the DOE Human Genome Program, for the project period 2/1/96 through 1/31/98, have provided major support for the curriculum development and field testing efforts for two high school level instructional units: Unit 1, ''Exploring Genetic Conditions: Genes, Culture and Choices''; and Unit 2, ''DNA Snapshots: Peaking at Your DNA''. In the original proposal, they requested DOE support for the partial salary and benefits of a Field Test Coordinator position to: (1) complete the field testing and revision of two high school curriculum units, and (2) initiate the education of teachers using these units. During the project period of this two-year DOE grant, a part-time Field-Test Coordinator was hired (Ms. Geraldine Horsma) and significant progress has been made in both of the original proposal objectives. Field testing for Unit 1 has occurred in over 12 schools (local and non-local sites with diverse student populations). Field testing for Unit 2 has occurred in over 15 schools (local and non-local sites) and will continue in 12-15 schools during the 96-97 school year. For both curricula, field-test sites and site teachers were selected for their interest in genetics education and in hands-on science education. Many of the site teachers had no previous experience with HGEP or the unit under development. Both of these first-year biology curriculum units, which contain genetics, biotechnology, societal, ethical and cultural issues related to HGP, are being implemented in many local and non-local schools (SF Bay Area, Southern California, Nebraska, Hawaii, and Texas) and in programs for teachers. These units will reach over 10,000 students in the SF Bay Area and continues to receive support from local corporate and private philanthropic organizations. Although HGEP unit development is nearing completion for both units, data is still being gathered and analyzed on unit effectiveness and student learning. The final field testing result from this analysis will contribute to the final revisions of each unit during the second-year of this grant.

  18. The Materials Genome Initiative September 25, 2013

    E-Print Network [OSTI]

    Nair, Sankar

    The Materials Genome Initiative September 25, 2013 Dr. Cyrus Wadia Assistant Director, Clean Energy're launching what we call the Materials Genome Initiative. The invention of silicon circuits and lithium ion

  19. Genome Engineering with TAL Effector Nucleases

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Genome Engineering with TAL Effector Nucleases Print Genome engineering (GE), an emerging discipline in which a DNA sequence is altered at a single position, has a wide variety of...

  20. INVESTIGATION Genomic Background and Generation Time

    E-Print Network [OSTI]

    Lynch, Michael

    INVESTIGATION Genomic Background and Generation Time Influence Deleterious Mutation Rates variation is generated and how selection shapes mutation rates over evolutionary time requires knowledge, genomic background and generation time, on deleterious mutation in Daphnia pulicaria, a cyclically