Sample records for bssd genomic science

  1. CROP & SOIL SCIENCES Quantitative Genomics

    E-Print Network [OSTI]

    Arnold, Jonathan

    CROP & SOIL SCIENCES Quantitative Genomics Committee Membership Dr. Scott Jackson - committee chair Dr. Peng-Wah Chee Department of Crop & Soil Sciences Department of Crop & Soil Sciences University of Horticulture Department of Crop & Soil Sciences University of Georgia University of Georgia 2360 Rainwater Rd

  2. Genome Science/Technologies

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

    McDonald Bioscience Communications Email State-of-the art technology and extensive genomics expertise Protein research Read caption + Los Alamos National Laboratory graduate...

  3. Biological Systems Science Division (BSSD) | U.S. DOE Office of 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: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645U.S. DOE Office511041clothAdvanced Materials Advanced Materials Find Find More LikeAndreasHelp(SC) Biological Systems

  4. 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: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645U.S. DOEThe Bonneville Power AdministrationField8,Dist.Newof EnergyFundingGeneGenome Engineering with TALGenome

  5. Genome Science and Personalized Cancer Treatment

    ScienceCinema (OSTI)

    Joe Gray

    2010-01-08T23:59:59.000Z

    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. Genomic Sciences | Clean Energy | ORNL

    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: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645U.S. DOEThe Bonneville Power AdministrationField8,Dist.Newof EnergyFundingGeneGenome Engineering with

  7. 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 the social sciences, and much more. This course will provide 1) an introduction to public health genomics, 2

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

    E-Print Network [OSTI]

    Setubal, JoĂŁo 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

  9. 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

  10. The Plant Genome [A Supplement to Crop Science] March 2008 No. 1 S-27 Genomic Origins of Potato

    E-Print Network [OSTI]

    Spooner, David

    The Plant Genome [A Supplement to Crop Science] March 2008 No. 1 S-27 Genomic Origins of Potato., and Shelley H. Jansky Abstract Chromosome pairing relationships within cultivated potato (Solanum tuberosum we reexamine potato genome hypotheses with the first phylogenetic analysis of all major genomes

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

    SciTech Connect (OSTI)

    Gray, Joe

    2009-08-04T23:59:59.000Z

    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.

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

    ScienceCinema (OSTI)

    Gray, Joe

    2011-04-28T23:59:59.000Z

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

    E-Print Network [OSTI]

    Standiford, Richard B.

    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

  14. Incorporating Genomics and Bioinformatics across the Life Sciences Curriculum

    E-Print Network [OSTI]

    Ditty, Jayna L.

    2012-01-01T23:59:59.000Z

    Page Incorporating Genomics and Bioinformatics across the2007) Discovering Genomics, Proteomics, and Bioinformatics,2003) Public access for teaching genomics, proteomics, and

  15. 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

  16. 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.

    2011-08-01T23:59:59.000Z

    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.

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

    E-Print Network [OSTI]

    Chen, Long-Qing

    evolution within a material are considered as the ``holy grail'' of materials science and engineering. Many of materials science and engineering. A microstructure may contain a wide variety of structural features such as an applied SPECIAL ISSUE: Materials Genome L.-Q. Chen (&) Department of Materials Science and Engineering

  18. Progress Report for Structural Genomics Science Theme, year 1

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

    University), Gaetano T. Montelione (Rutgers University) The Northeast Structural Genomics Consortium (NESGC, www.nesg.org) used EMSL's High Field NMR facility in 2006-2007 to...

  19. 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

    2013-01-15T23:59:59.000Z

    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.

  20. 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

    2012-03-21T23:59:59.000Z

    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.

  1. Los Alamos Science: The Human Genome Project. Number 20, 1992

    SciTech Connect (OSTI)

    Cooper, N G; Shea, N [eds.

    1992-01-01T23:59:59.000Z

    This article provides a broad overview of the Human Genome Project, with particular emphasis on work being done at Los Alamos. It tries to emphasize the scientific aspects of the project, compared to the more speculative information presented in the popular press. There is a brief introduction to modern genetics, including a review of classic work. There is a broad overview of the Genome Project, describing what the project is, what are some of its major five-year goals, what are major technological challenges ahead of the project, and what can the field of biology, as well as society expect to see as benefits from this project. Specific results on the efforts directed at mapping chromosomes 16 and 5 are discussed. A brief introduction to DNA libraries is presented, bearing in mind that Los Alamos has housed such libraries for many years prior to the Genome Project. Information on efforts to do applied computational work related to the project are discussed, as well as experimental efforts to do rapid DNA sequencing by means of single-molecule detection using applied spectroscopic methods. The article introduces the Los Alamos staff which are working on the Genome Project, and concludes with brief discussions on ethical, legal, and social implications of this work; a brief glimpse of genetics as it may be practiced in the next century; and a glossary of relevant terms.

  2. 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 ...

  3. 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: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level:Energy: Grid Integration Redefining What'sis Taking Over OurThe Iron4 Self-Scrubbing:,,of ScienceCurrentEmergencyU.S.U.S.(SC) From Human

  4. 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

  5. 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

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

    ScienceCinema (OSTI)

    Garrity, George

    2011-06-03T23:59:59.000Z

    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.

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

    SciTech Connect (OSTI)

    Garrity, George

    2009-09-09T23:59:59.000Z

    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.

  8. Computational methods and analyses in comparative genomics and epigenomics

    E-Print Network [OSTI]

    Peng, Qian

    2012-01-01T23:59:59.000Z

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

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

    ScienceCinema (OSTI)

    Rokhsar, Daniel

    2011-04-28T23:59:59.000Z

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

  10. Personal Genomics, Personalized Medicine,

    E-Print Network [OSTI]

    Napp, Nils

    Personal Genomics, Personalized Medicine, & YOU Carrie Iwema, PhD, MLS 21st May 2012 AAAS/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

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

    SciTech Connect (OSTI)

    Nichols, E.K.

    2000-02-17T23:59:59.000Z

    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. 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

  13. First Annual U.S. Department of Energy Office of Science Joint Genome Institute User Meeting

    E-Print Network [OSTI]

    Various

    2006-01-01T23:59:59.000Z

    Genome Analysis of MTBE-Degrading Beta- Proteobacteriummethyl tert- butyl ether (MTBE). Strain PM1 can alsooften co-contaminants with MTBE in groundwater, including

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

    E-Print Network [OSTI]

    Chen, Huaming

    2000-01-01T23:59:59.000Z

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

    E-Print Network [OSTI]

    Chen, Huaming

    2000-01-01T23:59:59.000Z

    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...

  16. Tissue sampling and standards for vertebrate genomics

    E-Print Network [OSTI]

    2012-01-01T23:59:59.000Z

    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

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

    E-Print Network [OSTI]

    Batzoglou, Serafim

    2000-01-01T23:59:59.000Z

    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 ...

  18. 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: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level:Energy: Grid Integration Redefining What'sis Taking Over OurTheBrookhaven NationalRegionalsResearch »Funding OpportunityGalleryGenome To

  19. DOE Joint Genome Institute: A DOE Office of Science User Facility of

    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: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645 3,625 1,006 492 742EnergyOnItem NotEnergy, science,SpeedingWu,IntelligenceYou are here ‹ › Science

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

    E-Print Network [OSTI]

    Kazakov, A.E.

    2011-01-01T23:59:59.000Z

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

  1. Translational Science Seminar The University of Illinois at Chicago (UIC) Center for Clinical and

    E-Print Network [OSTI]

    Illinois at Chicago, University of

    Science department applies multidisciplinary approaches involving human genetics, functional genomics

  2. Outlook GENOME ANALYSIS Errors in genome annotation 0168-9525/99/$ see front matter 1999 Elsevier Science All rights reserved. PII: S0168-9525(99)01706-0132

    E-Print Network [OSTI]

    Elsevier Science All rights reserved. PII: S0168-9525(99)01706-0132 At the time that Watson and Crick

  3. 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

  4. DOE Joint Genome Institute | 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: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level:Energy: Grid Integration Redefining What'sis Taking Over OurTheBrookhaven National Laboratory LaboratoryMaterials for EnergyU.S.ScienceDOE

  5. artificial genome model: Topics by E-print Network

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

    Dimension Slatton, Clint 5 Genomic computing: explanatory modelling for functional genomics Richard J. Gilbert Computer Technologies and Information Sciences Websites Summary:...

  6. Joint Genome Institute's Automation Approach and History

    SciTech Connect (OSTI)

    Roberts, Simon

    2006-07-05T23:59:59.000Z

    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.

  7. 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

  8. Genomic definition of species

    SciTech Connect (OSTI)

    Crkvenjakov, R.; Drmanac, R.

    1991-07-01T23:59:59.000Z

    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.

  9. 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

    2011-01-01T23:59:59.000Z

    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.

  10. 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

  11. 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

  12. 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

  13. U.S. Department of Energy's Office of Science

    E-Print Network [OSTI]

    Science, Engineering, & Technology - Hydrogen Production, Storage, and Use - Genomics: GTL, including

  14. Genomics and Systems Biology

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

    Genomics and Systems Biology Genomics and Systems Biology Los Alamos scientists perform research in functional genomics and structural genomics, and applications for such work...

  15. Molluscan Evolutionary Genomics

    E-Print Network [OSTI]

    Simison, W. Brian

    2010-01-01T23:59:59.000Z

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

  16. aa genome oryza: Topics by E-print Network

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

    , Jian Wang1,2* , Gane Ka-Shu Wong1,2,11* , Huanming Yang1,2* 1 Beijing Institute of Genomics of the Chinese Academy of Sciences, Beijing Genomics Institute, Beijing Proteomics...

  17. Genome Engineering

    SciTech Connect (OSTI)

    Voytas, Dan [University of Minnesota

    2014-03-20T23:59:59.000Z

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

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

    SciTech Connect (OSTI)

    Kuo, Alan; Grigoriev, Igor

    2012-06-17T23:59:59.000Z

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

  19. 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.

  20. accessing integrated genomic: Topics by E-print Network

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

    Last Page Topic Index 1 RESEARCH ARTICLE Open Access Integrating cytogenetics and genomics in Environmental Sciences and Ecology Websites Summary: RESEARCH ARTICLE Open Access...

  1. 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

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

    E-Print Network [OSTI]

    Penn, Kevin Matthew

    2012-01-01T23:59:59.000Z

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

  3. 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.

  4. Meeting report The changing face of genomics

    E-Print Network [OSTI]

    Kellis, Manolis

    , Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02138. MIT Computer Science the new challenges in genomics, particularly in the areas of gene regulation, cell dynamics, and genome evolution. (1) Regulation: Systematic discovery of all regulatory elements Given the primary sequence

  5. 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...

  6. JGI Fungal Genomics Program

    E-Print Network [OSTI]

    Grigoriev, Igor V.

    2012-01-01T23:59:59.000Z

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

  7. JGI Fungal Genomics Program

    E-Print Network [OSTI]

    Grigoriev, Igor V.

    2011-01-01T23:59:59.000Z

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

  8. Fungal Genomics Program

    E-Print Network [OSTI]

    Grigoriev, Igor

    2012-01-01T23:59:59.000Z

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

  9. 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

  10. 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

  11. 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

  12. 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: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645U.S. DOE Office of Science (SC) Environmental AssessmentsGeoffrey Campbelllong version)ConfinementGeneralGenomics and

  13. COMPUTATIONAL COMPARATIVE GENOMICS: GENES, REGULATION, EVOLUTION

    E-Print Network [OSTI]

    Kellis, Manolis

    COMPUTATIONAL COMPARATIVE GENOMICS: GENES, REGULATION, EVOLUTION by Manolis (Kellis) Kamvysselis B.S. Electrical Engineering and Computer Science; M. Eng. Computer Science and Engineering Massachusetts Institute at the Massachusetts Institute of Technology June 2003 © 2003 Massachusetts Institute of Technology All rights reserved

  14. 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: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level:Energy: Grid Integration Redefining What's PossibleRadiationImplementingnpitcheResearch BriefsTenney, Office of Science Office of Science β

  15. 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: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level:Energy: Grid Integration Redefining What's PossibleRadiationImplementingnpitcheResearch BriefsTenney, Office of Science Office of Science

  16. *** CANCELED *** SCIENCE ON SATURDAY- "Finding a Needle in A...

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

    Cure Cancer" Professor Olga G. Troyanskaya Lewis-Sigler Institute for Integrative Genomics & Department of Computer Science, Princeton University Science on Saturday is a...

  17. 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...

  18. Genomics and Bioinformatics Doug Brutlag

    E-Print Network [OSTI]

    IX #12;Genomics, Bioinformatics & Computational Biology Computational Biology Computational Molecular Biology BioinformaticsGenomics ProteomicsStructural Genomics #12;Genomics, Bioinformatics & Computational Biology Computational Biology Computational Molecular Biology BioinformaticsGenomics Proteomics

  19. 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

  20. Next-generation sequencing technologies have greatly reduced the cost of sequencing genomes. With the current sequencing technology, a genome is broken

    E-Print Network [OSTI]

    Campbell, A. Malcolm

    such as genome assembly. Key Words: Genome assembly; bioinformatics; computational biology; teaching tool. Genome the fields of mathematics and computer science. The rapid transformation in biological research has made Biology curriculum requires high school stu- dents to learn to use computational tools (College Board

  1. INTRODUCTION TO GENOMIC MEDICINE

    E-Print Network [OSTI]

    INTRODUCTION TO GENOMIC MEDICINE Genomics play a role in 21st century research and clinical related to genomic medicine. Tentative Schedule: WHEN: WHERE: WHO CAN ATTEND? INTRODUCTION January 31 Implications of Genomics in Clinical Medicine February 7 Molecular Biology/Genetics Refresher - 1 February 14

  2. 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: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645U.S. DOE Office of ScienceandMesa del Sol HomeFacebook Twitter Principalfuel cells" Find + AdvancedSignScience

  3. 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: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645 3,625 1,006 492 742EnergyOnItemResearch > TheNuclearHomeland Science Stockpile Stewardship National Security

  4. A GSC Global Genome Census (GSC8 Meeting)

    ScienceCinema (OSTI)

    Kyrpides, Nikos [DOE JGI

    2011-04-29T23:59:59.000Z

    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. ScienceS, TechnologieS AnD heAlTh TECHNOLOGIES

    E-Print Network [OSTI]

    Brest, Université de

    ­ Earth Science (STU)Bachelor's degree Building and construction Environmental Management and Construction Genetics, Genomics and Biotechnology (Vocational and Research) Food, Law, Nutrition and Health Innovation Movement, Sport and Health Genetics, Genomics and Biotechnology (Vocational and Research) electronics Micro

  6. Discovery of functional elements in 12 Drosophila genomes using evolutionary

    E-Print Network [OSTI]

    Bartel, David

    ,6 , Joseph W. Carlson7 , Madeline A. Crosby8 , Matthew D. Rasmussen2 , Sushmita Roy9 , Ameya N. Deoras2 , J, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK. 6 Institute of Computer Science, University

  7. Discovery of functional elements in 12 Drosophila genomes using evolutionary

    E-Print Network [OSTI]

    Kellis, Manolis

    Parts5,6 , Joseph W. Carlson7 , Madeline A. Crosby8 , Matthew D. Rasmussen2 , Sushmita Roy9 , Ameya N, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK. 6 Institute of Computer Science, Un

  8. aestivum bac genomic: Topics by E-print Network

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

    16 17 18 19 20 21 22 23 24 25 Next Page Last Page Topic Index 1 Tuatara (Sphenodon) Genomics: BAC Library Construction, Sequence Survey, Environmental Sciences and Ecology...

