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Sample records for genome institute walnut

  1. 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.

  2. 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.

  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. 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. Walnut Caterpillar 

    E-Print Network [OSTI]

    Ree, Bill

    2002-03-06

    This leaflet explains how to recognize and manage the walnut caterpillar in residential landscapes....

  6. 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

  7. 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

  8. 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.

  9. 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.

  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. 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.

  12. 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

  13. 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.

  14. 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

  15. 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.

  16. 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-

  17. 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

  18. 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.

  19. 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.

  20. 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

  1. 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

  2. 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...

  3. 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.

  4. 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

  5. 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

  6. 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

  7. 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

  8. 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...

  9. 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.

  10. 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.

  11. 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.

  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. 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)

  14. 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

  15. 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.

  16. 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.

  17. 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.

  18. Rich Genomics Resources Facilitate Progress in Understanding Wood Formation

    SciTech Connect (OSTI)

    Tuskan, Gerald [Oak Ridge National Laboratory

    2014-03-20

    Gerald Tuskan, Oak Ridge National Laboratory, at the 9th Annual Genomics of Energy & Environment Meeting on March 20, 2014 in Walnut Creek, Calif

  19. 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

  20. 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

  1. 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

  2. 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

  3. 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

  4. 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

  5. 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

  6. 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.

  7. Uncovering Signatures of Domestication Using Genomic Resequencing and Association Mapping of Common Bean

    SciTech Connect (OSTI)

    McClean, Phil [North Dakota State University

    2014-03-19

    Phil McClean, North Dakota State University, speaking at the 9th Annual Genomics of Energy & Environment Meeting on March 19, 2014 in Walnut Creek, Calif

  8. 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.

  9. 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.

  10. 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

  11. 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

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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

    PGF) in Walnut Creek, CA. Ergonomics: Program and PhilosophyIndustrial Engineers (IIE) Applied Ergonomics Conference. InEmpowering Employees in Ergonomics to improve training,

  1. 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

  2. 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

  3. 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.

  4. 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

  5. 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.

  6. 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.

  7. 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

  8. 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.

  9. Collaborative Monitoring in Walnut Creek, California1

    E-Print Network [OSTI]

    Standiford, Richard B.

    that they gained insight into priorities of Preserve users and knowledge of areas that might require new management regeneration and native grass populations in target management areas in the four Open Space Preserves and had to re-examine some of their own assumptions. The City of Walnut Creek managers stated

  10. 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.

  11. 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.

  12. 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.

  13. 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

  14. 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.

  15. Diamond Walnut Biomass Facility | Open Energy Information

    Open Energy Info (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 QA:QA J-E-1 SECTIONRobertsdale, Alabama (UtilityInstrumentsArea (DOE GTP) Jump to:SouthBar, California:Walnut Biomass

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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

  1. 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

  2. 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.

  3. 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.

  4. 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

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  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)

    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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. Obligate biotrophy features unraveled by the genomic analysis of rust fungi

    E-Print Network [OSTI]

    Gent, Universiteit

    , Walnut Creek, CA 94598; e Natural Resources Canada, Ste-Foy, QC, Canada G1V 4C7; f Institut National de la Recherche Agronomique, Unité de Recherche Génomique Info, 78026 Versailles Cedex, France; g Unité

  14. Wharton Undergraduate Division G95 Jon M. Huntsman Hall 3730 Walnut Street Philadelphia, PA 19104 spike.wharton.upenn.edu/ugrprogram

    E-Print Network [OSTI]

    George, Edward I.

    Wharton Undergraduate Division · G95 Jon M. Huntsman Hall · 3730 Walnut Street · Philadelphia, PA Division · G95 Jon M. Huntsman Hall · 3730 Walnut Street · Philadelphia, PA 19104 spike

  15. 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

  16. 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

  17. 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

  18. 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/

  19. 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.

  20. 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.

  1. 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

  2. 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).

  3. 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).

  4. 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).

  5. The Walnut Street Model of Ionospheric HF Radio Propagation Eric E. Johnson

    E-Print Network [OSTI]

    Johnson, Eric E.

    1 The Walnut Street Model of Ionospheric HF Radio Propagation Eric E. Johnson New Mexico State on radio frequency, latitude, time of day, season, the solar weather, and so on. Signals reach the receiver

  6. Case Study Walnut Hill United Methodist Church - Dallas, Texas, Chiller Replacement Analysis 

    E-Print Network [OSTI]

    Phillips, J.

    1998-01-01

    In March of 1992 Walnut Hill United Methodist Church in Dallas, Tx. decided that their existing thermal storage and electric reciprocating chiller system were both in need of replacement. After analyzing several options, they chose to install 150...

  7. 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

  8. 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.

  9. 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,

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. Facilities & Real Estate Services, 3101 Walnut Street, Philadelphia, PA 19104 Vehicular & Pedestrian Way-finding Directions

    E-Print Network [OSTI]

    Plotkin, Joshua B.

    Facilities & Real Estate Services, 3101 Walnut Street, Philadelphia, PA 19104 Vehicular area located at 3133 Jones Way. #12;Pedestrian Entry: Pedestrian entry to Facilities & Real Estate & Real Estate Services is located. The lower lobby level of Facilities & Real Estate Services can also

  15. 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

  16. 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...

  17. Walnut twig beetle (WTB), Pityophthorus juglandis, (Figure 1) is a small native phloeophagous (phloem-feeding) insect recently associated with

    E-Print Network [OSTI]

    Ishida, Yuko

    walnut orchard ecosystems with high population densities of WTB. Subsequently, however, the trapping methodology has been field tested and demonstrated in a variety of urban and wildland landscapes in California

  18. 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

  19. 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.

  20. 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

  1. 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.

  2. 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

  3. 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

  4. 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"

  5. 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

  6. 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

  7. 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...

  8. 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

  9. DOE - Office of Legacy Management -- Dow Chemical Co - Walnut Creek - CA 02

    Office of Legacy Management (LM)

    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 Gas &SCE-SessionsSouth Dakota Edgemont, SouthLaboratoryDiv - NY 40Units 3 andWalnut

  10. 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

  11. 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...

  12. 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

  13. 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

  14. 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

  15. 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

  16. 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

  17. 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

  18. 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...

  19. 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

  20. 56th and Walnut: A Philly Gut Rehab Development; Philadelphia, Pennsylvania (Fact Sheet)

    SciTech Connect (OSTI)

    Not Available

    2013-11-01

    Load-bearing brick-masonry multifamily buildings are prevalent in urban areas across much of the Northeast and mid-Atlantic. In most instances, these buildings are un-insulated unless they have been renovated within the past two decades. Affordable housing capital budgets typically limit what can be spent and energy improvements often take a back seat to basic capital improvements such as interior finish upgrades and basic repairs. The Consortium for Advanced Residential Buildings (CARB) is researching cost effective solution packages for significant energy efficiency and indoor air-quality improvements in these urban buildings. To explore how these low-cost retrofits can effectively integrate energy efficiency upgrades, CARB partnered with Columbus Property Management and Development, Inc. on a community-scale gut rehabilitation project located at 56th Street and Walnut Street in Philadelphia, consisting of 32 units in eleven 3-story buildings. These buildings were built in the early 1900s using stone foundations and solid brick-masonry walls. They were renovated in the 1990s to have interior light gauge metal framing with R-13 batt in the above-grade walls, induced-draft furnaces, and central air conditioning.

  1. 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

  2. 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

  3. 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,

  4. 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

  5. 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

  6. 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...

  7. 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

  8. 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

  9. 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

  10. 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

  11. 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

  12. 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.

  13. 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

  14. 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

  15. 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

  16. 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

  17. 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

  18. Genetic diversity in chestnuts of Kashmir valley Efficient managing practices require an understanding of the root distribution of crop in walnut (Juglans regia)-crop

    E-Print Network [OSTI]

    Xi, Weimin

    variation of roots for soybean (Glycine max) and peanut (Arachis hypogaea) grown with walnut trees. Crop. The RLD of intercropped peanut primarily located in the 0-10 cm soil layer, reaching the average of 52 peanut was achieved in the 10-20 cm soil layer. The RLDs of both intercropped soybean and peanut

  19. 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

  20. 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

  1. 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.

  2. 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)

  3. 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

  4. 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

  5. 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...

  6. 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.

  7. 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

  8. 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

  9. 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

  10. 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 ...

  11. 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

  12. 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.

  13. 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

  14. 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

  15. 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

  16. 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

  17. 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

  18. 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

  19. 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.

  20. 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.

  1. 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.

  2. 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:

  3. 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.

  4. 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 ...

  5. 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.

  6. 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

  7. 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.

  8. 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

  9. 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

  10. 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.

  11. 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...

  12. 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...

  13. 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...

  14. 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.

  15. 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

  16. 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

  17. Cooking with Walnuts (Spanish) 

    E-Print Network [OSTI]

    Anding, Jenna

    2001-09-10

    instituci?n se le prohibe discriminar en base de raza, color, origen nacional, sexo, edad, religion, creen- cias pol?ticas o discapacidad. Emitido en promoci?n del Trabajo Cooperativo de Extensi?n Agr?cola y Econom?a del Hogar, Decreto del Congreso del 18 de... mayo de 1914, seg?n enmienda, y del 30 de junio de 1914, en cooperaci?n con el Departamento de Agricultura de los Estados Unidos. Chester P. Fehlis, Director Comisionado, Extensi?n Cooperativa de Texas, El Sistema Universitario Texas A&M. Nuevo E-84S 9...

