Sample records for human genome project

  1. 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.

  2. 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:

  3. Implications of the Human Genome Project

    SciTech Connect (OSTI)

    Kitcher, P.

    1998-11-01T23:59:59.000Z

    The Human Genome Project (HGP), launched in 1991, aims to map and sequence the human genome by 2006. During the fifteen-year life of the project, it is projected that $3 billion in federal funds will be allocated to it. The ultimate aims of spending this money are to analyze the structure of human DNA, to identify all human genes, to recognize the functions of those genes, and to prepare for the biology and medicine of the twenty-first century. The following summary examines some of the implications of the program, concentrating on its scientific import and on the ethical and social problems that it raises. Its aim is to expose principles that might be used in applying the information which the HGP will generate. There is no attempt here to translate the principles into detailed proposals for legislation. Arguments and discussion can be found in the full report, but, like this summary, that report does not contain any legislative proposals.

  4. 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.

  5. 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.

  6. The Human Genome Project and eugenic concerns

    SciTech Connect (OSTI)

    Garver, K.L.; Garver, B. (Univ. of Pittsburgh, PA (United States))

    1994-01-01T23:59:59.000Z

    The US Human Genome Project is the largest scientific project funded by the federal government since the Apollo Moon Project. The overall effect from this project should be of great benefit to humankind because it will provide a better understanding both of single gene defects and multifactorial or familial diseases such as diabetes, arteriosclerosis, and cancer. At first this will lead to more exact ways of screening and diagnosing genetic disease, and later it will lead, in many if not most instances, to specific genetic cures. However, in the past, in both the US and German eugenic movements genetic information has been misused. Hopefully, by remembering and understanding the past injustices and inhumanity of negative eugenics, further misuse of scientific information can be avoided. 142 refs.

  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. 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.

  9. The Human Genome Project: Information access, management, and regulation. Final report

    SciTech Connect (OSTI)

    McInerney, J.D.; Micikas, L.B.

    1996-08-31T23:59:59.000Z

    The Human Genome Project is a large, internationally coordinated effort in biological research directed at creating a detailed map of human DNA. This report describes the access of information, management, and regulation of the project. The project led to the development of an instructional module titled The Human Genome Project: Biology, Computers, and Privacy, designed for use in high school biology classes. The module consists of print materials and both Macintosh and Windows versions of related computer software-Appendix A contains a copy of the print materials and discs containing the two versions of the software.

  10. Getting the Word Out on the Human Genome Project: A Course for Physicians

    SciTech Connect (OSTI)

    Sara L. Tobin

    2004-09-29T23:59:59.000Z

    Our project, ''Getting the Word Out on the Human Genome Project: A Course for Physicians,'' presented educational goals to convey the power and promise of the Human Genome Program to a variety of professional, educational, and public audiences. Our initial goal was to provide practicing physicians with a comprehensive multimedia tool to update their skills in the genomic era. We therefore created the multimedia courseware, ''The New Genetics: Courseware for Physicians. Molecular Concepts, Applications, and Ramifications.'' However, as the project moved forward, several unanticipated audiences found the courseware to be useful for instruction and for self-education, so an additional edition of the courseware ''The New Genetics: Medicine and the Human Genome. Molecular Concepts, Applications, and Ramifications'' was published simultaneously with the physician version. At the time that both versions of the courseware were being completed, Stanford's Office of Technology Licensing opted not to commercialize the courseware and offered a license-back agreement if the authors founded a commercial business. The authors thus became closely involved in marketing and sales, and several thousand copies of the courseware have been sold. Surprisingly, the non-physician version has turned out to be more in demand, and this has led us in several new directions, most of which involve undergraduate education. These are discussed in detail in the Report.

  11. 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 ...

  12. The human genome project: Information management, access, and regulation. Technical progress report, 1 April--31 August 1993

    SciTech Connect (OSTI)

    McInerney, J.D.; Micikas, L.B.

    1993-09-10T23:59:59.000Z

    Efforts are described to prepare educational materials including computer based as well as conventional type teaching materials for training interested high school and elementary students in aspects of Human Genome Project.

  13. The Human Genome Project and Mental Retardation: An Educational Program. Final Progress Report

    SciTech Connect (OSTI)

    Davis, Sharon

    1999-05-03T23:59:59.000Z

    The Arc, a national organization on mental retardation, conducted an educational program for members, many of whom have a family member with a genetic condition causing mental retardation. The project informed members about the Human Genome scientific efforts, conducted training regarding ethical, legal and social implications and involved members in issue discussions. Short reports and fact sheets on genetic and ELSI topics were disseminated to 2,200 of the Arc's leaders across the country and to other interested individuals. Materials produced by the project can e found on the Arc's web site, TheArc.org.

  14. 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.

  15. ELSI Bibliography: Ethical legal and social implications of the Human Genome Project

    SciTech Connect (OSTI)

    Yesley, M.S. [comp.

    1993-11-01T23:59:59.000Z

    This second edition of the ELSI Bibliography provides a current and comprehensive resource for identifying publications on the major topics related to the ethical, legal and social issues (ELSI) of the Human Genome Project. Since the first edition of the ELSI Bibliography was printed last year, new publications and earlier ones identified by additional searching have doubled our computer database of ELSI publications to over 5600 entries. The second edition of the ELSI Bibliography reflects this growth of the underlying computer database. Researchers should note that an extensive collection of publications in the database is available for public use at the General Law Library of Los Alamos National Laboratory (LANL).

  16. Biology for Students: Bioinformatics The Human Genome Project (HGP) is an international effort to determine the biochemical code for

    E-Print Network [OSTI]

    Weng, Zhiping

    Biology for Students: Bioinformatics The Human Genome Project (HGP) is an international effort, Bioinformatics focuses on computational approaches. One aspect of Bioinformatics involves the development and their regulatory elements that serve as the blueprint of human biology. The HGP has generated massive data

  17. 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.

  18. ELSI Bibliography: Ethical, legal and social implications of the Human Genome Project. 1994 Supplement

    SciTech Connect (OSTI)

    Yesley, M.S.; Ossorio, P.N. [comps.

    1994-09-01T23:59:59.000Z

    This report updates and expands the second edition of the ELSI Bibliography, published in 1993. The Bibliography and Supplement provides a comprehensive resource for identifying publications on the major topics related to the ethical, legal and social issues (ELSI) of the Human Genome Project. The Bibliography and Supplement are extracted from a database compiled at Los Alamos National Laboratory with the support of the Office of Energy Research, US Department of Energy. The second edition of the ELSI Bibliography was dated May 1993 but included publications added to the database until fall 1993. This Supplement reflects approximately 1,000 entries added to the database during the past year, bringing the total to approximately 7,000 entries. More than half of the new entries were published in the last year, and the remainder are earlier publications not previously included in the database. Most of the new entries were published in the academic and professional literature. The remainder are press reports from newspapers of record and scientific journals. The topical listing of the second edition has been followed in the Supplement, with a few changes. The topics of Cystic Fibrosis, Huntington`s Disease, and Sickle Cell Anemia have been combined in a single topic, Disorders. Also, all the entries published in the past year are included in a new topic, Publications: September 1993--September 1994, which provides a comprehensive view of recent reporting and commentary on the science and ELSI of genetics.