  9. JGI Fungal Genomics Program

    SciTech Connect (OSTI)

    Grigoriev, Igor V.

    2011-03-14T23:59:59.000Z

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

  10. Genomic Encyclopedia of Fungi

    SciTech Connect (OSTI)

    Grigoriev, Igor

    2012-08-10T23:59:59.000Z

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

  11. 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

  12. 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

  13. 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

  14. NERSC-ScienceHighlightsSeptember2014.pptx

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

    data analysis pipelines for DOE beamline facilities yield important science results. Genomics Novel algorithm running on Edison has resulted in unequaled processing speed for key...

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

    E-Print Network [OSTI]

    Kelsoe, J R

    2004-01-01T23:59:59.000Z

    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. 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

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

    ScienceCinema (OSTI)

    Chain, Patrick [DOE JGI

    2011-04-28T23:59:59.000Z

    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.

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

    SciTech Connect (OSTI)

    Chain, Patrick [DOE JGI] [DOE JGI

    2009-09-09T23:59:59.000Z

    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. REQUESTS FOR INDEPENDENT STUDY Trinity College of Arts & Sciences

    E-Print Network [OSTI]

    Richardson, David

    REQUESTS FOR INDEPENDENT STUDY Trinity College of Arts & Sciences (GENOME 293/294, GENOME 293 form is available at http://trinity.duke.edu/academic- requirements adheres to academic standards, policies, and procedures pertaining to undergraduate students in Trinity

  20. 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

  1. Insights from twenty years of bacterial genome sequencing

    SciTech Connect (OSTI)

    Land, Miriam L [ORNL; Hauser, Loren John [ORNL; Jun, Se Ran [ORNL; Nookaew, Intawat [ORNL; Leuze, Michael Rex [ORNL; Ahn, Tae-Hyuk [ORNL; Karpinets, Tatiana V [ORNL; Lund, Ole [Technical University of Denmark; Kora, Guruprasad H [ORNL; Wassenaar, Trudy [Molecular Microbiology & Genomics Consultants, Zotzenheim, Germany; Poudel, Suresh [ORNL; Ussery, David W [ORNL

    2015-01-01T23:59:59.000Z

    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.

  2. Fungal Genomics Program

    SciTech Connect (OSTI)

    Grigoriev, Igor

    2012-03-12T23:59:59.000Z

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

  3. 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.

  4. Genomic analysis of mouse tumorigenesis

    E-Print Network [OSTI]

    Tam, Mandy Chi-Mun

    2006-01-01T23:59:59.000Z

    The availability of the human and mouse genome sequences has spurred a growing interest in analyzing mouse models of human cancer using genomic techniques. Comparative genomic studies on mouse and human tumors can be ...

  5. Enhancer Identification through Comparative Genomics

    E-Print Network [OSTI]

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

    2006-01-01T23:59:59.000Z

    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

  6. The Future of Microbial Genomics

    SciTech Connect (OSTI)

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

    2010-06-02T23:59:59.000Z

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

  7. Evolutionary Genomics of Salmonella enterica Subspecies

    E-Print Network [OSTI]

    2013-01-01T23:59:59.000Z

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

  8. Automated Microbial Genome Annotation

    SciTech Connect (OSTI)

    Land, Miriam [DOE Joint Genome Institute at Oak Ridge National Laboratory

    2009-05-29T23:59:59.000Z

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

  9. DOE Office of Science Publishes Update of Landmark Plan: "Facilities...

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

    analysis, and analysis and modeling of cellular systems - to enable the Genomics:GTL program to achieve breakthroughs in basic science needed for cost-effective...

  10. Genomic Analysis of Burkholderia And Rhodococcus equi Bacteriophages

    E-Print Network [OSTI]

    Orchard II, Robert C.

    2011-08-04T23:59:59.000Z

    bacteriophages and pyrosequenced using 454 LifeSciences Technology. These phages are mosaic and sequencing traditional plasmid libraries were sufficient to deconvolute the 454 data. Also reported is the complete genomic sequencing of BcepNY3, a Burkholderia... cenocepacia bacteriophage via a Whole Genome Shotgun Approach. BcepNY3?s 47,382 bp genome was found to encode 70 proteins and 1 tRNA. It was determined that BcepNY3 is part of the previously described Bcep781 family of phages (26). Surprisingly...

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

    E-Print Network [OSTI]

    2013-01-01T23:59:59.000Z

    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

  12. 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.

  13. 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

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

    E-Print Network [OSTI]

    Wurtele, Eve Syrkin

    Comparative and Functional Genomics Comp Funct Genom 2003; 4: 239­245. Published online 1 April://www.botany.iastate.edu/mash/metnetex/metabolicnetex.html) is pub- licly available software in development for analysis of genome-wide RNA, protein and metabolite in the post-genome era is to understand how interactions among molecules in a cell determine its form

  15. 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

  16. 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

  17. Fuzzy Genome Sequence Assembly for Single and Environmental Genomes

    E-Print Network [OSTI]

    Nicolescu, Monica

    Fuzzy Genome Sequence Assembly for Single and Environmental Genomes Sara Nasser, Adrienne Breland. Traditional methods obtain a microorganism's DNA by culturing it in- dividually. Recent advances in genomics microbial commu- nities are often very complex with tens and hundreds of species. Assembling these genomes

  18. Human Genome Program

    SciTech Connect (OSTI)

    Not Available

    1993-01-01T23:59:59.000Z

    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.

  19. 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

  20. 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.

    2010-07-01T23:59:59.000Z

    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.

  1. 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

  2. Genomic library construction

    DOE Patents [OSTI]

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

    2011-07-26T23:59:59.000Z

    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.

  3. 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

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

    E-Print Network [OSTI]

    Posada-Buitrago, Martha Lucia

    2005-01-01T23:59:59.000Z

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

  5. 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

  6. Fueling the Future with Fungal Genomics

    E-Print Network [OSTI]

    Grigoriev, Igor V.

    2011-01-01T23:59:59.000Z

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

  7. 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

  8. VISTA - computational tools for comparative genomics

    E-Print Network [OSTI]

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

    2004-01-01T23:59:59.000Z

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

  9. 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

  10. 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

  11. 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.

  12. Life sciences and environmental sciences

    SciTech Connect (OSTI)

    Not Available

    1992-02-01T23:59:59.000Z

    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.

  13. Life sciences and environmental sciences

    SciTech Connect (OSTI)

    Not Available

    1992-02-01T23:59:59.000Z

    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.

  14. 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

  15. Clinical Microfluidics for Neutrophil Genomics and Proteomics...

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

    Clinical Microfluidics for Neutrophil Genomics and Proteomics. Clinical Microfluidics for Neutrophil Genomics and Proteomics. Abstract: Neutrophils play critical roles in...

  16. Mammalian comparative genomics and epigenomics

    E-Print Network [OSTI]

    Mikkelsen, Tarjei Sigurd, 1978-

    2009-01-01T23:59:59.000Z

    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 ...

  17. Genomics Division Home

    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: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645U.S. DOEThe Bonneville Power AdministrationField8,Dist.Newof EnergyFundingGeneGenome Engineering withfor Genomics

  18. 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: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level:Energy: Grid Integration Redefining What'sis Taking Over OurTheBrookhaven National LaboratoryJeffrey L

  19. 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

  20. Joint Genome Institute (JGI) Projects at NERSC

    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: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645U.S. DOE Office of Science (SC)Integrated Codes |Is Your Home as Ready for(SC)Joint Genome Institute (JGI) Joint

  1. RADIATION SCIENCE AND TECHNOLOGY | ROTARY WING AIRCRAfT | SANITARY -ENVIRONMENTAL

    E-Print Network [OSTI]

    RADIATION SCIENCE AND TECHNOLOGY | ROTARY WING AIRCRAfT | SANITARY - ENVIRONMENTAL ENGINEERING Computational Genomics & Proteomics 2008 Wearable Intelligent Devices for Human Health and Protection 2009

  2. 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

    2008-01-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    2014-01-01T23:59:59.000Z

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

  4. A physical map of the papaya genome with integrated genetic map and genome sequence

    E-Print Network [OSTI]

    2009-01-01T23:59:59.000Z

    genetic map and genome sequence Qingyi Yu 1 , Eric Tong 1 ,assist whole genome shotgun sequence assembly. Results: Thethe genetic map and genome sequence using BAC end sequences

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

    E-Print Network [OSTI]

    Mukhopadhyay, Aindrila

    2010-01-01T23:59:59.000Z

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

  6. acanthamoeba castellanii genome: Topics by E-print Network

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

    and Medicine Websites Summary: Prokaryotic Genomes Eurkaryotic Genomes Chapter 6. Genomics and Gene Identification Weigang Qiu Weigang Qiu Chapter 6. Genomics and Gene...

  7. aeromonas caviae genomic: Topics by E-print Network

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

    and Medicine Websites Summary: Prokaryotic Genomes Eurkaryotic Genomes Chapter 6. Genomics and Gene Identification Weigang Qiu Weigang Qiu Chapter 6. Genomics and Gene...

  8. Report on the Human Genome Initiative

    SciTech Connect (OSTI)

    Tinoco, I.; Cahill, G.; Cantor, C.; Caskey, T.; Dulbecco, R.; Engelhardt, D. L.; Hood, L.; Lerman, L. S.; Mendelsohn, M. L.; Sinsheimer, R. L.; Smith, T.; Soll, D.; Stormo, G.; White, R. L.

    1987-04-01T23:59:59.000Z

    The report urges DOE and the Nation to commit to a large. multi-year. multidisciplinary. technological undertaking to order and sequence the human genome. This effort will first require significant innovation in general capability to manipulate DNA. major new analytical methods for ordering and sequencing. theoretical developments in computer science and mathematical biology, and great expansions in our ability to store and manipulate the information and to interface it with other large and diverse genetic databases. The actual ordering and sequencing involves the coordinated processing of some 3 billion bases from a reference human genome. Science is poised on the rudimentary edge of being able to read and understand human genes. A concerted. broadly based. scientific effort to provide new methods of sufficient power and scale should transform this activity from an inefficient one-gene-at-a-time. single laboratory effort into a coordinated. worldwide. comprehensive reading of "the book of man". The effort will be extraordinary in scope and magnitude. but so will be the benefit to biological understanding. new technology and the diagnosis and treatment of human disease.

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

    E-Print Network [OSTI]

    2007-01-01T23:59:59.000Z

    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

  10. 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

  11. 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

  12. 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

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

    E-Print Network [OSTI]

    Gent, Universiteit

    GenomeView: a next-generation genome browser Thomas Abeel1,2,3, *, Thomas Van Parys1,2 , Yvan Saeys GenomeView, a stand-alone genome browser specifically designed to visualize and manipulate a multitude of genomics data. GenomeView enables users to dynamically browse high volumes of aligned short-read data

  14. Science Curriculum at HKUScience Curriculum at HKU What is a University?

    E-Print Network [OSTI]

    Tam, Vincent W. L.

    are results of synthesis of ideas in different disciplines ­ Human Genome Project ­ Environmental Science Bachelor of Science #12;Astronomy Biotechnology (for 3-year curriculum) Biochemistry Biology (for 3-year; Endocrinology: human physiology; Food microbiology; Environmental toxicology; Clinical microbiology and Applied

  15. The OME Framework for genome-scale systems biology

    SciTech Connect (OSTI)

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

    2014-12-19T23:59:59.000Z

    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.

  16. DOE Joint Genome Institute 2008 Progress Report

    SciTech Connect (OSTI)

    Gilbert, David

    2009-03-12T23:59:59.000Z

    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

  17. Yeast Genomic Library Genomic DNA Sau3AI partial digestion

    E-Print Network [OSTI]

    Odorizzi, Greg

    Yeast Genomic Library Concept: Genomic DNA ­ Sau3AI partial digestion Vector DNA ­ BamHI full digestion partial Ligate and transform above products Vector Information: · use centromeric plasmid to avoid of the mcs Preparing Vector: 1) digest 3-4ug of library vector with BamHI for 2-4hrs in a total volume of 20

  18. Genome 361: Fundamentals of Genetics and Genomics Spring 2014 Instructors

    E-Print Network [OSTI]

    Dunham, Maitreya

    testing for inherited diseases, human cloning, stem cell research, and genetically modified foods, to name1 Genome 361: Fundamentals of Genetics and Genomics Spring 2014 Instructors Maitreya Dunham.edu Course overview Genetics is the scientific study of heredity. In the last century, many genetic methods

  19. SCIENCE CHINA Technological Sciences

    E-Print Network [OSTI]

    Wang, Zhong L.

    SCIENCE CHINA Technological Sciences © Science China Press and Springer-Verlag Berlin Heidelberg and Nanosystems, Chinese Academy of Sciences, Beijing 100083, China; 2 Institute of Theoretical Physics, Lanzhou University, Lanzhou 730000, China; 3 School of Material Science and Engineering, Georgia Institute

  20. ORIGINAL PAPER The interdisciplinary engineering knowledge genome

    E-Print Network [OSTI]

    Shai, Offer

    ORIGINAL PAPER The interdisciplinary engineering knowledge genome Yoram Reich · Offer Shai Received, termed the ``Interdisciplinary Engineering Knowledge Genome'', which is an organized collection of system, the Interdisciplinary Engineering Knowledge Genome unifies many engineering disciplines, providing a basis

  1. Trichoderma: the genomics of opportunistic success

    E-Print Network [OSTI]

    Druzhinina, Irina S.

    2011-01-01T23:59:59.000Z

    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,

  2. Evolutionary Genomics of Salmonella enterica Subspecies

    E-Print Network [OSTI]

    2013-01-01T23:59:59.000Z

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

  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: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645U.S. DOEThe Bonneville Power AdministrationField8,Dist.Newof EnergyFundingGeneGenome Engineering withfor

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

    E-Print Network [OSTI]

    Church, George M.

