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Sample records for bssd genomic science

  1. 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...

  2. 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...

  3. Biological Systems Science Division (BSSD) | U.S. DOE Office of Science

    Office of Science (SC) Website

    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-effectWorkingLosThe 26thI D- 6 0GrantsThe LifeAtomic,Benjamin D.Betsythe(SC)

  4. Genome Science and Personalized Cancer Treatment

    ScienceCinema (OSTI)

    Gray, Joe

    2010-01-08

    August 4, 2009 Berkeley Lab lecture: Results from the Human Genome Project are enabling scientists to understand how individual cancers form and progress. This information, when combined with newly developed drugs, can optimize the treatment of individual cancers. Joe Gray, director of Berkeley Labs Life Sciences Division and Associate Laboratory Director for Life and Environmental Sciences, will focus on this approach, its promise, and its current roadblocks ? particularly with regard to breast cancer.

  5. Genome Science and Personalized Cancer Treatment

    SciTech Connect (OSTI)

    Gray, Joe

    2009-08-07

    August 4, 2009 Berkeley Lab lecture: Results from the Human Genome Project are enabling scientists to understand how individual cancers form and progress. This information, when combined with newly developed drugs, can optimize the treatment of individual cancers. Joe Gray, director of Berkeley Labs Life Sciences Division and Associate Laboratory Director for Life and Environmental Sciences, will focus on this approach, its promise, and its current roadblocks — particularly with regard to breast cancer.

  6. Genome Science and Personalized Cancer Treatment

    SciTech Connect (OSTI)

    Gray, Joe

    2009-08-04

    Summer Lecture Series 2009: Results from the Human Genome Project are enabling scientists to understand how individual cancers form and progress. This information, when combined with newly developed drugs, can optimize the treatment of individual cancers. Joe Gray, director of Berkeley Labs Life Sciences Division and Associate Laboratory Director for Life and Environmental Sciences, will focus on this approach, its promise, and its current roadblocks — particularly with regard to breast cancer.

  7. Bacterial phytopathogens and genome science Joa~ o C Setubal1

    E-Print Network [OSTI]

    Setubal, João Carlos

    Bacterial phytopathogens and genome science Joa~ o C Setubal1 , Leandro M Moreira2 and Ana CR da Silva3 There are now fourteen completed genomes of bacterial phytopathogens, all of which have been generated in the past six years. These genomes come from a phylogenetically diverse set of organisms

  8. DUKEInstituteForGenomeSciences&Policy Microbes R Us

    E-Print Network [OSTI]

    Richardson, David

    GenomeLIFE DUKEInstituteForGenomeSciences&Policy Microbes R Us Duke Faculty Explore the Microbiome of microbes. The microbial cells in and on our bodies outnumber human cells ten to one. In a contest Systems (GeMS), a new hub of activity inspired by renewed interest in the roles that microbes play

  9. Public Health Genomics Population Health Sciences 650 Section 023

    E-Print Network [OSTI]

    Sheridan, Jennifer

    Public Health Genomics Population Health Sciences 650 Section 023 Summer 2009, 07/20/09 ­ 07: Public health genomics is a new discipline that uses knowledge gained from genetic and molecular research and improve the health of the population often by enacting health services, programs, and policies

  10. 684 journal of law, medicine & ethics he new science of genomics endeavors to

    E-Print Network [OSTI]

    Church, George M.

    684 journal of law, medicine & ethics T he new science of genomics endeavors to chart the genomes and develop- ing countries, the promises and perils of genomic science appear against a backdrop of global attempting to decide about participating in genomic research or any other biomedical research. Genomic

  11. Standards in Genomic Sciences (2011) 4:257-270 DOI:10.4056/sigs.1664145 The Genomic Standards Consortium

    E-Print Network [OSTI]

    Shapiro, Mike

    2011-01-01

    Standards in Genomic Sciences (2011) 4:257-270 DOI:10.4056/sigs.1664145 The Genomic Standards Consortium A proposal to sequence the genome of a garter snake (Thamnophis sirtalis) Todd A. Castoe1* , Anne, Salt Lake City, UT 7 Genome Sequencing Center, Washington University School of Medicine, St. Louis, MO

  12. Genome Science and Personalized Cancer Treatment (LBNL Summer Lecture Series)

    ScienceCinema (OSTI)

    Gray, Joe

    2011-04-28

    Summer Lecture Series 2009: Results from the Human Genome Project are enabling scientists to understand how individual cancers form and progress. This information, when combined with newly developed drugs, can optimize the treatment of individual cancers. Joe Gray, director of Berkeley Labs Life Sciences Division and Associate Laboratory Director for Life and Environmental Sciences, will focus on this approach, its promise, and its current roadblocks ? particularly with regard to breast cancer.

  13. Genome Science and Personalized Cancer Treatment (LBNL Summer Lecture Series)

    SciTech Connect (OSTI)

    Gray, Joe

    2009-08-04

    Summer Lecture Series 2009: Results from the Human Genome Project are enabling scientists to understand how individual cancers form and progress. This information, when combined with newly developed drugs, can optimize the treatment of individual cancers. Joe Gray, director of Berkeley Labs Life Sciences Division and Associate Laboratory Director for Life and Environmental Sciences, will focus on this approach, its promise, and its current roadblocks — particularly with regard to breast cancer.

  14. Proceedings of the Sudden Oak Death Third Science Symposium Mitochondrial Genomics in the Genus

    E-Print Network [OSTI]

    Proceedings of the Sudden Oak Death Third Science Symposium 243 Mitochondrial Genomics in the Genus The mitochondrial genomes of Phytophthora infestans, P. ramorum and P. sojae have been sequenced and comparative genomics has provided an opportunity to examine the processes involved with genome evolution in the genus

  15. 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

  16. Post-Genomics Nanotechnology Is Gaining Momentum: Nanoproteomics and Applications in Life Sciences

    E-Print Network [OSTI]

    Tan, Weihong

    Post-Genomics Nanotechnology Is Gaining Momentum: Nanoproteomics and Applications in Life Sciences of nanotechnology applications, including nanoporous structures, functionalized nanoparticles, quantum dots

  17. 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.

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

    Office of Scientific and Technical Information (OSTI)

    and the environment, and to promote functional studies on a system level. Combining new sequencing technologies and comparative genomics tools, JGI is now leading the world...

  19. Progress Materials Science Phase-field method and Materials Genome Initiative (MGI)

    E-Print Network [OSTI]

    Chen, Long-Qing

    Progress Materials Science Phase-field method and Materials Genome Initiative (MGI) Long-Qing Chen evolution within a material are considered as the ``holy grail'' of materials science and engineering. Many impor- tant engineering materials are designed by controlling their phase transformations

  20. Large-Scale Sequencing: The Future of Genomic Sciences Colloquium

    SciTech Connect (OSTI)

    Margaret Riley; Merry Buckley

    2009-01-01

    Genetic sequencing and the various molecular techniques it has enabled have revolutionized the field of microbiology. Examining and comparing the genetic sequences borne by microbes - including bacteria, archaea, viruses, and microbial eukaryotes - provides researchers insights into the processes microbes carry out, their pathogenic traits, and new ways to use microorganisms in medicine and manufacturing. Until recently, sequencing entire microbial genomes has been laborious and expensive, and the decision to sequence the genome of an organism was made on a case-by-case basis by individual researchers and funding agencies. Now, thanks to new technologies, the cost and effort of sequencing is within reach for even the smallest facilities, and the ability to sequence the genomes of a significant fraction of microbial life may be possible. The availability of numerous microbial genomes will enable unprecedented insights into microbial evolution, function, and physiology. However, the current ad hoc approach to gathering sequence data has resulted in an unbalanced and highly biased sampling of microbial diversity. A well-coordinated, large-scale effort to target the breadth and depth of microbial diversity would result in the greatest impact. The American Academy of Microbiology convened a colloquium to discuss the scientific benefits of engaging in a large-scale, taxonomically-based sequencing project. A group of individuals with expertise in microbiology, genomics, informatics, ecology, and evolution deliberated on the issues inherent in such an effort and generated a set of specific recommendations for how best to proceed. The vast majority of microbes are presently uncultured and, thus, pose significant challenges to such a taxonomically-based approach to sampling genome diversity. However, we have yet to even scratch the surface of the genomic diversity among cultured microbes. A coordinated sequencing effort of cultured organisms is an appropriate place to begin, since not only are their genomes available, but they are also accompanied by data on environment and physiology that can be used to understand the resulting data. As single cell isolation methods improve, there should be a shift toward incorporating uncultured organisms and communities into this effort. Efforts to sequence cultivated isolates should target characterized isolates from culture collections for which biochemical data are available, as well as other cultures of lasting value from personal collections. The genomes of type strains should be among the first targets for sequencing, but creative culture methods, novel cell isolation, and sorting methods would all be helpful in obtaining organisms we have not yet been able to cultivate for sequencing. The data that should be provided for strains targeted for sequencing will depend on the phylogenetic context of the organism and the amount of information available about its nearest relatives. Annotation is an important part of transforming genome sequences into useful resources, but it represents the most significant bottleneck to the field of comparative genomics right now and must be addressed. Furthermore, there is a need for more consistency in both annotation and achieving annotation data. As new annotation tools become available over time, re-annotation of genomes should be implemented, taking advantage of advancements in annotation techniques in order to capitalize on the genome sequences and increase both the societal and scientific benefit of genomics work. Given the proper resources, the knowledge and ability exist to be able to select model systems, some simple, some less so, and dissect them so that we may understand the processes and interactions at work in them. Colloquium participants suggest a five-pronged, coordinated initiative to exhaustively describe six different microbial ecosystems, designed to describe all the gene diversity, across genomes. In this effort, sequencing should be complemented by other experimental data, particularly transcriptomics and metabolomics data, all of which

  1. 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.

  2. 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.

  3. Incorporating Genomics and Bioinformatics across the Life Sciences Curriculum

    E-Print Network [OSTI]

    Ditty, Jayna L.

    2012-01-01

    inquiry across the curriculum. Thousand Oaks, CA: Corwinacross the Life Sciences Curriculum Jayna L. Ditty 1 ,455. Altman RB (1998) A curriculum for bioinfor- matics: the

  4. Entrepreneurial experiments in science policy: Analyzing the Human Genome Project

    E-Print Network [OSTI]

    Huang, Kenneth G.

    We re-conceptualize the role of science policy makers, envisioning and illustrating their move from being simple investors in scientific projects to entrepreneurs who create the conditions for entrepreneurial experiments ...

  5. Current Genomics, 2004, 5, 299-308 1 1389-2029/04 $45.00+.00 2004 Bentham Science Publishers Ltd.

    E-Print Network [OSTI]

    Martin, Cristofre

    Current Genomics, 2004, 5, 299-308 1 1389-2029/04 $45.00+.00 ©2004 Bentham Science Publishers Ltd. Not Just a Fishing Trip ­ Environmental Genomics Using Zebrafish Louise E. Coverdale, David Lean and C. Cristofre Martin* Center for Advanced Research in Environmental Genomics, Department of Biology, University

  6. Current Genomics, 2002, 3, 000-000 1 1389-2029/02 $35.00+.00 2002 Bentham Science Publishers Ltd.

    E-Print Network [OSTI]

    Wendel, Jonathan F.

    Current Genomics, 2002, 3, 000-000 1 1389-2029/02 $35.00+.00 © 2002 Bentham Science Publishers Ltd. Non-Mendelian Phenomena in Allopolyploid Genome Evolution Bao Liu1 and Jonathan F. Wendel2,* 1. Recent evidence indicates that this genome doubling may be accompanied by a variety of non- Mendelian

  7. Small RNA analysis using the Genome SequencerTM The Genome SequencerTM FLX System from 454 Life SciencesTM and Roche Applied Science is a

    E-Print Network [OSTI]

    Cai, Long

    collection of molecules with several important biological functions. Genome Sequencer technology is ideally Genome Sequencer FLX DNA library preparation protocol. The Genome Sequencer process­specific A and B molecules.The resulting double-stranded library is transferred to the emulsion PCR (emPCRTM) step for clonal

  8. 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.

  9. 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–

  10. 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.

  11. Whitehead Policy Symposium. The Human Genome Project: Science, law, and social change in the 21st century

    SciTech Connect (OSTI)

    Nichols, E.K.

    2000-02-17

    Advances in the biomedical sciences, especially in human genomics, will dramatically influence law, medicine, public health, and many other sectors of our society in the decades ahead. The public already senses the revolutionary nature of genomic knowledge. In the US and Europe, we have seen widespread discussions about genetic discrimination in health insurance; privacy issues raised by the proliferation of DNA data banks; the challenge of interpreting new DNA diagnostic tests; changing definitions of what it means to be healthy; and the science and ethics of cloning animals and human beings. The primary goal of the Whitehead/ASLME Policy Symposium was to provide a bridge between the research community and professionals, who were just beginning to grasp the potential impact of new genetic technologies on their fields. The ''Human Genome Project: Science, Law, and Social Change in the 21st Century'' initially was designed as a forum for 300-500 physicians, lawyers, consumers, ethicists, and scientists to explore the impact of new genetic technologies and prepare for the challenges ahead.

  12. 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

  13. 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

  14. 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...

  15. 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

  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. Genome To Life Report | U.S. DOE Office of Science (SC)

    Office of Science (SC) Website

    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-effectWorkingLosThe 26thIWalterOptimizing(SC)FermiFundingGenome To Life Report

  18. Rapid genome resequencing of an atoxigenic strain of Aspergillus

    Office of Scientific and Technical Information (OSTI)

    de Barcelona, Bellaterra, Catalonia (Spain) 59 BASIC BIOLOGICAL SCIENCES fungal genomics; gene regulatory networks fungal genomics; gene regulatory networks In...

  19. Reference set of regulons in Desulfovibrionales inferred by comparative genomics approach

    E-Print Network [OSTI]

    Kazakov, A.E.

    2011-01-01

    inferred by comparative genomics approach 1 Lawrenceout large-scale comparative genomics analysis of regulatoryEnvironmental Research, Genomics:GTL Foundational Science

  20. Science on Saturday: Using Physics and Chemistry to Understand the Genome |

    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 RoomPreservation ofAlbuquerque| StanfordOffice of Science (SC) SULIPhysics

  1. 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

  2. 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-

  3. 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

  4. 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.