  19. 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.

  20. The New World of Human Genetics: A dialogue between Practitioners & the General Public on Ethical, Legal & Social Implications of the Human Genome Project

    SciTech Connect (OSTI)

    Schofield, Amy

    2014-12-08T23:59:59.000Z

    The history and reasons for launching the Human Genome project and the current uses of genetic human material; Identifying and discussing the major issues stemming directly from genetic research and therapy-including genetic discrimination, medical/ person privacy, allocation of government resources and individual finances, and the effect on the way in which we perceive the value of human life; Discussing the sometimes hidden ethical, social and legislative implications of genetic research and therapy such as informed consent, screening and preservation of genetic materials, efficacy of medical procedures, the role of the government, and equal access to medical coverage.

  1. Use of Optical Mapping to Aid in Assembly and Finishing of Human Microbiome Genome Projects

    SciTech Connect (OSTI)

    Wagner, Trevor [OpGen, Inc

    2010-06-03T23:59:59.000Z

    Trevor Wagner of OpGen, Inc. discusses the use of optical mapping to validate the assembly of HMP genomes on June 3, 2010 at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM

  2. An information and dialogue conference on the human genome project (HGP) for the minority communities in the state of Louisiana

    SciTech Connect (OSTI)

    NONE

    1999-06-01T23:59:59.000Z

    Zeta Phi Beta Sorority National Educational Foundation, in cooperation with Xavier University of New Orleans, and the New Orleans District Office of the United States Equal Employment Opportunity Commission, held the Information and Dialogue Conference on the Human Genome Project for the Minority Communities in the State of Louisiana on April 16-17, 1999. The Conference was held on the campus of Xavier University in New Orleans. Community leaders, government officials, minority professional and social organizations leaders, religious leaders, persons from the educational and academic community, and students were invited. Conference objectives included bringing HGP information and a focus in the minority community on the project, in clear and understandable terms, to spread the work in the minority community about the project; to explore the likely positive implications with respect to health care and related matters; to explore possible negative results and strategies to meet them; to discuss the social, legal, and ethical implications; and to facilitate minority input into the HGP as it develops.

  3. DOE human genome program contractor-grantee workshop VI

    SciTech Connect (OSTI)

    NONE

    1997-10-01T23:59:59.000Z

    Research is presented from the workshop on the Human Genome Project. Topics include sequencing, genetic mapping, informatics, ethical and legal issues, and infrastructure.

  4. An integrated encyclopedia of DNA elements in the human genome

    E-Print Network [OSTI]

    Altshuler, Robert Charles

    The human genome encodes the blueprint of life, but the function of the vast majority of its nearly three billion bases is unknown. The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of ...

  5. 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

  6. The Human Microbiome Project: A Community Resource for the Healthy Human Microbiome

    E-Print Network [OSTI]

    Gevers, Dirk

    The Human Microbiome Project (HMP) [1],[2] is a concept that was long in the making. After the Human Genome Project, interest grew in sequencing the “other genome" of microbes carried in and on the human body [3],[4]. ...

  7. A map of human genome variation from population-scale sequencing

    E-Print Network [OSTI]

    Lander, Eric S.

    The 1000 Genomes Project aims to provide a deep characterization of human genome sequence variation as a foundation for investigating the relationship between genotype and phenotype. Here we present results of the pilot ...

  8. 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.

  9. 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...

  10. Primer on molecular genetics. DOE Human Genome Program

    SciTech Connect (OSTI)

    Not Available

    1992-04-01T23:59:59.000Z

    This report is taken from the April 1992 draft of the DOE Human Genome 1991--1992 Program Report, which is expected to be published in May 1992. The primer is intended to be an introduction to basic principles of molecular genetics pertaining to the genome project. The material contained herein is not final and may be incomplete. Techniques of genetic mapping and DNA sequencing are described.

  11. 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

  12. DOE Human Genome Program contractor-grantee workshop

    SciTech Connect (OSTI)

    NONE

    1996-01-01T23:59:59.000Z

    This volume contains the proceedings for the DOE Human Genome Program`s Contractor-Grantee Workshop V held in Sante Fe, New Mexico January 28, February 1, 1996. Presentations were divided into sessions entitled Sequencing; Mapping; Informatics; Ethical, Legal, and Social Issues; and Infrastructure. Reports of individual projects described herein are separately indexed and abstracted for the database.

  13. 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

  14. 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.

  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. 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 ...

  17. 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 ...

  18. Report of the second Human Genome Diversity workshop

    SciTech Connect (OSTI)

    NONE

    1992-12-31T23:59:59.000Z

    The Second Human Genome Diversity Workshop was successfully held at Penn State University from October 29--31, 1992. The Workshop was essentially organized around 7 groups, each comprising approximately 10 participants, representing the sampling issues in different regions of the world. These groups worked independently, using a common format provided by the organizers; this was adjusted as needed by the individual groups. The Workshop began with a presentation of the mandate to the participants, and of the procedures to be followed during the workshop. Dr. Feldman presented a summary of the results from the First Workshop. He and the other organizers also presented brief comments giving their perspective on the objectives of the Second Workshop. Dr. Julia Bodmer discussed the study of European genetic diversity, especially in the context of the HLA experience there, and of plans to extend such studies in the coming years. She also discussed surveys of world HLA laboratories in regard to resources related to Human Genome Diversity. Dr. Mark Weiss discussed the relevance of nonhuman primate studies for understanding how demographic processes, such as mate exchange between local groups, affected the local dispersion of genetic variation. Primate population geneticists have some relevant experience in interpreting variation at this local level, in particular, with various DNA fingerprinting methods. This experience may be relevant to the Human Genome Diversity Project, in terms of practical and statistical issues.

  19. 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.

  20. The Cancer Genome Atlas Pan-Cancer analysis project

    E-Print Network [OSTI]

    Lander, Eric S.

    The Cancer Genome Atlas (TCGA) Research Network has profiled and analyzed large numbers of human tumors to discover molecular aberrations at the DNA, RNA, protein and epigenetic levels. The resulting rich data provide a ...

  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. 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

  3. 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.

  4. Monochromosomal hybrids for the analysis of the human genome

    SciTech Connect (OSTI)

    Athwal, R.S.