    2013-01-01T23:59:59.000Z

    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

  5. BER Science Network Requirements

    SciTech Connect (OSTI)

    Dart, Eli; Tierney, Brian

    2010-11-01T23:59:59.000Z

    The Energy Sciences Network (ESnet) is the primary provider of network connectivity for the US Department of Energy Office of Science, the single largest supporter of basic research in the physical sciences in the United States. In support of the Office of Science programs, ESnet regularly updates and refreshes its understanding of the networking requirements of the instruments, facilities, scientists, and science programs that it serves. This focus has helped ESnet to be a highly successful enabler of scientific discovery for over 20 years. In April 2010 ESnet and the Office of Biological and Environmental Research, of the DOE Office of Science, organized a workshop to characterize the networking requirements of the science programs funded by BER. The requirements identified at the workshop are summarized and described in more detail in the case studies and the Findings section. A number of common themes emerged from the case studies and workshop discussions. One is that BER science, like many other disciplines, is becoming more and more distributed and collaborative in nature. Another common theme is that data set sizes are exploding. Climate Science in particular is on the verge of needing to manage exabytes of data, and Genomics is on the verge of a huge paradigm shift in the number of sites with sequencers and the amount of sequencer data being generated.

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

    E-Print Network [OSTI]

    Lapidus, Alla L.

    2009-01-01T23:59:59.000Z

    a graphical tool for sequence finishing. Genome Research 8,Multiplexed genotyping with sequence- tagged molecularX. (1996). An improved sequence assembly program. Genomics

  7. Fueling Future with Algal Genomics

    SciTech Connect (OSTI)

    Grigoriev, Igor

    2012-07-05T23:59:59.000Z

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

  8. Identification and characterization of insect-specific proteins by genome data analysis

    E-Print Network [OSTI]

    Zhang, Guojie; Wang, Hongsheng; Shi, Junjie; Wang, Xiaoling; Zheng, Hongkun; Wong, Gane Ka-Shu; Clark, Terry; Wang, Wen; Wang, Jun; Kang, Le

    2007-04-04T23:59:59.000Z

    ral ssBioMed CentBMC Genomics Open AcceResearch article Identification and characterization of insect-specific proteins by genome data analysis Guojie Zhang†1,2,3, Hongsheng Wang†1, Junjie Shi†2, Xiaoling Wang2, Hongkun Zheng2, Gane Ka-Shu Wong2..., Terry Clark4, Wen Wang3, Jun Wang2,5 and Le Kang*1 Address: 1State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology Chinese Academy of Sciences, Haidian Beijing 100080, China, 2Beijing Institute of Genomics...

  9. Ecology and Evolutionary Biology The Wiess School of Natural Sciences

    E-Print Network [OSTI]

    Richards-Kortum, Rebecca

    Ecology and Evolutionary Biology The Wiess School of Natural Sciences Chair Evan Siemann Professors of Ecology and Evolutionary Biologyoffersabroadrangeofcoursesinthebiosciences:animalbehavior,animal biology, bioinformatics, conservation biology, diseases, ecology, evolutionary biology, field ecology, genetics, genomics

  10. Biological Production of Hydrogen DOE Office of Science,

    E-Print Network [OSTI]

    .Houghton@science.doe.gov #12;Biology transforms energy in a series ofBiology transforms energy in a series University Artificial Chromosome: Minimum Genome Oligo Assembly Microalgae production facility of Cyanotech

  11. Human genome. 1993 Program report

    SciTech Connect (OSTI)

    Not Available

    1994-03-01T23:59:59.000Z

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

  12. A Statistical Framework for Spatial Comparative Genomics

    E-Print Network [OSTI]

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

  13. 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

  14. Genomics and ornithology Scott V. Edwards

    E-Print Network [OSTI]

    Edwards, Scott

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

  15. SHORT REVIEW Ecological genomics: understanding gene and

    E-Print Network [OSTI]

    Kaufman, Glennis A.

    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

  16. 2004 Structural, Function and Evolutionary Genomics

    SciTech Connect (OSTI)

    Douglas L. Brutlag Nancy Ryan Gray

    2005-03-23T23:59:59.000Z

    This Gordon conference will cover the areas of structural, functional and evolutionary genomics. It will take a systematic approach to genomics, examining the evolution of proteins, protein functional sites, protein-protein interactions, regulatory networks, and metabolic networks. Emphasis will be placed on what we can learn from comparative genomics and entire genomes and proteomes.

  17. Assignment of Orthologous Genes via Genome Rearrangement

    E-Print Network [OSTI]

    Lonardi, Stefano

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

  18. 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

  19. 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

  20. 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

  1. 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

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

    SciTech Connect (OSTI)

    Kuo, Alan; Grigoriev, Igor

    2009-04-17T23:59:59.000Z

    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.

  3. 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

    2013-01-22T23:59:59.000Z

    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.

  4. 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

    2012-03-22T23:59:59.000Z

    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.

  5. Synthetic Genomics: Options for Governance

    E-Print Network [OSTI]

    Garfinkel, Michele

    2007-10-17T23:59:59.000Z

    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 ...

  6. The Center for integrative genomics

    E-Print Network [OSTI]

    Fankhauser, Christian

    , a new advenTure · a new institute with state-of-the-art technologies and facilities · Cutting edge roles for the human herpes simplex virus host cell factor HCF- in controlling genome duplication, transcription factors, a

  7. 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

  8. Implications of structural genomics target selection strategies: Pfam5000, whole genome, and random approaches

    E-Print Network [OSTI]

    Chandonia, John-Marc; Brenner, Steven E.

    2004-01-01T23:59:59.000Z

    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):

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

    SciTech Connect (OSTI)

    none,

    1988-04-01T23:59:59.000Z

    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.

  10. Genomics of emerging infectious disease: A PLoS collection.

    E-Print Network [OSTI]

    Eisen, Jonathan A; MacCallum, Catriona J

    2009-01-01T23:59:59.000Z

    Origins and evolutionary genomics of the 2009 swine-originan Infectious Diseases Genomics Project predict and preventRavel J (2009) The role of genomics in the identification,

  11. 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

    2010-01-01T23:59:59.000Z

    environment for structural genomics Dana Weekes 1† , S Srihigh-throughput structural genomics centers, despite theirbeing determined by structural genomics centers and high-

  12. Comparative genomics reveals diversity among xanthomonads infecting tomato and pepper

    E-Print Network [OSTI]

    2011-01-01T23:59:59.000Z

    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://

  13. Dissection of Plant Defense Mechanisms Using Chemical and Molecular Genomics

    E-Print Network [OSTI]

    Rodriguez-Salus, Melinda Sue

    2012-01-01T23:59:59.000Z

    of auxins by a chemical genomics approach." Journal ofadvances in chemical genomics." Current Medicinal Chemistrymolecular and chemical genomics." Phytopathology 97(7): S58-

  14. Validation in Genomics: CpG Island Methylation Revisited

    E-Print Network [OSTI]

    Segal, Mark R

    2006-01-01T23:59:59.000Z

    analysis. In: Functional Genomics: Methods and Protocols, M.Segal: Validation in Genomics: CpG Island Methylationpackage and applications to genomics. Bioinformatics and

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

    E-Print Network [OSTI]

    Arkin, Adam P.

    2014-01-01T23:59:59.000Z

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

  16. MicrobesOnline: an integrated portal for comparative functional genomics

    E-Print Network [OSTI]

    Joachimiak, Marcin P.

    2014-01-01T23:59:59.000Z

    comparative functional genomics Marcin P. Joachimiak 1,2 ,for comparative functional genomics of bacteria and archaea.publicly avail- able functional genomics data from published

  17. Microbes Online: an integrated portal for comparative functional genomics

    E-Print Network [OSTI]

    Arkin, Adam P.

    2014-01-01T23:59:59.000Z

    comparative functional genomics of bacteria, archaea, fungifor comparative functional genomics Paramvir S. Dehal 1,2* (and Environmental Research, Genomics:GTL program through

  18. additional structural genome: Topics by E-print Network

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

    a mitochondrial genome Archibald, John 3 Protein structure prediction and structural genomics CiteSeer Summary: Genome sequencing projects are producing linear amino acid...

  19. ancient human genome: Topics by E-print Network

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

    permafrost-preserved hair, the genome technologies have initiated an era of personal genomics. Eight human genome sequences have been reported so far Nielsen, Rasmus 3 A large...

  20. analyses genomes comparison: Topics by E-print Network

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

    %) of coding sequence, the human genome encodes only 3%, while 13 COMPUTATIONAL GENOMICS: MAPPING, COMPARISON, AND ANNOTATION OF GENOMES Biotechnology Websites Summary:...

  1. ancient genome duplication: Topics by E-print Network

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

    permafrost-preserved hair, the genome technologies have initiated an era of personal genomics. Eight human genome sequences have been reported so far Nielsen, Rasmus 8 Gene &...

  2. 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

  3. 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)

  4. 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

  5. SCIENCE CHINA Technological Sciences

    E-Print Network [OSTI]

    Simons, Jack

    SCIENCE CHINA Technological Sciences © Science China Press and Springer-Verlag Berlin Heidelberg. Density-functional-theory formulation of classical and quantum Hooke's law. Sci China Tech Sci, 2014, 57- sider an equilibrium lattice without strain (=0), but elec- #12;Hu H, et al. Sci China Tech Sci April

  6. 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

    2014-01-01T23:59:59.000Z

    Hubs: Web Accessible Browsers for Compar- ative Genomics 3.1Comparative Genomics Analyses . . . . . . . . . . . . . .browsers for comparative genomics” B.1 E. coli KO11FL 162099

  7. Explore Science

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

    Science Explore Science Explore Explore these Topics Activities Videos Cool Links Favorite Q&A invisible utility element Science is thinking in an organized way about things...

  8. Uncovering the dynamics of genome function at the organismal scale using

    E-Print Network [OSTI]

    Wisconsin at Madison, University of

    and Page, Science, 2000 Genetronic Replicator ­ Star Trek: TNG, 1992 #12;The genomic powerhouses ~20 facilitate the above ~25,000 genes #12;Workflow Data Capture Data Capture Data Storage (30 TB) Data Compression and Analysis Feature Extraction Data Storage (X TB) Schorr Center and OSG 0.5 TB/day Data

  9. Towards integrated clinico-genomic models for personalized medicine: combining gene

    E-Print Network [OSTI]

    West, Mike

    signatures and clinical factors in breast cancer outcomes prediction Joseph R. Nevins1,2,6,*, Erich S. Huang1 in the characterization of human cancers, including the ability to predict clinical outcomes. Nevertheless, most analyses predictions of clinical outcomes. INTRODUCTION Recent advances in genome science and technology define

  10. ; 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

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

    SciTech Connect (OSTI)

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

    2009-09-09T23:59:59.000Z

    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.

  12. 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

    2011-04-29T23:59:59.000Z

    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.

  13. 676 Combinatorial Chemistry & High Throughput Screening, 2007, 10, 676-697 1386-2073/07 $50.00+.00 2007 Bentham Science Publishers Ltd.

    E-Print Network [OSTI]

    Powers, Robert

    .00+.00 © 2007 Bentham Science Publishers Ltd. Functional Genomics and NMR Spectroscopy Robert Powers* Department genome project and the continued accomplishment in obtaining DNA se- quences for a vast array- nome-wide functional annotation (functional genomics) has evolved as the necessary next step. Nuclear

  14. 131Cognitive Science COGNITIVE SCIENCE

    E-Print Network [OSTI]

    Marsh, David

    131Cognitive Science COGNITIVE SCIENCE PROFESSOR ELMES* MAJOR A major in cognitive science leading courses: Cognitive Science 110, 395, 403, 473; Computer Science 111, 211; Philosophy 106, 313; Psychology Science: Com- puter Science 295 (LISP, PROLOG or C), 313, 315; Psychology 207 b. Philosophical Foundations

  15. Genomics :GTL project quarterly report April 2005.

    SciTech Connect (OSTI)

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

    2005-11-01T23:59:59.000Z

    This SAND report provides the technical progress through April 2005 of the Sandia-led project, ''Carbon Sequestration in Synechococcus Sp.: From Molecular Machines to Hierarchical Modeling'', funded by the DOE Office of Science GenomicsGTL 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 microamy 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.

  16. The Genome of the Epsilonproteobacterial Chemolithoautotroph Sulfurimonas dentrificans

    E-Print Network [OSTI]

    Sievert, Stefan M.; USF Genomics Class

    2008-01-01T23:59:59.000Z

    10 , Jörg Simon 11 , and the USF Genomics Class 2, ? Biologyof coverage at the Production Genomics Facility of the Joint

  17. Genome Size Varaiation in D. melanogaster

    E-Print Network [OSTI]

    Alfrejd, Benjamin

    2011-04-26T23:59:59.000Z

    in genome size may account for some of the missing heritability. We measured female genome sizes for 34 Drosophila melanogaster inbred strains that derived from isofemale lines established from a natural population in Raleigh, NC, in addition to a group...

  18. 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...

  19. GWIDD: Genome-wide protein docking database

    E-Print Network [OSTI]

    Kundrotas, Petras J.; Zhu, Zhengwei; Vasker, Ilya A.

    2009-11-09T23:59:59.000Z

    Structural information on interacting proteins is important for understanding life processes at the molecular level. Genome-wide docking database is an integrated resource for structural studies of protein–protein interactions on the genome scale...

  20. 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

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

    E-Print Network [OSTI]

    Goldschmidt, Christina

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

  2. 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

  3. 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

  4. From genomics to chemical genomics: new developments in KEGG

    E-Print Network [OSTI]

    Minoru Kanehisa; Susumu Goto; Masahiro Hattori; Kiyoko F. Aoki-kinoshita; Masumi Itoh; Shuichi Kawashima; Toshiaki Katayama; Michihiro Araki; Mika Hirakawa

    2006-01-01T23:59:59.000Z

    The increasing amount of genomic and molecular information is the basis for understanding higherorder biological systems, such as the cell and the 15 organism, and their interactions with the environment, as well as for medical, industrial and other practical applications. The KEGG resource

  5. Joint Genome Institute's Automation Approach and History

    E-Print Network [OSTI]

    Roberts, Simon

    2006-01-01T23:59:59.000Z

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

  6. 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

  7. 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

  8. 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

  9. INVITED: Comparative Microbial Genomics Giri Narasimhan

    E-Print Network [OSTI]

    Narasimhan, Giri

    INVITED: Comparative Microbial Genomics Giri Narasimhan Bioinformatics Research Group (Bio, comparative genomics holds the keys to decipher and mine this wealth of information. We discuss the diverse ways in which the availability of comparative genomics data allows us to answer more questions

  10. 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

  11. 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

  12. 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

  13. Prospects & Overviews Evolution of eukaryotic genome

    E-Print Network [OSTI]

    Babu, M. Madan

    , O. dioica has a rapidly evolving, highly compact genome with a divergent intron-exon organization. Additionally, O. dioica lacks the minor spli- ceosome and key DNA repair pathway genes. Even with a compact on various aspects of the global genome architecture and different genomic fea- tures such as intron

  14. Genome Biology 2005, 6:312 commentreviewsreportsdepositedresearchinteractionsinformationrefereedresearch

    E-Print Network [OSTI]

    Kellis, Manolis

    Genome Biology 2005, 6:312 commentreviewsreportsdepositedresearchinteractionsinformationrefereedresearch Meeting report Large-scale discovery and validation of functional elements in the human genome-mail: bbernst@fas.harvard.edu. Manolis Kellis. E-mail: manoli@mit.edu Published: 1 March 2005 Genome Biology

  15. Genome Biology 2006, 7:320 commentreviewsreportsdepositedresearchinteractionsinformationrefereedresearch

    E-Print Network [OSTI]

    Pritham, Ellen J.