  18. Cooking with Walnuts 

    E-Print Network [OSTI]

    Anding, Jenna

    2001-09-10

    , 1914, as amended, and June 30, 1914, in cooperation with the United States Department of Agriculture. Chester P. Fehlis, Deputy Director, Texas Cooperative Extension, The Texas A&M University System. New E-84 9/01 Easy Banana Bread (makes 1 loaf) What...

  19. 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

  20. 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

  1. 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:...

  2. 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.

  3. 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...

  4. 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

  5. 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

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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.

  11. 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

  12. 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

  13. 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

  14. 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.

  15. 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.

  16. 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

  17. 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...

  18. 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

  19. 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.

  20. 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.

  1. 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

  2. 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...

  3. 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.

  4. 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

  5. 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

  6. 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

  7. 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/).

  8. 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/).

  9. 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

  10. 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

  11. 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

  12. 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

  13. 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

  14. 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

  15. 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

  16. 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 ...

  17. 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

  18. 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 ...

  19. 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 ...

  20. 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

  1. 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

  2. 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

  3. 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

  4. 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

  5. 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

  6. 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

  7. Single-cell and metagenomic analyses indicate a fermentative and saccharolytic lifestyle for members of the OP9 lineage

    E-Print Network [OSTI]

    Quake, Stephen R.

    of California, Merced, Merced, CA, 95343, USA 4US Department of Energy Joint Genome Institute, Walnut Creek, CA of Earth and Space Exploration, Arizona State University, Tempe, AZ, 85287, USA Abstract OP9 is a yet this article: (pending) NIH Public Access Author Manuscript Nat Commun. Author

  8. PORPHYRA (BANGIOPHYCEAE) TRANSCRIPTOMES PROVIDE INSIGHTS INTO RED ALGAL DEVELOPMENT AND METABOLISM1

    E-Print Network [OSTI]

    Lane, Chris

    3G1, Canada John W. Stiller Department of Biology, East Carolina University, Greenville, North Lindquist U.S. Department of Energy, Joint Genome Institute, Walnut Creek, California 94958, USA Senjie Lin Carolina 27834, USA Susan H. Brawley School of Marine Sciences, University of Maine, Orono, Maine 04469

  9. 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

  10. 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.

  11. 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...

  12. 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,...

  13. 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,...

  14. 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–

  15. 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

  16. 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

  17. 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

  18. 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

  19. 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...

  20. 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

  1. 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

  2. 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

  3. 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

  4. 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.

  5. 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...

  6. 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...

  7. 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.

  8. 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

  9. 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

  10. 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,

  11. 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

  12. 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

  13. 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.

  14. 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.

  15. 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

  16. 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.

  17. 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

  18. 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

  19. 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.

  20. 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

  1. 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,...

  2. 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...

  3. 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

  4. 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

  5. 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

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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

  11. 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

  12. 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

  13. 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.

  14. 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

  15. 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

  16. 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

  17. 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

  18. 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

  19. 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

  20. 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

  1. 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

  2. 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

  3. 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

  4. 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.

  5. 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

  6. 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.

  7. 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 &...

  8. 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...

  9. 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...

  10. 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 ...

  11. 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...

  12. 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.

  13. 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...

  14. 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...

  15. 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...

  16. 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

  17. 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):

  18. 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

  19. 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

  20. 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

  1. 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

  2. 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

  3. 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://

  4. 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,

  5. 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

  6. 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-

  7. 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

  8. 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

  9. 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-

  10. 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

  11. 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

  12. 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. ..

  13. 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.

  14. 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

  15. 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

  16. 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

  17. 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.

  18. 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

  19. 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.

  20. 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.

  1. ; 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

  2. 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.

  3. 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

  4. 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...

  5. 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

  6. 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

  7. 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.

  8. 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,...

  9. 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.

  10. 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

  11. 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...

  12. 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

  13. Strategies and tools for whole genome alignments

    SciTech Connect (OSTI)

    Couronne, Olivier; Poliakov, Alexander; Bray, Nicolas; Ishkhanov,Tigran; Ryaboy, Dmitriy; Rubin, Edward; Pachter, Lior; Dubchak, Inna

    2002-11-25

    The availability of the assembled mouse genome makespossible, for the first time, an alignment and comparison of two largevertebrate genomes. We have investigated different strategies ofalignment for the subsequent analysis of conservation of genomes that areeffective for different quality assemblies. These strategies were appliedto the comparison of the working draft of the human genome with the MouseGenome Sequencing Consortium assembly, as well as other intermediatemouse assemblies. Our methods are fast and the resulting alignmentsexhibit a high degree of sensitivity, covering more than 90 percent ofknown coding exons in the human genome. We have obtained such coveragewhile preserving specificity. With a view towards the end user, we havedeveloped a suite of tools and websites for automatically aligning, andsubsequently browsing and working with whole genome comparisons. Wedescribe the use of these tools to identify conserved non-coding regionsbetween the human and mouse genomes, some of which have not beenidentified by other methods.

  14. Unlocking the Secrets of the Genome

    E-Print Network [OSTI]

    Celniker, Susan E.

    The primary objective of the Human Genome Project was to produce high-quality sequences not just for the human genome but also for those of the chief model organisms: Escherichia coli, yeast (Saccharomyces cerevisiae), ...

  15. Genome Sequence of the Pea Aphid Acyrthosiphon The International Aphid Genomics Consortium"

    E-Print Network [OSTI]

    Paris-Sud XI, Université de

    Genome Sequence of the Pea Aphid Acyrthosiphon pisum The International Aphid Genomics Consortium we present the 464 Mb draft genome assembly of the pea aphid Acyrthosiphon pisum. This first published whole genome sequence of a basal hemimetabolous insect provides an outgroup to the multiple

  16. Population genomics20-02-2009 Antnio Rodrigues; Bruno Santos / 59 Population Genomics

    E-Print Network [OSTI]

    Goldschmidt, Christina

    Population genomics20-02-2009 António Rodrigues; Bruno Santos / 59 Population Genomics 1 António Rodrigues (PDBC 2008) Bruno Santos (PDBC 2008) #12;Population genomics20-02-2009 António Rodrigues; Bruno Santos / 59 Contents 2 2 1000 genome project 1 Motivation and Introduction New generation sequencing

  17. Correction for measurement error from genotyping-by-sequencing in genomic variance and genomic prediction models

    E-Print Network [OSTI]

    Schierup, Mikkel Heide

    Correction for measurement error from genotyping-by-sequencing in genomic variance and genomic for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University Denmark DLF-Trfolium, Store Heddinge, Denmark CENTER FOR QUANTITATIVE GENETICS AND GENOMICS F2 F2 Simulate sequencing Genotype

  18. The importance of reptilian genomics The study of reptilian genomes is essential if we are to

    E-Print Network [OSTI]

    Georgia, University of

    The importance of reptilian genomics The study of reptilian genomes is essential if we are to understand the patterns of genomic evolution across amniotes (mammals, birds and non-avian reptiles). Non of genome sequencing efforts [2,3]. The green anole (Anolis caroli nensis) is the only non-avian reptilian

  19. A Possible Genome To Architecture Project (GenToA) [The Meta-Genome Project?

    E-Print Network [OSTI]

    Sloman, Aaron

    concern about the Human Genome project, comparing it with buying a book written in a language nobodyA Possible Genome To Architecture Project (GenToA) [The Meta-Genome Project?] Installed: 2 Aug 2010 can a genome specify an information-processing architecture that grows itself guided by interaction

  20. Comparative Sequencing of Plant Genomes: Choices to Make The first sequenced genome of a plant,

    E-Print Network [OSTI]

    Purugganan, Michael D.

    COMMENTARY Comparative Sequencing of Plant Genomes: Choices to Make The first sequenced genome of a plant, Arabidopsis thaliana, was published ,6 years ago (Arabidopsis Genome Initiative, 2000). Since that time, the complete rice genome (Oryza sativa; Goff et al., 2002; Yu et al., 2002; International Rice

  1. Genomic potential for polysaccharide deconstruction in bacteria

    E-Print Network [OSTI]

    Berlemont, R; Martiny, AC; Martiny, AC

    2015-01-01

    improved data processing and web-based tools. Nucleic Acidsthe SEED genome databases via Web services API: tools for

  2. GDB - Human Genome Database final report

    SciTech Connect (OSTI)

    Talbot, C. Conover, Jr.

    2002-01-08

    This is the DOE final report for the GDB, Human Genome Database, project at the Johns Hopkins University.

  3. Materials Genome Initiative for Global Competitiveness

    E-Print Network [OSTI]

    Chandy, John A.