    1990-01-01T23:59:59.000Z

    In this research project the authors proposed to develop rodent/human hybrid cell lines each containing a single different human chromosome. The human chromosomes will be marked with Ecogpt and stably maintained by selection in the hybrid cells. The experimental approach to produce the proposed cell lines involve the following: they will first transfer a cloned selectable marker, Ecogpt (an E. coli gene for xanthine-guanine phosphoribosyltransferase: XGPRT) to normal diploid human cells using a retroviral vector. The transferred gene will integrate at random into multiple sites in the recipient cell genome. Clonal cell lines from independent transgenotes will each carry the selectable marker integrated into a different site and perhaps a different chromosome. The chromosome carrying the selectable marker will then be transferred further to mouse cells by microcell fusion. In addition they also use directed integration of Ecogpt into the chromosome present in rodent cells, otherwise not marked with a selectable marker. This allows them to complete the bank of proposed cell line. The human chromosome, since it will be marked with a selectable marker, can be transferred to any other cell line of interest for complementation analysis. Clones of each cell line, containing varying size segments of the same chromosome produced by selection for the retention or loss of the selectable marker following x-irradiation or by metaphase chromosome transfer method will facilitate physical mapping and determination of gene order on a chromosome. 1 fig.

  5. 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

  6. Materials Project: A Materials Genome Approach

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

    Ceder, Gerbrand (MIT); Persson, Kristin (LBNL)

    Technological innovation - faster computers, more efficient solar cells, more compact energy storage - is often enabled by materials advances. Yet, it takes an average of 18 years to move new materials discoveries from lab to market. This is largely because materials designers operate with very little information and must painstakingly tweak new materials in the lab. Computational materials science is now powerful enough that it can predict many properties of materials before those materials are ever synthesized in the lab. By scaling materials computations over supercomputing clusters, this project has computed some properties of over 80,000 materials and screened 25,000 of these for Li-ion batteries. The computations predicted several new battery materials which were made and tested in the lab and are now being patented. By computing properties of all known materials, the Materials Project aims to remove guesswork from materials design in a variety of applications. Experimental research can be targeted to the most promising compounds from computational data sets. Researchers will be able to data-mine scientific trends in materials properties. By providing materials researchers with the information they need to design better, the Materials Project aims to accelerate innovation in materials research.[copied from http://materialsproject.org/about] You will be asked to register to be granted free, full access.

  7. The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata

    SciTech Connect (OSTI)

    Liolios, Konstantinos; Chen, Amy; Mavromatis, Konstantinos; Tavernarakis, Nektarios; Hugenholtz, Phil; Markowitz, Victor; Kyrpides, Nikos C.

    2009-09-01T23:59:59.000Z

    The Genomes On Line Database (GOLD) is a comprehensive resource for centralized monitoring of genome and metagenome projects worldwide. Both complete and ongoing projects, along with their associated metadata, can be accessed in GOLD through precomputed tables and a search page. As of September 2009, GOLD contains information for more than 5800 sequencing projects, of which 1100 have been completed and their sequence data deposited in a public repository. GOLD continues to expand, moving toward the goal of providing the most comprehensive repository of metadata information related to the projects and their organisms/environments in accordance with the Minimum Information about a (Meta)Genome Sequence (MIGS/MIMS) specification.

  8. The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata

    SciTech Connect (OSTI)

    Fenner, Marsha W; Liolios, Konstantinos; Mavromatis, Konstantinos; Tavernarakis, Nektarios; Kyrpides, Nikos C.

    2007-12-31T23:59:59.000Z

    The Genomes On Line Database (GOLD) is a comprehensive resource of information for genome and metagenome projects world-wide. GOLD provides access to complete and ongoing projects and their associated metadata through pre-computed lists and a search page. The database currently incorporates information for more than 2900 sequencing projects, of which 639 have been completed and the data deposited in the public databases. GOLD is constantly expanding to provide metadata information related to the project and the organism and is compliant with the Minimum Information about a Genome Sequence (MIGS) specifications.

  9. Beyond The Human Genome: What's Next? (LBNL Summer Lecture Series)

    ScienceCinema (OSTI)

    Rokhsar, Daniel

    2014-05-06T23:59:59.000Z

    UC Berkeley's Daniel Rokhsar and his colleagues were instrumental in contributing the sequences for three of the human body's chromosomes in the effort to decipher the blueprint of life- the completion of the DNA sequencing of the human genome. Now he is turning to the structure and function of genes in other organisms, some of them no less important to the planet's future than the human map. Hear the latest in this lecture from Lawrence Berkeley National Laboratory.

  10. The Data Center (DC) Genome project is a collaborative effort with Microsoft Research

    E-Print Network [OSTI]

    Amir, Yair

    that IT equipment needs abundant cooling to operate reliably, the CRAC systems in many data centers are set to very, Project Genome: Wireless Sensor Network for Data Center Cooling , The Architecture Journal volume 18, 2009DC Genome The Data Center (DC) Genome project is a collaborative effort with Microsoft Research

  11. Genomic mosaicism in the human brain

    E-Print Network [OSTI]

    Westra, Jurjen Willem

    2008-01-01T23:59:59.000Z

    Zlokovic BV (2008) The blood-brain barrier in health andmosaicism in the human brain ………………………………………. Chapter Threethe Alzheimer’s disease brain ………………………………. Chapter Five DNA

  12. Human genome program report. Part 1, overview and progress

    SciTech Connect (OSTI)

    NONE

    1997-11-01T23:59:59.000Z

    This report contains Part 1 of a two-part report to reflect research and progress in the U.S. Department of Energy Human Genome Program from 1994 through 1996, with specified updates made just before publication. Part 1 consists of the program overview and report on progress.

  13. Human genome program report. Part 2, 1996 research abstracts

    SciTech Connect (OSTI)

    NONE

    1997-11-01T23:59:59.000Z

    This report contains Part 2 of a two-part report to reflect research and progress in the US Department of Energy Human Genome Program from 1994 through 1996, with specified updates made just before publication. Part 2 consists of 1996 research abstracts. Attention is focused on the following: sequencing; mapping; informatics; ethical, legal, and social issues; infrastructure; and small business innovation research.

  14. 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

  15. Identification and analysis of functional elements in 1% of the human genome by

    E-Print Network [OSTI]

    Lieb, Jason

    ARTICLES Identification and analysis of functional elements in 1% of the human genome by the ENCODE frommultiple,diverseexperimentsperformedonatargeted 1%ofthe human genome as part of the pilot phase and computational analyses. Together, our results advance the collective knowledge about human genome function

  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. 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"

  18. Developing Grid-based Systems for Microbial Genome Comparisons: The Microbase Project

    E-Print Network [OSTI]

    Newcastle upon Tyne, University of

    Developing Grid-based Systems for Microbial Genome Comparisons: The Microbase Project Anil Wipat, University of Newcastle upon Tyne Abstract Comparative analysis of genomes allows the rich source of biological genome sequence data to be most efficiently exploited. However, the rate at which microbial

  19. 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.

  20. Human Resources Organizational Readiness Project: An Overview

    E-Print Network [OSTI]

    Finzi, Adrien

    and easily interface with SAP software Managed by a special Human Resources project team Will be undertaken in close coordination with the BUworks program team HR Organizational Readiness Project BUworks / SAP of SAP Enhanced data security within the new system Current job "system" is 30 years old ­ it must

  1. 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.