  5. Genome Science/Technologies

    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 (Journal

  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;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

  7. 1 It is often said that genomics science is on a Moore's law, 1 (Professor of Mathematics and Computer

    E-Print Network [OSTI]

    Mishra, Bud

    , NY, USA)growing exponentially in data throughput, number of assem- bled genomes, lowered cost, etc of innovations due to Watt and others, which improved the engines' efficiency over Thomas Newcomen's existing design, rapidly coal became much more cost-effective as a source of energy and the steam engine found

  8. National Laboratory] Basic Biological Sciences(59) Biological...

    Office of Scientific and Technical Information (OSTI)

    Achievements of structural genomics Terwilliger, Thomas C. Los Alamos National Laboratory Basic Biological Sciences(59) Biological Science Biological Science Abstract Not...

  9. Systems Biology | More Science | ORNL

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

    ORNL brings together multidisciplinary expertise and special facilities in genomics, computational biology, plant sciences, microbiology, microbial ecology, biophysics,...

  10. 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.

  11. 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.

  12. 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

  13. Reference-Free Comparative Genomics of 174 Chloroplasts

    E-Print Network [OSTI]

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

  14. Comparative Microbial Genomics group CenterforBiologicalSequenceAnalysisTheTechnicalUniversityofDenmarkDTU

    E-Print Network [OSTI]

    Ussery, David W.

    Comparative Microbial Genomics group Centerfor systematics - is it relevant to modern science? Istanbul, Turkey 8 August, 2008 - or - What can genomics tell us about Vibrio species? Discovering natural groups in Vibrio #12;Comparative Microbial Genomics

  15. 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

  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. 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.

  18. 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

  19. November 2004 / Vol. 54 No. 11 BioScience 991 Atidal wave in the biological sciences, caused by

    E-Print Network [OSTI]

    Liu, Zhongchi

    , caused by the advent of genomic techniques and data, has begun to sweep across the fields of evolutionary of genome biology,or genomics, surged in the late 1980s under the impetus of the Human Genome Project and functional questions. The National Plant Genome Initiative, which brought genomics to the plant sciences

  20. 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...

  1. 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...

  2. INTEGRATED GENOME-BASED STUDIES OF SHEWANELLA ECOPHYSIOLOGY TIEDJE...

    Office of Scientific and Technical Information (OSTI)

    BIOLOGICAL SCIENCES The aim of the work reported is to study Shewanella population genomics, and to understand the evolution, ecophysiology, and speciation of Shewanella. The...

  3. Rapid genome resequencing of an atoxigenic strain of Aspergillus...

    Office of Scientific and Technical Information (OSTI)

    United States Language: English Subject: 59 BASIC BIOLOGICAL SCIENCES fungal genomics; gene regulatory networks Word Cloud More Like This Free Publicly Accessible Full...

  4. Community-wide analysis of microbial genome sequence signatures

    E-Print Network [OSTI]

    2009-01-01

    acidophile important in acid mine drainage. Science 2000,genome signatures in acid mine drainage communities. Thus,chemolithoautotrophic acid mine drainage (AMD) ecosystem in

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

    E-Print Network [OSTI]

    Penn, Kevin Matthew

    2012-01-01

    rplB smpB Comparative genomics Gene gain Gene loss Totalbiology and comparative genomics. BMC Bioinformatics 10(1):Intersection of Evolution and Genomics. Science 300(5626):

  6. The context and content of the human genome project and the American eugenics movement: An analytical, case study approach

    E-Print Network [OSTI]

    Mandel, Sarah M

    1993-01-01

    40 Four: The human genome project and its implications forimplications of the human genome project: where did we come109 Davis, BD. Human Genome Project: is big science bad for

  7. 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.

  8. Science

    E-Print Network [OSTI]

    Department of Mathematics, Statistics, and Computer Science, University of Illinois. at Chicago, Chicago, IL, 60607, USA. 2 Department of Mathematics, Purdue ...

  9. 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

  10. Genomes containing Duplicates are Hard to compare (Extended abstract)

    E-Print Network [OSTI]

    Chauve, Cedric

    1 Genomes containing Duplicates are Hard to compare (Extended abstract) Cedric Chauve LaCIM, CGL, D and Applications, IWBRA 2006, volume 3992 of Lecture Notes in Computer Science, pages 783--790. #12; Genomes)similarity measures between two genomes when they contain duplicated genes. In that case, there are usually two main

  11. Translational genomics of Vegetable Crops Las Vegas, NV

    E-Print Network [OSTI]

    Douches, David S.

    Translational genomics of Vegetable Crops Las Vegas, NV July 21, 2005 David Francis and Allen Van Deynze At the recent ASHS meetings in Las Vegas, a workshop "Translational Genomics of Vegetable Crops interventions" (Minna and Gazdar, 1996). In applied plant science, "translational genomics" implies

  12. Current developments in genomics challenge the established framework of

    E-Print Network [OSTI]

    Church, George M.

    Current developments in genomics challenge the established framework of biomedical ethics because the empirical facts of the genomic science change too fast for the reflections of ethics to keep pace with for pragmatic moral guidance1 . Recent revelations about the human genome, such as the abundance of copy

  13. 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,

  14. 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

  15. Fungal Genomics Program

    E-Print Network [OSTI]

    Grigoriev, Igor

    2012-01-01

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

  16. 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

  17. 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

  18. Biomedical Sciences Orientation Autumn 2014

    E-Print Network [OSTI]

    Doty, Sharon Lafferty

    Biomedical Sciences Orientation Autumn 2014 Diana Louden ­ dknl@uw.edu 206-221-3480 ­ libguides & Humanities, Biological Structure, Biomedical Informatics & Medical Education, Genome Sciences, Immunology databases, electronic journals & books, help guides, news about resources & services, and the Biomedical

  19. Science

    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 of NaturalDukeWakefieldSulfateSciTechtail.Theory ofDidDevelopment Top LDRDUniversitySchedules Print Current Science

  20. Science

    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 RoomPreservation ofAlbuquerque| Stanford SynchrotronVideo-Contest Sign In AboutBiologicalScience

  1. 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

  2. Genomics and Systems Biology

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

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

  3. The Dynamic Nature of Eukaryotic Genomes Laura Wegener Parfrey,* Daniel J. G. Lahr,* and Laura A. Katz*

    E-Print Network [OSTI]

    Katz, Laura

    The Dynamic Nature of Eukaryotic Genomes Laura Wegener Parfrey,* Daniel J. G. Lahr,* and Laura A of Biological Sciences, Smith College, Northampton, MA Analyses of diverse eukaryotes reveal that genomes of examples of genome dynamism is accelerating as genome sequences are completed from diverse eukaryotes

  4. 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.

  5. MycoCosm, an Integrated Fungal Genomics Resource Shabalov, Igor...

    Office of Scientific and Technical Information (OSTI)

    Resource Shabalov, Igor; Grigoriev, Igor 59 BASIC BIOLOGICAL SCIENCES MycoCosm is a web-based interactive fungal genomics resource, which was first released in March 2010, in...

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

    E-Print Network [OSTI]

    Borenstein, Elhanan

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

  7. 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

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

    E-Print Network [OSTI]

    Müller, Hans-Georg

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

  9. specificity of genomics-based protein-function prediction, although whether specific experimental testing of protein

    E-Print Network [OSTI]

    Lässig, Michael

    specificity of genomics-based protein-function prediction, although whether specific experimental interactome. Proc. Natl. Acad. Sci. U. S. A. 98, 4569­4574 9 Dwight, S.S. et al. (2002) Saccharomyces Genome for predicting protein­protein interactions from genomic data. Science 302, 449­453 17 Troyanskaya, O.G. et al

  10. Assembly free comparative genomics of short-read sequence data discovers the needles in the haystack

    E-Print Network [OSTI]

    Assembly free comparative genomics of short-read sequence data discovers the needles of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA Abstract Most comparative genomic analyses an assembly free analysis of SRS data that discovers sequence variants among focal genomes by tabulating

  11. Representing Genomic Knowledge in the UMLS Semantic Network , Carol Friedman, Ph.D.2,1

    E-Print Network [OSTI]

    Yu, Hong

    Representing Genomic Knowledge in the UMLS Semantic Network Hong Yu1 , Carol Friedman, Ph.D.2 2 Department of Computer Science, Queens College CUNY 3 Center for Genomics Research, Columbia University 4 Yeshiva University Genomics research has a significant impact on the understanding and treatment

  12. 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

  13. Science and Management of Pest Insects, Plant Pathogens and Goal: Colorado State University will enhance its focus and depth in undergraduate education, graduate education, research,

    E-Print Network [OSTI]

    , and ecology, bioinformatics, genomics, and population genetics of pests. Undergraduate education will include and applied science regarding pest species (their taxonomy, genomics, population genetics, and ecology

  14. 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

  15. 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:

  16. Genomic Sequence Comparisons, 1987-2003 Final Report

    SciTech Connect (OSTI)

    George M. Church

    2004-07-29

    This project was to develop new DNA sequencing and RNA and protein quantitation methods and related genome annotation tools. The project began in 1987 with the development of multiplex sequencing (published in Science in 1988), and one of the first automated sequencing methods. This lead to the first commercial genome sequence in 1994 and to the establishment of the main commercial participants (GTC then Agencourt) in the public DOE/NIH genome project. In collaboration with GTC we contributed to one of the first complete DOE genome sequences, in 1997, that of Methanobacterium thermoautotropicum, a species of great relevance to energy-rich gas production.

  17. Science and Public Policy

    SciTech Connect (OSTI)

    Handler, Thomas [University of Tennessee

    2012-11-28

    The United States faces many issues that involve science. Issues ranging from climate change to nano-technology, from human genomics to modified food crops. What is the role that science plays in determining what the public policy for these issues should be? How as scientists should we respond to requests for advice?

  18. 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.

  19. 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 ...

  20. 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.

  1. 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

  2. Transformational advances in knowledge and technology come from discovery science. As the nation's largest funder of basic

    E-Print Network [OSTI]

    . Completed in 2003, the Human Genome Project has been succeeded by DOE's Genomic Science program, which years from Earth. An initial map of the human genome was completed in 2003. The Human Genome Project has collaborated with the National Institutes of Health in a 13-year effort to fully map the human genome

  3. Comparative genomics in acid mine drainage biofilm communities reveals metabolic and structural differentiation of co-occurring archaea

    E-Print Network [OSTI]

    2013-01-01

    genomics in acid mine drainage biofilm communities revealsextreme acidophiles from acid mine drainage and industrialacidophile important in acid mine drainage. Science 2000,

  4. DOI: 10.1126/science.1229549 , 1060 (2012);338Science

    E-Print Network [OSTI]

    2012-01-01

    with the National Renewable Energy Laboratory. We acknowledge research support from the BioEnergy Science Center, a DOE Bioenergy Research Center, and the Genomic Science Program (ER65258), both supported by the Office

  5. Biology & Biomedical Sciences ACADEMIC PROGRAM

    E-Print Network [OSTI]

    Gereau, Robert W. IV

    Biology & Biomedical Sciences ACADEMIC PROGRAM GUIDELINES Programs in Cell & Molecular Biology Developmental, Regenerative and Stem Cell Biology Molecular Cell Biology Molecular Genetics & Genomics Molecular Microbiology & Microbial Pathogenesis #12;PAGE 2 GUIDELINES TO THE PROGRAMS IN CELL AND MOLECULAR BIOLOGY

  6. Algorithms for Gene Clustering Analysis on Genomes 

    E-Print Network [OSTI]

    Yi, Gang Man

    2012-07-16

    CLUSTERING ANALYSIS ON GENOMES A Dissertation by GANG MAN YI Submitted to the O ce of Graduate Studies of Texas A&M University in partial ful llment of the requirements for the degree of DOCTOR OF PHILOSOPHY May 2011 Major Subject: Computer Science... ALGORITHMS FOR GENE CLUSTERING ANALYSIS ON GENOMES A Dissertation by GANG MAN YI Submitted to the O ce of Graduate Studies of Texas A&M University in partial ful llment of the requirements for the degree of DOCTOR OF PHILOSOPHY Approved by: Chair...

  7. 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

  8. Insights from twenty years of bacterial genome sequencing

    SciTech Connect (OSTI)

    Land, Miriam L; Hauser, Loren John; Jun, Se Ran; Nookaew, Intawat; Leuze, Michael Rex; Ahn, Tae-Hyuk; Karpinets, Tatiana V; Lund, Ole; Kora, Guruprasad H; Wassenaar, Trudy; Poudel, Suresh; Ussery, David W

    2015-01-01

    Since the first two complete bacterial genome sequences were published in 1995, the science of bacteria has dramatically changed. Using third-generation DNA sequencing, it is possible to completely sequence a bacterial genome in a few hours and identify some types of methylation sites along the genome as well. Sequencing of bacterial genome sequences is now a standard procedure, and the information from tens of thousands of bacterial genomes has had a major impact on our views of the bacterial world. In this review, we explore a series of questions to highlight some insights that comparative genomics has produced. To date, there are genome sequences available from 50 different bacterial phyla and 11 different archaeal phyla. However, the distribution is quite skewed towards a few phyla that contain model organisms. But the breadth is continuing to improve, with projects dedicated to filling in less characterized taxonomic groups. The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas system provides bacteria with immunity against viruses, which outnumber bacteria by tenfold. How fast can we go? Second-generation sequencing has produced a large number of draft genomes (close to 90 % of bacterial genomes in GenBank are currently not complete); third-generation sequencing can potentially produce a finished genome in a few hours, and at the same time provide methlylation sites along the entire chromosome. The diversity of bacterial communities is extensive as is evident from the genome sequences available from 50 different bacterial phyla and 11 different archaeal phyla. Genome sequencing can help in classifying an organism, and in the case where multiple genomes of the same species are available, it is possible to calculate the pan- and core genomes; comparison of more than 2000 Escherichia coli genomes finds an E. coli core genome of about 3100 gene families and a total of about 89,000 different gene families. Why do we care about bacterial genome sequencing? There are many practical applications, such as genome-scale metabolic modeling, biosurveillance, bioforensics, and infectious disease epidemiology. In the near future, high-throughput sequencing of patient metagenomic samples could revolutionize medicine in terms of speed and accuracy of finding pathogens and knowing how to treat them.

  9. November | U.S. DOE Office of Science (SC)

    Office of Science (SC) Website

    with appointments as professor at the University of Chicago, described "Computing and Biology: Toward Predictive Theory in the Life Sciences" as part of the Genomics-Driven...

  10. 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

  11. 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

  12. 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.

  13. 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...

  14. 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...

  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. 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

  17. 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

  18. 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

  19. DOI: 10.1126/science.1205822 , 348 (2011);333Science

    E-Print Network [OSTI]

    Church, George M.