    Materials Genome Initiative for Global Competitiveness June 2011 #12;2 Materials Genome Initiative information visit www.ostp.gov. #12;3Materials Genome Initiative for Global Competitiveness EXECUTIVE OFFICE, the development of advanced materials will fuel many of the emerging industries that will address challenges

  4. One day seminar: Genetics and Genomics of

    E-Print Network [OSTI]

    Brierley, Andrew

    SCHOOL OF MEDICINE One day seminar: Genetics and Genomics of Infectious Diseases Malaria and TB 14th June 2013 University of St Andrews - School of Medicine Pathogen genome research allows exquisite to understanding disease progression. Pathogen genome sequencing is accessible to most. Outputs have broad

  5. UNL Core for Applied Genomics and Ecology

    E-Print Network [OSTI]

    Farritor, Shane

    UNL Core for Applied Genomics and Ecology Bioinformatics training Roche 454 GS-FLX Registration, Microbiomes, Variant Analysis, Whole Genomes, Transcriptomes Data Analysis and Statistics CAGE database and employer. University of Nebraska-Lincoln*Core for Applied Genomics and Ecology* 323 Filley Hall *Lincoln

  6. Computational Approaches Towards Human Genome Annotation

    E-Print Network [OSTI]

    Singh, Jaswinder Pal

    Computational Approaches Towards Human Genome Annotation Mark Gerstein Molecular Biophysics of the human genome. My talk will be concerned with topics within this area, in particular annotating pseudogenes (protein fossils) in the genome. I will discuss a comprehensive pseudogene identification pipeline

  7. Genome Biology 2007, 8:R34 commentreviewsreportsdepositedresearchrefereedresearchinteractionsinformation

    E-Print Network [OSTI]

    Shneiderman, Ben

    Genome Biology 2007, 8:R34 analytics tool for genome assemblies Michael C Schatz*, Adam M Phillippy*, Ben Shneiderman and Steven L the original work is properly cited. Hawkeye: a visual analytics tool for genome assembliesHawkeye is a new

  8. The Human Genome Project: Sequencing the Future

    E-Print Network [OSTI]

    genome programs--Genomes to Life, the Microbial Genome Program, and the Microbial Cell Project on fossil fuels. The new findings also have the potential to provide tools for enhanced biothreat agent detection and response and for using genetically engineered microbes to clean up toxic wastes in contaminat

  9. Genome Biology 2004, 6:302 commentreviewsreportsdepositedresearchinteractionsinformationrefereedresearch

    E-Print Network [OSTI]

    Gent, Universiteit

    Genome Biology 2004, 6, Technologiepark 927, B-9052 Ghent, Belgium. E-mail: Yves.vandepeer@psb.ugent.be Published: 21 December 2004 Genome at http://genomebiology.com/2004/6/1/302 © 2004 BioMed Central Ltd A report on the Plant Genomics European

  10. Bridging mycorrhizal genomics, metagenomics and forest ecology

    E-Print Network [OSTI]

    Pringle, Anne

    Meetings Bridging mycorrhizal genomics, metagenomics and forest ecology 6th New Phytologist of easily cultured saprotrophic fungi (among the first three published genomes were the models Saccharomyces or biotechnological interest, genomics is now poised to rapidly permeate the fields of fungal ecology and evolution

  11. Introduction to Theme "Genomics in Ecology,

    E-Print Network [OSTI]

    Shaffer, H. Bradley

    Introduction to Theme "Genomics in Ecology, Evolution, and Systematics" H. Bradley Shaffer1, Los Angeles, California 90095; email: brad.shaffer@ucla.edu 2 Center for Genomics and Systems Biology.1146/annurev-ecolsys-081913-123118 Copyright c 2013 by Annual Reviews. All rights reserved Keywords genome

  12. Genome Biology 2005, 6:312 commentreviewsreportsdepositedresearchinteractionsinformationrefereedresearch

    E-Print Network [OSTI]

    Kellis, Manolis

    Genome Biology 2005, 6-mail: bbernst@fas.harvard.edu. Manolis Kellis. E-mail: manoli@mit.edu Published: 1 March 2005 Genome Biology- tium, which aims to identify a comprehensive `Encyclopedia of DNA elements' in the human genome [http

  13. Methodological Review Data integration and genomic medicine

    E-Print Network [OSTI]

    Petropoulos, Michalis

    Methodological Review Data integration and genomic medicine Brenton Louie a,*, Peter Mork b 2006 Abstract Genomic medicine aims to revolutionize health care by applying our growing understanding the opportunities of genomic medicine as well as identify the informatics challenges in this domain. We also review

  14. DATA QUALITY IN GENOME DATABASES (Research Paper)

    E-Print Network [OSTI]

    Freytag, Johann-Christoph

    DATA QUALITY IN GENOME DATABASES (Research Paper) Heiko Müller Humboldt University Berlin, Germany@dbis.informatik.hu-berlin.de Abstract: Genome databases store data about molecular biological entities such as genes, proteins, diseases is their importance in the process of drug discovery. Genome data is analyzed and interpreted to gain so-called leads

  15. Genomic Comparisons of Humans and Chimpanzees

    E-Print Network [OSTI]

    Genomic Comparisons of Humans and Chimpanzees Ajit Varki1 and David L. Nelson2 1 Glycobiology, anthropogeny, genetics, evolution, hominid Abstract The genome consists of the entire DNA present of the chimpanzee genome is now available, providing opportunities to better understand genetic contributions

  16. Genome Biology 2006, 7:320 commentreviewsreportsdepositedresearchinteractionsinformationrefereedresearch

    E-Print Network [OSTI]

    Feschotte, Cedric

    Genome Biology 2006, 7:320 commentreviewsreportsdepositedresearchinteractionsinformationrefereedresearch Meeting report Mobile DNA: genomes under the influence Cédric Feschotte and Ellen J Pritham Feschotte. Email: cedric@uta.edu Published: 30 June 2006 Genome Biology 2006, 7:320 (doi:10.1186/gb-2006

  17. Inferring Ancestral Chloroplast Genomes with Inverted Repeat

    E-Print Network [OSTI]

    Tang, Jijun

    Inferring Ancestral Chloroplast Genomes with Inverted Repeat Liying Cui # , Feng Yue + , Claude W 87131 Abstract--- Genome evolution is shaped not only by nucleotide substitutions, but also by structural changes including gene and genome duplications, inser­ tions/deletions and gene order

  18. PRITZKER INSTITUTE FOR BIOMEDICAL SCIENCE

    E-Print Network [OSTI]

    Heller, Barbara

    PRITZKER INSTITUTE FOR BIOMEDICAL SCIENCE AND ENGINEERING Strategic Plan Summary #12;Pritzker Institute for Biomedical Science and Engineering for Strategic Plan Summary | 1 PRITZKER INSTITUTE FOR BIOMEDICAL SCIENCE AND ENGINEERING STRATEGIC PLAN SUMMARY 1. Grow the student body · Provide financial

  19. American Institute of Aeronautics Astronautics

    E-Print Network [OSTI]

    American Institute of Aeronautics Astronautics Study Cylindrical Thruster Low Power Space scaling of magnetic circuit leaves almost no magnetic Copyright American Institute Aeronautics; American Institute of Aeronautics Astronautics ability coaxial thrusters achieve performance moderate power

  20. Strategies for Achieving Institutional Change

    Broader source: Energy.gov [DOE]

    Many strategies—including those derived from Institutional Change Principles–may be used to effect institutional change in support of energy and sustainability objectives.

  1. Los Alamos National Laboratory Institutes

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

    Consortium consists of the University of New Mexico, New Mexico State University, and New Mexico Tech. The Engineering Institute Information Science and Technology Institute...

  2. Nuclear Organization and Genome Function

    E-Print Network [OSTI]

    Corces, Victor G.

    Nuclear Organization and Genome Function Kevin Van Bortle and Victor G. Corces Department-range interactions and have proposed roles in nuclear organization. In this review, we explore recent findings for the roles of insulators in nuclear organization. 163 Annu.Rev.CellDev.Biol.2012.28:163-187.Downloadedfromwww

  3. The ecoresponsive genome of Daphnia pulex

    SciTech Connect (OSTI)

    Colbourne, John K.; Pfrender, Michael E.; Gilbert, Donald; Thomas, W. Kelley; Tucker, Abraham; Oakley, Todd H.; Tokishita, Shinichi; Aerts, Andrea; Arnold, Georg J.; Basu, Malay Kumar; Bauer, Darren J.; Caceres, Carla E.; Carmel, Liran; Casola, Claudio; Choi, Jeong-Hyeon; Detter, John C.; Dong, Qunfeng; Dusheyko, Serge; Eads, Brian D.; Frohlich, Thomas; Geiler-Samerotte, Kerry A.; Gerlach, Daniel; Hatcher, Phil; Jogdeo, Sanjuro; Krijgsveld, Jeroen; Kriventseva, Evgenia V; Kültz, Dietmar; Laforsch, Christian; Lindquist, Erika; Lopez, Jacqueline; Manak, Robert; Muller, Jean; Pangilinan, Jasmyn; Patwardhan, Rupali P.; Pitluck, Samuel; Pritham, Ellen J.; Rechtsteiner, Andreas; Rho, Mina; Rogozin, Igor B.; Sakarya, Onur; Salamov, Asaf; Schaack, Sarah; Shapiro, Harris; Shiga, Yasuhiro; Skalitzky, Courtney; Smith, Zachary; Souvorov, Alexander; Sung, Way; Tang, Zuojian; Tsuchiya, Dai; Tu, Hank; Vos, Harmjan; Wang, Mei; Wolf, Yuri I.; Yamagata, Hideo; Yamada, Takuji; Ye, Yuzhen; Shaw, Joseph R.; Andrews, Justen; Crease, Teresa J.; Tang, Haixu; Lucas, Susan M.; Robertson, Hugh M.; Bork, Peer; Koonin, Eugene V.; Zdobnov, Evgeny M.; Grigoriev, Igor V.; Lynch, Michael; Boore, Jeffrey L.