  2. DOE/ER-0382 THE HUMAN GENOME INITIATIVE OF THE

    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 Administration wouldDECOMPOSITION OF CALCIUMCOSTDOENuclear1382 THE HUMAN GENOME INITIATIVE

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

    E-Print Network [OSTI]

    Arnold, Jonathan

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

  4. ANTH 376: GENOMICS & ANTHROPOLOGY 4 credit hours (satisfies an SC requirement)

    E-Print Network [OSTI]

    1 ANTH 376: GENOMICS & ANTHROPOLOGY 4 credit hours (satisfies an SC variation, health and evolution. Extended Course Description The Human Genome Project and recent advances in genome sequencing techniques have made it possible

  5. Genome-wide In-silico Identification of Transcriptional Regulators Controlling Cell Cycle in Human Cells

    E-Print Network [OSTI]

    Shamir, Ron

    - 1 - Genome-wide In-silico Identification of Transcriptional Regulators Controlling Cell Cycle-3-6409760 Fax: 972-3-6407471 e-mail: yossih@post.tau.ac.il Running title: Transcriptional regulation of human cell cycle Key words: Transcriptional regulation, cell cycle, functional genomics. #12;- 2 - Abstract

  6. FCTO Projects and the Materials Genome Initiative Webinar

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

    non-precious functional materials. The electrochemical conditions are relevant to fuel cells. Project Technical Approach & Example Results * Theory-guided HiTp evaluation...

  7. DOE Human Genome Program: Contractor-Grantee Workshop IV, November 13--17, 1994, Santa Fe, New Mexico

    SciTech Connect (OSTI)

    Not Available

    1994-10-01T23:59:59.000Z

    This volume contains the proceedings of the fourth Contractor-Grantee Workshop for the Department of Energy (DOE) Human Genome Program. Of the 204 abstracts in this book, some 200 describe the genome research of DOE-funded grantees and contractors located at the multidisciplinary centers at Lawrence Berkeley Laboratory, Lawrence Livermore National Laboratory, and Los Alamos National Laboratory; other DOE-supported laboratories; and more than 54 universities, research organizations, and companies in the United States and abroad. Included are 16 abstracts from ongoing projects in the Ethical, Legal, and Social Issues (ELSI) component, an area that continues to attract considerable attention from a wide variety of interested parties. Three abstracts summarize work in the new Microbial Genome Initiative launched this year by the Office of Health and Environmental Research (OHER) to provide genome sequence and mapping data on industrially important microorganisms and those that live under extreme conditions. Many of the projects will be discussed at plenary sessions held throughout the workshop, and all are represented in the poster sessions.

  8. EA-0856: Construction and Operation of a Human Genome Laboratory at Lawrence Berkeley Laboratory Berkeley, California

    Broader source: Energy.gov [DOE]

    This EA evaluates the environmental impacts of a proposal to construct and operate a new laboratory for consolidation of current and future activities of the Human Genome Center at the U.S....

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

    ScienceCinema (OSTI)

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

    2011-04-29T23:59:59.000Z

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

  10. The DNA Files: Report from Genome Radio Project, March--June 1995

    SciTech Connect (OSTI)

    NONE

    1995-07-10T23:59:59.000Z

    The Genome Radio Project (GRP) core staff are now all in place and the office infrastructure has been set up. The project logo, stationery, and letterhead have all been approved. The name of the series has been identified: The DNA Files. Weekly staff planning meetings and work plans have been initiated; the research component has been launched; interviews of potential production personnel are being conducted. The first three months of the GRP were principally devoted to the further development of the entire two-year project, specifically by pursuing full funding for this project from sources other than DOE. The principal purpose of this planning grant includes the following: produce a pilot documentary which can be used to strengthen the marketing strategy of the overall project; create concrete strategies for best engaging the talents and energies of the project`s advisors; and identify concrete collaborations that maximize the efficacy of a well-designed set of ancillary materials. During this period, GRP collaborated with the Exploratorium in San Francisco to record their series of evening lectures on the social implications of genetic research and its applications. Project staff also attended Lawrence Berkeley Lab.`s Genome Educators Workshops, and the Public Radio Conference.

  11. The genomic complexity of primary human prostate cancer

    E-Print Network [OSTI]

    Carter, Scott Lambert

    Prostate cancer is the second most common cause of male cancer deaths in the United States. However, the full range of prostate cancer genomic alterations is incompletely characterized. Here we present the complete sequence ...

  12. FCTO Projects and the Materials Genome Initiative | Department of Energy

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Home Page on Google Bookmark EERE: Alternative Fuels DataDepartment of Energy Your Density Isn't YourTransport in Representative Geologic MediaTreatment |Safeguards andBG-PLN-0036FCTO Projects

  13. Bioinformatics for the human microbiome project

    E-Print Network [OSTI]

    Gevers, Dirk

    Microbes inhabit virtually all sites of the human body, yet we know very little about the role they play in our health. In recent years, there has been increasing interest in studying human-associated microbial communities, ...

  14. 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,

  15. Project 3 Integrative Genomics (IG) Objective: To give a presentation of about 40-90 minutes duration at the end of the week covering the

    E-Print Network [OSTI]

    Goldschmidt, Christina

    Project 3 ­ Integrative Genomics (IG) Objective: To give a presentation of about 40-90 minutes duration at the end of the week covering the key aspects of the integrative genomics, which is the combined) "Integrative Genomics and Functional Explanation" downloadable from http://www.stats.ox.ac.uk/research/genome

  16. MSc Human-Computer Interaction with Ergonomics MSc Project

    E-Print Network [OSTI]

    Blandford, Ann

    MSc Human-Computer Interaction with Ergonomics MSc Project Web analytics and think aloud studies-Computer Interaction with Ergonomics) in the Faculty of Life Sciences, University College London, [2007]. NOTE

  17. Mexico recently joined the global community in investing in human genomic variation

    E-Print Network [OSTI]

    Cai, Long

    Mexico recently joined the global community in investing in human genomic variation studies through for Mexico to create innovative solutions to its own health challenges as it will focus on the link between in a country like Mexico. INMEGEN will also play a part in economic development. Mexico's recent draft proposal

  18. Patterns of linkage disequilibrium in the human genome

    E-Print Network [OSTI]

    Liu-Cordero, Shau Neen, 1970-

    2002-01-01T23:59:59.000Z

    Although enormous progress has occurred in the field of human genetics, the cloning of complex trait mutations remains a challenging and unresolved process. This continuing difficulty is responsible for an ever-increasing ...

  19. Analysis of alterations in the human cancer genome

    E-Print Network [OSTI]

    Carter, Scott L. (Scott Lambert)

    2011-01-01T23:59:59.000Z

    Aneuploidy, an abnormal complement of chromosomes, is present in approximately 90% of human malignancies. Despite over 100 years of research, many questions remain regarding the contribution of aneuploidy to the cancer ...