    2011-01-01

    DOI: 10.1126/science.1205822 , 348 (2011);333Science , et al.Farren J. Isaacs Genome-Wide Codon://www.sciencemag.org/cgi/collection/genetics Genetics subject collections:This article appears in the following registered trademark of AAAS. is aScience2011 by the American Association for the Advancement of Science; all rights reserved. The title

  20. 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

  1. 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

  2. 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:...

  3. School of Computing Science, University of Newcastle upon Tyne

    E-Print Network [OSTI]

    Newcastle upon Tyne, University of

    School of Computing Science, University of Newcastle upon Tyne Exploring Microbial Genome Sequences upon Tyne, NE1 7RU, UK. #12;1 Exploring Microbial Genome Sequences to Identify Protein Families Abstract--The analysis of microbial genome sequences can identify protein families that provide potential

  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. NREL Support for a Functional Genomics Approach to Investigate Regulation of Phenolic Glycoside: Cooperative Research and Development Final Report, CRADA number CRD-07-00218

    SciTech Connect (OSTI)

    Davis, M.

    2010-07-01

    NREL and MTU collaborated on a proposal 'A Functional Genomics Approach to Investigate Regulation of Phenolic Glycoside Metabolism in Populus' funded by the National Science Foundation.

  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 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

  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. 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

  9. 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

  10. 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

  11. 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

  12. 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

  13. 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.

  14. Science Park Science Park

    E-Print Network [OSTI]

    Koolen, Marijn

    Science Park Science Park Science Park Science Park Science Park Kruislaan Kruislaan Science Park SURFsara NLeSC Polder Anna Hoeve Telecity Matrix Innovation Center AUC AMOLF ARCNL UvA Faculty of Science Equinix Universum CWI UvA Oerknal Meet & Eat Maslow Spar ACE Venture Lab IXA ILCA NS Amsterdam Science

  15. 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

  16. 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.

  17. Life sciences and environmental sciences

    SciTech Connect (OSTI)

    Not Available

    1992-02-01

    The DOE laboratories play a unique role in bringing multidisciplinary talents -- in biology, physics, chemistry, computer sciences, and engineering -- to bear on major problems in the life and environmental sciences. Specifically, the laboratories utilize these talents to fulfill OHER`s mission of exploring and mitigating the health and environmental effects of energy use, and of developing health and medical applications of nuclear energy-related phenomena. At Lawrence Berkeley Laboratory (LBL) support of this mission is evident across the spectrum of OHER-sponsored research, especially in the broad areas of genomics, structural biology, basic cell and molecular biology, carcinogenesis, energy and environment, applications to biotechnology, and molecular, nuclear and radiation medicine. These research areas are briefly described.

  18. Life sciences and environmental sciences

    SciTech Connect (OSTI)

    Not Available

    1992-02-01

    The DOE laboratories play a unique role in bringing multidisciplinary talents -- in biology, physics, chemistry, computer sciences, and engineering -- to bear on major problems in the life and environmental sciences. Specifically, the laboratories utilize these talents to fulfill OHER's mission of exploring and mitigating the health and environmental effects of energy use, and of developing health and medical applications of nuclear energy-related phenomena. At Lawrence Berkeley Laboratory (LBL) support of this mission is evident across the spectrum of OHER-sponsored research, especially in the broad areas of genomics, structural biology, basic cell and molecular biology, carcinogenesis, energy and environment, applications to biotechnology, and molecular, nuclear and radiation medicine. These research areas are briefly described.

  19. 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

  20. 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

  1. Granularity of genomics data in genome visualisation

    E-Print Network [OSTI]

    Jakubowska, J.; Hunt, E.

    Jakubowska,J. Hunt,E. Chalmers,M.J. DCS Technical Report Series pp 10 Dept of Computing Science, University of Glasgow

  2. 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

  3. 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.

  4. Science Outreach Science Outreach

    E-Print Network [OSTI]

    Kavanagh, Karen L.

    Science Outreach Science Outreach AT SFU'S FACULTY OF SCIENCE OUR PASSION IS SCIENCE EDUCATION At SFU's Faculty of Science our passion is science education #12;coming sooncoming soon The Trottier 2015. The Trottier Observatory will be an anchor for a science plaza located in front of Strand Hall

  5. 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.

  6. Fast Identification of Gene Clusters in Prokaryotic Genomes Karine StOnge (1,2) , Anne Bergeron (1,3) , Cedric Chauve (1,2,3)

    E-Print Network [OSTI]

    Chauve, Cedric

    Fast Identification of Gene Clusters in Prokaryotic Genomes Karine St­Onge (1,2) , Anne Bergeron (1,3) , Cedric Chauve (1,2,3) (1) Comparative genomics laboratory, UQAM (2) LaCIM, UQAM (3) Computer Science Department, UQAM Poster at 3rd RECOMB Workshop on Comparative Genomics, 2005. #12; Fast Identification

  7. 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...

  8. 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.

  9. 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

  10. 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

  11. 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

  12. 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

  13. Franois Pompanon and Aurlie Bonin (eds.), Data Production and Analysis in Population Genomics: Methods and Protocols, Methods in Molecular Biology, vol. 888, DOI 10.1007/978-1-61779-870-2_17, Springer Science+Business Media New York 2012

    E-Print Network [OSTI]

    correlate allelic frequencies and environmental variables such as precipitation, temperature, or sun, temperature, sun radia- tion, etc.) (4, 5). In this case, the geographic coordinates (spatial variables Variables in the Context of Allele Distribution Models: Detecting Signatures of Selection in the Genome

  14. 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)

  15. Genomic Science | U.S. DOE Office of Science (SC)

    Office of Science (SC) Website

    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-effectWorkingLosThe 26thIWalter H. Zinn,ChristopherDOE Office of

  16. Predictive Genomics, Biology, Medicine Learning theory: SLT what is it?

    E-Print Network [OSTI]

    Kon, Mark

    ­ small number of parameters ­ appropriate to small amounts of data Ex. Find mean m and standard deviation to large amounts of data Ex. Neural Network, RBF network, support vector machine Genomics: Current). · Computational demands require the high performance resources of Center for Computational Science at BU

  17. RESEARCH Open Access Decoding the massive genome of loblolly pine

    E-Print Network [OSTI]

    Maryland at College Park, University of

    @ucdavis.edu 1 Department of Plant Sciences, University of California, Davis, CA, USA Full list of author demonstrates a novel approach to sequencing the large and complex genomes of this important group of plants genera [1]), are one of the oldest of the major plant clades, having arisen from ancestral seed plants

  18. 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

  19. 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.

  20. 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

  1. 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 ...

  2. 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 ...

  3. 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

  4. 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

  5. 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

  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. 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

  8. 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.

  9. Genomic Structure in Europeans dating back at least 36,200 years

    E-Print Network [OSTI]

    Seguin-Orlando, Andaine; Korneliussen, Thorfinn S.; Sikora, Martin; Malaspinas, Anna-Sapfo; Manica, Andrea; Moltke, Ida; Albrechtsen, Anders; Ko, Amy; Margaryan, Ashot; Moiseyev, Vyacheslav; Goebel, Ted; Westaway, Michael; Lambert, David; Khartanovich, Valeri; Wall, Jeffrey D.; Nigst, Philip R.; Foley, Robert A.; Lahr, Marta Mirazon; Nielsen, Rasmus; Orlando, Ludovic; Willerslev, Eske

    2014-11-06

    and Genetic Legacy of Neolithic Farmers and Hunter-Gatherers in Europe. Science. 336, 466–469 (2012). 20. P. Skoglund et al., Genomic diversity and admixture differs for Stone-Age Scandinavian foragers and farmers. Science. 344, 747–750 (2014). 21. I...

  10. SCIENCE CHINA Technological Sciences

    E-Print Network [OSTI]

    Liu, Yijun

    turbines, jet engines, nuclear power plants and space crafts, have placed severe demands on highSCIENCE CHINA Technological Sciences © Science China Press and Springer-Verlag Berlin Heidelberg

  11. 10.1101/gr.2227704Access the most recent version at doi: 2004 14: 1014-1024Genome Res.

    E-Print Network [OSTI]

    Schnaufer, Achim

    School of Pathology, University of Oxford, Oxford, OX1 3RE, United Kingdom; 2 School of Biological Sciences, University of Manchester, Manchester, M13 9PT, United Kingdom Most eukaryotic genomes contain, but remain largely absent from genome projects because of difficulties in cloning and sequence assembly

  12. 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

  13. DOI: 10.1126/science.1241459 , 357 (2013);342Science

    E-Print Network [OSTI]

    Church, George M.

    2013-01-01

    DOI: 10.1126/science.1241459 , 357 (2013);342Science et al.Marc J. Lajoie Genomically Recoded.html#related found at: can berelated to this articleA list of selected additional articles on the Science Web sites articles hosted by HighWire Press; see:cited byThis article has been registered trademark of AAAS. is aScience

  14. Findiing Science with Science Page 1 Finding Science with Science

    E-Print Network [OSTI]

    Stock, Kristin

    Findiing Science with Science Page 1 Finding Science with Science: Evaluating the Use Stojanovicd , Femke Reitsmae , Lukasz Korczynskif and Boyan Brodaricg a Centre for Geospatial Science of Earth and Ocean Sciences, Cardiff University, Cardiff, UK; e Department of Geography, University

  15. 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

  16. 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

  17. 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

  18. 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

  19. 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

  20. 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

  1. 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...

  2. The OME Framework for genome-scale systems biology

    SciTech Connect (OSTI)

    Palsson, Bernhard O.; Ebrahim, Ali; Federowicz, Steve

    2014-12-19

    The life sciences are undergoing continuous and accelerating integration with computational and engineering sciences. The biology that many in the field have been trained on may be hardly recognizable in ten to twenty years. One of the major drivers for this transformation is the blistering pace of advancements in DNA sequencing and synthesis. These advances have resulted in unprecedented amounts of new data, information, and knowledge. Many software tools have been developed to deal with aspects of this transformation and each is sorely needed [1-3]. However, few of these tools have been forced to deal with the full complexity of genome-scale models along with high throughput genome- scale data. This particular situation represents a unique challenge, as it is simultaneously necessary to deal with the vast breadth of genome-scale models and the dizzying depth of high-throughput datasets. It has been observed time and again that as the pace of data generation continues to accelerate, the pace of analysis significantly lags behind [4]. It is also evident that, given the plethora of databases and software efforts [5-12], it is still a significant challenge to work with genome-scale metabolic models, let alone next-generation whole cell models [13-15]. We work at the forefront of model creation and systems scale data generation [16-18]. The OME Framework was borne out of a practical need to enable genome-scale modeling and data analysis under a unified framework to drive the next generation of genome-scale biological models. Here we present the OME Framework. It exists as a set of Python classes. However, we want to emphasize the importance of the underlying design as an addition to the discussions on specifications of a digital cell. A great deal of work and valuable progress has been made by a number of communities [13, 19-24] towards interchange formats and implementations designed to achieve similar goals. While many software tools exist for handling genome-scale metabolic models or for genome-scale data analysis, no implementations exist that explicitly handle data and models concurrently. The OME Framework structures data in a connected loop with models and the components those models are composed of. This results in the first full, practical implementation of a framework that can enable genome-scale design-build-test. Over the coming years many more software packages will be developed and tools will necessarily change. However, we hope that the underlying designs shared here can help to inform the design of future software.

  3. 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

  4. 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

  5. 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,

  6. Human Genome: DOE Origins

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

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

  7. 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,...

  8. 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...

  9. 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

  10. Earth Sciences Environmental Earth Sciences,

    E-Print Network [OSTI]

    Brierley, Andrew

    86 Earth Sciences­ Environmental Earth Sciences, Geology Degree options MGeol (Single Honours Degrees) Earth Sciences BSc (Single Honours Degrees) Environmental Earth Sciences Geology BSc (Joint. * The Geology and Environmental Earth Sciences degrees are accredited by the Geological Society of London

  11. Earth Sciences Environmental Earth Sciences,

    E-Print Network [OSTI]

    Brierley, Andrew

    94 Earth Sciences­ Environmental Earth Sciences, Geology Degree options MGeol (Single Honours Degrees) Earth Sciences BSc (Single Honours Degrees) Environmental Earth Sciences Geology BSc (Joint placement. * The Geology and Environmental Earth Sciences degrees are accredited by the Geological Society

  12. SCIENCE CHINA Technological Sciences

    E-Print Network [OSTI]

    Ahmad, Sajjad

    SCIENCE CHINA Technological Sciences © Science China Press and Springer-Verlag Berlin Heidelberg HU HongChang, TIAN FuQiang* & HU HePing Department of Hydraulic Engineering, State Key Laboratory as a key soil physical parameter and has been widely used to predict soil hydraulic and other related

  13. 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.

  14. Data mining and the human genome

    SciTech Connect (OSTI)

    Abarbanel, Henry [The MITRE Corporation, McLean, VA (US). JASON Program Office; Callan, Curtis [The MITRE Corporation, McLean, VA (US). JASON Program Office; Dally, William [The MITRE Corporation, McLean, VA (US). JASON Program Office; Dyson, Freeman [The MITRE Corporation, McLean, VA (US). JASON Program Office; Hwa, Terence [The MITRE Corporation, McLean, VA (US). JASON Program Office; Koonin, Steven [The MITRE Corporation, McLean, VA (US). JASON Program Office; Levine, Herbert [The MITRE Corporation, McLean, VA (US). JASON Program Office; Rothaus, Oscar [The MITRE Corporation, McLean, VA (US). JASON Program Office; Schwitters, Roy [The MITRE Corporation, McLean, VA (US). JASON Program Office; Stubbs, Christopher [The MITRE Corporation, McLean, VA (US). JASON Program Office; Weinberger, Peter [The MITRE Corporation, McLean, VA (US). JASON Program Office

    2000-01-07

    As genomics research moves from an era of data acquisition to one of both acquisition and interpretation, new methods are required for organizing and prioritizing the data. These methods would allow an initial level of data analysis to be carried out before committing resources to a particular genetic locus. This JASON study sought to delineate the main problems that must be faced in bioinformatics and to identify information technologies that can help to overcome those problems. While the current influx of data greatly exceeds what biologists have experienced in the past, other scientific disciplines and the commercial sector have been handling much larger datasets for many years. Powerful datamining techniques have been developed in other fields that, with appropriate modification, could be applied to the biological sciences.

  15. 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.

  16. 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.

  17. 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

  18. 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

  19. 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

  20. 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

  1. 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

  2. SHORT REVIEW Ecological genomics: understanding gene and

    E-Print Network [OSTI]

    Herman, Mike

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

  3. 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

  4. 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

  5. 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

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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

  11. 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

  12. 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

  13. 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

  14. 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.

  15. 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.