    2011-02-04

    This document provides supporting material related to the sequencing of the ecoresponsive genome of Daphnia pulex. This material includes information on materials and methods and supporting text, as well as supplemental figures, tables, and references. The coverage of materials and methods addresses genome sequence, assembly, and mapping to chromosomes, gene inventory, attributes of a compact genome, the origin and preservation of Daphnia pulex genes, implications of Daphnia's genome structure, evolutionary diversification of duplicated genes, functional significance of expanded gene families, and ecoresponsive genes. Supporting text covers chromosome studies, gene homology among Daphnia genomes, micro-RNA and transposable elements and the 46 Daphnia pulex opsins. 36 figures, 50 tables, 183 references.

  4. Genome informatics: Requirements and challenges

    SciTech Connect (OSTI)

    Robbins, R.J.

    1993-12-31

    Informatics of some kind will play a role in every aspect of the Human Genome Project (HGP); data acquisition, data analysis, data exchange, data publication, and data visualization. What are the real requirements and challenges? The primary requirement is clear thinking and the main challenge is design. If good design is lacking, the price will be failure of genome informatics and ultimately failure of the genome project itself. Scientists need good designs to deliver the tools necessary for acquiring and analyzing DNA sequences. As these tools become more efficient, they will need new tools for comparative genomic analyses. To make the tools work, the scientists will need to address and solve nomenclature issues that are essential, if also tedious. They must devise systems that will scale gracefully with the increasing flow of data. The scientists must be able to move data easily from one system to another, with no loss of content. As scientists, they will have failed in their responsibility to share results, should repeating experiments ever become preferable to searching the literature. Their databases must become a new kind of scientific literature and the scientists must develop ways to make electronic data publishing as routine as traditional journal publishing. Ultimately, they must build systems so advanced that they are virtually invisible. In summary, the HGP can be considered the most ambitious, most audacious information-management project ever undertaken. In the HGP, computers will not merely serve as tools for cataloging existing knowledge. Rather, they will serve as instruments, helping to create new knowledge by changing the way the scientists see the biological world. Computers will allow them to see genomes, just as radio telescopes let them see quasars and electron microscopes let them see viruses.

  5. 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.

  6. Insights from Human/Mouse genome comparisons

    SciTech Connect (OSTI)

    Pennacchio, Len A.

    2003-03-30

    Large-scale public genomic sequencing efforts have provided a wealth of vertebrate sequence data poised to provide insights into mammalian biology. These include deep genomic sequence coverage of human, mouse, rat, zebrafish, and two pufferfish (Fugu rubripes and Tetraodon nigroviridis) (Aparicio et al. 2002; Lander et al. 2001; Venter et al. 2001; Waterston et al. 2002). In addition, a high-priority has been placed on determining the genomic sequence of chimpanzee, dog, cow, frog, and chicken (Boguski 2002). While only recently available, whole genome sequence data have provided the unique opportunity to globally compare complete genome contents. Furthermore, the shared evolutionary ancestry of vertebrate species has allowed the development of comparative genomic approaches to identify ancient conserved sequences with functionality. Accordingly, this review focuses on the initial comparison of available mammalian genomes and describes various insights derived from such analysis.

  7. Institutional Change Basics for Sustainability | Department of...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Institutional Change Basics for Sustainability Institutional Change Basics for Sustainability Institutional change integrates technology, policy, and behavior to make new...

  8. Resources on Institutional Change for Sustainability | Department...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Institutional Change Resources on Institutional Change for Sustainability Resources on Institutional Change for Sustainability The Federal Energy Management Program (FEMP)...

  9. Use of Institutional Controls

    Broader source: Directives, Delegations, and Requirements [Office of Management (MA)]

    2003-04-09

    The Policy ensures that the Department of Energy will use institutional controls in the management of resources, facilities and properties under its control, and in implementing its programmatic responsibilities. Certified 1-28-11. Superseded by Chg 1 (Admin Chg), dated 12-7-15.

  10. Use of Institutional Controls

    Broader source: Directives, Delegations, and Requirements [Office of Management (MA)]

    2003-04-09

    The Policy ensures that the Department of Energy will use institutional controls in the management of resources, facilities and properties under its control, and in implementing its programmatic responsibilities. Certified 1-28-11. Supersedes DOE P 454.1, dated 4-9-03.

  11. Commitment Institutional Change Principle

    Broader source: Energy.gov [DOE]

    Commitment can be a crucial element that helps federal agencies inject and emphasize sustainability in their organizational culture. Institutions and people change when they have made definite commitments to change, especially when those commitments relate to future conditions. Research shows that explicit commitments improve the rate at which people adopt energy-efficient behaviors.

  12. 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.

  13. Initial sequencing and comparative analysis of the mouse genome

    E-Print Network [OSTI]

    Eddy, Sean

    Initial sequencing and comparative analysis of the mouse genome Mouse Genome Sequencing Consortium ........................................................................................................................................................................................................................... The sequence of the mouse genome is a key informational tool for understanding the contents of the human genome collaboration to produce a high-quality draft sequence of the mouse genome. We also present an initial

  14. Prediction of Membrane Proteins in Post-Genomic Era

    E-Print Network [OSTI]

    Kihara, Daisuke

    by the report that the human genome sequencing project has been completed [1,2]. Beyond the human genome, a surge of world-wide genome projects in the last decade have been producing complete genome sequences1 Prediction of Membrane Proteins in Post-Genomic Era Daisuke Kihara1* & Minoru Kanehisa2 1) Donald

  15. Human-mouse comparative genomics: successes and failures to reveal functional regions of the human genome

    SciTech Connect (OSTI)

    Pennacchio, Len A.; Baroukh, Nadine; Rubin, Edward M.

    2003-05-15

    Deciphering the genetic code embedded within the human genome remains a significant challenge despite the human genome consortium's recent success at defining its linear sequence (Lander et al. 2001; Venter et al. 2001). While useful strategies exist to identify a large percentage of protein encoding regions, efforts to accurately define functional sequences in the remaining {approx}97 percent of the genome lag. Our primary interest has been to utilize the evolutionary relationship and the universal nature of genomic sequence information in vertebrates to reveal functional elements in the human genome. This has been achieved through the combined use of vertebrate comparative genomics to pinpoint highly conserved sequences as candidates for biological activity and transgenic mouse studies to address the functionality of defined human DNA fragments. Accordingly, we describe strategies and insights into functional sequences in the human genome through the use of comparative genomics coupled wit h functional studies in the mouse.

  16. Institutions or, who does what and why

    E-Print Network [OSTI]

    Handy, Susan L.

    it is infused with value" ­ Philip Selznick #12;Importance of Institutions Institutional characteristics

  17. Editorial: Human and Evolutionary Genomics Human Genomics has, from its outset, included a great deal of evolutionary analysis. The

    E-Print Network [OSTI]

    Pollock, David

    Editorial: Human and Evolutionary Genomics Human Genomics has, from its outset, included a great genomics. This inclusion is the result of an obvious trend in the field of genomics to incorporate more. The world now has over one hundred complete bacterial genomes, and with human, roundworm, multiple

  18. Unlocking the secrets of the genome Despite the successes of genomics, little is known about how genetic information produces complex

    E-Print Network [OSTI]

    Kellis, Manolis

    Unlocking the secrets of the genome Despite the successes of genomics, little is known about how genomes could change that. T he primary objective of the Human Genome Project was to produce high- quality sequences not just for the human genome but also for those of the chief model organisms:Escherichia coli

  19. Abstract--As the human genome project progresses and some microbial and eukaryotic genomes are recognized, a

    E-Print Network [OSTI]

    Zelikovsky, Alexander

    1 of 4 Abstract--As the human genome project progresses and some microbial and eukaryotic genomes. This technology promises to monitor the whole genome at once, so that researchers can study the whole genome virus as well as simulated data. Our experiments show that the genomic data follow the pattern predicted

  20. GenomePro -Processing Genomic Files Of All Sizes Technical Report FIU-SCIS-2015-01-20-1

    E-Print Network [OSTI]

    Robinson, Michael

    to further understand not only our humane genome but any life form genome. Keywords ­ Gigabytes, Terabytes, Genome, Sub-Sequence, I.INTRODUCTION The Genome Project, started in 1990 and completed in April 2003, sequenced the human genome producing files of about 3.2 Gigabytes. During the next 10 years a new sequencing

  1. 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

  2. Metagenomics, metatranscriptomics and single cell genomics reveal...

    Office of Scientific and Technical Information (OSTI)

    and single cell genomics reveal functional response of active Oceanospirillales to Gulf oil spill Citation Details In-Document Search Title: Metagenomics, metatranscriptomics and...