  20. Comparative Genomic Analysis of Human Fungal Pathogens Causing Paracoccidioidomycosis

    E-Print Network [OSTI]

    Holder, Jason W.

    Paracoccidioides is a fungal pathogen and the cause of paracoccidioidomycosis, a health-threatening human systemic mycosis endemic to Latin America. Infection by Paracoccidioides, a dimorphic fungus in the order Onygenales, ...

  1. Genomic medicine in primary care: Texas physicians' adoption of an innovation

    E-Print Network [OSTI]

    Suther, Sandra Gayle

    2004-09-30T23:59:59.000Z

    New applications of genomic medicine stemming from the Human Genome Project are predicted to become routine components of primary care. Primary care physicians (PCPs) will increasingly become responsible for screening patients for inherited...

  2. Project ATHENA creates surrogate human organ systems

    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)IntegratedSpeedingTechnical News,Program DirectionProject ATHENA creates surrogate

  3. Project ATHENA creates surrogate human organ systems

    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 Possible forPortsmouth/Paducah47,193.70 Hg Mercury 35InformationProgrammingProgress on anProject

  4. Population Genomics Objective: To give a presentation of about 40-90 minutes duration at the end of the week covering the key aspects

    E-Print Network [OSTI]

    Goldschmidt, Christina

    Population Genomics Objective: To give a presentation of about 40-90 minutes duration at the end of the week covering the key aspects of the population genomics of humans. This 1000 genomes project is devoted to the exciting project, where the genomes of a 1000 individuals are to be sequenced in the next

  5. Mapping cis-Regulatory Domains in the Human Genome UsingMulti-Species Conservation of Synteny

    SciTech Connect (OSTI)

    Ahituv, Nadav; Prabhakar, Shyam; Poulin, Francis; Rubin, EdwardM.; Couronne, Olivier

    2005-06-13T23:59:59.000Z

    Our inability to associate distant regulatory elements with the genes that they regulate has largely precluded their examination for sequence alterations contributing to human disease. One major obstacle is the large genomic space surrounding targeted genes in which such elements could potentially reside. In order to delineate gene regulatory boundaries we used whole-genome human-mouse-chicken (HMC) and human-mouse-frog (HMF) multiple alignments to compile conserved blocks of synteny (CBS), under the hypothesis that these blocks have been kept intact throughout evolution at least in part by the requirement of regulatory elements to stay linked to the genes that they regulate. A total of 2,116 and 1,942 CBS>200 kb were assembled for HMC and HMF respectively, encompassing 1.53 and 0.86 Gb of human sequence. To support the existence of complex long-range regulatory domains within these CBS we analyzed the prevalence and distribution of chromosomal aberrations leading to position effects (disruption of a genes regulatory environment), observing a clear bias not only for mapping onto CBS but also for longer CBS size. Our results provide a genome wide data set characterizing the regulatory domains of genes and the conserved regulatory elements within them.

  6. 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

  7. Projecting human development and CO2 emissions

    E-Print Network [OSTI]

    Costa, Luís; Kropp, Jürgen P

    2012-01-01T23:59:59.000Z

    We estimate cumulative CO2 emissions during the period 2000 to 2050 from developed and developing countries based on the empirical relationship between CO2 per capita emissions (due to fossil fuel combustion and cement production) and corresponding HDI. In order to project per capita emissions of individual countries we make three assumptions which are detailed below. First, we use logistic regressions to fit and extrapolate the HDI on a country level as a function of time. This is mainly motivated by the fact that the HDI is bounded between 0 and 1 and that it decelerates as it approaches 1. Second, we employ for individual countries the correlations between CO2 per capita emissions and HDI in order to extrapolate their emissions. This is an ergodic assumption. Third, we let countries with incomplete data records evolve similarly as their close neighbors (in the emissions-HDI plane, see Fig. 1 in the main text) with complete time series of CO2 per capita emissions and HDI. Country-based emissions estimates a...

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

    SciTech Connect (OSTI)

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

    2012-03-21T23:59:59.000Z

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

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

    ScienceCinema (OSTI)

    Willerslev, Eske [University of Copenhagen

    2013-01-15T23:59:59.000Z

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

  10. 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.

  11. 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

  12. 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

  13. 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.

  14. 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.

  15. 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 ...

  16. Human Resources Organizational Readiness Project Over the past 18 months, hundreds of employees from across the University brought their institutional

    E-Print Network [OSTI]

    Finzi, Adrien

    Human Resources Organizational Readiness Project Over the past 18 months, hundreds of employees implement SAP. What is the Human Resources Organizational Readiness Project? In preparation for the BUworks Program, the Human Resources Organizational Readiness Project will collect, organize and standardize

  17. 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.

  18. Large-scale discovery and validation of functional elements in the human genome

    E-Print Network [OSTI]

    Kellis, Manolis

    A report on the genomics workshop 'Identification of Functional Elements in Mammalian Genomes', Cold Spring Harbor, New York, 11-13 November 2004.

  19. 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,

  20. COORDINATING HUMAN AND MATERIAL RESOURCES Construction project management is the art of directing and coordinating human and material

    E-Print Network [OSTI]

    Simaan, Nabil

    COORDINATING HUMAN AND MATERIAL RESOURCES Construction project management is the art of directing and coordinating human and material resources throughout the life of a project by using modern management. Today's construction engineers and managers are faced with unprecedented challenges in planning

  1. Architecture and anatomy of the genomic locus encoding the human leukemia-associated transcription factor RUNX1/AML1q

    E-Print Network [OSTI]

    Groner, Yoram

    involved in acute myeloid leukemia. Interestingly, the FLI1 homologous sequence contains a breakpoint.elsevier.com/locate/gene Abbreviations: All, acute lymphoid leukemia; AML, acute myeloid leukemia; CBFb, core binding factor b; DS, DownArchitecture and anatomy of the genomic locus encoding the human leukemia-associated transcription

  2. Trans-Study Projection of Genomic Biomarkers in Analysis of Oncogene Deregulation and Breast Cancer

    E-Print Network [OSTI]

    West, Mike

    , to animal model experiments, to human outcome studies and clinical trials. The question of how to translate experiments, and the in vivo context is gene expression studies with data generated from human breast tumours Abstract In cancer studies as in many areas of human disease research, gene expression microarray technol

  3. Assessing corporate project impacts in changeable contexts: A human rights perspective

    SciTech Connect (OSTI)