    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

  16. DATA QUALITY IN GENOME DATABASES (Research Paper)

    E-Print Network [OSTI]

    Weske, Mathias

    DATA QUALITY IN GENOME DATABASES (Research Paper) Heiko MĂĽller 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

  17. 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

  18. 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

  19. 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

  20. U.S. Department of Energy's Office of Science

    E-Print Network [OSTI]

    Infrastructure................ 37,125 42,735 43,590 Science Program Direction........................... 149..................................................................241,100 257,310 246,882 257,310 Science Laboratories Infrastructure the Hydrogen Economy: Materials, Catalysis, Modeling, Electrochemistry, Genomes to Life, Fusion production, etc

  1. Managing the genome data deluge

    SciTech Connect (OSTI)

    Aldhous, P.

    1993-10-22T23:59:59.000Z

    This article describes efforts to integrate all the databases containing sequence information generated by the Human Genome Project. Projects range from putting all the information in one central source, to creating systems for allowing the user to communicate with the different databases in one operation.

  2. Nuclear Organization and Genome Function

    E-Print Network [OSTI]

    Corces, Victor G.

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

  3. Microfluidic Devices for Genomic Analysis

    E-Print Network [OSTI]

    the puzzle of interactions between proteins is far more complicated than deciphering genomes, due to the lack, and industry. Fractionation of biological molecules, such as nucleic acids and proteins, plays a central role of proteins' equivalent of amplification, fractionation and sequencing techniques. Micro- and nano

  4. 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.

    2011-02-04T23:59:59.000Z

    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.

  5. 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

  6. 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

  7. The human genome: Some assembly required. Final report

    SciTech Connect (OSTI)

    NONE

    1994-12-31T23:59:59.000Z

    The Human Genome Project promises to be one of the most rewarding endeavors in modern biology. The cost and the ethical and social implications, however, have made this project the source of considerable debate both in the scientific community and in the public at large. The 1994 Graduate Student Symposium addresses the scientific merits of the project, the technical issues involved in accomplishing the task, as well as the medical and social issues which stem from the wealth of knowledge which the Human Genome Project will help create. To this end, speakers were brought together who represent the diverse areas of expertise characteristic of this multidisciplinary project. The keynote speaker addresses the project`s motivations and goals in the larger context of biological and medical sciences. The first two sessions address relevant technical issues, data collection with a focus on high-throughput sequencing methods and data analysis with an emphasis on identification of coding sequences. The third session explores recent advances in the understanding of genetic diseases and possible routes to treatment. Finally, the last session addresses some of the ethical, social and legal issues which will undoubtedly arise from having a detailed knowledge of the human genome.

  8. E-Print Network 3.0 - applying whole-genome studies Sample Search...

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

    (Lec 19) Picture Copyright: AccessExcellence @ the National Museum of Health Summary: Genomics Comparison of whole genomes. - Whole genome sequencing - Whole genome annotation &...

  9. 10. international mouse genome conference

    SciTech Connect (OSTI)

    Meisler, M.H.

    1996-12-31T23:59:59.000Z

    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.

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

    ScienceCinema (OSTI)

    Neal Lane

    2010-09-01T23:59:59.000Z

    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.

  11. Genome Improvement at JGI-HAGSC

    SciTech Connect (OSTI)

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

    2012-03-03T23:59:59.000Z

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

  12. 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...

  13. Life sciences: Lawrence Berkeley Laboratory, 1988

    SciTech Connect (OSTI)

    Not Available

    1989-07-01T23:59:59.000Z

    Life Sciences Research at LBL has both a long history and a new visibility. The physics technologies pioneered in the days of Ernest O. Lawrence found almost immediate application in the medical research conducted by Ernest's brother, John Lawrence. And the tradition of nuclear medicine continues today, largely uninterrupted for more than 50 years. Until recently, though, life sciences research has been a secondary force at the Lawrence Berkeley Laboratory (LBL). Today, a true multi-program laboratory has emerged, in which the life sciences participate as a full partner. The LBL Human Genome Center is a contribution to the growing international effort to map the human genome. Its achievements represent LBL divisions, including Engineering, Materials and Chemical Sciences, and Information and Computing Sciences, along with Cell and Molecular Biology and Chemical Biodynamics. The Advanced Light Source Life Sciences Center will comprise not only beamlines and experimental end stations, but also supporting laboratories and office space for scientists from across the US. This effort reflects a confluence of scientific disciplines --- this time represented by individuals from the life sciences divisions and by engineers and physicists associated with the Advanced Light Source project. And finally, this report itself, the first summarizing the efforts of all four life sciences divisions, suggests a new spirit of cooperation. 30 figs.

  14. Annotation-based genome-wide SNP discovery in the large and complex Aegilops tauschii genome using next-generation sequencing without a reference genome sequence

    E-Print Network [OSTI]

    2011-01-01T23:59:59.000Z

    the soybean whole genome sequence. BMC Genomics 2010, 11:38.SNPs without a reference sequence. BMC Bioinformatics 2010,identification of repetitive sequences in plants. Nucleic

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

    SciTech Connect (OSTI)

    Rounsley, Steve [University of Arizona

    2014-03-20T23:59:59.000Z

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

  16. 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

  17. 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

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

    ScienceCinema (OSTI)

    Zimmer, Carl [New York Times

    2013-01-22T23:59:59.000Z

    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

  19. Genome Announcement1 Draft genome sequence of the electricity producing3

    E-Print Network [OSTI]

    Hazen, Terry

    1 Genome Announcement1 2 Draft genome sequence of the electricity producing3 Thermincola potens of insoluble electron acceptors by model Gram-negative64 bacteria such as Geobacter or Shewanella species (4

  20. 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

    2012-03-20T23:59:59.000Z

    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

  1. TRENDS in Genetics Vol.18 No.11 November 2002 http://tig.trends.com 0168-9525/02/$ see front matter 2002 Elsevier Science Ltd. All rights reserved. PII

    E-Print Network [OSTI]

    Fernandez, Thomas

    matter © 2002 Elsevier Science Ltd. All rights reserved. PII: 555Opinion One result of genome-9525/02/$ ­ see front matter © 2002 Elsevier Science Ltd. All rights reserved. PII: S0168-9525(02)02765-8 Genotype

  2. Diatom Genomics (2009 JGI User Meeting)

    ScienceCinema (OSTI)

    Ambrust, Ginger

    2011-04-25T23:59:59.000Z

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

  3. One Bacterial Cell, One Complete Genome

    E-Print Network [OSTI]

    Woyke, Tanja

    2010-01-01T23:59:59.000Z

    displacement amplification (MDA). Sanger-based finishingour single cell genome and exclude MDA-derived artifacts, wedisplacement amplification (MDA) [4,14], enabling random

  4. Faculty of Science Environmental Science

    E-Print Network [OSTI]

    quality control and monitoring · Environmental management and conservation · Education with additionalFaculty of Science Environmental Science If you have a natural curiosity and concern about the environment, Environmental Science offers you exciting career opportunities. It applies scientific tools from

  5. GENOMIC RESOURCES NOTE Genomic Resources Notes accepted 1 February 201331 March

    E-Print Network [OSTI]

    Rieseberg, Loren

    GENOMIC RESOURCES NOTE Genomic Resources Notes accepted 1 February 2013­31 March 2013 GENOMIC RESOURCES DEVELOPMENT CONSORTIUM,1 MATTHEW G. KING,2 SE´ BASTIEN RENAUT,3 LOREN H. RIESEBERG2,4 and HEATHER C. ROWE3 1 Molecular Ecology Resources Editorial Office, 6270 University Blvd, Vancouver, BC V6T 1Z4

  6. Genomic Responses to the Loss of LRPPRC MITOCHONDRIAL AND NUCLEAR GENOMIC RESPONSES TO LOSS OF LRPPRC

    E-Print Network [OSTI]

    Mootha, Vamsi K.

    of Systems Biology, Harvard Medical School, Boston, MA 02446 USA Running head: Genomic Responses to the LossGenomic Responses to the Loss of LRPPRC 1 MITOCHONDRIAL AND NUCLEAR GENOMIC RESPONSES TO LOSS with the loss of LRPPRC. Using this strategy, we discovered a specific role for LRPPRC in the expression of all

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

    E-Print Network [OSTI]

    Pachter, Lior

    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

  8. ORIGINAL ARTICLE Comparative genomics of two newly isolated

    E-Print Network [OSTI]

    Alvarez-Cohen, Lisa

    ORIGINAL ARTICLE Comparative genomics of two newly isolated Dehalococcoides strains of Microbiology, Cornell University, Ithaca, NY, USA Comparative genomics of Dehalococcoides strains and an enrichment were performed using a microarray targeting genes from all available sequenced genomes

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

    E-Print Network [OSTI]

    Boore, Jeffrey L.

    2009-01-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Penn, Kevin; Jensen, Paul R

    2012-01-01T23:59:59.000Z

    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

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

    SciTech Connect (OSTI)

    Chain, Patrick [DOE-JGI

    2009-05-27T23:59:59.000Z

    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"

  12. Structural Genomics of Minimal Organisms: Pipeline and Results

    E-Print Network [OSTI]

    Kim, Sung-Hou

    2008-01-01T23:59:59.000Z

    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

  13. UV Decontamination of MDA Reagents for Single Cell Genomics

    E-Print Network [OSTI]

    Lee, Janey

    2011-01-01T23:59:59.000Z

    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

  14. Phytozome: A Comparative Platform for Green Plant Genomics

    E-Print Network [OSTI]

    Goodstein, David M.

    2012-01-01T23:59:59.000Z

    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-

  15. The Impact of Structural Genomics: Expectations and Outcomes

    E-Print Network [OSTI]

    Chandonia, John-Marc; Brenner, Steven E.

    2005-01-01T23:59:59.000Z

    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

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

    E-Print Network [OSTI]

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

    2005-01-01T23:59:59.000Z

    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

  17. The common ground of genomics and systems biology

    E-Print Network [OSTI]

    Conesa, Ana; Mortazavi, Ali

    2014-01-01T23:59:59.000Z

    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.

  18. asian diploid genome: Topics by E-print Network

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

    coverage, and guided by the reference genome, we used uniquely mapped for personal genomics. The completion of a highly refined, encyclopaedic human genome sequence1,2 was a...

  19. Science | Argonne National Laboratory

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

    Science Computing, Environment & Life Sciences Energy & Global Security Photon Sciences Physical Sciences & Engineering Energy Frontier Research Centers Institute for Molecular...

  20. The completion and near completion of the sequencing phase of genome projects has ushered in the age of proteomics, the

    E-Print Network [OSTI]

    Gerstein, Mark

    articles The completion and near completion of the sequencing phase of genome projects has ushered Science, PO Box 208114, Yale University, New Haven, Connecticut 06520, USA. 5Environmental Molecular, USA. 6Departments of Biochemistry and Molecular Biology, Chemistry, and the Biotechnology Laboratory

  1. 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.

    2014-01-01T23:59:59.000Z

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

  2. SciTech Connect: Achievements of structural genomics

    Office of Scientific and Technical Information (OSTI)

    Achievements of structural genomics Citation Details In-Document Search Title: Achievements of structural genomics You are accessing a document from the Department of Energy's...

  3. SciTech Connect: Multiplex automated genome engineering

    Office of Scientific and Technical Information (OSTI)

    Multiplex automated genome engineering Citation Details In-Document Search Title: Multiplex automated genome engineering You are accessing a document from the Department of...

  4. Combining Functional and Structural Genomics to Sample the Essential...

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

    Functional and Structural Genomics to Sample the Essential Burkholderia Structome. Combining Functional and Structural Genomics to Sample the Essential Burkholderia Structome....

  5. The Seattle Structure Genomics Center for Infectious Disease...

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

    The Seattle Structure Genomics Center for Infectious Disease (SSGCID). The Seattle Structure Genomics Center for Infectious Disease (SSGCID). Abstract: The NIAID-funded Seattle...

  6. DOE JGI Whole Genome Shotgun Sequencing, part 1

    ScienceCinema (OSTI)

    Miranda Harmon-Smith

    2010-09-01T23:59:59.000Z

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

  7. DOE JGI Whole Genome Shotgun Sequencing, part 3

    ScienceCinema (OSTI)

    Miranda Harmon-Smith

    2010-09-01T23:59:59.000Z

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

  8. DOE JGI Whole Genome Shotgun Sequencing, part 2

    ScienceCinema (OSTI)

    Miranda Harmon-Smith

    2010-09-01T23:59:59.000Z

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

  9. Comparative Omics-Driven Genome Annotation Refinement: Application...

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

    Abstract: Genome sequencing continues to be a rapidly evolving technology, yet most downstream aspects of genome annotation pipelines remain relatively stable or are even being...

  10. analysis incorporating genomic: Topics by E-print Network

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

    Theses and Dissertations Summary: ??Genome sequence analysis is central to todays genomics research, and sequence alignment and Single-Nucleotide Polymorphism (SNP) detection...

  11. atlantic salmon genome: Topics by E-print Network

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

    maps of the Atlantic salmon (Salmo salar) genome derived from RAD sequencing BMC Genomics 2014, 15 Millar, Andrew J. 2 Sex Determination in Tasmanian Atlantic Salmon. Open...

  12. acyrthosiphon pisum genome: Topics by E-print Network

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

    2008-01-01 3 Genome Sequence of the Pea Aphid Acyrthosiphon The International Aphid Genomics Consortium" Physics Websites Summary: by anyone for any lawful purpose. Funding: Work...

  13. aspergillus genome database: Topics by E-print Network

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

    and avoid outdated data. Heiko Mller 11 Integrative database analysis in structural genomics CiteSeer Summary: Abstract (2 sentences) An important aspect of structural genomics...

  14. accelerated genome evolution: Topics by E-print Network

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

    Theses and Dissertations Summary: ??Genome sequence analysis is central to todays genomics research, and sequence alignment and Single-Nucleotide Polymorphism (SNP) detection...