  3. Nuclear and mitochondrial genome defects in autisms.

    E-Print Network [OSTI]

    Smith, M; Spence, MA; Flodman, P

    2009-01-01

    435– 439. Smith et al. : Nuclear and Mitochondrial Genomebe advantageous. Smith et al. : Nuclear and MitochondrialAND MEDICAL GENETICS 2009 Nuclear and Mitochondrial Genome

  4. Massachusetts Institute of Technology MIT Web Survey Service Institutional Research,

    E-Print Network [OSTI]

    Reif, Rafael

    Massachusetts Institute of Technology MIT Web Survey Service Institutional Research, Office.mit.edu/ist/isnews/v21/n02/210210.html 1. Coordination with the MIT Institutional Research & Web Survey Service. The MIT, intended audience, and desired schedule. The Web Survey Service will host certain web surveys

  5. Materials Research Institute 199 Materials Research Institute Building

    E-Print Network [OSTI]

    Lee, Dongwon

    promise to transform the field of materials research in areas such as energy, health, and the environment of Materials Research A New Building for the 21st Century he Materials Research Institute promotes interdisciMaterials Research Institute 199 Materials Research Institute Building The Pennsylvania State

  6. Statistical Challenges in Functional Genomics Paola Sebastiani and Marco Ramoni

    E-Print Network [OSTI]

    Spang, Rainer

    in Functional Genomics 1. The Human Genome Project The Human Genome Project (HGP) is a multi-year effort in 1990, the HGP is expected to render its final results in 2005, but the staggering technological

  7. ComBo : a visualization tool for comparative genomic data

    E-Print Network [OSTI]

    Yu, Tamara H. (Tamara Hui)

    2004-01-01

    Propelled by advances in sequencing technology, the advent of the genomic era brings the challenge of managing and interpreting massive amount of genomic data. A number of single-genome browsers have been developed for ...

  8. Genome sequence of the Brown Norway rat yields insights into

    E-Print Network [OSTI]

    Payseur, Bret

    Genome sequence of the Brown Norway rat yields insights into mammalian evolution Rat Genome Norway (BN) rat strain. The sequence represents a high-quality `draft' covering over 90% of the genome

  9. Evolutionary Genomics of Life in (and from) the Sea

    E-Print Network [OSTI]

    Boore, Jeffrey L.

    2009-01-01

    291: 1304-1351. Table 1. Genomics information on the webLBNL-59356 Evolutionary Genomics of Life in (and from) thean engine for comparative genomics. The six largest centers

  10. The common ground of genomics and systems biology

    E-Print Network [OSTI]

    Conesa, Ana; Mortazavi, Ali

    2014-01-01

    8/S2. Authors’ details Genomics of Gene Expression Lab,systems biology. Annu Rev. Genomics Hum. Genet 2001, 2:343-projection strategies. Genomics 2008, 92(6):373-83. 31.

  11. UV Decontamination of MDA Reagents for Single Cell Genomics

    E-Print Network [OSTI]

    Lee, Janey

    2011-01-01

    Reagents for Single Cell Genomics Janey Lee 1* , Damon TigheReagents for Single Cell Genomics Janey Lee 1 , Damon TigheAbstract Single cell genomics, the amplification and

  12. Phytozome: A Comparative Platform for Green Plant Genomics

    E-Print Network [OSTI]

    Goodstein, David M.

    2012-01-01

    a growing plant comparative genomics resource. Nucleic AcidsL.A. (2011) The Sol Genomics Network (solgenomics.net):for comparative plant genomics. Nucleic Acids Res, 36, D959-

  13. Structural Genomics of Minimal Organisms: Pipeline and Results

    E-Print Network [OSTI]

    Kim, Sung-Hou

    2008-01-01

    of recombinant proteins. J. Struct. Funct. Genomics 5:69-74.proteins. J. Struct. Funct. Genomics 5:69-74. Oganesyan,Structural Genomics of Minimal Organisms: Pipeline and

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

    E-Print Network [OSTI]

    Penn, Kevin; Jensen, Paul R

    2012-01-01

    Orcutt B, et al: Ecological genomics of marine roseobacters.1037-1042. Penn and Jensen BMC Genomics 2012, 13:86 http://and Jensen: Comparative genomics reveals evidence of marine

  15. Evolutionary Genomics of Life in (and from) the Sea

    E-Print Network [OSTI]

    Boore, Jeffrey L.

    2009-01-01

    built for the Human Genome Project (Lander et al. , 2001;developed for the Human Genome Project can now best behuman genome, and nearly all of this is directed at projects

  16. The Impact of Structural Genomics: Expectations and Outcomes

    E-Print Network [OSTI]

    Chandonia, John-Marc; Brenner, Steven E.

    2005-01-01

    Choi et al. , J Struct Funct Genomics 4, 31-4 (2003). H. M.Center for Structural Genomics, sequence families of unknownMCSG) Northeast Structural Genomics Consortium, Novel folds

  17. Finding conserved patterns in biological sequences, networks and genomes 

    E-Print Network [OSTI]

    Yang, Qingwu

    2009-05-15

    approach for investigating clustering of related genes across multiple genomes for a given gene cluster. By analyzing gene clustering in 400 bacterial genomes, we show that our algorithm is efficient enough to study gene clusters across hundreds of genomes....

  18. Target Selection and Deselection at the Berkeley Structural Genomics Center

    E-Print Network [OSTI]

    Chandonia, John-Marc; Kim, Sung-Hou; Brenner, Steven E.

    2005-01-01

    gene-set concept. Annu Rev Genomics Hum Genet 2000;1:99-116.SE. A tour of structural genomics. Nat Rev Genet 2001;2(10):M, Wang LK. Structural genomics: a pipeline for providing

  19. Goodlad Institute for Educational Renewal

    E-Print Network [OSTI]

    Matrajt, Graciela

    Goodlad Institute for Educational Renewal Annual Report October 2010 #12; Page | 1 PREFACE The Goodlad Institute for Educational Renewal honors the remarkable. Goodlad initiated a national effort to support educational quality and renewal. Looking beyond high

  20. Institutions G.C. Sciara

    E-Print Network [OSTI]

    Handy, Susan L.

    an institution when it is infused with value" ­ Philip Selznick #12;Why they matter... ·They plan, implement

  1. 1. Awarding Institution/Body Imperial College London 2. Teaching Institution Imperial College London

    E-Print Network [OSTI]

    in the following areas. ` Knowledge and understanding A. Knowledge and understanding of: 1. Key topics in Genomics and Bioinformatics, including genome mapping, sequence analysis, transcriptomics, host/pathogen genomics, use of DNA/protein databases, functional and comparative genomics, phylogenetic analysis. 2. Key topics in Macromolecular

  2. Advanced Studies 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 News Publications Traditional Knowledge KiosksAboutHelp &Advanced Simulation andInstitute

  3. INSTITUTE COLLOQUIA AND SEMINARS

    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 (JournalvivoHighHussein KhalilResearch8 IEEEINL5-March 31, 2006INSTITUTE

  4. INSTITUTE OF PHYSICS PUBLISHING

    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 (JournalvivoHighHussein KhalilResearch8 IEEEINL5-March 31, 2006INSTITUTE4

  5. INSTITUTE OF PHYSICS PUBLISHING

    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 (JournalvivoHighHussein KhalilResearch8 IEEEINL5-March 31, 2006INSTITUTE46

  6. Comparative genomics analysis of Liberibacter species to elucidate pathogenesis and culturability

    E-Print Network [OSTI]

    Leonard, Michael T.; Fagen, Jennie R.; McCullough, Connor M.; Davis-Richardson, Austin G.; Davis, Michael J.; Triplett, Eric W.

    2014-01-01

    Vol. 1 (2014) Comparative genomics analysis of Liberibacterof citrus, comparative genomics of this strain with other

  7. Target Selection and Deselection at the Berkeley StructuralGenomics...

    Office of Scientific and Technical Information (OSTI)

    and Deselection at the Berkeley StructuralGenomics Center At the Berkeley Structural Genomics Center (BSGC), our goalis to obtain a near-complete structural complement of proteins...

  8. 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...