  16. Improving primary science great science

    E-Print Network [OSTI]

    Rambaut, Andrew

    Improving primary science Developing great science subject leadershipGreat ideas for primary science leaders from schools that value science. #12;2 | Primary science Where science has a good profile, investigative science with access to high-quality expertise, children are likely to enjoy learning the subject

  17. 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 ...

  18. The recent times have seen a surge in computational modeling of materials and processes. New research initiatives like the Materials Genome Initiative (MGI)

    E-Print Network [OSTI]

    Ghosh, Somnath

    . New research initiatives like the Materials Genome Initiative (MGI) and the Integrated Computational Materials Science & Engineering (ICMSE) are creating unprecedented opportunities for unraveling new1 PREFACE The recent times have seen a surge in computational modeling of materials and processes

  19. Science and Science Fiction

    ScienceCinema (OSTI)

    Scherrer, Robert [Vanderbilt University, Nashville, Tennessee, United States

    2009-09-01

    I will explore the similarities and differences between the process of writing science fiction and the process of 'producing' science, specifically theoretical physics. What are the ground rules for introducing unproven new ideas in science fiction, and how do they differ from the corresponding rules in physics? How predictive is science fiction? (For that matter, how predictive is theoretical physics?) I will also contrast the way in which information is presented in science fiction, as opposed to its presentation in scientific papers, and I will examine the relative importance of ideas (as opposed to the importance of the way in which these ideas are presented). Finally, I will discuss whether a background as a research scientist provides any advantage in writing science fiction.

  20. 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

  1. 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):

  2. Mapping our genes: The genome projects: How big, how fast

    SciTech Connect (OSTI)

    none,

    1988-04-01

    For the past 2 years, scientific and technical journals in biology and medicine have extensively covered a debate about whether and how to determine the function and order of human genes on human chromosomes and when to determine the sequence of molecular building blocks that comprise DNA in those chromosomes. In 1987, these issues rose to become part of the public agenda. The debate involves science, technology, and politics. Congress is responsible for /open quotes/writing the rules/close quotes/ of what various federal agencies do and for funding their work. This report surveys the points made so far in the debate, focusing on those that most directly influence the policy options facing the US Congress. Congressional interest focused on how to assess the rationales for conducting human genome projects, how to fund human genome projects (at what level and through which mechanisms), how to coordinate the scientific and technical programs of the several federal agencies and private interests already supporting various genome projects, and how to strike a balance regarding the impact of genome projects on international scientific cooperation and international economic competition in biotechnology. OTA prepared this report with the assistance of several hundred experts throughout the world. 342 refs., 26 figs., 11 tabs.

  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. 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-

  6. 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

  7. 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

  8. 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-

  9. 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

  10. 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

  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. Science Mathematics Engineering

    E-Print Network [OSTI]

    Hamlet, Richard

    Science Mathematics Engineering . ­ p.1 #12;Science Mathematics Engineering Science, Computer `Science', . ­ p.1 #12;Science Mathematics Engineering Science, Computer `Science', Mathematics, . ­ p.1 #12;Science Mathematics Engineering Science, Computer `Science', Mathematics, and Software Development

  14. 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

  15. 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.

  16. 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)

  17. Wine Science Wine Sciencee Science

    E-Print Network [OSTI]

    Wine Science Wine Sciencee Science Thomas Henick-Kling Professor of Enology Director of Viticulture & Enology Program #12;Wine Science Wine Science Growth of Washington Wine Industry #12;Wine Science Wine Science Wine Grapes utilized 2007 2008 2009 2010 WA 127,000 145,000 156,000 160,000 NY 24,000 26,000 30

  18. Faculty of Science General Science

    E-Print Network [OSTI]

    Faculty of Science General Science The General Science program gives you maximum flexibility to explore the sciences, plus the core requirements you need for on-going, specialized studies. www.uwindsor.ca/science Rigorous, Enriching Programs The BSc General Science program is a great way to explore your many interests

  19. 1 Biomedical Sciences BIOMEDICAL SCIENCES

    E-Print Network [OSTI]

    Vertes, Akos

    1 Biomedical Sciences BIOMEDICAL SCIENCES The interdisciplinary doctoral programs in the biomedical sciences are organized within the Institute for Biomedical Sciences. The first full year of study toward are admitted directly into the Institute for Biomedical Sciences through Columbian College of Arts and Sciences

  20. Biomarker discovery via dependency analysis of multi-view functional genomics data

    E-Print Network [OSTI]

    Kaski, Samuel

    School of Science, Finland University of Helsinki, Finland ali.faisal@aalto.fi riku University of Helsinki Genome-scale Biology Research Program Finland University of Helsinki, Finland leo University and University of Helsinki, Finland samuel.kaski@hiit.fi Abstract Cancers are complex diseases

  1. 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

  2. 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.

  3. 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.

  4. ; 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

  5. Graduate School of Arts and Sciences

    E-Print Network [OSTI]

    #12;#12;Procession Brass Ensemble Welcome Thomas Pollard Sterling Professor of Molecular, Cellular for exceptional achievement in research is awarded to a graduate student within the Council of Engineering. nicole mcneer Engineering and Applied Science "Nanoparticles for Site-Specific Genome Editing" Nicole's work

  6. 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.

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

    E-Print Network [OSTI]

    Penn, Kevin; Jensen, Paul R

    2012-01-01

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

  8. The 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

  9. 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

  10. 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...

  11. 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

  12. 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.

  13. 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), ...

  14. 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

  15. 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

  16. 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

  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. Computer Science Computer Science?

    E-Print Network [OSTI]

    Cafarella, Michael J.

    -M Programming, U-M Solar Car, Hybrid Racing, and the Mars Rover Team. Other groups that advance societal good. Michigan Hackers: Experimenting with technology gEECS: Girls in electrical engineering and computer science

  2. Is sustainability science really a science?

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

    Is sustainability science really a science? Is sustainability science really a science? The team's work shows that although sustainability science has been growing explosively...

  3. Materials Science & Engineering | More Science | ORNL

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

    More Science Home | Science & Discovery | More Science | Materials Science and Engineering SHARE Materials Science and Engineering ORNL's core capability in applied materials...

  4. 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

  5. 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

  6. 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.

  7. 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

  8. 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

  9. 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

  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. 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

  12. 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

  13. 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

  14. 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

  15. 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

  16. 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

  17. 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

  18. 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

  19. 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

  20. 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

  1. 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

  2. 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

  3. 1 Political Science POLITICAL SCIENCE

    E-Print Network [OSTI]

    Vertes, Akos

    1 Political Science POLITICAL SCIENCE With Capitol Hill nearby and the White House just blocks away, GW is the ideal place to study political science. Students in the program benefit from rigorous study and behavioral sciences discipline in the Columbian College of Arts and Sciences, the program examines politics

  4. Neal Lane: Confessions of a President's Science Advisor

    ScienceCinema (OSTI)

    Neal Lane

    2010-09-01

    Former science advisor to president Bill Clinton Neal Lane briefly reviews the history of the job of Science Advisor to the President and give some examples of issues he had to deal with when he was in that position, including climate change, stem cell research, the human genome, nanotechnology and research funding. He will also give his opinions about the present and future state of science in the U.S.

  5. 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

  6. Computer Science

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

    Cite Seer Department of Energy provided open access science research citations in chemistry, physics, materials, engineering, and computer science IEEE Xplore Full text...

  7. Statistical Sciences

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

    LeeAnn Martinez (505) 667-3308 Email Find Expertise header Search our employee skills database Statistical Sciences Statistical Sciences provides statistical reasoning and...

  8. 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.

  9. 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.

  10. 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.

  11. Nuclear Sciences | More Science | ORNL

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

    Nuclear Sciences SHARE Nuclear Sciences In World War II's Manhattan Project, ORNL helped usher in the nuclear age. Today, laboratory scientists are leaders in using nuclear...

  12. Nuclear Sciences | More Science | ORNL

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

    Sciences SHARE Nuclear Sciences In World War II's Manhattan Project, ORNL helped usher in the nuclear age. Today, laboratory scientists are leaders in using nuclear technologies...

  13. Nuclear Science | More Science | ORNL

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

    Science SHARE Nuclear Science In World War II's Manhattan Project, ORNL helped usher in the nuclear age. Today, laboratory scientists are leaders in using nuclear technologies and...

  14. SCIENCE CHINA Technological Sciences

    E-Print Network [OSTI]

    Wang, Zhong L.

    University, Lanzhou 730000, China; 3 School of Material Science and Engineering, Georgia Institute on the piezoelectric semiconductor materials, such as ZnO, ZnS, CdS and GaN. With the usage of these piezoelectric.37 eV and large free-exciton binding energy of 60 meV at room temperature. Furthermore, splendid one

  15. From Human Genome to Materials "Genome" | U.S. DOE Office of Science

    Office of Science (SC) Website

    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-effectWorkingLosThe 26thIWalterOptimizing(SC)Fermi NationalFermiFlorida(SC)

  16. 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.

  17. 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.

  18. Faculty of Science Computer Science

    E-Print Network [OSTI]

    Faculty of Science Computer Science Computer software engineering, network and system analysis.uwindsor.ca/computerscience The University of Windsor offers a variety of computer science programs to prepare students for a career in the technology industry or in research and academia. A computer science degree provides an in-depth understanding

  19. Earth Sciences Environmental Earth Sciences,

    E-Print Network [OSTI]

    Brierley, Andrew

    84 Earth Sciences­ Environmental Earth Sciences, Geology MGeol (Single Honours Degrees) Earth Sciences BSc (Single Honours Degrees) Environmental Earth Sciences Geology BSc (Joint Honours Degrees) and among the most research-intensive in Europe. Features * The Department of Earth and Environmental

  20. Faculty of Science Computer Science

    E-Print Network [OSTI]

    Faculty of Science Computer Science Software engineering, network and system analysis continue a variety of computer science programs to prepare students for a career in the technology industry or in research and academia. A computer science degree provides an in-depth understanding of the fundamentals

  1. 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.

  2. 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

  3. 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

  4. 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

  5. Science Education Programs | Neutron Science | ORNL

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

    Scattering Tutorials Kids' Corner NScD Careers Supporting Organizations Neutron Science Home | Science & Discovery | Neutron Science | Science and Education SHARE Inspiring...

  6. Biology | More Science | ORNL

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

    Atmospheric Sciences Materials Science and Engineering Mathematics Physics Environment Safety and Health More Science Home | Science & Discovery | More Science | Biology SHARE...

  7. NERSC Science Gateways

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

    Users Science Gateways Science Gateways About Science Gateways A science gateway is a web based interface to access HPC computers and storage systems. Gateways allow science...

  8. 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

  9. 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

  10. 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.

  11. 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

  12. 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

  13. 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

  14. 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

  15. 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

  16. 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...

  17. 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

  18. 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

  19. BER Science Network Requirements

    E-Print Network [OSTI]

    Dart, Eli

    2011-01-01

    base • Genome annotation • Laboratory information management system • DNA sequencing • Sequence data

  20. 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

  1. 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 ...

  2. 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

  3. 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

  4. 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.

  5. 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

  6. 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-

  7. 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

  8. 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

  9. 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

  10. 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

  11. 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....

  12. 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"

  13. 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

  14. Big Science

    ScienceCinema (OSTI)

    Dr. Thomas Zacharia

    2010-01-08

    Big science seeks big solutions for the most urgent problems of our times. Video courtesy Cray, Inc.

  15. 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

  16. 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).

  17. 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).

  18. 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...

  19. 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...

  20. 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).

  1. 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...

  2. Information Science, Computing, Applied Math

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

    Information Science, Computing, Applied Math science-innovationassetsimagesicon-science.jpg Information Science, Computing, Applied Math National security depends on science...

  3. 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.

  4. 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.

  5. 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

  6. 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

  7. 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).

  8. 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

  9. STOKED ABOUT SCIENCE? Science Summer

    E-Print Network [OSTI]

    Machel, Hans

    ) · Sunscreen & Bug Spray · www.science.ualberta.ca/summercamps Proper footwear (no flip flops) #12;Half Day

  10. The Science of Science Dr. Katy Brner

    E-Print Network [OSTI]

    Menczer, Filippo

    1 The Science of Science Dr. Katy Börner Cyberinfrastructure for Network Science Center, Director Information Visualization Laboratory, Director School of Library and Information Science Indiana University February 20th, 2008 Computational Scientometrics: Studying Science by Scientific Means Börner, Katy, Chen

  11. 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).

  12. 1 Geological Sciences GEOLOGICAL SCIENCES

    E-Print Network [OSTI]

    Vertes, Akos

    1 Geological Sciences GEOLOGICAL SCIENCES Geological sciences' faculty members are engaged in research on the geology and paleontology of the Appalachian and Rocky mountains, Asia and elsewhere. They collaborate with scientists from the U.S. Geological Survey and other international organizations. Research

  13. 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,

  14. 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

  15. 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.

  16. 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,

  17. 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/

  18. 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.

  19. 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.

  20. [Faculty of Science Information and Computing Sciences

    E-Print Network [OSTI]

    Löh, Andres

    [Faculty of Science Information and Computing Sciences] Terminating combinator parsers in Agda and Computing Sciences Utrecht University June 12, 2008 #12;[Faculty of Science Information and Computing Information and Computing Sciences] 3 Totality #12;[Faculty of Science Information and Computing Sciences] 4

  1. Academy of Integrated Science College of Science

    E-Print Network [OSTI]

    Zallen, Richard

    FALL 2015 Academy of Integrated Science College of Science Virginia Tech Integrated Science SCIENCE CURRICULUM COMPILED BY NORA SULLIVAN PROGRAM ACADEMIC ADVISOR ACADEMY OF INTEGRATED SCIENCE COLLEGE OF SCIENCE VIRGINIA TECH NORA84@VT.EDU 540-231-2442 WWW.SCIENCE.VT.EDU/AIS/ISC #12

  2. Nuclear Science | ORNL

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

    and Reports News and Awards Supporting Organizations Home | Science & Discovery | Nuclear Science Nuclear Science | Nuclear Science SHARE In World War II's Manhattan Project,...

  3. Information Science

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

    Information Science and Technology (ASIS&T) American Society for Indexing (ASI) Digital Library Federation (DLF) National Archives and Records Administration (NARA) Special...

  4. 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

  5. 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

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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

  11. 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

  12. 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

  13. 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

  14. |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

  15. 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

  16. 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

  17. 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

  18. 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

  19. What Makes Science, Science? Research, Shared Effort ... & A...

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

    Makes Science, Science? Research, Shared Effort ... & A New Office of Science Website What Makes Science, Science? Research, Shared Effort ... & A New Office of Science Website...