  15. aphid genome absence: Topics by E-print Network

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

    Topic Index 1 Genome Sequence of the Pea Aphid Acyrthosiphon The International Aphid Genomics Consortium" Physics Websites Summary: by anyone for any lawful purpose. Funding: Work...

  16. accurate structural genome: Topics by E-print Network

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

    door de promotor: unknown authors 8 Protein structure prediction and structural genomics CiteSeer Summary: Genome sequencing projects are producing linear amino acid...

  17. af146527 genomic repeat: Topics by E-print Network

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

    of Repeats, Signatures, and Patterns in Genomic Sequences Michael Robinson of genomics, proteomics, and many other "-omics," vast quantities of information are generated...

  18. Uses of antimicrobial genes from microbial genome

    DOE Patents [OSTI]

    Sorek, Rotem; Rubin, Edward M.

    2013-08-20T23:59:59.000Z

    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.

  19. Genome of Geobacter sulfurreducens: Metal Reduction

    E-Print Network [OSTI]

    Lovley, Derek

    and in the generation of electricity. G. sulfurreducens, a member of the - Proteobacteria and of the family GeobacterGenome of Geobacter sulfurreducens: Metal Reduction in Subsurface Environments B. A. Methe´,1 * K. Utterback,1 S. E. Van Aken,1 D. R. Lovley,2 C. M. Fraser1 The complete genome sequence of Geobacter

  20. Genome Biology 2003, 4:R43 commentreviewsreportsdepositedresearchrefereedresearchinteractionsinformation

    E-Print Network [OSTI]

    Kellis, Manolis

    , Massachusetts Institute of Technology, Cambridge, MA 02139, USA. §Whitehead/MIT Center for Genome Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. ¶Department of Genome conserved word pairs associated with gene-expression changes in yeastsTranscriptional regulation

  1. Computational Identification of Operons in Microbial Genomes

    E-Print Network [OSTI]

    computational pipeline is proposed to find potential operons in microbial genomes. The algorithm relies activities and regulation, it is encouraged by selection. By group regu- lation of certain highly expressed expenditure. In most bacterial genomes, func- tionally coupled gene clusters are often regulated under

  2. Fungal biology: compiling genomes and exploiting them

    SciTech Connect (OSTI)

    Labbe, Jessy L [ORNL; Uehling, Jessie K [ORNL; Payen, Thibaut [INRA; Plett, Jonathan [University of Western Sydney, Australia

    2014-01-01T23:59:59.000Z

    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).

  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

    2011-04-29T23:59:59.000Z

    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. Genomic definition of species. Revision 2

    SciTech Connect (OSTI)

    Crkvenjakov, R.; Drmanac, R.

    1993-03-01T23:59:59.000Z

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

  5. Database Requirements for Workflow Management in a HighThroughput Genome Laboratory 1

    E-Print Network [OSTI]

    Bonner, Anthony

    @genome.wi.mit.edu 2 University of Toronto Department of Computer Science 10 King's College Rd Toronto, ON, Canada M5S constitutes an audit trail, or event history, and has much the same function as a laboratory notebook number P50 HG00098, and from the U.S. Department of Energy under contract DE­FG02­95ER62101. 1 #12

  6. 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

  7. Faculty of Science Environmental Science

    E-Print Network [OSTI]

    Faculty of Science Environmental Science If you have a natural curiosity and concern about the environment, Environmental Science offers you exciting career opportunities. It applies scientific tools from.uwindsor.ca/earth #12;Environmental Science We look forward to meeting you! You will receive a solid grounding

  8. 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

  9. 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

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

    E-Print Network [OSTI]

    Castellana, Natalie

    2012-01-01T23:59:59.000Z

    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,

  11. Technetium Chemistry Science Challenges in Environmental Science

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

    Technetium Chemistry Science Challenges in Environmental Science and Waste Processing Workshop Sponsored by Environmental Molecular Science Laboratory Richland, Washington July...

  12. 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/

  13. Genome resequencing in Populus: Revealing large-scale genome variation and implications on specialized-trait genomics

    SciTech Connect (OSTI)

    Muchero, Wellington [ORNL] [ORNL; Labbe, Jessy L [ORNL] [ORNL; Priya, Ranjan [University of Tennessee, Knoxville (UTK)] [University of Tennessee, Knoxville (UTK); DiFazio, Steven P [West Virginia University, Morgantown] [West Virginia University, Morgantown; Tuskan, Gerald A [ORNL] [ORNL

    2014-01-01T23:59:59.000Z

    To date, Populus ranks among a few plant species with a complete genome sequence and other highly developed genomic resources. With the first genome sequence among all tree species, Populus has been adopted as a suitable model organism for genomic studies in trees. However, far from being just a model species, Populus is a key renewable economic resource that plays a significant role in providing raw materials for the biofuel and pulp and paper industries. Therefore, aside from leading frontiers of basic tree molecular biology and ecological research, Populus leads frontiers in addressing global economic challenges related to fuel and fiber production. The latter fact suggests that research aimed at improving quality and quantity of Populus as a raw material will likely drive the pursuit of more targeted and deeper research in order to unlock the economic potential tied in molecular biology processes that drive this tree species. Advances in genome sequence-driven technologies, such as resequencing individual genotypes, which in turn facilitates large scale SNP discovery and identification of large scale polymorphisms are key determinants of future success in these initiatives. In this treatise we discuss implications of genome sequence-enable technologies on Populus genomic and genetic studies of complex and specialized-traits.

  14. NERSC Science Gateways

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

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

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

    E-Print Network [OSTI]

    2008-01-01T23:59:59.000Z

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

  16. COMPUTER SCIENCE INFORMATION TECHNOLOGY

    E-Print Network [OSTI]

    Dunstan, Neil

    COMPUTER SCIENCE and INFORMATION TECHNOLOGY POSTGRADUATE STUDIES 2006 School of Mathematics of Information Systems with Honours Master of Science (Computer Science) Professional Doctorate in Science (Computer Science) PhD (Computer Science) The postgraduate programs in Computer Science and Information

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

    SciTech Connect (OSTI)

    Lapidus, Alla L.

    2009-01-01T23:59:59.000Z

    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.

  18. Automatic annotation of organellar genomes with DOGMA

    SciTech Connect (OSTI)

    Wyman, Stacia; Jansen, Robert K.; Boore, Jeffrey L.

    2004-06-01T23:59:59.000Z

    Dual Organellar GenoMe Annotator (DOGMA) automates the annotation of extra-nuclear organellar (chloroplast and animal mitochondrial) genomes. It is a web-based package that allows the use of comparative BLAST searches to identify and annotate genes in a genome. DOGMA presents a list of putative genes to the user in a graphical format for viewing and editing. Annotations are stored on our password-protected server. Complete annotations can be extracted for direct submission to GenBank. Furthermore, intergenic regions of specified length can be extracted, as well the nucleotide sequences and amino acid sequences of the genes.

  19. An Integrated Program in Microbial Genome Sequencing and Analysis

    SciTech Connect (OSTI)

    Claire M. Fraser, Ph.D.; J.E. Eisen, Ph.D.; W. Nierman, Ph.D.; K. Nelson, Ph.D.; H. Tettelin, Ph.D.; J. Heidelberg, Ph.D.; O. White, Ph.D.; B. Methe, Ph.D.; N. El-Sayed, Ph.D.; S. Gill, Ph.D.; S. Peterson, Ph.D.; J. Quackenbush, Ph.D.; T. Read, Ph.D.

    2005-11-30T23:59:59.000Z

    Under this award, numerous genome sequences were generated, analyzed, published and made publicly available.

  20. 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

  1. 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

  2. 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

  3. 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

  4. 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

  5. Initial sequencing and analysis of the human genome

    E-Print Network [OSTI]

    Eddy, Sean

    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

  6. 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

  7. Genome-wide mapping and analysis of mammalian promoters

    E-Print Network [OSTI]

    Barrera, Leah Ortiz-Luis

    2007-01-01T23:59:59.000Z

    ed. Bioinformatics and Computational Biology Solutions usingfor computational biology and bioinformatics. Genome Biol

  8. Big Science

    ScienceCinema (OSTI)

    Dr. Thomas Zacharia

    2010-01-08T23:59:59.000Z

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

  9. Big Science

    SciTech Connect (OSTI)

    Dr. Thomas Zacharia

    2008-12-01T23:59:59.000Z

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

  10. Assistant Director Physical Science and Engineering

    E-Print Network [OSTI]

    Genomics Plant Genome Physics of the Universe Education & Workforce Dev. Research Business Models Global

  11. 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

  12. 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

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

    SciTech Connect (OSTI)

    Swaminathan, Kankshita [Energy Biosciences Institute

    2014-03-20T23:59:59.000Z

    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.

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

    SciTech Connect (OSTI)

    Lennie, Peter

    2006-06-29T23:59:59.000Z

    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.

  15. Information Science, Computing, Applied Math

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

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

  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. First international E. coli genome meeting

    SciTech Connect (OSTI)

    Not Available

    1992-01-01T23:59:59.000Z

    This volume is a collection of abstracts of oral presentations and poster sessions of studies reported at the First International E. Coli Genome Meeting, held September 10-14, 1992 at the University of Wisconsin.

  18. First international E. coli genome meeting

    SciTech Connect (OSTI)

    Not Available

    1992-12-31T23:59:59.000Z

    This volume is a collection of abstracts of oral presentations and poster sessions of studies reported at the First International E. Coli Genome Meeting, held September 10-14, 1992 at the University of Wisconsin.

  19. 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

  20. 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.

  1. Next-generation information systems for genomics 

    E-Print Network [OSTI]

    Mungall, Christopher

    2011-06-27T23:59:59.000Z

    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. DOE Joint Genome Institute 2008 Progress Report

    E-Print Network [OSTI]

    Gilbert, David

    2009-01-01T23:59:59.000Z

    Genomics of cellulosic biofuels. Nature, 454 (7206):841-845,2008 Termite Bellies and Biofuels (Published in Smithsonian,in the quest for viable biofuels. An estimated 10,000 marine

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

    E-Print Network [OSTI]

    Kheradpour, Pouya

    2012-01-01T23:59:59.000Z

    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 ...

  4. Cancer Vulnerabilities Unveiled by Genomic Loss

    E-Print Network [OSTI]

    Nijhawan, Deepak

    Due to genome instability, most cancers exhibit loss of regions containing tumor suppressor genes and collateral loss of other genes. To identify cancer-specific vulnerabilities that are the result of copy number losses, ...

  5. 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)

  6. Justice and the Human Genome Project

    SciTech Connect (OSTI)

    Murphy, T.F.; Lappe, M. [eds.] [eds.

    1992-12-31T23:59:59.000Z

    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.

  7. Justice and the Human Genome Project

    SciTech Connect (OSTI)

    Murphy, T.F.; Lappe, M. (eds.)

    1992-01-01T23:59:59.000Z

    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.

  8. Somatic retrotransposition in the cancer genome

    E-Print Network [OSTI]

    Helman, Elena

    2014-01-01T23:59:59.000Z

    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 ...

  9. Genomic analysis of control of cell type

    E-Print Network [OSTI]

    Frampton, Garrett M

    2011-01-01T23:59:59.000Z

    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 ...

  10. 1 Organizational Sciences and Communication ORGANIZATIONAL SCIENCES

    E-Print Network [OSTI]

    Vertes, Akos

    1 Organizational Sciences and Communication ORGANIZATIONAL SCIENCES AND COMMUNICATION The communication and organizational sciences majors are offered by the Department of Organizational Sciences. The Department of Organizational Sciences and Communication offers interdisciplinary programs leading

  11. 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

  12. The Calyptogena magnifica chemoautotrophic symbiont genome

    SciTech Connect (OSTI)

    Newton, I.L.; Woyke, T.; Auchtung, T.A.; Dilly, G.F.; Dutton,R.J.; Fisher, M.C.; Fontanez, K.M.; Lau, E.; Stewart, F.J.; Richardson,P.M.; Barry, K.W.; Saunders, E.; Detter, J.C.; Wu, D.; Eisen, J.A.; Cavanaugh, C.M.

    2007-03-01T23:59:59.000Z

    Chemoautotrophic endosymbionts are the metabolic cornerstone of hydrothermal vent communities, providing invertebrate hosts with nearly all of their nutrition. The Calyptogena magnifica (Bivalvia: Vesicomyidae) symbiont, Candidatus Ruthia magnifica, is the first intracellular sulfur-oxidizing endosymbiont to have its genome sequenced, revealing a suite of metabolic capabilities. The genome encodes major chemoautotrophic pathways as well as pathways for biosynthesis of vitamins, cofactors, and all 20 amino acids required by the clam.

  13. SEMANTIC WEB APPROACH TO DATABASE INTEGRATION IN THE LIFE SCIENCES

    E-Print Network [OSTI]

    Gerstein, Mark

    . Key words: RDF database, integration. Semantic Web, molecular biology. INTRODUCTION The success of the Human Genome Project (HGP) [1] together with the popularity of the Web (or World Wide Web) [2] has madeChapter 1 SEMANTIC WEB APPROACH TO DATABASE INTEGRATION IN THE LIFE SCIENCES Kei-Hoi Cheung

  14. The Human Genome Diversity Project

    SciTech Connect (OSTI)

    Cavalli-Sforza, L. [Stanford Univ., CA (United States)

    1994-12-31T23:59:59.000Z

    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.

  15. 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

    2005-02-01T23:59:59.000Z

    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

  16. Genomes to Life Project Quarterly Report April 2005.

    SciTech Connect (OSTI)

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

    2006-02-01T23:59:59.000Z

    This SAND report provides the technical progress through April 2005 of the Sandia-led project, %22Carbon Sequestration in Synechococcus Sp.: From Molecular Machines to Hierarchical Modeling,%22 funded by the DOE Office of Science Genomics:GTL 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 can be found at www.genomes-to-life.org Acknowledgment We want to gratefully acknowledge the contributions of: Grant Heffelfinger1*, Anthony Martino2, Brian Palenik6, Andrey Gori

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

    E-Print Network [OSTI]

    Ho, Hsiang; Milenkovi?, Tijana; Memiševi?, Vesna; Aruri, Jayavani; Pržulj, Nataša; Ganesan, Anand K

    2010-01-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Novichkov, Pavel S.

    2010-01-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Winickoff, David E

    2008-01-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Dehal, Paramvir

    2013-01-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Neale, David

    2011-01-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Sain, Divya

    2013-01-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Wohlbach, Dana J.

    2011-01-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    2010-01-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    2011-01-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Ellison, Christopher

    2011-01-01T23:59:59.000Z

    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.