  9. The Arabidopsis lyrata genome sequence and the basis of rapid genome size change

    SciTech Connect (OSTI)

    Hu, Tina T.; Pattyn, Pedro; Bakker, Erica G.; Cao, Jun; Cheng, Jan-Fang; Clark, Richard M.; Fahlgren, Noah; Fawcett, Jeffrey A.; Grimwood, Jane; Gundlach, Heidrun; Haberer, Georg; Hollister, Jesse D.; Ossowski, Stephan; Ottilar, Robert P.; Salamov, Asaf A.; Schneeberger, Korbinian; Spannagl, Manuel; Wang, Xi; Yang, Liang; Nasrallah, Mikhail E.; Bergelson, Joy; Carrington, James C.; Gaut, Brandon S.; Schmutz, Jeremy; Mayer, Klaus F. X.; Van de Peer, Yves; Grigoriev, Igor V.; Nordborg, Magnus; Weigel, Detlef; Guo, Ya-Long

    2011-04-29

    In our manuscript, we present a high-quality genome sequence of the Arabidopsis thaliana relative, Arabidopsis lyrata, produced by dideoxy sequencing. We have performed the usual types of genome analysis (gene annotation, dN/dS studies etc. etc.), but this is relegated to the Supporting Information. Instead, we focus on what was a major motivation for sequencing this genome, namely to understand how A. thaliana lost half its genome in a few million years and lived to tell the tale. The rather surprising conclusion is that there is not a single genomic feature that accounts for the reduced genome, but that every aspect centromeres, intergenic regions, transposable elements, gene family number is affected through hundreds of thousands of cuts. This strongly suggests that overall genome size in itself is what has been under selection, a suggestion that is strongly supported by our demonstration (using population genetics data from A. thaliana) that new deletions seem to be driven to fixation.

  10. Uses of antimicrobial genes from microbial genome

    DOE Patents [OSTI]

    Sorek, Rotem; Rubin, Edward M.

    2013-08-20

    We describe a method for mining microbial genomes to discover antimicrobial genes and proteins having broad spectrum of activity. Also described are antimicrobial genes and their expression products from various microbial genomes that were found using this method. The products of such genes can be used as antimicrobial agents or as tools for molecular biology.

  11. Genome Biology 2004, 5:343 commentreviewsreportsdepositedresearchinteractionsinformationrefereedresearch

    E-Print Network [OSTI]

    ://genomebiology.com/2004/5/9/343 © 2004 BioMed Central Ltd A report on the Keystone Symposium `Structural Genomics', held-dollar-plus folly? Two concurrent Keystone Symposia, `Structural Genomics' and `Frontiers in Structural Biology set up an auto- mated pipeline to annotate proteins of known structure but unknown function. The push

  12. INVITED: Comparative Microbial Genomics Giri Narasimhan

    E-Print Network [OSTI]

    Narasimhan, Giri

    with greater ease and greater confidence. Keywords-microbes; comparative genomics; I. INTRODUCTION Microbes, and functional capabilities, often in order to adapt to their harsh environments, compete with other microbes, or to reproduce. While there do exist microbes with enormous genomes, most microbes have smaller and simpler

  13. Fungal biology: compiling genomes and exploiting them

    SciTech Connect (OSTI)

    Labbe, Jessy L; Uehling, Jessie K; Payen, Thibaut; Plett, Jonathan

    2014-01-01

    The last 10 years have seen the cost of sequencing complete genomes decrease at an incredible speed. This has led to an increase in the number of genomes sequenced in all the fungal tree of life as well as a wide variety of plant genomes. The increase in sequencing has permitted us to study the evolution of organisms on a genomic scale. A number of talks during the conference discussed the importance of transposable elements (TEs) that are present in almost all species of fungi. These TEs represent an especially large percentage of genomic space in fungi that interact with plants. Thierry Rouxel (INRA, Nancy, France) showed the link between speciation in the Leptosphaeria complex and the expansion of TE families. For example in the Leptosphaeria complex, one species associated with oilseed rape has experienced a recent and massive burst of movement by a few TE families. The alterations caused by these TEs took place in discrete regions of the genome leading to shuffling of the genomic landscape and the appearance of genes specific to the species, such as effectors useful for the interactions with a particular plant (Rouxel et al., 2011). Other presentations showed the importance of TEs in affecting genome organization. For example, in Amanita different species appear to have been invaded by different TE families (Veneault-Fourrey & Martin, 2011).

  14. Genome Biology 2004, 5:250 commentreviewsreportsdepositedresearchinteractionsinformationrefereedresearch

    E-Print Network [OSTI]

    Gent, Universiteit

    :250 commentreviewsreportsdepositedresearchinteractionsinformationrefereedresearch Minireview Tetraodon genome confirms Takifugu findings: most fish are ancient polyploids Yves Van pufferfish Tetraodon nigroviridis. Ray-finned fish underwent a whole-genome duplication some 350 million have also yielded a surprising finding: ray-finned fish (Actinopterygii), such as pufferfish might have

  15. WASHINGTON UNIVERSITY SEVER INSTITUTE OF TECHNOLOGY

    E-Print Network [OSTI]

    Rouchka, Eric

    ______________________________________________________ Assembly and Compositional Analysis of Human Genomic Data by Eric C. Rouchka Prepared under the direction _____________________________________ ABSTRACT _____________________________________ Assembly and Compositional Analysis of Human Genomic Data Genome Project was initiated as a fifteen-year endeavor to sequence the approximately three billion bases

  16. Functional Insights from Structural Genomics

    SciTech Connect (OSTI)

    Forouhar,F.; Kuzin, A.; Seetharaman, J.; Lee, I.; Zhou, W.; Abashidze, M.; Chen, Y.; Montelione, G.; Tong, L.; et al

    2007-01-01

    Structural genomics efforts have produced structural information, either directly or by modeling, for thousands of proteins over the past few years. While many of these proteins have known functions, a large percentage of them have not been characterized at the functional level. The structural information has provided valuable functional insights on some of these proteins, through careful structural analyses, serendipity, and structure-guided functional screening. Some of the success stories based on structures solved at the Northeast Structural Genomics Consortium (NESG) are reported here. These include a novel methyl salicylate esterase with important role in plant innate immunity, a novel RNA methyltransferase (H. influenzae yggJ (HI0303)), a novel spermidine/spermine N-acetyltransferase (B. subtilis PaiA), a novel methyltransferase or AdoMet binding protein (A. fulgidus AF{_}0241), an ATP:cob(I)alamin adenosyltransferase (B. subtilis YvqK), a novel carboxysome pore (E. coli EutN), a proline racemase homolog with a disrupted active site (B. melitensis BME11586), an FMN-dependent enzyme (S. pneumoniae SP{_}1951), and a 12-stranded {beta}-barrel with a novel fold (V. parahaemolyticus VPA1032).

  17. Ecogenomics Sheds Light on Synergistic Networks of Microbial Dark Matter in a

    SciTech Connect (OSTI)

    Nobu, Masaru [University of Illinois at Urbana-Champaign

    2014-03-19

    Masaru Nobu, University of Illinois at Urbana-Champaign, speaking at the 9th Annual Genomics of Energy & Environment Meeting on March 19, 2014 in Walnut Creek, Calif.

  18. Unlocking Plant Metabolic Diversity

    SciTech Connect (OSTI)

    Osbourn, Anne [John Innes Centre

    2014-03-19

    Anne Osbourn, John Innes Centre, UK, at the 9th Annual Genomics of Energy & Environment Meeting on March 19, 2014 in Walnut Creek, Calif.

  19. Understanding the Forest Microbiome: A Fungal Perspective

    SciTech Connect (OSTI)

    Vilgalys, Rytas [Duke University

    2014-03-19

    Rytas Vilgalys, Duke University, speaking at the 9th Annual Genomics of Energy & Environment Meeting on March 19, 2014 in Walnut Creek, Calif

  20. Mapping Soil Carbon from Cradle to Grave: Identifying the Microbial Blueprint for Root-carbon Transformations in Soil

    SciTech Connect (OSTI)

    Nuccio, Erin [Lawrence Livermore National Laboratory

    2014-03-19

    Erin Nuccio, Lawrence Livermore National Laboratory, at the 9th Annual Genomics of Energy & Environment Meeting on March 19, 2014 in Walnut Creek, Calif.

  1. Pectinases Link Early Fungal Evolution to the Land Plant Lineage

    SciTech Connect (OSTI)

    Berbee, Mary [University of British Columbia

    2014-03-19

    Mary Berbee, University of British Columbia, Canada, speaking at the 9th Annual Genomics of Energy & Environment Meeting on March 19, 2014 in Walnut Creek, Calif.

  2. Proteogenomics : applications of mass spectrometry at the interface of genomics and proteomics

    E-Print Network [OSTI]

    Castellana, Natalie

    2012-01-01

    of proteomics and genomics to unravel the specificities ofetry and comparative genomics to analyze multiple genomes,”genome,” Comp. Funct. Genomics, vol. 3, no. 3, pp. 244–253,

  3. How Pseudo-Boolean Programming can help Genome Rearrangement Distance Computation

    E-Print Network [OSTI]

    Fertin, Guillaume

    How Pseudo-Boolean Programming can help Genome Rearrangement Distance Computation S vialette@lri.fr Abstract. Computing genomic distances between whole genomes is a fundamental problem in comparative genomics. Recent researches have resulted in different genomic distance definitions: number

  4. Genomic definition of species. Revision 2

    SciTech Connect (OSTI)

    Crkvenjakov, R.; Drmanac, R.

    1993-03-01

    A genome is the sum total of the DNA sequences in the cells of an individual organism. The common usage that species possess genomes comes naturally to biochemists, who have shown that all protein and nucleic acid molecules are at the same time species- and individual-specific, with minor individual variations being superimposed on a consensus sequence that is constant for a species. By extension, this property is attributed to the common features of DNA in the chromosomes of members of a given species and is called species genome. Our proposal for the definition of a biological species is as follows: A species comprises a group of actual and potential biological organisms built according to a unique genome program that is recorded, and at least in part expressed, in the structures of their genomic nucleic acid molecule(s), having intragroup sequence differences which can be fully interconverted in the process of organismal reproduction.