  20. NREL: Energy Sciences - Chemical and Materials Science

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

    in the U.S. Department of Energy (DOE) National Photovoltaic Program and DOE Basic Energy Sciences Program. Materials Science. The Materials Science Group's research...

  1. 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

  2. 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

  3. Genome MedicineGenome Medicine This Provisional PDF corresponds to the article as it appeared upon acceptance. Fully formatted

    E-Print Network [OSTI]

    ) is a key tool in genomics, in particular to study inherited and acquired human genetic disorders [1]. Multiple projects now aim at mapping the human genetic variation on a large scale, such as the 1,000 Genomes Project [2], the UK 100 k Genome Project [3], or the Genome of the Netherlands [4]. Meanwhile

  4. 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.

  5. Facilities and Equipment for Genomics/Comparative Functional Genomics at New York University

    SciTech Connect (OSTI)

    Lennie, Peter

    2006-06-29

    This award was for partial support for the renovation of space to house research laboratories and moveable scientific equipment for genomics/functional geonomics at New York University.

  6. Life sciences

    SciTech Connect (OSTI)

    Day, L. (ed.)

    1991-04-01

    This document is the 1989--1990 Annual Report for the Life Sciences Divisions of the University of California/Lawrence Berkeley Laboratory. Specific progress reports are included for the Cell and Molecular Biology Division, the Research Medicine and Radiation Biophysics Division (including the Advanced Light Source Life Sciences Center), and the Chemical Biodynamics Division. 450 refs., 46 figs. (MHB)

  7. Comparative genomics and bioenergetics Jose Castresana *

    E-Print Network [OSTI]

    Castresana, Jose

    Review Comparative genomics and bioenergetics Jose Castresana * European Molecular Biology conclusions about the phylogenetic distribution and evolution of bioenergetic pathways to be drawn conservation used by prokaryotes. In addition, a thorough phylogenetic analysis of other bioenergetic protein

  8. Family Law and the Genomic Revolution

    E-Print Network [OSTI]

    Torrance, Andrew W.

    2010-01-01

    , personalized genomics, and gene therapy, coupled with the flux in the law of gene patents (and patents on related inventions), will ensure the substantial transformation of the legal milieu in which parents make reproductive choices. Family law...

  9. Privacy in the Genomic Era Muhammad Naveed*

    E-Print Network [OSTI]

    International Association for Cryptologic Research (IACR)

    with the announcement twelve years ago that the Human Genome Project (HGP) had completed its goals [Guttmacher at the advent of the HGP. In parallel with this trend there has been significant progress on understanding

  10. The Genome Sequencing Center at NCGR

    SciTech Connect (OSTI)

    Schilkey, Faye [National Center for Genome Resources

    2010-06-02

    Faye Schilkey from the National Center for Genome Resources discusses NCGR's research, sequencing and analysis experience on June 2, 2010 at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM

  11. Justice and the Human Genome Project

    SciTech Connect (OSTI)

    Murphy, T.F.; Lappe, M.

    1992-12-31

    Most of the essays gathered in this volume were first presented at a conference, Justice and the Human Genome, in Chicago in early November, 1991. The goal of the, conference was to consider questions of justice as they are and will be raised by the Human Genome Project. To achieve its goal of identifying and elucidating the challenges of justice inherent in genomic research and its social applications the conference drew together in one forum members from academia, medicine, and industry with interests divergent as rate-setting for insurance, the care of newborns, and the history of ethics. The essays in this volume address a number of theoretical and practical concerns relative to the meaning of genomic research.

  12. Justice and the Human Genome Project

    SciTech Connect (OSTI)

    Murphy, T.F.; Lappe, M.

    1992-01-01

    Most of the essays gathered in this volume were first presented at a conference, Justice and the Human Genome, in Chicago in early November, 1991. The goal of the, conference was to consider questions of justice as they are and will be raised by the Human Genome Project. To achieve its goal of identifying and elucidating the challenges of justice inherent in genomic research and its social applications the conference drew together in one forum members from academia, medicine, and industry with interests divergent as rate-setting for insurance, the care of newborns, and the history of ethics. The essays in this volume address a number of theoretical and practical concerns relative to the meaning of genomic research.

  13. Genomic analysis of the horse Y chromosome 

    E-Print Network [OSTI]

    Santani, Avni Bhawan

    2005-02-17

    Stallion fertility is of significant economic importance in the multibillion dollar equine industry. Presently, the underlying genetic causes of infertility in stallions are unknown. Analysis of the human genome has shown that in more than 25...

  14. Computational regulatory genomics : motifs, networks, and dynamics

    E-Print Network [OSTI]

    Kheradpour, Pouya

    2012-01-01

    Gene regulation, the process responsible for taking a static genome and producing the diversity and complexity of life, is largely mediated through the sequence specific binding of regulators. The short, degenerate nature ...

  15. Genomic definition of species. Revision 1

    SciTech Connect (OSTI)

    Crkvenjakov, R.; Dramanac, R.

    1992-06-01

    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. The definition of species based on chromosomes, genes, or genome common to its member organisms has been implied or mentioned in passing numerous times. Some population biologists think that members of species have similar ``homeostatic genotypes,`` which are to a degree resistant to mutation or environmental change in the production of a basic phenotype.

  16. lincRNAs: Genomics, Evolution, and Mechanisms

    E-Print Network [OSTI]

    Ulitsky, Igor

    Long intervening noncoding RNAs (lincRNAs) are transcribed from thousands of loci in mammalian genomes and might play widespread roles in gene regulation and other cellular processes. This Review outlines the emerging ...

  17. Webinar December 2: Materials Genome Initiative

    Broader source: Energy.gov [DOE]

    The Energy Department will present a live webinar entitled "Materials Genome Initiative" on Tuesday, December 2, from 12:00 to 1:00 p.m. Eastern Standard Time.

  18. Statistical Methods for Integrating Genomics Data 

    E-Print Network [OSTI]

    McGuffey, Elizabeth Jennings

    2015-04-16

    membership information and utilizes hierarchical shrinkage to simultaneously select important genes and assign pathway scores. The integration of multiple genomic platforms again allows us to determine which platform is regulating each important gene...

  19. Genomic analysis of control of cell type

    E-Print Network [OSTI]

    Frampton, Garrett M

    2011-01-01

    In mammalian development, a single fertilized egg grows into a complex organism, comprised of organs and tissues made up of hundreds of different specialized cell types. All of these cells contain the same genome, but ...

  20. Prokaryotic Genomes from Microbes Online Database

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

    Alm, Eric J.; Huang, Katherine H.; Price, Morgan N.; Koche, Richard P.; Keller, Keith; Dubchak, Inna L.; Arkin, Adam P.

    To describe the potential functions of genes, MicrobesOnline includes protein family analyses (from InterPro and COG), metabolic maps (from KEGG), links to research papers (from UniProt and PubMed), and operon predictions for every genome. To examine each gene's evolutionary history, MicrobesOnline includes precomputed phylogenetic trees for all the gene families. It displays gene trees with genomic context or it compares the gene tree to the species tree. The tools provided with MicrobesOnline allow users to: compute customized motifs, sequence alignments, and phylogenetic trees change expression patterns in metabolic maps annotate genes in various ways The database contains more than 430 genomes. A browse tree tool and a genome browser are available, along with specialized search capabilities. (Specialized Interface)

  1. Next-generation information systems for genomics 

    E-Print Network [OSTI]

    Mungall, Christopher

    2011-06-27

    The advent of next-generation sequencing technologies is transforming biology by enabling individual researchers to sequence the genomes of individual organisms or cells on a massive scale. In order to realize the ...

  2. Somatic retrotransposition in the cancer genome

    E-Print Network [OSTI]

    Helman, Elena

    2014-01-01

    Cancer is a complex disease of the genome exhibiting myriad somatic mutations, from single nucleotide changes to various chromosomal rearrangements. The technological advances of next-generation sequencing enable high-throughput ...

  3. Bachelor of Science & Bachelor of Science (Technology)

    E-Print Network [OSTI]

    Waikato, University of

    Bachelor of Science & Bachelor of Science (Technology) SpecialiSationS Environmental Microbiology environment. This specialisation can be attached to the Environmental Sciences major. Environmental Modelling Sciences major. Land and Freshwater Environments This specialisation is for students interested

  4. Science Learning+: Phase 1 projects Science Learning+

    E-Print Network [OSTI]

    Rambaut, Andrew

    Science Learning+: Phase 1 projects Science Learning+ Phase 1 projects 2 December 2014 #12..............................................................................................................4 Youth access and equity in informal science learning: developing a research and practice agenda..................................................................................................5 Enhancing informal learning through citizen science..............................................6

  5. 2632 WWW.CROPS.ORG CROP SCIENCE, VOL. 50, NOVEMBERDECEMBER 2010 Seashore paspalum is a warm-season turfgrass that is adapted

    E-Print Network [OSTI]

    Parrott, Wayne

    , Univ. of Georgia, Griffin Campus, 1109 Experiment St., Griffin, GA 30223. This research was supported Genetics and Genomics and Dep. of Crop and Soil Sciences, Univ. of Georgia, 111 Riverbend Rd., Athens, GA

  6. Genomes to Life Project Quartely Report October 2004.

    SciTech Connect (OSTI)

    Heffelfinger, Grant S.; Martino, Anthony; Rintoul, Mark Daniel; Geist, Al; Gorin, Andrey; Xu, Ying; Palenik, Brian

    2005-02-01

    This SAND report provides the technical progress through October 2004 of the Sandia-led project, %22Carbon Sequestration in Synechococcus Sp.: From Molecular Machines to Hierarchical Modeling,%22 funded by the DOE Office of Science Genomes to Life Program. Understanding, predicting, and perhaps manipulating carbon fixation in the oceans has long been a major focus of biological oceanography and has more recently been of interest to a broader audience of scientists and policy makers. It is clear that the oceanic sinks and sources of CO2 are important terms in the global environmental response to anthropogenic atmospheric inputs of CO2 and that oceanic microorganisms play a key role in this response. However, the relationship between this global phenomenon and the biochemical mechanisms of carbon fixation in these microorganisms is poorly understood. In this project, we will investigate the carbon sequestration behavior of Synechococcus Sp., an abundant marine cyanobacteria known to be important to environmental responses to carbon dioxide levels, through experimental and computational methods. This project is a combined experimental and computational effort with emphasis on developing and applying new computational tools and methods. Our experimental effort will provide the biology and data to drive the computational efforts and include significant investment in developing new experimental methods for uncovering protein partners, characterizing protein complexes, identifying new binding domains. We will also develop and apply new data measurement and statistical methods for analyzing microarray experiments. Computational tools will be essential to our efforts to discover and characterize the function of the molecular machines of Synechococcus. To this end, molecular simulation methods will be coupled with knowledge discovery from diverse biological data sets for high-throughput discovery and characterization of protein-protein complexes. In addition, we will develop a set of novel capabilities for inference of regulatory pathways in microbial genomes across multiple sources of information through the integration of computational and experimental technologies. These capabilities will be applied to Synechococcus regulatory pathways to characterize their interaction map and identify component proteins in these - 4 - pathways. We will also investigate methods for combining experimental and computational results with visualization and natural language tools to accelerate discovery of regulatory pathways. The ultimate goal of this effort is develop and apply new experimental and computational methods needed to generate a new level of understanding of how the Synechococcus genome affects carbon fixation at the global scale. Anticipated experimental and computational methods will provide ever-increasing insight about the individual elements and steps in the carbon fixation process, however relating an organism's genome to its cellular response in the presence of varying environments will require systems biology approaches. Thus a primary goal for this effort is to integrate the genomic data generated from experiments and lower level simulations with data from the existing body of literature into a whole cell model. We plan to accomplish this by developing and applying a set of tools for capturing the carbon fixation behavior of complex of Synechococcus at different levels of resolution. Finally, the explosion of data being produced by high-throughput experiments requires data analysis and models which are more computationally complex, more heterogeneous, and require coupling to ever increasing amounts of experimentally obtained data in varying formats. These challenges are unprecedented in high performance scientific computing and necessitate the development of a companion computational infrastructure to support this effort. More information about this project, including a copy of the original proposal, can be found at www.genomes-to-life.org Acknowledgment We want to gratefully acknowledge the contributions of the GTL Project Te

  7. Security Science & Technology | Nuclear Science | ORNL

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

    Security Treaty Verification Nuclear Systems Modeling, Simulation & Validation Nuclear Systems Technology Reactor Technology Nuclear Science Home | Science & Discovery |...

  8. Earth and Atmospheric Sciences | More Science | ORNL

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

    Earth and Atmospheric Sciences Nuclear Forensics Climate & Environment Sensors and Measurements Chemical & Engineering Materials Computational Earth Science Systems Modeling...

  9. Genomics-based breeding in forest trees: are we there yet?

    E-Print Network [OSTI]

    Neale, David

    2011-01-01

    PRESENTATION Open Access Genomics-based breeding in forestEfforts to realize genomics-based breeding in conifer treeUSDA. The Conifer Translational Genomics Network Coordinated

  10. Protein interaction network topology uncovers melanogenesis regulatory network components within functional genomics datasets

    E-Print Network [OSTI]

    Ho, Hsiang; Milenkovic, Tijana; Memisevic, Vesna; Aruri, Jayavani; Przulj, Natasa; Ganesan, Anand K

    2010-01-01

    components within functional genomics datasets BMC SystemssiRNA-based functional genomics of pigmentation identifiesrelated functional genomics data. J R Soc Interface Motulsky

  11. 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,

  12. Applications of the Pipeline Environment for Visual Informatics and Genomics Computations

    E-Print Network [OSTI]

    2011-01-01

    for visual informatics and genomics computations. BMCfor visual informatics and genomics computations Ivo D DinovContemporary informatics and genomics research require

  13. MicrobesOnline: an integrated portal for comparative and functional genomics

    E-Print Network [OSTI]

    Dehal, Paramvir

    2013-01-01

    for comparative and functional genomics Paramvir S. DehalUS Department of Energy Genomics: GTL program (grant DE-approach to comparative genomics, including a tree-based

  14. Evolutionary genomics of divergence and adaptation within the model fungi Neurospora crassa and Neurospora tetrasperma

    E-Print Network [OSTI]

    Ellison, Christopher

    2011-01-01

    Taylor JW. 2011. Population genomics and local adaptation inpromise of population genomics: from genotyping to genomeera. Annual Review of Genomics and Human Genetics 11:265-89.

  15. A Tomato Detached Leaf Assay for Chemical Genomics of an HLB Model System

    E-Print Network [OSTI]

    Patne, S.; Eulgem, T.; Roose, M. L.