    Salcito, Kendyl, E-mail: kendyl.salcito@unibas.ch [Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, P.O. Box, CH-4002 Basel (Switzerland); University of Basel, P.O. Box, CH-4003 Basel (Switzerland); NomoGaia, 1900 Wazee Street, Suite 303, Denver, CO 80202 (United States); NewFields, LLC, Denver, CO 80202 (United States); Singer, Burton H., E-mail: bhsinger@epi.ufl.edu [Emerging Pathogens Institute, University of Florida, Gainesville, FL 32610 (United States); Krieger, Gary R., E-mail: gkrieger@newfields.com [NewFields, LLC, Denver, CO 80202 (United States); Weiss, Mitchell G., E-mail: mitchell-g.weiss@unibas.ch [Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, P.O. Box, CH-4002 Basel (Switzerland); University of Basel, P.O. Box, CH-4003 Basel (Switzerland); Wielga, Mark, E-mail: wielga@nomogaia.org [NomoGaia, 1900 Wazee Street, Suite 303, Denver, CO 80202 (United States); NewFields, LLC, Denver, CO 80202 (United States); Utzinger, Jürg, E-mail: juerg.utzinger@unibas.ch [Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, P.O. Box, CH-4002 Basel (Switzerland); University of Basel, P.O. Box, CH-4003 Basel (Switzerland)

    2014-07-01T23:59:59.000Z

    Project-level impact assessment was originally conceived as a snapshot taken in advance of project implementation, contrasting current conditions with a likely future scenario involving a variety of predicted impacts. Current best practice guidance has encouraged a shift towards longitudinal assessments from the pre-project stage through the implementation and operating phases. Experience and study show, however, that assessment of infrastructure-intensive projects rarely endures past the project's construction phase. Negative consequences for environmental, social and health outcomes have been documented. Such consequences clarify the pressing need for longitudinal assessment in each of these domains, with human rights impact assessment (HRIA) as an umbrella over, and critical augmentation of, environmental, social and health assessments. Project impacts on human rights are more closely linked to political, economic and other factors beyond immediate effects of a company's policy and action throughout the project lifecycle. Delineating these processes requires an adequate framework, with strategies for collecting longitudinal data, protocols that provide core information for impact assessment and guidance for adaptive mitigation strategies as project-related effects change over time. This article presents general principles for the design and implementation of sustained, longitudinal HRIA, based on experience assessing and responding to human rights impact in a uranium mining project in Malawi. The case study demonstrates the value of longitudinal assessment both for limiting corporate risk and improving human welfare. - Graphical abstract: Assessing changes in human rights condition as affected by both project and context, over time. - Highlights: • Corporate capital projects affect human rights in myriad ways. • Ongoing, longitudinal impact assessment techniques are needed. • We present an approach for conducting longitudinal human rights impact assessment. • Our methodology allows distinguishing corporate impacts from contextual changes. • Promptly observing context changes and impacts enables companies to react nimbly.

  4. Genome scan identifies a locus affecting gamma-globin expression in human beta-cluster YAC transgenic mice

    SciTech Connect (OSTI)

    Lin, S.D.; Cooper, P.; Fung, J.; Weier, H.U.G.; Rubin, E.M.

    2000-03-01T23:59:59.000Z

    Genetic factors affecting post-natal g-globin expression - a major modifier of the severity of both b-thalassemia and sickle cell anemia, have been difficult to study. This is especially so in mice, an organism lacking a globin gene with an expression pattern equivalent to that of human g-globin. To model the human b-cluster in mice, with the goal of screening for loci affecting human g-globin expression in vivo, we introduced a human b-globin cluster YAC transgene into the genome of FVB mice . The b-cluster contained a Greek hereditary persistence of fetal hemoglobin (HPFH) g allele resulting in postnatal expression of human g-globin in transgenic mice. The level of human g-globin for various F1 hybrids derived from crosses between the FVB transgenics and other inbred mouse strains was assessed. The g-globin level of the C3HeB/FVB transgenic mice was noted to be significantly elevated. To map genes affecting postnatal g-globin expression, a 20 centiMorgan (cM) genome scan of a C3HeB/F VB transgenics [prime] FVB backcross was performed, followed by high-resolution marker analysis of promising loci. From this analysis we mapped a locus within a 2.2 cM interval of mouse chromosome 1 at a LOD score of 4.2 that contributes 10.4% of variation in g-globin expression level. Combining transgenic modeling of the human b-globin gene cluster with quantitative trait analysis, we have identified and mapped a murine locus that impacts on human g-globin expression in vivo.

  5. Approaches to advancing quantitative human health risk assessment of environmental chemicals in the post-genomic era

    SciTech Connect (OSTI)

    Chiu, Weihsueh A., E-mail: chiu.weihsueh@epa.gov [National Center for Environmental Assessment, U.S. Environmental Protection Agency, Washington DC, 20460 (United States); Euling, Susan Y.; Scott, Cheryl Siegel; Subramaniam, Ravi P. [National Center for Environmental Assessment, U.S. Environmental Protection Agency, Washington DC, 20460 (United States)

    2013-09-15T23:59:59.000Z

    The contribution of genomics and associated technologies to human health risk assessment for environmental chemicals has focused largely on elucidating mechanisms of toxicity, as discussed in other articles in this issue. However, there is interest in moving beyond hazard characterization to making more direct impacts on quantitative risk assessment (QRA) — i.e., the determination of toxicity values for setting exposure standards and cleanup values. We propose that the evolution of QRA of environmental chemicals in the post-genomic era will involve three, somewhat overlapping phases in which different types of approaches begin to mature. The initial focus (in Phase I) has been and continues to be on “augmentation” of weight of evidence — using genomic and related technologies qualitatively to increase the confidence in and scientific basis of the results of QRA. Efforts aimed towards “integration” of these data with traditional animal-based approaches, in particular quantitative predictors, or surrogates, for the in vivo toxicity data to which they have been anchored are just beginning to be explored now (in Phase II). In parallel, there is a recognized need for “expansion” of the use of established biomarkers of susceptibility or risk of human diseases and disorders for QRA, particularly for addressing the issues of cumulative assessment and population risk. Ultimately (in Phase III), substantial further advances could be realized by the development of novel molecular and pathway-based biomarkers and statistical and in silico models that build on anticipated progress in understanding the pathways of human diseases and disorders. Such efforts would facilitate a gradual “reorientation” of QRA towards approaches that more directly link environmental exposures to human outcomes.

  6. New families of human regulatory RNA structures identified by comparative analysis of vertebrate genomes

    E-Print Network [OSTI]

    Kellis, Manolis

    Regulatory RNA structures are often members of families with multiple paralogous instances across the genome. Family members share functional and structural properties, which allow them to be studied as a whole, facilitating ...

  7. Draft Genome Sequences of Six Enterohepatic Helicobacter Species Isolated from Humans and One from Rhesus Macaques

    E-Print Network [OSTI]

    Shen, Zeli

    Draft genome sequences of seven enterohepatic Helicobacter species, H. bilis, H. canadensis, H. canis, H. cinaedi, H. winghamensis, H. pullorum, and H. macacae, are presented. These isolates were obtained from clinical ...

  8. 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

  9. Boston University Office of the Executive Vice President Human Resources Organizational Readiness Project

    E-Print Network [OSTI]

    Finzi, Adrien

    in a coordinated format required by the SAP enterprise resource planning (ERP) system. The collection of this data Project represents an important first step in the successful launch of SAP and modernizing our human Project To: Vice Presidents, Deans, Directors and Department Heads From: Joseph P. Mercurio, Executive

  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. 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...