  5. The Virtual Institute of Microbial Stress and Survival VIMSS:ESPP Overview

    E-Print Network [OSTI]

    Arkin, Adam P.

    2014-01-01

    established in 2002 through DOE Genomics:GTL funding of theMicrobiology Core, Functional Genomics and Imaging Core, andof VIMSS in comparative genomics, functional genomics, and

  6. Genome-Wide siRNA-Based Functional Genomics of Pigmentation Identifies Novel Genes and Pathways That Impact Melanogenesis in Human Cells

    E-Print Network [OSTI]

    2008-01-01

    siRNA-Based Functional Genomics of Pigmentation Identifiespoorly understood. Functional genomics based on RNA-mediatedof RNAi-based functional genomics to identify novel genes,

  7. Genome Structure Gallery from the Mycobacterium Tuberculosis Structual Genomics Consortium

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

    The TB Structural Genomics Consortium works with the structures of proteins from M. tuberculosis, analyzing these structures in the context of functional information that currently exists and that the Consortium generates. The database of linked structural and functional information constructed from this project will form a lasting basis for understanding M. tuberculosis pathogenesis and for structure-based drug design. The Consortium's structural and functional information is publicly available. The Structures Gallery makes more than 650 total structures available by PDB identifier. Some of these are not consortium targets, but all are viewable in 3D color and can be manipulated in various ways by Jmol, an open-source Java viewer for chemical structures in 3D from http://www.jmol.org/

  8. Institutional Change for Sustainability Case Studies | Department...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Institutional Change for Sustainability Case Studies Institutional Change for Sustainability Case Studies These case studies show examples of institutional change successfully...

  9. Cyclotron Institute Upgrade Project

    SciTech Connect (OSTI)

    Clark, Henry; Yennello, Sherry; Tribble, Robert

    2014-08-26

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

  10. Complete genome sequence of the halophilic and highly halotolerant Chromohalobacter salexigens type strain (1H11T)

    SciTech Connect (OSTI)

    Copeland, A [U.S. Department of Energy, Joint Genome Institute; O'Connor, Kathleen [Purdue University; Lucas, Susan [U.S. Department of Energy, Joint Genome Institute; Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute; Berry, Kerrie W. [United States Department of Energy Joint Genome Institute; Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Glavina Del Rio, Tijana [U.S. Department of Energy, Joint Genome Institute; Hammon, Nancy [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; Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Bruce, David [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Han, Cliff [Los Alamos National Laboratory (LANL); Tapia, Roxanne [Los Alamos National Laboratory (LANL); Saunders, Elizabeth H [Los Alamos National Laboratory (LANL); Schmutz, Jeremy [Stanford University; Brettin, Thomas S [ORNL; Larimer, Frank W [ORNL; Land, Miriam L [ORNL; Hauser, Loren John [ORNL; Vargas, Carmen [University of Seville; Nieto, Joaquin J. [University of Seville; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; 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; Csonka, Laszlo N. [Purdue University; Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute

    2011-01-01

    Chromohalobacter salexigens is one of nine currently known species of the genus Chromoha- lobacter in the family Halomonadaceae. It is the most halotolerant of the so-called mod- erately halophilic bacteria currently known and, due to its strong euryhaline phenotype, it is an established model organism for prokaryotic osmoadaptation. C. salexigens strain 1H11T and Halomonas elongata are the first and the second members of the family Halomonada- ceae with a completely sequenced genome. The 3,696,649 bp long chromosome with a total of 3,319 protein-coding and 93 RNA genes was sequenced as part of the DOE Joint Genome Institute Program DOEM 2004.

  11. Tokyo Institute of Technology Tokyo Institute of Technology

    E-Print Network [OSTI]

    Shimodaira, Hidetoshi

    Tokyo Institute of Technology 2004 #12; Tokyo Institute of Technology k O(n-k/2) (Efron et al 1996) 2O(B) (Shimodaira 2002, 2004) O(B) #12; Tokyo Institute of Technology of Technology 1 2 3 4 5 1 2 3 4 5 1 2 3 4 5 1 23 4 5 1 2 3 4 5 1 2 3 4 5 1 2 3 4 5 1 23 4 5 1 2 3 4 5

  12. 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

  13. Genome Sequence of the Palaeopolyploid soybean

    SciTech Connect (OSTI)

    Schmutz, Jeremy; Cannon, Steven B.; Schlueter, Jessica; Ma, Jianxin; Mitros, Therese; Nelson, William; Hyten, David L.; Song, Qijian; Thelen, Jay J.; Cheng, Jianlin; Xu, Dong; Hellsten, Uffe; May, Gregory D.; Yu, Yeisoo; Sakura, Tetsuya; Umezawa, Taishi; Bhattacharyya, Madan K.; Sandhu, Devinder; Valliyodan, Babu; Lindquist, Erika; Peto, Myron; Grant, David; Shu, Shengqiang; Goodstein, David; Barry, Kerrie; Futrell-Griggs, Montona; Abernathy, Brian; Du, Jianchang; Tian, Zhixi; Zhu, Liucun; Gill, Navdeep; Joshi, Trupti; Libault, Marc; Sethuraman, Anand; Zhang, Xue-Cheng; Shinozaki, Kazuo; Nguyen, Henry T.; Wing, Rod A.; Cregan, Perry; Specht, James; Grimwood, Jane; Rokhsar, Dan; Stacey, Gary; Shoemaker, Randy C.; Jackson, Scott A.

    2009-08-03

    Soybean (Glycine max) is one of the most important crop plants for seed protein and oil content, and for its capacity to fix atmospheric nitrogen through symbioses with soil-borne microorganisms. We sequenced the 1.1-gigabase genome by a whole-genome shotgun approach and integrated it with physical and high-density genetic maps to create a chromosome-scale draft sequence assembly. We predict 46,430 protein-coding genes, 70percent more than Arabidopsis and similar to the poplar genome which, like soybean, is an ancient polyploid (palaeopolyploid). About 78percent of the predicted genes occur in chromosome ends, which comprise less than one-half of the genome but account for nearly all of the genetic recombination. Genome duplications occurred at approximately 59 and 13 million years ago, resulting in a highly duplicated genome with nearly 75percent of the genes present in multiple copies. The two duplication events were followed by gene diversification and loss, and numerous chromosome rearrangements. An accurate soybean genome sequence will facilitate the identification of the genetic basis of many soybean traits, and accelerate the creation of improved soybean varieties.

  14. Genome Sequence Databases (Overview): Sequencing and Assembly

    SciTech Connect (OSTI)

    Lapidus, Alla L.

    2009-01-01

    From the date its role in heredity was discovered, DNA has been generating interest among scientists from different fields of knowledge: physicists have studied the three dimensional structure of the DNA molecule, biologists tried to decode the secrets of life hidden within these long molecules, and technologists invent and improve methods of DNA analysis. The analysis of the nucleotide sequence of DNA occupies a special place among the methods developed. Thanks to the variety of sequencing technologies available, the process of decoding the sequence of genomic DNA (or whole genome sequencing) has become robust and inexpensive. Meanwhile the assembly of whole genome sequences remains a challenging task. In addition to the need to assemble millions of DNA fragments of different length (from 35 bp (Solexa) to 800 bp (Sanger)), great interest in analysis of microbial communities (metagenomes) of different complexities raises new problems and pushes some new requirements for sequence assembly tools to the forefront. The genome assembly process can be divided into two steps: draft assembly and assembly improvement (finishing). Despite the fact that automatically performed assembly (or draft assembly) is capable of covering up to 98% of the genome, in most cases, it still contains incorrectly assembled reads. The error rate of the consensus sequence produced at this stage is about 1/2000 bp. A finished genome represents the genome assembly of much higher accuracy (with no gaps or incorrectly assembled areas) and quality ({approx}1 error/10,000 bp), validated through a number of computer and laboratory experiments.

  15. APPLIED GENOMICS TECHNOLOGY CENTER www.agtc.med.wayne.edu

    E-Print Network [OSTI]

    Berdichevsky, Victor

    APPLIED GENOMICS TECHNOLOGY CENTER www.agtc.med.wayne.edu CURRENT SERVICES CONTACT INFORMATION Dr. Susan J. Land, Ph.D. Laboratory Director ABOUT THE FACILITY The Applied Genomics Technology Center (AGTC-of-the-art, fee-for-service genomics center that provides a wide range of genomic technologies to the medical

  16. Genome Organization and Gene Expression Shape the Transposable Element Distribution

    E-Print Network [OSTI]

    Alvarez, Nadir

    Genome Organization and Gene Expression Shape the Transposable Element Distribution The distribution of transposable elements (TEs) in a genome reflects a balance between insertion rate and selection shaping the organization of genomes. Past research has shown that TEs tend to accumulate in genomic

  17. Prediction of Contiguous Regions in the Amniote Ancestral Genome

    E-Print Network [OSTI]

    Chauve, Cedric

    Prediction of Contiguous Regions in the Amniote Ancestral Genome A¨ida Ouangraoua1 , Fr (CARs) of the genome of the last common ancestor of all extant amniotes, based on the currently sequenced and assembled am- niote genomes as ingroups and three teleost fish genomes as outgroups. We

  18. Target selection and current status of structural genomics for the

    E-Print Network [OSTI]

    Babu, M. Madan

    33 Target selection and current status of structural genomics for the completed microbial genomes 3.2 Structural status of completed microbial genomes in the PDB................ 3.3 Metabolic pathways as targets for structural genomics.......................... 3.3.1 Glycolytic pathway

  19. 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

  20. Functional Genomics: It's All How You Read It

    E-Print Network [OSTI]

    Boguski, Mark S.