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

    E-Print Network [OSTI]

    2013-01-01T23:59:59.000Z

    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

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

    E-Print Network [OSTI]

    2011-01-01T23:59:59.000Z

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

  9. 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

    2013-01-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    2006-01-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Chivian, Dylan

    2008-01-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Joachimiak, Marcin Pawel

    2008-01-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

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

    2014-01-01T23:59:59.000Z

    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

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

    E-Print Network [OSTI]

    Hsiao, Albert

    2005-01-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Mukhopadhyay, Aindrila

    2014-01-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Zhang, Yafeng

    2014-01-01T23:59:59.000Z

    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

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

    E-Print Network [OSTI]

    Nohzadeh-Malakshah, Sahar

    2012-01-01T23:59:59.000Z

    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.

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

    E-Print Network [OSTI]

    Novichkov, Pavel S.

    2014-01-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    2014-01-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Chandonia, John-Marc; Brenner, Steven E.

    2005-01-01T23:59:59.000Z

    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

  1. Discovering and validating biological hypotheses from coherent patterns in functional genomics data using associative biclustering

    E-Print Network [OSTI]

    Joachimiak, Marcin P.

    2014-01-01T23:59:59.000Z

    patterns in functional genomics data using associativeand Environmental Research, Genomics:GTL program throughof Energy Functional genomics confronts researchers with a

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

    E-Print Network [OSTI]

    Deutschbauer, Adam

    2014-01-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    2009-01-01T23:59:59.000Z

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

  4. Mass spectrometry-guided genome mining of peptidic and glycosylated microbial natural products

    E-Print Network [OSTI]

    Kersten, Roland David

    mass spectrometry-guided genome mining approach for naturalBioactivity-guided genome mining identifies the lomaiviticinspectrometry and genome mining via short sequence tagging

  5. ENVIRONMENTAL SCIENCE AND

    E-Print Network [OSTI]

    ENVIRONMENTAL SCIENCE AND MANAGEMENT www.esr.pdx.edu Undergraduate Program: Environmental Science an emphasis on natural sciences and mathematics (Environmental Science) or emphasis on policy, geography and social sciences (Environmental Studies). Undergraduate Degrees Offered: Environmental Science Bachelor

  6. 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.

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

    SciTech Connect (OSTI)

    Schulman, Al

    2009-08-09T23:59:59.000Z

    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

  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. [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

  10. Information science is neither

    E-Print Network [OSTI]

    Furner, J

    2015-01-01T23:59:59.000Z

    Julian. “Semiotics, information science, documents andof library and information sciences, 3rd ed. , edited bykind of science can information science be? ” Journal of the

  11. Science Highlights

    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: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level:Energy: Grid Integration Redefining What's PossibleRadiationImplementingnpitcheResearch BriefsTenney, Office ofScienceScienceScience

  12. Processing Science

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

    Processing Science Related to the Electron Beam Melting Additive Manufacturing Process October 14 th , 2014 Ryan Dehoff Metal Additive Manufacturing Thrust Lead Manufacturing...

  13. A Compressed Self-Index for Genomic Databases

    E-Print Network [OSTI]

    Gagie, Travis; Nekrich, Yakov; Puglisi, Simon J

    2011-01-01T23:59:59.000Z

    Advances in DNA sequencing technology will soon result in databases of thousands of genomes. Within a species, individuals' genomes are almost exact copies of each other; e.g., any two human genomes are 99.9% the same. Relative Lempel-Ziv (RLZ) compression takes advantage of this property: it stores the first genome uncompressed or as an FM-index, then compresses the other genomes with a variant of LZ77 that copies phrases only from the first genome. RLZ achieves good compression and supports fast random access; in this paper we show how to support fast search as well, thus obtaining an efficient compressed self-index.

  14. Bradbury Science Museum - Science on Wheels

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

    Bradbury Science Museum - Science on Wheels Our Mission: To stimulate interest in and enthusiasm for science, technology, engineering and mathematics and promote public...

  15. www.emsl.pnnl.gov New Science, New Tools: GENOMIC SCIENCES

    E-Print Network [OSTI]

    of the Environmental TEM and Scanning/TEM permit the highest resolution imaging of biological samples. Combined

  16. Multiple Whole Genome Alignments Without a Reference Organism

    SciTech Connect (OSTI)

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

    2009-01-16T23:59:59.000Z

    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.

  17. 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

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

    E-Print Network [OSTI]

    Dehal, Paramvir S.

    2010-01-01T23:59:59.000Z

    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* ,

  19. 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

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

    E-Print Network [OSTI]

    Huang, Y. Wayne

    2014-01-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Earl, Dent A.

    2014-01-01T23:59:59.000Z

    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. ,

  2. 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

  3. Cognitive Science 1 Cognitive Science

    E-Print Network [OSTI]

    (Linguistics), Laurie Santos (Psychology), Brian Scassellati (Computer Science) Assistant Professors Daylian and cognition based on patterns of breakdown in pathology, computational and robotic research that strives

  4. Life sciences

    SciTech Connect (OSTI)

    Day, L. (ed.)

    1991-04-01T23:59:59.000Z

    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)

  5. Sequencing and comparing whole mitochondrial genomes ofanimals

    SciTech Connect (OSTI)

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

    2005-04-22T23:59:59.000Z

    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.

  6. Physical mapping of complex genomes

    DOE Patents [OSTI]

    Evans, G.A.

    1993-06-15T23:59:59.000Z

    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.

  7. Physical mapping of complex genomes

    DOE Patents [OSTI]

    Evans, Glen A. (Encinitas, CA)

    1993-01-01T23:59:59.000Z

    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.

  8. 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.

  9. Bringing large-scale multiple genome analysis one step closer: ScalaBLAST and beyond

    SciTech Connect (OSTI)

    Oehmen, Christopher S.; Sofia, Heidi J.; Baxter, Douglas; Szeto, Ernest; Hugenholtz, Philip; Kyrpides, Nikos; Markowitz, Victor; Straatsma, Tjerk P.

    2007-06-01T23:59:59.000Z

    Genome sequence comparisons of exponentially growing data sets form the foundation for the comparative analysis tools provided by community biological data resources such as the Integrated Microbial Genome (IMG) system at the Joint Genome Institute (JGI). We present an example of how ScalaBLAST, a high-throughput sequence analysis program harnesses increasingly critical high-performance computing to perform sequence analysis which is a critical component of maintaining a state-of-the-art sequence data repository. The Integrated Microbial Genomes (IMG) system1 is a data management and analysis platform for microbial genomes hosted at the JGI. IMG contains both draft and complete JGI genomes integrated with other publicly available microbial genomes of all three domains of life. IMG provides tools and viewers for interactive analysis of genomes, genes and functions, individually or in a comparative context. Most of these tools are based on pre-computed pairwise sequence similarities involving millions of genes. These computations are becoming prohibitively time consuming with the rapid increase in the number of newly sequenced genomes incorporated into IMG and the need to refresh regularly the content of IMG in order to reflect changes in the annotations of existing genomes. Thus, building IMG 2.0 (released on December 1st 2006) entailed reloading from NCBI's RefSeq all the genomes in the previous version of IMG (IMG 1.6, as of September 1st, 2006) together with 1,541 new public microbial,viral and eukaryal genomes, bringing the total of IMG genomes to 2,301. A critical part of building IMG 2.0 involved using PNNL ScalaBLAST software for computing pairwise similarities for over 2.2 million genes in under 26 hours on 1,000 processors, thus illustrating the impact that new generation bioinformatics tools are poised to make in biology. The BLAST algorithm2, 3 is a familiar bioinformatics application for computing sequence similarity, and has become a workhorse in large-scale genomics projects. The rapid growth of genome resources such as IMG cannot be sustained without more powerful tools such as ScalaBLAST that use more effectively large scale computing resources to perform the core BLAST calculations. ScalaBLAST is a high performance computing algorithm designed to give high throughput BLAST results on high-end supercomputers. Other parallel sequence comparison applications have been developed4-6. However problems with scaling generally prevent these applications from being used for very large searches. ScalaBLAST7 is the first BLAST application to be both highly scaleable against the size of the database as well as the number of computer processors on high-end hardware and on commodity clusters. ScalaBLAST achieves high throughput by parsing a large collection of query sequences into independent subgroups. These smaller tasks are assigned to independent process groups. Efficient scaling is achieved by (transparently to the user) sharing only one copy of the target database across all processors using the Global Array toolkit 8, 9, which provides software implementation of shared memory interface. ScalaBLAST was initially deployed on the 1,960 processor MPP2 cluster in the Wiliam R. Wiley Environmental Molecular Sciences Laboratory at Pacific Northwest National Laboratory, and has since been ported to a variety of linux-based clusters and shared memory architectures, including SGI Altix, AMD opteron, and Intel Xeon-based clusters. Future targets include IBM BlueGene, Cray, and SGI Altix XE architectures. The importance of performing high-throughput calculations rapidly lies in the rate of growth of sequence data. For a genome sequencing center to provide multiple-genome comparison capabilities, it must keep pace with exponentially growing collection of protein data, both from its own genomes, and from the public genome information as well. As sequence data continues to grow exponentially, this challenge will only increase with time. Solving the BLAST throughput challenge for centralized data resources like IMG has the poten

  10. Genomes to life project quarterly report June 2004.

    SciTech Connect (OSTI)

    Heffelfinger, Grant S.

    2005-01-01T23:59:59.000Z

    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.

  11. A Complete Neandertal Mitochondrial Genome Sequence Determined

    E-Print Network [OSTI]

    Good, Jeffrey M.

    Rothberg Institute for Childhood Diseases, Guilford, CT 06437, USA 7Croatian Academy of Sciences and Arts, Zrinski trg 11, HR-10000 Zagreb, Croatia 8Croatian Academy of Sciences and Arts, Institute for Quaternary

  12. 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

  13. 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

  14. 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 ...

  15. An object-oriented framework to organize genomic data

    E-Print Network [OSTI]

    Wei, Ning

    2009-05-15T23:59:59.000Z

    Bioinformatics resources should provide simple and flexible support for genomics research. A huge amount of gene mapping data, micro-array expression data, expressed sequence tags (EST), BAC sequence data and genome sequence data are already...

  16. Identifying Recent Adaptations in Large-Scale Genomic Data

    E-Print Network [OSTI]

    Andersen, Kristian G.

    Although several hundred regions of the human genome harbor signals of positive natural selection, few of the relevant adaptive traits and variants have been elucidated. Using full-genome sequence variation from the 1000 ...

  17. Novel phylogenetic approaches to problems in microbial genomics

    E-Print Network [OSTI]

    David, Lawrence A. (Lawrence Anthony)

    2010-01-01T23:59:59.000Z

    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 ...

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

    SciTech Connect (OSTI)

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

    2009-05-28T23:59:59.000Z

    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

  19. Use of Optical Mapping in Bacterial Genome Finishing

    SciTech Connect (OSTI)

    Kumar, Dibyendu [University of Florida

    2010-06-03T23:59:59.000Z

    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

  20. MycoCosm, an Integrated Fungal Genomics Resource

    SciTech Connect (OSTI)

    Shabalov, Igor; Grigoriev, Igor

    2012-03-16T23:59:59.000Z

    MycoCosm is a web-based interactive fungal genomics resource, which was first released in March 2010, in response to an urgent call from the fungal community for integration of all fungal genomes and analytical tools in one place (Pan-fungal data resources meeting, Feb 21-22, 2010, Alexandria, VA). MycoCosm integrates genomics data and analysis tools to navigate through over 100 fungal genomes sequenced at JGI and elsewhere. This resource allows users to explore fungal genomes in the context of both genome-centric analysis and comparative genomics, and promotes user community participation in data submission, annotation and analysis. MycoCosm has over 4500 unique visitors/month or 35000+ visitors/year as well as hundreds of registered users contributing their data and expertise to this resource. Its scalable architecture allows significant expansion of the data expected from JGI Fungal Genomics Program, its users, and integration with external resources used by fungal community.

  1. Reference genome sequence of the model plant Setaria

    E-Print Network [OSTI]

    2012-01-01T23:59:59.000Z

    segregation of nuclear genes in plants. Bot. Gaz. 147, 26.in the nuclear genome of Fragaria vesca. Plant Genome 2, 93–Nuclear DNA isolation from Setaria. A single, highly inbred Yugu1 plant

  2. 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 ...

  3. average genome size: Topics by E-print Network

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

    ancestry in the nuclear genomes of plastid underscore the power of comparative genomics and, at the same time, reveal how little we know with certainty 15 An Upper Bound on...

  4. analysis full genome: Topics by E-print Network

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

    Maize Human (partial) "I came into the class with little to no understanding of what genomics entailedGoals Full Genome Microarrays Data Analysis Bioinformatics RNA-free Teaching...

  5. Initial sequencing and comparative analysis of the mouse genome

    SciTech Connect (OSTI)

    Waterston, Robert H.; Lindblad-Toh, Kerstin; Birney, Ewan; Rogers, Jane; Abril, Josep F.; Agarwal, Pankaj; Agarwala, Richa; Ainscough, Rachel; Alexandersson, Marina; An, Peter; Antonarakis, Stylianos E.; Attwood, John; Baertsch, Robert; Bailey, Jonathon; Barlow, Karen; Beck, Stephan; Berry, Eric; Birren, Bruce; Bloom, Toby; Bork, Peer; Botcherby, Marc; Bray, Nicolas; Brent, Michael R.; Brown, Daniel G.; Brown, Stephen D.; Bult, Carol; Burton, John; Butler, Jonathan; Campbell, Robert D.; Carninci, Piero; Cawley, Simon; Chiaromonte, Francesca; Chinwalla, Asif T.; Church, Deanna M.; Clamp, Michele; Clee, Christopher; Collins, Francis S.; Cook, Lisa L.; Copley, Richard R.; Coulson, Alan; Couronne, Olivier; Cuff, James; Curwen, Val; Cutts, Tim; Daly, Mark; David, Robert; Davies, Joy; Delehaunty, Kimberly D.; Deri, Justin; Dermitzakis, Emmanouil T.; Dewey, Colin; Dickens, Nicholas J.; Diekhans, Mark; Dodge, Sheila; Dubchak, Inna; Dunn, Diane M.; Eddy, Sean R.; Elnitski, Laura; Emes, Richard D.; Eswara, Pallavi; Eyras, Eduardo; Felsenfeld, Adam; Fewell, Ginger A.; Flicek, Paul; Foley, Karen; Frankel, Wayne N.; Fulton, Lucinda A.; Fulton, Robert S.; Furey, Terrence S.; Gage, Diane; Gibbs, Richard A.; Glusman, Gustavo; Gnerre, Sante; Goldman, Nick; Goodstadt, Leo; Grafham, Darren; Graves, Tina A.; Green, Eric D.; Gregory, Simon; Guigo, Roderic; Guyer, Mark; Hardison, Ross C.; Haussler, David; Hayashizaki, Yoshihide; Hillier, LaDeana W.; Hinrichs, Angela; Hlavina, Wratko; Holzer, Timothy; Hsu, Fan; Hua, Axin; Hubbard, Tim; Hunt, Adrienne; Jackson, Ian; Jaffe, David B.; Johnson, L. Steven; Jones, Matthew; Jones, Thomas A.; Joy, Ann; Kamal, Michael; Karlsson, Elinor K.; Karolchik, Donna; Kasprzyk, Arkadiusz; Kawai, Jun; Keibler, Evan; Kells, Cristyn; Kent, W. James; Kirby, Andrew; Kolbe, Diana L.; Korf, Ian; Kucherlapati, Raju S.; Kulbokas III, Edward J.; Kulp, David; Landers, Tom; Leger, J.P.; Leonard, Steven; Letunic, Ivica; Levine, Rosie; et al.