  12. 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:...

  13. 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 &...

  14. Targets of Balancing Selection in the Human Genome Aida M. Andres,* 1

    E-Print Network [OSTI]

    Nielsen, Rasmus

    proposed for several human diseases, including the ß-globin gene and sickle cell anemia (Pasvol et al. 1978

  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. 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

  17. 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.

  18. Chromosome region-specific libraries for human genome analysis. Final progress report, 1 March 1991--28 February 1994

    SciTech Connect (OSTI)

    Kao, F.T.

    1994-04-01T23:59:59.000Z

    The objectives of this grant proposal include (1) development of a chromosome microdissection and PCR-mediated microcloning technology, (2) application of this microtechnology to the construction of region-specific libraries for human genome analysis. During this grant period, the authors have successfully developed this microtechnology and have applied it to the construction of microdissection libraries for the following chromosome regions: a whole chromosome 21 (21E), 2 region-specific libraries for the long arm of chromosome 2, 2q35-q37 (2Q1) and 2q33-q35 (2Q2), and 4 region-specific libraries for the entire short arm of chromosome 2, 2p23-p25 (2P1), 2p21-p23 (2P2), 2p14-p16 (wP3) and 2p11-p13 (2P4). In addition, 20--40 unique sequence microclones have been isolated and characterized for genomic studies. These region-specific libraries and the single-copy microclones from the library have been used as valuable resources for (1) isolating microsatellite probes in linkage analysis to further refine the disease locus; (2) isolating corresponding clones with large inserts, e.g. YAC, BAC, P1, cosmid and phage, to facilitate construction of contigs for high resolution physical mapping; and (3) isolating region-specific cDNA clones for use as candidate genes. These libraries are being deposited in the American Type Culture Collection (ATCC) for general distribution.

  19. CID-miRNA: A web server for prediction of novel miRNA precursors in human genome

    SciTech Connect (OSTI)

    Tyagi, Sonika; Vaz, Candida [Centre for Computational Biology and Bioinformatics, School of Information Technology, Jawaharlal Nehru University, New Mehrauli Road, New Delhi 110067 (India); Gupta, Vipin; Bhatia, Rohit [Department of Computer Sciences, Netaji Subhash Institute of Technology, New Delhi (India); Maheshwari, Sachin [Department of Computer Sciences, Indian Institute of Technology, New Delhi (India); Srinivasan, Ashwin [IBM Research Lab, Indian Institute of Technology, New Delhi (India); Bhattacharya, Alok [Centre for Computational Biology and Bioinformatics, School of Information Technology, Jawaharlal Nehru University, New Mehrauli Road, New Delhi 110067 (India); School of Life Sciences, Jawaharlal Nehru University, New Delhi (India)], E-mail: alok.bhattacharya@gmail.com

    2008-08-08T23:59:59.000Z

    microRNAs (miRNA) are a class of non-protein coding functional RNAs that are thought to regulate expression of target genes by direct interaction with mRNAs. miRNAs have been identified through both experimental and computational methods in a variety of eukaryotic organisms. Though these approaches have been partially successful, there is a need to develop more tools for detection of these RNAs as they are also thought to be present in abundance in many genomes. In this report we describe a tool and a web server, named CID-miRNA, for identification of miRNA precursors in a given DNA sequence, utilising secondary structure-based filtering systems and an algorithm based on stochastic context free grammar trained on human miRNAs. CID-miRNA analyses a given sequence using a web interface, for presence of putative miRNA precursors and the generated output lists all the potential regions that can form miRNA-like structures. It can also scan large genomic sequences for the presence of potential miRNA precursors in its stand-alone form. The web server can be accessed at (http://mirna.jnu.ac.in/cidmirna/)

  20. 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.

  1. 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...

  2. Genome Wide Evaluation of Normal Human Tissue in Response to Controlled, In

    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 TALGenomevivo

  3. Habitat for Humanity: La Grange, Georgia, 2003 Jimmy Carter Work Project

    SciTech Connect (OSTI)

    Not Available

    2005-06-01T23:59:59.000Z

    The Troup-Chambers Habitat for Humanity built a Habitat house to ENERGY STAR standards in LaGrange, Georgia, in 2003. The project was so successfully that all Troup-Chambers houses will now be built to ENERGY STAR standards.

  4. 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 ...

  5. Gray, W. D. (2003). Cognitive factors in homeland defense: The role of human factors in the novel intelligence from massive data (NIMD) project, Human Factors and Ergonomics Society (pp. 1017-1018). Santa Monica, CA: Human

    E-Print Network [OSTI]

    Gray, Wayne

    2003-01-01T23:59:59.000Z

    intelligence from massive data (NIMD) project, Human Factors and Ergonomics Society (pp. 1017-1018). Santa Monica, CA: Human Factors and Ergonomics Society. COGNITIVE FACTORS IN HOMELAND DEFENSE: THE ROLE

  6. Origins of chromosomal rearrangement hotspots in the human genome: evidence from the AZFadeletion hotspots

    E-Print Network [OSTI]

    Hurles, Matthew E; Willey, David; Matthews, Lucy; Hussain, Syed Sufyan

    2004-07-14T23:59:59.000Z

    switched in error. Analysis of gene conversion tract length After determining the minimum number of gene conversion events using the phylogeny (see text), observed tract lengths were estimated using the method of Betrán et al. (1997) as implemented... readily utilized substrate for NAHR. Second, because different conversion events occur in different chromosomes, 5 it can generate excess sequence diversity among them – a phenomenon recognized in organisms as diverse as humans, flies and protozoans...

  7. 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.

  8. 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.

  9. 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

  10. 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

  11. 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...

  12. NCBI Handout Series | BioProject | Last Update August 19, 2013 Contact: info@ncbi.nlm.nih.gov Biological studies in the post-genome era often produce large volumes of complex and high-throughput

    E-Print Network [OSTI]

    Levin, Judith G.

    Project. Registering a project requires credentials from an MyNCBI, NIH or eRA login. Searching with "Chinchilla [orgn of Health · Department of Health and Human Services B A C E D Chinchilla [organism] #12;The Bio

  13. 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.

  14. Human Genome: DOE Origins

    Office of Scientific and Technical Information (OSTI)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645 3,625 1,006 492 742EnergyOn AprilAElectronic InputRudolphMATERIALSInformationUniversity)W

  15. A clamp ligation method for point mutational spectrometry : marked increase in scanning range for the human genome

    E-Print Network [OSTI]

    Kim, Andrea Seungsun, 1971-

    2002-01-01T23:59:59.000Z

    The study of human mutagenesis requires methods of measuring somatic mutations in normal human tissues and inherited mutations in human populations. Such methods should permit measurement of rare mutations in the presence ...

  16. 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.

  17. 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...