    2014-01-01

    Leaf Assay for Chemical Genomics of an HLB Model Systemapproach known as chemical genomics with Tomato “Psyllida model of HLB. Chemical genomics involves three key stages

  16. RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach

    E-Print Network [OSTI]

    Novichkov, Pavel S.

    2010-01-01

    motifs by comparative genomics. Nucleic Acids Res. , 28,M.S. (2009) Comparative genomics of regulation of fatty acidcomparative and functional genomics. Nucleic Acids Res. ,

  17. Pigeonpea genomics initiative (PGI): an international effort to improve crop productivity of pigeonpea (Cajanus cajan L.)

    E-Print Network [OSTI]

    2010-01-01

    009-9327-2 Pigeonpea genomics initiative (PGI): anIndia R. K. Varshney (&) Genomics Towards Gene Discoverycrop legume’. To enable genomics-assisted breeding in this

  18. ESPP Functional Genomics and Imaging Core: Cell wide analysis of Metal-Reducing Bacteria

    E-Print Network [OSTI]

    Mukhopadhyay, Aindrila

    2014-01-01

    and Environmental Research, Genomics:GTL Program throughESPP Functional Genomics and Imaging Core: Cell widemetals. The Functional Genomics and Imaging Core (FGIC)

  19. Comparative genomics of xylose-fermenting fungi for enhanced biofuel production

    E-Print Network [OSTI]

    Wohlbach, Dana J.

    2011-01-01

    et al. (2009) Comparative genomics of the fungal pathogensComparative genomics of xylose-fermenting fungi for enhancedapplications. BMC Genomics Wisselink HW, Toirkens MJ, Wu Q,

  20. Discovery of Fungal Cell Wall Components Using Evolutionary and Functional Genomics

    E-Print Network [OSTI]

    Sain, Divya

    2013-01-01

    profiling and comparative genomics approaches." Eukaryotcerevisiae." Comp Funct Genomics 2(3): 124-42. Dinsdale, E.profiling and comparative genomics approaches." Eukaryot

  1. Metabolic complementarity and genomics of the dual bacterial symbiosis of sharpshooters

    E-Print Network [OSTI]

    2006-01-01

    Metabolic Complementarity and Genomics of the Dual BacterialMetabolic complementarity and genomics of the dual bacterialthe other. ) Comparative genomics. The predicted proteomes

  2. Target selection and annotation for the structural genomics of the amidohydrolase and enolase superfamilies

    E-Print Network [OSTI]

    2009-01-01

    J Struct Funct Genomics (2009) 10:107–125 DOIannotation for the structural genomics of the amidohydrolaseCenter for Structural Genomics (NYSGXRC) that aims to

  3. From Benefit Sharing to Power Sharing: Partnership Governance in Population Genomics Research

    E-Print Network [OSTI]

    Winickoff, David E

    2008-01-01

    T. Greely, ‘Iceland's Plan for Genomics Research: Facts andMike Fortun, Promising Genomics: Iceland and deCODE Geneticsabout commercialization in genomics research. 18 In this

  4. Comparative genomics of metabolic capacities of regulons controlled by cis-regulatory RNA motifs in bacteria

    E-Print Network [OSTI]

    Sun, Eric I; Leyn, Semen A; Kazanov, Marat D; Saier, Milton H; Novichkov, Pavel S; Rodionov, Dmitry A

    2013-01-01

    RH, Breaker RR: Comparative genomics reveals 104 candidateof transporters. BMC Genomics 2008, 9:330. 16. Green NJ,in proteobacteria: comparative genomics analysis. FEMS

  5. Resource for the exploration of regulons accurately predicted by the methods of comparative genomics

    E-Print Network [OSTI]

    Novichkov, Pavel S.

    2014-01-01

    the methods of comparative genomics. Pavel S. Novichkov 1 ,Environmental Research, Genomics:GTL program through con-a computational comparative genomics approach is coming of

  6. A Novel Candidate Vaccine for Cytauxzoonosis Inferred from Comparative Apicomplexan Genomics

    E-Print Network [OSTI]

    2013-01-01

    from Comparative Apicomplexan Genomics Jaime L. Tarigo 1 ,the use of comparative genomics to computationally andthe use of comparative genomics as an accelerated path to

  7. Applications of the pipeline environment for visual informatics and genomics computations

    E-Print Network [OSTI]

    2011-01-01

    for visual informatics and genomics computations. BMCfor visual informatics and genomics computations Ivo D DinovContemporary informatics and genomics research require

  8. Integrative Genomics Reveals Novel Molecular Pathways and Gene Networks for Coronary Artery Disease

    E-Print Network [OSTI]

    2014-01-01

    Integrative Genomics Reveals Novel Molecular Pathways and7 | e1004502 Integrative Genomics of Coronary Artery Disease2012) Use of functional genomics to identify candidate genes

  9. Discovering and validating biological hypotheses from coherent patterns in functional genomics data

    E-Print Network [OSTI]

    Joachimiak, Marcin Pawel

    2008-01-01

    patterns in functional genomics data Marcin P. Joachimiakpatterns in functional genomics data” Marcin P. Joachimiakand Environmental Research, Genomics Program:GTL through

  10. Clustering and Registration of Functional Data with Applications in Time Course Genomics Data

    E-Print Network [OSTI]

    Zhang, Yafeng

    2014-01-01

    of Clustering Methods for Time Course Genomics Data . .Methods for Time Course Genomics Data. To be submitted S.human subjects. BMC Genomics, 13, 2012. 636. Kongming Wang

  11. Consortium biology in immunology: the perspective from the Immunological Genome Project.

    E-Print Network [OSTI]

    Benoist, C; Lanier, L; Merad, M; Mathis, D

    2012-01-01

    significance, the Human Genome Project (1990–2003) is1990s against the Human Genome Project 5 , and more recentlycompletion of the Human Genome Project, Eric Lander argued

  12. From Benefit Sharing to Power Sharing: Partnership Governance in Population Genomics Research

    E-Print Network [OSTI]

    Winickoff, David E

    2008-01-01

    failures of the Human Genome Diversity Project, communitysampling, and the Human Genome Diversity Project eventuallyCommunity of the Human Genome Diversity Project, ‘Proposed

  13. Evolutionary Study of Genome Features in Cereals: a Focus on Endogenous Small RNA Generation

    E-Print Network [OSTI]

    Nohzadeh-Malakshah, Sahar

    2012-01-01

    overlapping genes in Metazoa. In BMC Genomics, pp. 174.B. (2012). Compressive genomics. In Nat Biotechnol , pp.Ibarra, J. (2011). Crop genomics: advances and applications.

  14. Comparative functional genomics of energy metabolism and insulin resistance in mammalian systems

    E-Print Network [OSTI]

    Hsiao, Albert

    2005-01-01

    of two-channel functional genomics data.  (in review).  and differentiation.   Genomics, 2004.   84 (5): p.  876-Comparative Functional Genomics   of Energy Metabolism and 

  15. The development and application of an integrated functional genomics platform in Desulfovibrio desulfuricans G20

    E-Print Network [OSTI]

    Deutschbauer, Adam

    2014-01-01

    integrated functional genomics data will be used to build aan integrated functional genomics platform in Desulfovibrioand Environmental Research, Genomics:GTL program through

  16. Update on the Pfam5000 Strategy for Selection of Structural Genomics Targets

    E-Print Network [OSTI]

    Chandonia, John-Marc; Brenner, Steven E.

    2005-01-01

    Mizuguchi, "Structural genomics: an overview," Prog BiophysA tour of structural genomics," Nat Rev Genet, vol. 2, pp.Montelione, "Structural genomics: an approach to the protein

  17. The Human Genome Diversity Project

    SciTech Connect (OSTI)

    Cavalli-Sforza, L.

    1994-12-31

    The Human Genome Diversity Project (HGD Project) is an international anthropology project that seeks to study the genetic richness of the entire human species. This kind of genetic information can add a unique thread to the tapestry knowledge of humanity. Culture, environment, history, and other factors are often more important, but humanity`s genetic heritage, when analyzed with recent technology, brings another type of evidence for understanding species` past and present. The Project will deepen the understanding of this genetic richness and show both humanity`s diversity and its deep and underlying unity. The HGD Project is still largely in its planning stages, seeking the best ways to reach its goals. The continuing discussions of the Project, throughout the world, should improve the plans for the Project and their implementation. The Project is as global as humanity itself; its implementation will require the kinds of partnerships among different nations and cultures that make the involvement of UNESCO and other international organizations particularly appropriate. The author will briefly discuss the Project`s history, describe the Project, set out the core principles of the Project, and demonstrate how the Project will help combat the scourge of racism.

  18. College of Health Sciences Health Sciences Connection

    E-Print Network [OSTI]

    Barrash, Warren

    College of Health Sciences Health Sciences Connection 1 Dean's Message College of Health Sciences Health Sciences Connection February 2011 Volume IX (3) Since the last COHS newsletter, the faculty Dr. Tim Dunnagan, Dean #12;Health Sciences Connection 2 College News College of Health Sciences

  19. Web of Science Web of ScienceWeb of Science

    E-Print Network [OSTI]

    Wang, Yayu

    Web of Science 2015-3-25 #12;Web of ScienceWeb of Science 93 2 22 7 Web of Science #12; 3.com/WOS_GeneralSearch_input.do?product=WOS&search_ mode=GeneralSearch&SID=4CLD1VklEapSgBPAiM8&preferencesSaved= Web of Science Web of Science core; #12; IDS IDS IDS #12; 50 "" #12; #12; 1. 2. 3. #12;4. 5. #12;6. Web of ScienceSCI 2

  20. Computer Science UNDERGRADUATE

    E-Print Network [OSTI]

    Suzuki, Masatsugu

    447 Computer Science UNDERGRADUATE PROGRAMS The Department of Computer Science provides undergraduate instruction leading to the bachelor's degree in computer science. This program in computer science is accredited by the Computer Science Accreditation Board (CSAB), a specialized accrediting body recognized

  1. Department of Materials Science &

    E-Print Network [OSTI]

    Zhigilei, Leonid V.

    Developing Leaders of Innovation Department of Materials Science & Engineering #12;At the University of Virginia, students in materials science, engineering physics and engineering science choose to tackle compelling issues in materials science and engineering or engineering science

  2. COMPUTER SCIENCE EECS Department

    E-Print Network [OSTI]

    COMPUTER SCIENCE EECS Department The Electrical Engineering and Computer Science (EECS) Department at WSU offers undergraduate degrees in electrical engineering, computer engineering and computer science. The EECS Department offers master of science degrees in computer science, electrical engineering

  3. Psychology is a Developmental Science

    E-Print Network [OSTI]

    Greenberg, Gary; Partridge, Ty; Mosack, Victoria; Lambdin, Charles

    2006-01-01

    of the Brain and the Human Genome Project. Both purported toyears later and one Human Genome Project behind us, we areenormous success of the Human Genome Project—one of the most

  4. 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.

  5. Supporting Organizations | Nuclear Science | ORNL

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

    Nuclear Science Engineering Fusion & Materials for Nuclear Systems Nuclear Science Home | Science & Discovery | Nuclear Science | Supporting Organizations SHARE Supporting...

  6. Genome sequence analysis of the model grass Brachypodium distachyon: insights into grass genome evolution

    SciTech Connect (OSTI)

    Schulman, Al

    2009-08-09

    Three subfamilies of grasses, the Erhardtoideae (rice), the Panicoideae (maize, sorghum, sugar cane and millet), and the Pooideae (wheat, barley and cool season forage grasses) provide the basis of human nutrition and are poised to become major sources of renewable energy. Here we describe the complete genome sequence of the wild grass Brachypodium distachyon (Brachypodium), the first member of the Pooideae subfamily to be completely sequenced. Comparison of the Brachypodium, rice and sorghum genomes reveals a precise sequence- based history of genome evolution across a broad diversity of the grass family and identifies nested insertions of whole chromosomes into centromeric regions as a predominant mechanism driving chromosome evolution in the grasses. The relatively compact genome of Brachypodium is maintained by a balance of retroelement replication and loss. The complete genome sequence of Brachypodium, coupled to its exceptional promise as a model system for grass research, will support the development of new energy and food crops

  7. GenomePeek—an online tool for prokaryotic genome and metagenome analysis

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    McNair, Katelyn; Edwards, Robert A.

    2015-06-16

    As increases in prokaryotic sequencing take place, a method to quickly and accurately analyze this data is needed. Previous tools are mainly designed for metagenomic analysis and have limitations; such as long runtimes and significant false positive error rates. The online tool GenomePeek (edwards.sdsu.edu/GenomePeek) was developed to analyze both single genome and metagenome sequencing files, quickly and with low error rates. GenomePeek uses a sequence assembly approach where reads to a set of conserved genes are extracted, assembled and then aligned against the highly specific reference database. GenomePeek was found to be faster than traditional approaches while still keeping errormore »rates low, as well as offering unique data visualization options.« less

  8. Genomic Sequence or Signature Tags (GSTs) from the Genome Group at Brookhaven National Laboratory (BNL)

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

    Dunn, John J.; McCorkle, Sean R.; Praissman, Laura A.; Hind, Geoffrey; Van der Lelie, Daniel; Bahou, Wadie F.; Gnatenko, Dmitri V.; Krause, Maureen K.

    Genomic Signature Tags (GSTs) are the products of a method we have developed for identifying and quantitatively analyzing genomic DNAs. The DNA is initially fragmented with a type II restriction enzyme. An oligonucleotide adaptor containing a recognition site for MmeI, a type IIS restriction enzyme, is then used to release 21-bp tags from fixed positions in the DNA relative to the sites recognized by the fragmenting enzyme. These tags are PCR-amplified, purified, concatenated and then cloned and sequenced. The tag sequences and abundances are used to create a high resolution GST sequence profile of the genomic DNA. [Quoted from Genomic Signature Tags (GSTs): A System for Profiling Genomic DNA, Dunn, John J.; McCorkle, Sean R.; Praissman, Laura A.; Hind, Geoffrey; Van der Lelie, Daniel; Bahou, Wadie F.; Gnatenko, Dmitri V.; Krause, Maureen K., Revised 9/13/2002

  9. The Los Alamos Science Pillars The Science of Signatures

    SciTech Connect (OSTI)

    Smith, Joshua E.; Peterson, Eugene J.