    2002-12-15T23:59:59.000Z

    The sequence of the mouse genome is a key informational tool for understanding the contents of the human genome and a key experimental tool for biomedical research. Here, we report the results of an international collaboration to produce a high-quality draft sequence of the mouse genome. We also present an initial comparative analysis of the mouse and human genomes, describing some of the insights that can be gleaned from the two sequences. We discuss topics including the analysis of the evolutionary forces shaping the size, structure and sequence of the genomes; the conservation of large-scale synteny across most of the genomes; the much lower extent of sequence orthology covering less than half of the genomes; the proportions of the genomes under selection; the number of protein-coding genes; the expansion of gene families related to reproduction and immunity; the evolution of proteins; and the identification of intraspecies polymorphism.

  6. Ancient human genome sequence of an extinct Palaeo-Eskimo

    E-Print Network [OSTI]

    Rasmussen, Morten; Li, Yingrui; Lindgreen, Stinus; Pedersen, Jakob Skou; Albrechtsen, Anders; Moltke, Ida; Metspalu, Mait; Metspalu, Ene; Kivisild, Toomas; Gupta, Ramneek; Bertalan, Marcelo; Nielsen, Kasper; Gilbert, M. Thomas P.; Wang, Yong; Raghavan, Maanasa; Campos, Paula F.; Kamp, Hanne Munkholm; Wilson, Andrew S.; Gledhill, Andrew; Tridico, Silvana; Bunce, Michael; Lorenzen, Eline D.; Binladen, Jonas; Guo, Xiaosen; Zhao, Jing; Zhang, Xiuqing; Zhang, Hao; Li, Zhuo; Chen, Minfeng; Orlando, Ludovic; Kristiansen, Karsten; Bak, Mads; Tommerup, Niels; Bendixen, Christian; Pierre, Tracey L.; Gronnow, Bjarne; Meldgaard, Morten; Andreasen, Claus; Fedorova, Sardana A.; Osipova, Ludmila P.; Higham, Thomas F. G.; Ramsey, Christopher Bronk; Hansen, Thomas v. O.; Nielsen, Finn C.; Crawford, Michael H.; Brunak, Soren; Sicheritz-Ponten, Thomas; Villems, Richard; Nielsen, Rasmus; Krogh, Anders; Wang, Jun; Willerslev, Eske

    2010-02-11T23:59:59.000Z

    We report here the genome sequence of an ancient human. Obtained from ?4,000-year-old permafrost-preserved hair, the genome represents a male individual from the first known culture to settle in Greenland. Sequenced to an ...

  7. Genomics-Bioinformatics Day: "Bioinformatics, Computational Biology, Systems Biology & Mathematical

    E-Print Network [OSTI]

    Goldschmidt, Christina

    3rd Genomics-Bioinformatics Day: "Bioinformatics, Computational Biology, Systems Biology on "Bioinformatics, Computational Biology, Systems Biology & Mathematical Biology: Their Relationship". Genomics, Bioinformatics, Computational Biology have a tremendous appeal and these fields have originated or grown

  8. 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.)

  9. Genomic islands predict functional adaptation in marine actinobacteria

    E-Print Network [OSTI]

    Penn, Kevin

    2010-01-01T23:59:59.000Z

    Ecological adaptations among bacterial populations have been linked to genomic islands, strain-specific regions of DNA that house

  10. The Asian Citrus Psyllid Genome (Diaphorina citri, Hemiptera)

    E-Print Network [OSTI]

    Hunter, Wayne B.; Reese, Justin; International Psyllid Genome Consortium, The

    2014-01-01T23:59:59.000Z

    Genome (Diaphorina citri, Hemiptera) Hunter, W.B. 1 , Reese,psyllid, Diaphorina citri (Hemiptera), is an important pest

  11. des Sciences le magazine des activits de diffusion des sciences

    E-Print Network [OSTI]

    Cerf, Nicolas

    Solvay ........................................................................ 17 Classes Sciences au

  12. Web of Science Welcome to the Web of Science................................................................................................ 2

    E-Print Network [OSTI]

    Huang, Su-Yun

    Web of Science #12; Welcome to the Web of Science................................................................................................ 2 Web of Science.............................................................................................. 4 Web of Science

  13. Faculty of Science Computer Science Handbook

    E-Print Network [OSTI]

    Sun, Jing

    Faculty of Science Computer Science Handbook 2013 #12;Welcome to Computer Science Welcome from the Head of Department 2 What is Computer Science? 2 Careers in Computer Science 3 What can you do with a Computer Science degree? 4 Meet our students 5 Academic information Important dates 7 Admission

  14. A rapid whole genome sequencing and analysis system supporting genomic epidemiology (7th Annual SFAF Meeting, 2012)

    ScienceCinema (OSTI)

    FitzGerald, Michael [Broad Institute

    2013-02-12T23:59:59.000Z

    Michael FitzGerald on "A rapid whole genome sequencing and analysis system supporting genomic epidemiology" at the 2012 Sequencing, Finishing, Analysis in the Future Meeting held June 5-7, 2012 in Santa Fe, New Mexico.

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

    ScienceCinema (OSTI)

    Goldberg, Robert [UCLA

    2013-01-22T23:59:59.000Z

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

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

    SciTech Connect (OSTI)

    Goldberg, Robert [UCLA] [UCLA

    2012-03-21T23:59:59.000Z

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

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

    SciTech Connect (OSTI)

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

    2012-03-21T23:59:59.000Z

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

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

    SciTech Connect (OSTI)

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

    2012-03-21T23:59:59.000Z

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

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

    SciTech Connect (OSTI)

    Bermingham, Eldredge [STRI-Panama

    2013-03-27T23:59:59.000Z

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

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

    ScienceCinema (OSTI)

    Schatz, Michael C [Cold Spring Harbor Laboratory

    2013-01-15T23:59:59.000Z

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

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

    ScienceCinema (OSTI)

    Rieseberg, Loren [University of British Columbia

    2013-01-15T23:59:59.000Z

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

  2. Genome-Wide In Silico Identification of Transcriptional Regulators Controlling

    E-Print Network [OSTI]

    Shamir, Ron

    Genome-Wide In Silico Identification of Transcriptional Regulators Controlling the Cell Cycle networks that control gene transcription is one of the greatest challenges of functional genomics. Using human genomic sequences, models for binding sites of known transcription factors, and gene expression

  3. Using genomics to improve Bacillus anthracis diagnostics and

    E-Print Network [OSTI]

    Using genomics to improve Bacillus anthracis diagnostics and outbreak investigations Joakim Ĺgren;Using genomics to improve Bacillus anthracis diagnostics and outbreak investigations Abstract-generation sequencing (NGS) has revolutionized the way DNA is sequenced and the whole genome (i.e., all the DNA

  4. ORIGINAL ARTICLE Comparative genomics-guided loop-mediated isothermal

    E-Print Network [OSTI]

    Hsiang, Tom

    ORIGINAL ARTICLE Comparative genomics-guided loop-mediated isothermal amplification sequencing and analytical techniques, genomic sequence data of prok- aryotes are accumulating at a very rapid pace. As of October 2008, there are 873 complete and pub- lished genome sequences, as well as 2025

  5. Hindawi Publishing Corporation International Journal of Plant Genomics

    E-Print Network [OSTI]

    California at Santa Cruz, University of

    Hindawi Publishing Corporation International Journal of Plant Genomics Volume 2008, Article ID 412875, 7 pages doi:10.1155/2008/412875 Research Article TreeGenes: A Forest Tree Genome Database Jill L are to (1) provide a comprehensive resource for forest tree genomics data to facilitate gene discovery

  6. Genomics and Transcriptomics of Plant Beneficial Serratia spp.

    E-Print Network [OSTI]

    Genomics and Transcriptomics of Plant Beneficial Serratia spp. Saraswoti Neupane Faculty of Natural. proteamaculans S4 (photo: S. Neupane) #12;Genomics and transcriptomics of plant beneficial Serratia spp. Abstract, and have potential as possible biocontrol agents in agriculture. This thesis provides the detailed genomic

  7. Genomics and computational molecular biology Douglas L Brutlag

    E-Print Network [OSTI]

    Brutlag, Doug

    340 Genomics and computational molecular biology Douglas L Brutlag There has been a dramatic increase in the number of completely sequenced bacterial genomes during the past two years as a result of the efforts both of public genome agencies and the pharmaceutical industry. The availability of completely

  8. Potential of metabolomics as a functional genomics tool

    E-Print Network [OSTI]

    Wurtele, Eve Syrkin

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

  9. AIHS Translational Research Chair in Child Health Genomics

    E-Print Network [OSTI]

    Calgary, University of

    AIHS Translational Research Chair in Child Health Genomics The Department of Medical Genetics) invite applications for full-time academic position in Child Health Genomics. This position represents a major investment in genomic research and the successful applicant will join a program with a vision

  10. Clique-detection Models in Computational Biochemistry and Genomics

    E-Print Network [OSTI]

    Butenko, Sergiy

    Clique-detection Models in Computational Biochemistry and Genomics S. Butenko and W. E. Wilhelm,wilhelm}@tamu.edu Abstract Many important problems arising in computational biochemistry and genomics have been formulated and genomic aspects of the problems as well as to the graph-theoretic aspects of the solution approaches. Each

  11. Feature selection in high dimensional regression problems for genomics

    E-Print Network [OSTI]

    Paris-Sud XI, Université de

    Feature selection in high dimensional regression problems for genomics Julie Hamon1,2,3 , Clarisse, France julien.jacques@lifl.fr Abstract. In the context of genomic selection in animal breeding and "closed to real" datasets. Keywords: Feature selection, combinatorial optimization, regression, genomic. 1

  12. Production Efficiency of Beef Cows through Mathematical Modeling and Genomics

    E-Print Network [OSTI]

    Production Efficiency of Beef Cows through Mathematical Modeling and Genomics For decades cows reside. With recent advances in genomics, the identification of intrinsic genetic factors Develop and evaluate the individual-based model· for production efficiency of beef cows using genomic

  13. Reconciling Utility with Privacy in Genomics Mathias Humbert Erman Ayday

    E-Print Network [OSTI]

    Thévenaz, Jacques

    Reconciling Utility with Privacy in Genomics Mathias Humbert Erman Ayday Jean-Pierre Hubaux.telenti@chuv.ch ABSTRACT Direct-to-consumer genetics makes it possible for everyone to obtain their genome sequences. In order to contribute to medical research, a growing number of people publish their genomic data

  14. Sequence and comparative analysis of the chicken genome provide unique

    E-Print Network [OSTI]

    Edwards, Scott

    Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution International Chicken Genome Sequencing Consortium* *Lists of participants and affiliations appear ........................................................................................................................................................................................................................... We present here a draft genome sequence of the red jungle fowl, Gallus gallus. Because the chicken

  15. Genome Sequence of Mercury-Methylating and Pleomorphic Desulfovibrio africanus

    E-Print Network [OSTI]

    Genome Sequence of Mercury-Methylating and Pleomorphic Desulfovibrio africanus Contact: Steven D. africanus genome sequence to allow us to gain insights into the physiological states genomics using the sequence information for D. africanus and the previously sequenced mercury methylator D

  16. Genome Technology, No.56 October 2005 CROSSING OVER

    E-Print Network [OSTI]

    Ferrara, Katherine W.

    Genome Technology, No.56 October 2005 CROSSING OVER ACADEMIA OR INDUSTRY? WWW.GENOME-TECHNOLOGY importantly, if I try it out and don't like it, can I come back? Genome Technology interviewed a number-scientist types who chase down answers to impossibly huge (and sometimes useless) questions at the expense

  17. Toward genome-enabled mycology David S. Hibbett1

    E-Print Network [OSTI]

    Hibbett, David S.

    #12;Toward genome-enabled mycology David S. Hibbett1 Biology Department, Clark University State University, Corvallis, Oregon 97331 Abstract: Genome-enabled mycology is a rapidly expanding field that is characterized by the pervasive use of genome-scale data and associated computa- tional tools in all aspects

  18. The Exemplar Breakpoint Distance for nontrivial genomes cannot be approximated

    E-Print Network [OSTI]

    Fertin, Guillaume

    The Exemplar Breakpoint Distance for non­trivial genomes cannot be approximated Guillaume Blin 1 ­ France guillaume.fertin@univ­nantes.fr Abstract. A promising and active field of comparative genomics con­ sists in comparing two genomes by establishing a one­to­one correspon­ dence (i.e., a matching) between

  19. Genome Rearrangement and Planning: Revisited Tansel Uras and Esra Erdem

    E-Print Network [OSTI]

    Erdem, Esra

    Genome Rearrangement and Planning: Revisited Tansel Uras and Esra Erdem Faculty of Engineering be reconstructed by pair- wise comparison of their entire genomes. Such a comparison can be quantified by determining the number of events that change the order of genes in a genome. Earlier Erdem and Tillier

  20. Genome Rearrangement and Planning Institute of Information Systems

    E-Print Network [OSTI]

    Erdem, Esra

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

  1. Reconstructing the Genomic Architecture of Ancestral Mammals: Lessons From Human,

    E-Print Network [OSTI]

    Batzoglou, Serafim

    Reconstructing the Genomic Architecture of Ancestral Mammals: Lessons From Human, Mouse, and Rat Genomes Guillaume Bourque,1 Pavel A. Pevzner,2 and Glenn Tesler3,4 1 Centre de Recherches Mathe of Mathematics, University of California­San Diego, La Jolla, California 92093, USA Recent analysis of genome

  2. Rearrangements in genomes with centromeres part I: translocations

    E-Print Network [OSTI]

    Shamir, Ron

    Rearrangements in genomes with centromeres part I: translocations Michal Ozery-Flato and Ron Shamir. Every new chromosome created by a genome rearrange- ment event must have a centromere in order to survive. This constraint has been ignored in the computational modeling and analysis of genome

  3. Proof and evolutionary analysis of ancient genome duplication in the

    E-Print Network [OSTI]

    Kellis, Manolis

    Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae ........................................................................................................................................................................................................................... Whole-genome duplication followed by massive gene loss and specialization has long been postulated by searching complete genome sequence for signs of ancient duplication. Here, we show that the yeast

  4. Genome Rearrangement: A Planning Approach Tansel Uras and Esra Erdem

    E-Print Network [OSTI]

    Erdem, Esra

    Genome Rearrangement: A Planning Approach Tansel Uras and Esra Erdem Faculty of Engineering be reconstructed by pair- wise comparison of their entire genomes. Such a comparison can be quantified by determining the number of events that change the order of genes in a genome. Earlier Erdem and Tillier

  5. A Comparative Evaluation of XML Difference Algorithms with Genomic Data

    E-Print Network [OSTI]

    Paton, Norman

    A Comparative Evaluation of XML Difference Algorithms with Genomic Data Cornelia Hedeler and Norman, UK {chedeler,npaton}@cs.manchester.ac.uk Abstract. Genome sequence data and annotations are subject difference algorithms, namely X-Diff, JXyDiff and 3DM, can be used to identify and document genome changes

  6. 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

  7. Department of Materials Science &

    E-Print Network [OSTI]

    Acton, Scott

    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

  8. 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

  9. Science Highlights

    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: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645U.S. DOE Office of ScienceandMesa del Sol HomeFacebook Twitter Principalfuel cells" Find ScienceDemos ScienceScience

  10. The Los Alamos Science Pillars The Science of Signatures

    SciTech Connect (OSTI)

    Smith, Joshua E. [Los Alamos National Laboratory; Peterson, Eugene J. [Los Alamos National Laboratory

    2012-09-13T23:59:59.000Z

    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.