    Functional Genomics: It's All How You Read It Philip Hieter and Mark Boguski "Functional genomics to functional genomics? An informal poll of colleagues indicates that the term is widely used, but has many genomics websites that have sprung up over the last 12 months clearly demonstrates that interpretations

  1. Phylogenetics of modern birds in the era of genomics

    E-Print Network [OSTI]

    Edwards, Scott

    Review Phylogenetics of modern birds in the era of genomics Scott V. Edwards*, W. Bryan Jennings and maturation of the genomics era, the completion of the chicken genome and a suite of technologies that promise genomics strategies, including adoption of objective quality scores for sequence data, analysis

  2. Initial sequencing and comparative analysis of the mouse genome

    E-Print Network [OSTI]

    Hardison, Ross C.

    and knockin techniques17­22 . For these and other reasons, the Human Genome Project (HGP) recognized from its ........................................................................................................................................................................................................................... The sequence of the mouse genome is a key informational tool for understanding the contents of the human genome comparative analysis of the mouse and human genomes, describing some of the insights that can be gleaned from

  3. Examining the Current Problems of Whole Genome Comparison: A Review

    E-Print Network [OSTI]

    Examining the Current Problems of Whole Genome Comparison: A Review Biochemistry 218 Project://www.ncbi.nlm.nih.gov/Genbank/genbankstats.html). The first two publications of microbial whole genome sequencing projects were published in 1995. Only six. Bacterial genomes consist mostly (85-95 %) of coding sequence, the human genome encodes only ~3%, while

  4. Assembly and Analysis of Extended Human Genomic Contig Regions

    E-Print Network [OSTI]

    Rouchka, Eric

    @ibc.wustl.edu; states@ibc.wustl.edu Abstract The Human Genome Project (HGP) has led to the deposit of human genomic The U.S. Human Genome Project, coordinated by the United States Department of Energy (DOEAssembly and Analysis of Extended Human Genomic Contig Regions Eric C. Rouchka and David J. States

  5. |Research Focus In search of the minimal Escherichia coli genome

    E-Print Network [OSTI]

    Conway, Tyrrell

    for a `second human genome project' to compile an inventory of the genomes of the human microflora, Stanley|Research Focus In search of the minimal Escherichia coli genome Darren J. Smalley, Marvin Whiteley and Tyrrell Conway Advanced Center for Genome Technology, The University of Oklahoma, Norman, OK 73019

  6. RASMUS NIELSEN he goal of the 1000 Genomes Project1

    E-Print Network [OSTI]

    Nielsen, Rasmus

    RASMUS NIELSEN T he goal of the 1000 Genomes Project1 is to find most of the variants in the human's take a step back. A decade ago, the reference copy of the human genome was sequenced3 of the human genome, therefore, a second phase of human genomics emerged

  7. Programme Specification Title of programme: MSc Genomic Medicine

    E-Print Network [OSTI]

    Huang, Xun

    1 Programme Specification Title of programme: MSc Genomic Medicine This specification provides Medicine Interim Exit awards Postgraduate Diploma in Genomic Medicine / Postgraduate Certificate in Genomic Medicine/ Postgraduate Certificate in the Principles of Genomic Medicine. FHEQ level of final award 7 UCAS

  8. Initial sequencing and analysis of the human genome

    E-Print Network [OSTI]

    Boetticher, Gary D.

    Initial sequencing and analysis of the human genome International Human Genome Sequencing. ............................................................................................................................................................................................................................................................................ The human genome holds an extraordinary trove of information about human development, physiology, medicine a draft sequence of the human genome. We also present an initial analysis of the data, describing some

  9. Comparing Bacterial Genomes by Searching their Common Intervals

    E-Print Network [OSTI]

    Fertin, Guillaume

    Comparing Bacterial Genomes by Searching their Common Intervals S´ebastien Angibaud, Damien. Comparing bacterial genomes implies the use of a dedicated measure. It relies on comparing circular genomes genomes that takes into account duplications. Its application on a concrete case, comparing E. coli and V

  10. Georgia Institute of Laboratory Safety

    E-Print Network [OSTI]

    ENVIRONMENTAL HEALTH AND SAFETY POLICY.......................................10 Purpose Institute Council for Environmental Health and Safety (IC.........................................................................................12 Chemical and Environmental Safety Committee (CESC

  11. Fiscal Year 2012 Peer Institution

    E-Print Network [OSTI]

    Fiscal Year 2012 Highlights Peer Institution Comparisons Cost to Students Economic Impact access to the University's audited financial information and openly share how we deploy resources

  12. Continuous Change Institutional Change Principle

    Broader source: Energy.gov [DOE]

    ecause it takes time to establish institutional change, federal agencies need multiyear plans that continuously work to achieve, reinforce, and improve significant and persistent sustainability goals.

  13. Essays in Economics and Institutions

    E-Print Network [OSTI]

    Schihl, Michael Kristjian

    2010-01-01

    to (the New) Institutional Economics . . . . .3.4.2Governance. Journal of Law, Economics, and Organization, 7:Journal of Development Economics, 77(2):341–366, August

  14. Clean Energy Manufacturing Innovation Institute for Composites...

    Office of Environmental Management (EM)

    Clean Energy Manufacturing Innovation Institute for Composites Materials and Structures Clean Energy Manufacturing Innovation Institute for Composites Materials and Structures...

  15. Clean Energy Manufacturing Innovation Institute for Composite...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Clean Energy Manufacturing Innovation Institute for Composite Materials And Structures Webinar Clean Energy Manufacturing Innovation Institute for Composite Materials And...

  16. Southface Energy Institute: Advanced Commercial Buildings Initiative...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Southface Energy Institute: Advanced Commercial Buildings Initiative - 2015 Peer Review Southface Energy Institute: Advanced Commercial Buildings Initiative - 2015 Peer Review...

  17. Integrative Bioengineering Institute

    SciTech Connect (OSTI)

    Eddington, David; Magin,L,Richard; Hetling, John; Cho, Michael

    2009-01-09

    Microfabrication enables many exciting experimental possibilities for medicine and biology that are not attainable through traditional methods. However, in order for microfabricated devices to have an impact they must not only provide a robust solution to a current unmet need, but also be simple enough to seamlessly integrate into standard protocols. Broad dissemination of bioMEMS has been stymied by the common aim of replacing established and well accepted protocols with equally or more complex devices, methods, or materials. The marriage of a complex, difficult to fabricate bioMEMS device with a highly variable biological system is rarely successful. Instead, the design philosophy of my lab aims to leverage a beneficial microscale phenomena (e.g. fast diffusion at the microscale) within a bioMEMS device and adapt to established methods (e.g. multiwell plate cell culture) and demonstrate a new paradigm for the field (adapt instead of replace). In order for the field of bioMEMS to mature beyond novel proof-of-concept demonstrations, researchers must focus on developing systems leveraging these phenomena and integrating into standard labs, which have largely been ignored. Towards this aim, the Integrative Bioengineering Institute has been established.

  18. Navigating Mnoa Institutional Research Website Mnoa Institutional Research Office (MIRO)

    E-Print Network [OSTI]

    ;Surveys #12;FACTS ­ Fast Facts #12;FACTS ­College Navigator #12;Information Sources: MIRO reportsNavigating Mnoa Institutional Research Website Mnoa Institutional Research Office (MIRO) University of information #12;Two Dimensions of Navigation HOME REPORTS RANKINGS SURVEYS FACTS DECISION SUPPORT Fast Facts

  19. Mapping the Human Reference Genome's Missing Sequence by Three-Way Admixture in Latino Genomes

    E-Print Network [OSTI]

    McCarroll, Steve

    ARTICLE Mapping the Human Reference Genome's Missing Sequence by Three-Way Admixture in Latino Genomes Giulio Genovese,1,2,3,* Robert E. Handsaker,2,3 Heng Li,2,3 Eimear E. Kenny,4,5,6,7,8 and Steven A. McCarroll1,2,3,* A principal obstacle to completing maps and analyses of the human genome involves

  20. 1st Genomics-Bioinformatics Day on "Comparative Genomics" April 24th 2003 in the Medawar Building in the

    E-Print Network [OSTI]

    Goldschmidt, Christina

    1st Genomics-Bioinformatics Day on "Comparative Genomics" April 24th 2003 in the Medawar Building. There is a need, however, for researchers interested in genomics and bioinformatics to meet, so Jotun Hein, Richard Mott and Chris Ponting have organised the first Genomics/Bioinformatics day. It is our intention