    2012-09-13

    As a national security science laboratory, Los Alamos is often asked to detect and measure the characteristics of complex systems and to use the resulting information to quantify the system's behavior. The Science of Signatures (SoS) pillar is the broad suite of technical expertise and capability that we use to accomplish this task. With it, we discover new signatures, develop new methods for detecting or measuring signatures, and deploy new detection technologies. The breadth of work at Los Alamos National Laboratory (LANL) in SoS is impressive and spans from the initial understanding of nuclear weapon performance during the Manhattan Project, to unraveling the human genome, to deploying laser spectroscopy instrumentation on Mars. Clearly, SoS is a primary science area for the Laboratory and we foresee that as it matures, new regimes of signatures will be discovered and new ways of extracting information from existing data streams will be developed. These advances will in turn drive the development of sensing instrumentation and sensor deployment. The Science of Signatures is one of three science pillars championed by the Laboratory and vital to supporting our status as a leading national security science laboratory. As with the other two pillars, Materials for the Future and Information Science and Technology for Predictive Science (IS&T), SoS relies on the integration of technical disciplines and the multidisciplinary science and engineering that is our hallmark to tackle the most difficult national security challenges. Over nine months in 2011 and 2012, a team of science leaders from across the Laboratory has worked to develop a SoS strategy that positions us for the future. The crafting of this strategy has been championed by the Chemistry, Life, and Earth Sciences Directorate, but as you will see from this document, SoS is truly an Institution-wide effort and it has engagement from every organization at the Laboratory. This process tapped the insight and imagination of many LANL staff and managers and resulted in a strategy which focuses on our strengths while recognizing that the science of signatures is dynamic. This report highlights the interdependence between SoS, advances in materials science, and advances in information technology. The intent is that SoS shape and inform Los Alamos investments in nuclear forensics, nuclear diagnostics, climate, space, energy, and biosurveillence; the areas of leadership that you will read about in this strategy document. The Science of Signatures is still a relatively new strategic direction for the Laboratory. The primary purpose of this document is tell Laboratory staff how SoS is being managed and give them a chance to get involved. A second important purpose is to inform the Department of Energy and our customers of our capability growth in this important scientific area. Questions concerning the SoS strategy and input to it are welcomed and may be directed to any member of the SoS Leadership Council or to the Chemistry, Life, and Earth Science Directorate Office.

  10. Intellectual Property and eScience

    E-Print Network [OSTI]

    Burk, DL

    2007-01-01

    on Properties of the Human Genome Project (pp. 97–122). SanStreet meets the human genome project: Intellectual propertycollaboratory? ’’ The human genome mapping project and the

  11. Science Magazine

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

    & ANALYSIS www.sciencemag.org SCIENCE VOL 339 8 FEBRUARY 2013 635 Steven Chu, the fi rst Nobel-winning scien- tist to lead the sprawling U.S. Department of Energy (DOE), has rarely...

  12. Science Museum

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

    Nanotechnology and algae biofuels exhibits open July 26 at the Bradbury Science Museum July 22, 2013 LOS ALAMOS, N.M., July 22, 2013-Los Alamos National Laboratory's Bradbury...

  13. The Meaning of Cell Genealogy The meaning of stem The meaning of Zygote, Mitotic ages and Genome Data Methods Applica Somatic Cell Genealogies and Differentiation

    E-Print Network [OSTI]

    Goldschmidt, Christina

    The Meaning of Cell Genealogy The meaning of stem The meaning of Zygote, Mitotic ages and Genome Data Methods Applica Somatic Cell Genealogies and Differentiation Olina Geofrey Martijn African Institute for Mathematical Sciences 2008 #12;The Meaning of Cell Genealogy The meaning of stem The meaning

  14. VISTA - computational tools for comparative genomics

    SciTech Connect (OSTI)

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

    2004-01-01

    Comparison of DNA sequences from different species is a fundamental method for identifying functional elements in genomes. Here we describe the VISTA family of tools created to assist biologists in carrying out this task. Our first VISTA server at http://www-gsd.lbl.gov/VISTA/ was launched in the summer of 2000 and was designed to align long genomic sequences and visualize these alignments with associated functional annotations. Currently the VISTA site includes multiple comparative genomics tools and provides users with rich capabilities to browse pre-computed whole-genome alignments of large vertebrate genomes and other groups of organisms with VISTA Browser, submit their own sequences of interest to several VISTA servers for various types of comparative analysis, and obtain detailed comparative analysis results for a set of cardiovascular genes. We illustrate capabilities of the VISTA site by the analysis of a 180 kilobase (kb) interval on human chromosome 5 that encodes for the kinesin family member3A (KIF3A) protein.

  15. Microbial Protein-Protein Interactions (MiPPI) Data from the Genomics: GTL Center for Molecular and Cellular Systems (CMCS)

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

    The Genomic Science Center for Molecular and Cellular Systems (CMCS), established in 2002, seeks to identify and characterize the complete set of protein complexes within a cell to provide a mechanistic basis for the understanding of biochemical functions. The CMCS is anchored at ORNL and PNNL. CMCS initially focused on the identification and characterization of protein complexes in two microbial systems,Rhodopseudomonas palustris (R. palustris) and Shewanella oneidensis (S. oneidensis). These two organisms have also been the focus of major DOE Genomic Science/Microbial Cell Program (MCP) projects. To develop an approach for identifying the diverse types of complexes present in microbial organisms, CMCS incorporates a number of molecular biology, microbiology, analytical and computational tools in an integrated pipeline.

  16. Faculty of Science Environmental Science

    E-Print Network [OSTI]

    for career success. An Environmental Science degree is also appropriate background training for professions Resources A new and integrated set of state-of-the-art laboratory and field equipment has been designed

  17. Neutron Science | More Science | ORNL

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

    ORNL's long history of neutron science began in the 1940s with the pioneering neutron scattering studies of Ernest Wollan and Clifford Shull. Shull was co-recipient of...

  18. Understanding our genetic inheritance: The US Human Genome Project, The first five years FY 1991--1995

    SciTech Connect (OSTI)

    1990-04-01

    The Human Genome Initiative is a worldwide research effort with the goal of analyzing the structure of human DNA and determining the location of the estimated 100,000 human genes. In parallel with this effort, the DNA of a set of model organisms will be studied to provide the comparative information necessary for understanding the functioning of the human genome. The information generated by the human genome project is expected to be the source book for biomedical science in the 21st century and will by of immense benefit to the field of medicine. It will help us to understand and eventually treat many of the more than 4000 genetic diseases that affect mankind, as well as the many multifactorial diseases in which genetic predisposition plays an important role. A centrally coordinated project focused on specific objectives is believed to be the most efficient and least expensive way of obtaining this information. The basic data produced will be collected in electronic databases that will make the information readily accessible on convenient form to all who need it. This report describes the plans for the U.S. human genome project and updates those originally prepared by the Office of Technology Assessment (OTA) and the National Research Council (NRC) in 1988. In the intervening two years, improvements in technology for almost every aspect of genomics research have taken place. As a result, more specific goals can now be set for the project.

  19. Bioinformatician position available Integrative Genomics of Ageing Group, University of Liverpool

    E-Print Network [OSTI]

    Bioinformatician position available Integrative Genomics of Ageing Group, University of Liverpool A bioinformatician position is available in the Integrative Genomics of Ageing Group at the University of Liverpool) systems biology, functional genomics, network analysis, and genome evolution. Applicants should have

  20. Computational Prediction of Genomic Functional Cores Specific to Different Alessandra Carbone

    E-Print Network [OSTI]

    Carbone, Alessandra

    Computational Prediction of Genomic Functional Cores Specific to Different Microbes Alessandra of available complete genomes, comparative genomics has concluded that the universal core contains as reference organisms to infer essentiality in other microbial species. The case of small parasitic genomes

  1. Decoding Plant and Animal Genome Plasticity from Differential Paleo-Evolutionary Patterns and Processes

    E-Print Network [OSTI]

    Gent, Universiteit

    Decoding Plant and Animal Genome Plasticity from Differential Paleo-Evolutionary Patterns Continuing advances in genome sequencing technologies and computational methods for comparative genomics currently allow inferring the evolutionary history of entire plant and animal genomes. Based

  2. MicrobesOnline: An Integrated Portal For Comparative Functional Genomics (R-018)

    E-Print Network [OSTI]

    Huang, Y. Wayne

    2014-01-01

    and Environmental Research,  Genomics:GTL Program  through Comparative Functional Genomics (R-018) Y. Wayne Huang 1,2 ,genome using comparative genomics and sequence  motif 

  3. MicrobesOnline: an integrated portal for comparative and functional genomics

    E-Print Network [OSTI]

    Dehal, Paramvir S.

    2010-01-01

    the US Department of Energy Genomics: GTL program (DE-AC02-Web site for comparative genomics. Genome Res, 15, 1015-comparative and functional genomics Paramvir S. Dehal 1,2* ,

  4. Hippocrates and Helices The Importance of Integrating Genomics, Epigenomics, and Personalized Medicine into Systems

    E-Print Network [OSTI]

    Brutlag, Doug

    Hippocrates and Helices The Importance of Integrating Genomics, Epigenomics, and Personalized an increased emphasis on personalized medicine. Succinctly, medical educators should integrate genomics of the Human Genome Project: personalized medical disciplines, particularly genomic medicine and epigenomic

  5. Evaluation And Application Of The Three A's Of Genomics: Assembly, Alignment, Annotation.

    E-Print Network [OSTI]

    Earl, Dent A.

    2014-01-01

    genome assembly. BMC Genomics, 10:180. [Locke et al. , 2011]of the three A’s of Genomics: Assembly, Alignment,among vertebrates. BMC Genomics, 11:21. [Blakesley et al. ,

  6. Multiple Whole Genome Alignments Without a Reference Organism

    SciTech Connect (OSTI)

    Dubchak, Inna; Poliakov, Alexander; Kislyuk, Andrey; Brudno, Michael

    2009-01-16

    Multiple sequence alignments have become one of the most commonly used resources in genomics research. Most algorithms for multiple alignment of whole genomes rely either on a reference genome, against which all of the other sequences are laid out, or require a one-to-one mapping between the nucleotides of the genomes, preventing the alignment of recently duplicated regions. Both approaches have drawbacks for whole-genome comparisons. In this paper we present a novel symmetric alignment algorithm. The resulting alignments not only represent all of the genomes equally well, but also include all relevant duplications that occurred since the divergence from the last common ancestor. Our algorithm, implemented as a part of the VISTA Genome Pipeline (VGP), was used to align seven vertebrate and sixDrosophila genomes. The resulting whole-genome alignments demonstrate a higher sensitivity and specificity than the pairwise alignments previously available through the VGP and have higher exon alignment accuracy than comparable public whole-genome alignments. Of the multiple alignment methods tested, ours performed the best at aligning genes from multigene families?perhaps the most challenging test for whole-genome alignments. Our whole-genome multiple alignments are available through the VISTA Browser at http://genome.lbl.gov/vista/index.shtml.

  7. The Science of Team Science: Origins and Themes The Science of Team Science

    E-Print Network [OSTI]

    Finley Jr., Russell L.

    The Science of Team Science: Origins and Themes The Science of Team Science Overview of the Field, PhD Abstract: The science of team science encompasses an amalgam of conceptual and methodologic about the cost effectiveness of public- and private-sector investments in team-based science

  8. Statistics and Actuarial Science

    E-Print Network [OSTI]

    Chauve, Cedric

    SCIENCE SFU.CA/ SCIENCE Statistics and Actuarial Science #12;Further Information Student info, academic calendar, registration students.sfu.ca Science advising sfu.ca/science/undergrad/advising Statistics and Actuarial Science The Department of Statistics and Actuarial Science offers the degree

  9. Genomes to life project quarterly report June 2004.

    SciTech Connect (OSTI)

    Heffelfinger, Grant S.

    2005-01-01

    This SAND report provides the technical progress through June 2004 of the Sandia-led project, ''Carbon Sequestration in Synechococcus Sp.: From Molecular Machines to Hierarchical Modeling'', funded by the DOE Office of Science Genomes to Life Program. Understanding, predicting, and perhaps manipulating carbon fixation in the oceans has long been a major focus of biological oceanography and has more recently been of interest to a broader audience of scientists and policy makers. It is clear that the oceanic sinks and sources of CO{sub 2} are important terms in the global environmental response to anthropogenic atmospheric inputs of CO{sub 2} and that oceanic microorganisms play a key role in this response. However, the relationship between this global phenomenon and the biochemical mechanisms of carbon fixation in these microorganisms is poorly understood. In this project, we will investigate the carbon sequestration behavior of Synechococcus Sp., an abundant marine cyanobacteria known to be important to environmental responses to carbon dioxide levels, through experimental and computational methods. This project is a combined experimental and computational effort with emphasis on developing and applying new computational tools and methods. Our experimental effort will provide the biology and data to drive the computational efforts and include significant investment in developing new experimental methods for uncovering protein partners, characterizing protein complexes, identifying new binding domains. We will also develop and apply new data measurement and statistical methods for analyzing microarray experiments. Computational tools will be essential to our efforts to discover and characterize the function of the molecular machines of Synechococcus. To this end, molecular simulation methods will be coupled with knowledge discovery from diverse biological data sets for high-throughput discovery and characterization of protein-protein complexes. In addition, we will develop a set of novel capabilities for inference of regulatory pathways in microbial genomes across multiple sources of information through the integration of computational and experimental technologies. These capabilities will be applied to Synechococcus regulatory pathways to characterize their interaction map and identify component proteins in these pathways. We will also investigate methods for combining experimental and computational results with visualization and natural language tools to accelerate discovery of regulatory pathways. The ultimate goal of this effort is develop and apply new experimental and computational methods needed to generate a new level of understanding of how the Synechococcus genome affects carbon fixation at the global scale. Anticipated experimental and computational methods will provide ever-increasing insight about the individual elements and steps in the carbon fixation process, however relating an organism's genome to its cellular response in the presence of varying environments will require systems biology approaches. Thus a primary goal for this effort is to integrate the genomic data generated from experiments and lower level simulations with data from the existing body of literature into a whole cell model. We plan to accomplish this by developing and applying a set of tools for capturing the carbon fixation behavior of complex of Synechococcus at different levels of resolution. Finally, the explosion of data being produced by high-throughput experiments requires data analysis and models which are more computationally complex, more heterogeneous, and require coupling to ever increasing amounts of experimentally obtained data in varying formats. These challenges are unprecedented in high performance scientific computing and necessitate the development of a companion computational infrastructure to support this effort.

  10. Justice and the human genome project

    SciTech Connect (OSTI)

    Murphy, T.F.; Lappe, M.A.