  11. POSTDOCTORAL OR RESEARCH ASSISTANT POSITIONS--Bioinformatics, comparative genomics, endosymbiosis and genome evolution

    E-Print Network [OSTI]

    Archibald, John

    of nuclear genome sequences from two unicellular algae (http://www.jgi.doe.gov/sequencing/why/CSP2007 are essential, as are strong written and oral communication abilities. The positions are available starting May

  12. Third International E. coli genome meeting

    SciTech Connect (OSTI)

    NONE

    1994-12-31T23:59:59.000Z

    Proceedings of the Third E. Coli Genome Meeting are provided. Presentations were divided into sessions entitled (1) Large Scale Sequencing, Sequence Analysis; (2) Databases; (3) Sequence Analysis; (4) Sequence Divergence in E. coli Strains; (5) Repeated Sequences and Regulatory Motifs; (6) Mutations, Rearrangements and Stress Responses; and (7) Origins of New Genes. The document provides a collection of abstracts of oral and poster presentations.

  13. A genomic integration method to visualize

    E-Print Network [OSTI]

    Cai, Long

    technique for the sustained visualization of endogenous mRNA in vivo is required. PCR-based strategies for genomic tagging in yeast, via homo- logous recombination, have yielded deletion libraries7 as well as GFP- and epitope-tagged protein expression libraries8,9. To develop a similar resource for the systematic mapping

  14. Genome Biology 2005, 6:R72 commentreviewsreportsdepositedresearchrefereedresearchinteractionsinformation

    E-Print Network [OSTI]

    and conservation information. This enabled us to build a better multispecies promoter annotation pipeline and hence Gene transcription is regulated by transcription factors (TFs), binding mostly and specifically to the promoter regions. Recent developments of technologies for studying genome- wide transcriptional regulation

  15. Genome Biology 2004, 5:R102 commentreviewsreportsdepositedresearchrefereedresearchinteractionsinformation

    E-Print Network [OSTI]

    Brendel, Volker

    RNAs and other splicingrelated proteins, together with information on gene structure, alternative splicing, gene genes encoding splicing-related proteins were identified in the Arabidopsis genome by sequence. Plant RNA splicing mechanisms remain comparatively poorly understood, due in part to the lack

  16. Comparative Analysis of Genome Sequences with VISTA

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

    Dubchak, Inna

    VISTA is a comprehensive suite of programs and databases developed by and hosted at the Genomics Division of Lawrence Berkeley National Laboratory. They provide information and tools designed to facilitate comparative analysis of genomic sequences. Users have two ways to interact with the suite of applications at the VISTA portal. They can submit their own sequences and alignments for analysis (VISTA servers) or examine pre-computed whole-genome alignments of different species. A key menu option is the Enhancer Browser and Database at http://enhancer.lbl.gov/. The VISTA Enhancer Browser is a central resource for experimentally validated human noncoding fragments with gene enhancer activity as assessed in transgenic mice. Most of these noncoding elements were selected for testing based on their extreme conservation with other vertebrates. The results of this enhancer screen are provided through this publicly available website. The browser also features relevant results by external contributors and a large collection of additional genome-wide conserved noncoding elements which are candidate enhancer sequences. The LBL developers invite external groups to submit computational predictions of developmental enhancers. As of 10/19/2009 the database contains information on 1109 in vivo tested elements - 508 elements with enhancer activity.

  17. Bioinformatics The Maize Genetics and Genomics Database.

    E-Print Network [OSTI]

    Brendel, Volker

    relationships; and to provide an array of computational tools that address biological questions in an easyBioinformatics The Maize Genetics and Genomics Database. The Community Resource for Access, Development and Cell Biology (C.J.L., V.B.), and Department of Statistics (V.B.), Iowa State University, Ames

  18. FOXM1 binds directly to non-consensus sequences in the human genome

    E-Print Network [OSTI]

    Sanders, Deborah A.; Gormally, Michael V.; Marsico, Giovanni; Beraldi, Dario; Tannahill, David; Balasubramanian, Shankar

    2015-06-23T23:59:59.000Z

    , Addenbrooke’s Hospital, Hills Road, Cambridge CB2 0SP, UK 4 Present address: Domainex, 162 Cambridge Science Park, Milton Road, Cambridge CB4 0GH, UK Abstract Background The Forkhead (FKH) transcription factor FOXM1 is a key regulator of the cell cycle... . Additionally, some transcription factors show different modes of recruitment to chromatin at specific sub-sets of genomic binding sites. For example, the ETS family member ELK1 [23] has two distinct types of binding modes, either binding redundantly...

  19. Genome-level homology and phylogeny of Vibrionaceae (Gammaproteobacteria: Vibrionales) with three new complete genome sequences

    E-Print Network [OSTI]

    Dikow, R. B.; Smith, William Leo

    2013-04-11T23:59:59.000Z

    . Wachsmuth IK, Blake PA, Olsvik O: Vibrio cholerae and Cholera. Molecular to Global Perspectives. Washington: ASM Press; 1994. Dikow and Smith BMCMicrobiology 2013, 13:80 Page 13 of 13 http://www.biomedcentral.com/1471-2180/13/80 7. CDC: Vibrio vulnificus...Dikow and Smith BMCMicrobiology 2013, 13:80 http://www.biomedcentral.com/1471-2180/13/80 RESEARCH ARTICLE Open Access Genome-level homology and phylogeny of Vibrionaceae (Gammaproteobacteria: Vibrionales) with three new complete genome sequences...

  20. Science Museum

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

    Maintaining nuclear stability in times of transition focus of talk at Bradbury Science Museum January 9, 2014 First in series of evening lectures open to public LOS ALAMOS, N.M.,...

  1. Chemical Science

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

    Chemical Science Compton double ionization of helium in the region of the cross-section maximum B. Krssig, R.W. Dunford, D.S. Gemmell, S. Hasegawa, E.P. Kanter, H....

  2. 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...

  3. Science Highlights

    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: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level:Energy: Grid Integration Redefining What's PossibleRadiationImplementingnpitcheResearch BriefsTenney, Office ofScienceScience

  4. Science Summary

    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: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level:Energy: Grid Integration Redefining What's PossibleRadiationImplementingnpitcheResearch BriefsTenney, OfficeScienceEarlyScience On

  5. Science Summary

    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: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level:Energy: Grid Integration Redefining What's PossibleRadiationImplementingnpitcheResearch BriefsTenney, OfficeScienceEarlyScience On9,

  6. Science Summary

    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: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level:Energy: Grid Integration Redefining What's PossibleRadiationImplementingnpitcheResearch BriefsTenney, OfficeScienceEarlyScience

  7. Science Summary

    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: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level:Energy: Grid Integration Redefining What's PossibleRadiationImplementingnpitcheResearch BriefsTenney, OfficeScienceEarlyScience7, 2008

  8. Science Summary

    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: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level:Energy: Grid Integration Redefining What's PossibleRadiationImplementingnpitcheResearch BriefsTenney, OfficeScienceEarlyScience7, 200830,

  9. Science Summary

    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: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level:Energy: Grid Integration Redefining What's PossibleRadiationImplementingnpitcheResearch BriefsTenney, OfficeScienceEarlyScience7,

  10. College of Veterinary Medicine and Biomedical Sciences

    E-Print Network [OSTI]

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

  11. DOE Human Genome Program report of the second contractor-grantee workshop

    SciTech Connect (OSTI)

    Not Available

    1991-08-01T23:59:59.000Z

    The number of genome-funded projects has increased rapidly, and the Human Genome Initiative has grown into a flourishing program, with a complementary counterpart at the National Institutes of Health. The impact of the Human Genome Project on science and society will be substantial as significant achievements become frequent occurrences. New physical mapping strategies have allowed our national laboratories and university grantees to move ahead in a timely manner, and development of innovative approaches to determining the base sequence of chromosomes is proceeding at an encouraging rate. Our computational capabilities are improving. New networking workstations and methods of inputting and analyzing mapping and sequencing data are being developed to allow investigators easy access to data from major databanks. Investigations are under way into the ethical, legal, and social implications of the use of data generated by this program. Program management needs, such as project coordination and the desire to create an environment in which the program's investigators could interact, formed the basis for this workshop. The 1991 workshop had many stimulating presentations, and numerous collaborative efforts have developed, but we anticipate that its successor, scheduled for the all of 1992, will provide additional concepts, strategies, and technologies that are not yet imagined and that are based on multidisciplinary interactions. This document provides the abstracts of all talks and poster sessions.

  12. 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 @...

  13. Genomics:GTL Bioenergy Research Centers White Paper

    SciTech Connect (OSTI)

    Mansfield, Betty Kay [ORNL; Alton, Anita Jean [ORNL; Andrews, Shirley H [ORNL; Bownas, Jennifer Lynn [ORNL; Casey, Denise [ORNL; Martin, Sheryl A [ORNL; Mills, Marissa [ORNL; Nylander, Kim [ORNL; Wyrick, Judy M [ORNL; Drell, Dr. Daniel [Office of Science, Department of Energy; Weatherwax, Sharlene [U.S. Department of Energy; Carruthers, Julie [U.S. Department of Energy

    2006-08-01T23:59:59.000Z

    In his Advanced Energy Initiative announced in January 2006, President George W. Bush committed the nation to new efforts to develop alternative sources of energy to replace imported oil and fossil fuels. Developing cost-effective and energy-efficient methods of producing renewable alternative fuels such as cellulosic ethanol from biomass and solar-derived biofuels will require transformational breakthroughs in science and technology. Incremental improvements in current bioenergy production methods will not suffice. The Genomics:GTL Bioenergy Research Centers will be dedicated to fundamental research on microbe and plant systems with the goal of developing knowledge that will advance biotechnology-based strategies for biofuels production. The aim is to spur substantial progress toward cost-effective production of biologically based renewable energy sources. This document describes the rationale for the establishment of the centers and their objectives in light of the U.S. Department of Energy's mission and goals. Developing energy-efficient and cost-effective methods of producing alternative fuels such as cellulosic ethanol from biomass will require transformational breakthroughs in science and technology. Incremental improvements in current bioenergy-production methods will not suffice. The focus on microbes (for cellular mechanisms) and plants (for source biomass) fundamentally exploits capabilities well known to exist in the microbial world. Thus 'proof of concept' is not required, but considerable basic research into these capabilities remains an urgent priority. Several developments have converged in recent years to suggest that systems biology research into microbes and plants promises solutions that will overcome critical roadblocks on the path to cost-effective, large-scale production of cellulosic ethanol and other renewable energy from biomass. The ability to rapidly sequence the DNA of any organism is a critical part of these new capabilities, but it is only a first step. Other advances include the growing number of high-throughput techniques for protein production and characterization; a range of new instrumentation for observing proteins and other cell constituents; the rapid growth of commercially available reagents for protein production; a new generation of high-intensity light sources that provide precision imaging on the nanoscale and allow observation of molecular interactions in ultrafast time intervals; major advances in computational capability; and the continually increasing numbers of these instruments and technologies within the national laboratory infrastructure, at universities, and in private industry. All these developments expand our ability to elucidate mechanisms present in living cells, but much more remains to be done. The Centers are designed to accomplish GTL program objectives more rapidly, more effectively, and at reduced cost by concentrating appropriate technologies and scientific expertise, from genome sequence to an integrated systems understanding of the pathways and internal structures of microbes and plants most relevant to developing bioenergy compounds. The Centers will seek to understand the principles underlying the structural and functional design of selected microbial, plant, and molecular systems. This will be accomplished by building technological pathways linking the genome-determined components in an organism with bioenergy-relevant cellular systems that can be characterized sufficiently to generate realistic options for biofuel development. In addition, especially in addressing what are believed to be nearer-term approaches to renewable energy (e.g., producing cellulosic ethanol cost-effectively and energy-efficiently), the Center research team must understand in depth the current industrial-level roadblocks and bottlenecks (see section, GTL's Vision for Biological Energy Alternatives, below). For the Centers, and indeed the entire BER effort, to be successful, Center research must be integrated with individual investigator research, and coordination of activities,

  14. Science Advisory Committee | EMSL

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

    Science Advisory Committee About EMSL Leadership Scientific Impact EMSL's Evolution Science Advisory Committee User Executive Committee Strategy and Operations Science Advisory...

  15. Top Science of 2013

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

    Liquid-scanning technology boosts airport security science-innovationassetsimagesicon-science.jpg Top Science of 2013 Our strong interdisciplinary teaming and unique research...

  16. Citizen science in archaeology

    E-Print Network [OSTI]

    Smith, ML

    2014-01-01T23:59:59.000Z

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

  17. BER Science Network Requirements

    E-Print Network [OSTI]

    Dart, Eli

    2011-01-01T23:59:59.000Z

    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

  18. Science Gateway Databases

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

    Science Databases Science Database Services NERSC supports the provisioning of databases to hold large scientific datasets, as part of the science gateways effort. Data-centric...

  19. [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

  20. College of Health Sciences Health Sciences Connection

    E-Print Network [OSTI]

    Barrash, Warren

    , College of Health Sciences. · "Innovative Ways to Address Idaho's Healthcare Needs: Long-Term CareCollege 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