    1995-04-01

    This book is a collection of nine essays originally presented at a conference entitled {open_quotes}Justice and the Human Genome{close_quotes} held in Chicago in late 1991. The goal of the articles in this collection is to explore questions of justice raised by developments in genomic research and by applications of genetic knowledge and technology. The Human Genome Project (HGP) is used as a starting point for exploring these questions, but, as Marc Lappe recognizes, the database generated by HGP research will have implications far beyond the medical applications frequently used to justify this research effort. Thus, the book`s contributors consider questions of justice in relation to screening and testing for various predispositions, conditions, and diseases and gene therapy but also examine testing for other characteristics, forensic uses of genetic information, issues associated with DNA banks, and (hypothetical) genetic enhancement possibilities.

  11. Sequencing and comparing whole mitochondrial genomes ofanimals

    SciTech Connect (OSTI)

    Boore, Jeffrey L.; Macey, J. Robert; Medina, Monica

    2005-04-22

    Comparing complete animal mitochondrial genome sequences is becoming increasingly common for phylogenetic reconstruction and as a model for genome evolution. Not only are they much more informative than shorter sequences of individual genes for inferring evolutionary relatedness, but these data also provide sets of genome-level characters, such as the relative arrangements of genes, that can be especially powerful. We describe here the protocols commonly used for physically isolating mtDNA, for amplifying these by PCR or RCA, for cloning,sequencing, assembly, validation, and gene annotation, and for comparing both sequences and gene arrangements. On several topics, we offer general observations based on our experiences to date with determining and comparing complete mtDNA sequences.

  12. Physical mapping of complex genomes

    DOE Patents [OSTI]

    Evans, G.A.

    1993-06-15

    A method for the simultaneous identification of overlapping cosmid clones among multiple cosmid clones and the use of the method for mapping complex genomes are provided. A library of cosmid clones that contains the DNA to be mapped is constructed and arranged in a manner such that individual clones can be identified and replicas of the arranged clones prepared. In preferred embodiments, the clones are arranged in a two dimensional matrix. In such embodiments, the cosmid clones in a row are pooled, mixed probes complementary to the ends of the DNA inserts in the pooled clones are synthesized, hybridized to a first replica of the library. Hybridizing clones, which include the pooled row, are identified. A second portion of clones is prepared by pooling cosmid clones that correspond to a column in the matrix. The second pool thereby includes one clone from the first portion pooled clones. This common clone is located on the replica at the intersection of the column and row. Mixed probes complementary to the ends of the DNA inserts in the second pooled portion of clones are prepared and hybridized to a second replica of the library. The hybridization pattern on the first and second replicas of the library are compared and cross-hybridizing clones, other than the clones in the pooled column and row, that hybridize to identical clones in the first and second replicas are identified. These clones necessarily include DNA inserts that overlap with the DNA insert in the common clone located at the intersection of the pooled row and pooled column. The DNA in the entire library may be mapped by pooling the clones in each of the rows and columns of the matrix, preparing mixed end-specific probes and hybridizing the probes from each row or column to a replica of the library. Since all clones in the library are located at the intersection of a column and a row, the overlapping clones for all clones in the library may be identified and a physical map constructed.

  13. Physical mapping of complex genomes

    DOE Patents [OSTI]

    Evans, Glen A. (Encinitas, CA)

    1993-01-01

    Method for simultaneous identification of overlapping cosmid clones among multiple cosmid clones and the use of the method for mapping complex genomes are provided. A library of cosmid clones that contains the DNA to be mapped is constructed and arranged in a manner such that individual clones can be identified and replicas of the arranged clones prepared. In preferred embodiments, the clones are arranged in a two dimensional matrix. In such embodiments, the cosmid clones in a row are pooled, mixed probes complementary to the ends of the DNA inserts int he pooled clones are synthesized, hybridized to a first replica of the library. Hybridizing clones, which include the pooled row, are identified. A second portion of clones is prepared by pooling cosmid clones that correspond to a column in the matrix. The second pool thereby includes one clone from the first portion pooled clones. This common clone is located on the replica at the intersection of the column and row. Mixed probes complementary to the ends of the DNA inserts in the second pooled portion of clones are prepared and hybridized to a second replica of the library. The hybridization pattern on the first and second replicas of the library are compared and cross-hybridizing clones, other than the clones in the pooled column and row, that hybridize to identical clones in the first and second replicas are identified. These clones necessarily include DNA inserts that overlap with the DNA insert int he common clone located at the intersection of the pooled row and pooled column. The DNA in the entire library may be mapped by pooling the clones in each of the rows and columns of the matrix, preparing mixed end-specific probes and hybridizing the probes from each row or column to a replica of the library. Since all clones in the library are located at the intersection of a column and a row, the overlapping clones for all clones in the library may be identified and a physical map constructed. In other preferred embodiments, the cosmid clones are arranged in a three dimensional matrix, pooled and compared in threes according to intersecting planes of the three dimensional matrix. Arrangements corresponding to geometries of higher dimensions may also be prepared and used to simultaneously identify overlapping clones in highly complex libraries with relatively few hybridization reactions.

  14. Science DMZ Implemented at NERSC

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

    NERSC Science Engagement Move your data Programs & Workshops Science Requirements Reviews Case Studies OSCARS Case Studies Science DMZ Case Studies Science DMZ @ UF Science DMZ @...

  15. Finishing the euchromatic sequence of the human genome

    E-Print Network [OSTI]

    Brutlag, Doug

    foundation for biomedical research in the decades ahead. The Human Genome Project (HGP) was launched in 1990 this component of the HGP. In February 2001, the IHGSC15 and Celera Genomics16 each reported draft sequences

  16. Error and Error Mitigation in Low-Coverage Genome Assemblies

    E-Print Network [OSTI]

    Hubisz, Melissa J.

    The recent release of twenty-two new genome sequences has dramatically increased the data available for mammalian comparative genomics, but twenty of these new sequences are currently limited to ~2× coverage. Here we examine ...

  17. Defining functional DNA elements in the human genome

    E-Print Network [OSTI]

    Kellis, Manolis

    With the completion of the human genome sequence, attention turned to identifying and annotating its functional DNA elements. As a complement to genetic and comparative genomics approaches, the Encyclopedia of DNA Elements ...

  18. Novel phylogenetic approaches to problems in microbial genomics

    E-Print Network [OSTI]

    David, Lawrence A. (Lawrence Anthony)

    2010-01-01

    Present day microbial genomes are the handiwork of over 3 billion years of evolution. Comparisons between these genomes enable stepping backwards through past evolutionary events, and can be formalized using binary tree ...

  19. Tools for Extracting Actionable Medical Knowledge from Genomic Big Data

    E-Print Network [OSTI]

    Goldstein, Theodore Charles

    2013-01-01

    KNOWLEDGE FROM GENOMIC BIG DATA A dissertation submitted inKNOWLEDGE FROM GENOMIC BIG DATA By Theodore C. Goldsteinby the quantities of big data from these assays and cannot

  20. MycoCosm, an Integrated Fungal Genomics Resource (Conference...

    Office of Scientific and Technical Information (OSTI)

    In-Document Search Title: MycoCosm, an Integrated Fungal Genomics Resource MycoCosm is a web-based interactive fungal genomics resource, which was first released in March 2010, in...

  1. 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

  2. Use of Optical Mapping in Bacterial Genome Finishing

    SciTech Connect (OSTI)

    Kumar, Dibyendu [University of Florida

    2010-06-03

    Dibyendu Kumar from the University of Florida discusses whole-genome optical mapping to help validate bacterial genome assemblies on June 3, 2010 at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM

  3. Information science is neither

    E-Print Network [OSTI]

    Furner, J

    2015-01-01

    of library and information sciences, 3rd ed. , edited byAmerican Society for Information Science and Technology 63,Annual Review of Information Science and Technology 41, no.

  4. Physics | More Science | ORNL

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

    Physics ORNL Physics Environment Safety and Health More Science Home | Science & Discovery | More Science | Physics SHARE Physics Bottom view of the 25 million volt tandem...

  5. Science & Discovery | ORNL

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

    Advanced Materials Clean Energy National Security Neutron Science Nuclear Science Supercomputing and Computation More Science Hubs, Centers and Institutes US ITER Mars 'Curiosity'...

  6. ORISE: Forensic Science

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

    Forensic Science Forensic Science The Oak Ridge Institute for Science and Education (ORISE) provides direct forensic analytical support, consulting and training services to United...

  7. Computational Science and Engineering

    E-Print Network [OSTI]

    Giger, Christine

    Computational Science and Engineering Research Profile The Computational Science and Engineering and Process Engineering Computational Science and Engineering Laboratory Prof. Dr. Petros Koumoutsakos petros

  8. Earth & Environmental Science

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

    Earth & Environmental Science Earth & Environmental Science1354608000000Earth & Environmental ScienceSome of these resources are LANL-only and will require Remote Access.No...

  9. BER Science Network Requirements

    E-Print Network [OSTI]

    Dart, Eli

    2011-01-01

    of Energy, Office of Science, Office of Advanced Scientificthe Directors of the Office of Science, Office of Advanced5 Simulation Data Key Remote Science Drivers Instruments and

  10. Neural Social Science

    E-Print Network [OSTI]

    Lakoff, George

    2013-01-01

    interpersonal warmth . ” Science, 322, 2008, 606–607 . Atcold? ” Psychological Science , 19, 2008, 838–842. Subjectsand physical cleansing. Science, 313, 1451–1452. Students

  11. Citizen science in archaeology

    E-Print Network [OSTI]

    Smith, ML

    2014-01-01

    Melinda A. Zeder Smith] CITIZEN SCIENCE IN ARCHAEOLOGY 2014and Application of Citizen Science. Biological ConservationHilchey 2011 A Review of Citizen Science and Community-Based

  12. Nuclear Science & Technology

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

    Nuclear Science & Technology Nuclear Science & Technology1354608000000Nuclear Science & TechnologySome of these resources are LANL-only and will require Remote Access. No...

  13. [Faculty of Science Information and Computing Sciences

    E-Print Network [OSTI]

    Löh, Andres

    [Faculty of Science Information and Computing Sciences] 1 Types in Functional Programming Languages Andres L¨oh Department of Information and Computing Sciences Utrecht University UU General Math Colloquium ­ May 8, 2008 #12;[Faculty of Science Information and Computing Sciences] 2 Overview What

  14. History of Science 157 Sociology of Science

    E-Print Network [OSTI]

    Shapin, Steven

    1 History of Science 157 Sociology of Science Fall 2009 Steven Shapin Science Center 469 Tuesdays to thinking about science, its historical development, its relations to society and other forms of culture: Science Center 451 Office hours: Mondays 8:30 -> 10.15, or by arrangement #12;2 E-mail: shapin

  15. College of Health Sciences Health Sciences Connection

    E-Print Network [OSTI]

    Barrash, Warren

    College of Health Sciences Health Sciences Connection 1 Dean's Message College of Health Sciences Health Sciences Connection Back to School edition September 2010 Volume IX (1) Dr. Tim Dunnagan, Dean of the College of Health Sciences (COHS) at Boise State University (BSU). It is truly an honor to have

  16. Genomic Data and Annotation from the SEED

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

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

    The SEED Project has been extended to support metagenomic samples and concomitant analytical tools. Moreover, the number of genomes being introduced into SEED is growing very rapidly. Building a framework to support this growth while providing highly accurate annotations is centrally important to SEED. The project’s subsystem-based annotation strategy has become the technological foundation for addressing these challenges.(copied from Appendix 7 of Systems Biology Knowledgebase for a New Era in Biology, A Genomics:GTL Report from the May 2008 Workshop, DOE/SC-0113, Grequrick, S; Fredrickson, J.K.; Stevens, R., Pub March 1, 2009.)

  17. Genome-Facilitated Analyses of Geomicrobial Processes

    SciTech Connect (OSTI)

    Kenneth H. Nealson

    2012-05-02

    This project had the goal(s) of understanding the mechanism(s) of extracellular electron transport (EET) in the microbe Shewanella oneidensis MR-1, and a number of other strains and species in the genus Shewanella. The major accomplishments included sequencing, annotation, and analysis of more than 20 Shewanella genomes. The comparative genomics enabled the beginning of a systems biology approach to this genus. Another major contribution involved the study of gene regulation, primarily in the model organism, MR-1. As part of this work, we took advantage of special facilities at the DOE: e.g., the synchrotron radiation facility at ANL, where we successfully used this system for elemental characterization of single cells in different metabolic states (1). We began work with purified enzymes, and identification of partially purified enzymes, leading to initial characterization of several of the 42 c-type cytochromes from MR-1 (2). As the genome became annotated, we began experiments on transcriptome analysis under different conditions of growth, the first step towards systems biology (3,4). Conductive appendages of Shewanella, called bacterial nanowires were identified and characterized during this work (5, 11, 20,21). For the first time, it was possible to measure the electron transfer rate between single cells and a solid substrate (20), a rate that has been confirmed by several other laboratories. We also showed that MR-1 cells preferentially attach to cells at a given charge, and are not attracted, or even repelled by other charges. The interaction with the charged surfaces begins with a stimulation of motility (called electrokinesis), and eventually leads to attachment and growth. One of the things that genomics allows is the comparative analysis of the various Shewanella strains, which led to several important insights. First, while the genomes predicted that none of the strains looked like they should be able to degrade N-acetyl glucosamine (NAG), the monomer that makes up chitin, virtually all of the strains were in fact capable. This led to the discovery of a great many new genes involved with chitin and NAG metabolism (7). In a similar vein, a detailed study of the sugar utilization pathway revealed a major new insight into the regulation of sugar metabolism in this genus (19). Systems Biology and Comparative Genomics of the shewanellae: Several publications were put together describing the use of comparative genomics for analyses of the group Shewanella, and these were a logical culmination of our genomic-driven research (10,15,18). Eight graduate students received their Ph.D. degrees doing part of the work described here, and four postdoctoral fellows were supported. In addition, approximately 20 undergraduates took part in projects during the grant period.

  18. Genome Majority Vote (GMV), Version 0.x

    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 (Journal Article)ForthcomingGENERALProblemsGeneralGenericGeneticsGenomeGenome

  19. College of Veterinary Medicine and Biomedical Sciences

    E-Print Network [OSTI]

    , protein, lipid and carbohydrate biochemistry, medicinal chemistry, enzymology, metabolomics, genomics

  20. Divide and (epigenetic) rule: Chromatin domains as functional and structural units of genomes

    E-Print Network [OSTI]

    Giri, Ranjit K.

    of these in development, differentiation, and disease are also discussed. 1. The Genome era The Human Genome Project the genome sequencing projects revealed, that the total number of genes in human genome was not more than produced a refer- ence sequence of the euchromatic human genome, which was the first major genome sequenced