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

    E-Print Network [OSTI]

    Goldschmidt, Christina

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

  19. 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

  20. 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.

  1. 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.

  2. GOLD: The Genomes Online Database

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

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

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

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

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

    (Specialized Interface)

  3. Identification of the major structural and nonstructural proteins encoded by human parvovirus B19 and mapping of their genes by procaryotic expression of isolated genomic fragments

    SciTech Connect (OSTI)

    Cotmore, S.F.; McKie, V.C.; Anderson, L.J.; Astell, C.R.; Tattersall, P.

    1986-11-01T23:59:59.000Z

    Plasma from a child with homozygous sickle-cell disease, sampled during the early phase of an aplastic crisis, contained human parvovirus B19 virions. Plasma taken 10 days later (during the convalescent phase) contained both immunoglobulin M and immunoglobulin G antibodies directed against two viral polypeptides with apparent molecular weights for 83,000 and 58,000 which were present exclusively in the particulate fraction of the plasma taken during the acute phase. These two protein species comigrated at 110S on neutral sucrose velocity gradients with the B19 viral DNA and thus appear to constitute the viral capsid polypeptides. The B19 genome was molecularly cloned into a bacterial plasmid vector. Two expression constructs containing B19 sequences from different halves of the viral genome were obtained, which directed the synthesis, in bacteria, of segments of virally encoded protein. These polypeptide fragments were then purified and used to immunize rabbits. Antibodies against a protein sequence specified between nucleotides 2897 and 3749 recognized both the 83- and 58-kilodalton capsid polypeptides in aplastic plasma taken during the acute phase and detected similar proteins in the similar proteins in the tissues of a stillborn fetus which had been infected transplacentally with B19. Antibodies against a protein sequence encoded in the other half of the B19 genome (nucleotides 1072 through 2044) did not react specifically with any protein in plasma taken during the acute phase but recognized three nonstructural polypeptides of 71, 63, and 52 kilodaltons present in the liver and, at lower levels, in some other tissues of the transplacentally infected fetus.

  4. 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

  5. The Human Genome Project and other biological research efforts are creating an avalanche of new data about the chemical makeu

    Office of Scientific and Technical Information (OSTI)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645 3,625 1,006 492 742EnergyOnItem Not FoundInformation DOEInformation Summary Big*The Effective Field

  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. 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

  8. 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

  9. 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...

  10. 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

  11. Why Human Disease-Associated Residues Appear as the Wild-Type in Other Species: Genome-Scale Structural

    E-Print Network [OSTI]

    Zhang, Jianzhi

    : Jeffrey Thorne Abstract Many human-disease associated amino acid residues (DARs) appear as the wild in these other species that alleviate the deleterious effects of the DARs. The general validity the compensation hypothesis by assembling and analyzing 1,077 DARs located in 177 proteins of known crystal

  12. 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

  13. 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.

  14. Evolution and comparative genomics of subcellular specializations: EST sequencing of Torpedo electric organ

    E-Print Network [OSTI]

    Vertes, Akos

    Evolution and comparative genomics of subcellular specializations: EST sequencing of Torpedo discovery Open reading frame (ORF) Uncharacterized open reading frames (ORFs) in human genomic sequence Elsevier B.V. All rights reserved. 1. Introduction The availability of complete genomic sequences

  15. 12 IEEE TRANSACTIONS ON NANOTECHNOLOGY, VOL. 1, NO. 1, MARCH 2002 Scanning the Controls: Genomics and

    E-Print Network [OSTI]

    12 IEEE TRANSACTIONS ON NANOTECHNOLOGY, VOL. 1, NO. 1, MARCH 2002 Scanning the Controls: Genomics and topological complexity is the complexity of the genome itself, consisting of about one billion basepairs. The Human Genome Proj

  16. Considerations Related To Human Intrusion In The Context Of Disposal Of Radioactive Waste-The IAEA HIDRA Project

    SciTech Connect (OSTI)

    Seitz, Roger; Kumano, Yumiko; Bailey, Lucy; Markley, Chris; Andersson, Eva; Beuth, Thomas

    2014-01-09T23:59:59.000Z

    The principal approaches for management of radioactive waste are commonly termed ‘delay and decay’, ‘concentrate and contain’ and ‘dilute and disperse’. Containing the waste and isolating it from the human environment, by burying it, is considered to increase safety and is generally accepted as the preferred approach for managing radioactive waste. However, this approach results in concentrated sources of radioactive waste contained in one location, which can pose hazards should the facility be disrupted by human action in the future. The International Commission on Radiological Protection (ICRP), International Atomic Energy Agency (IAEA), and Organization for Economic Cooperation and Development/Nuclear Energy Agency (OECD/NEA) agree that some form of inadvertent human intrusion (HI) needs to be considered to address the potential consequences in the case of loss of institutional control and loss of memory of the disposal facility. Requirements are reflected in national regulations governing radioactive waste disposal. However, in practice, these requirements are often different from country to country, which is then reflected in the actual implementation of HI as part of a safety case. The IAEA project on HI in the context of Disposal of RadioActive waste (HIDRA) has been started to identify potential areas for improved consistency in consideration of HI. The expected outcome is to provide recommendations on how to address human actions in the safety case in the future, and how the safety case may be used to demonstrate robustness and optimize siting, design and waste acceptance criteria within the context of a safety case.

  17. The human molecular clock and mutation process : a characterization using microsatellite DNA

    E-Print Network [OSTI]

    Sun, James Xin

    2012-01-01T23:59:59.000Z

    In the past decade, thousands of human genomes have been catalogued, either by whole-genome sequencing or by targeted genotyping. The variability between human genomes encodes invaluable information about human traits and ...

  18. 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

  19. 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 ...

  20. 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...

  1. 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.

  2. Hybrid Human Powered Vehicle (Phase 3) The Zero EMission (ZEM) Vehicle Project

    E-Print Network [OSTI]

    Su, Xiao

    Continuous charging batteries by solar PV while driving the vehicle in sunny days, and parking in open lot and testing P-2 Sponsors: SJSU-COE, SunPower Corp. San Jose, and Clean Battery Technologies Inc. Santa Clara Base: 4' wide x 8'-6" long Power Sources: Human pedaling/ Electricity/Solar PV Freight Weight: 1200 lbs

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

    E-Print Network [OSTI]

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

  4. 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

  5. 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

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

    E-Print Network [OSTI]

    2013-01-01T23:59:59.000Z

    co-occurring archaea. BMC Genomics 2013 14:485. Submit yourgenomes. Yelton et al. BMC Genomics 2013, 14:485 http://work was supported by DOE Genomics: GTL project Grant No.

  7. Redbird Red Habitat for Humanity Net Zero Energy Home Project Summary

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

    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 742EnergyOn April 23, 2014, an OHASeptember 2010InJanuary 29, 2013Redbird Red Habitat for Humanity

  8. Screening Assessment of Potential Human-Health Risk from Future Natural-Gas Drilling Near Project Rulison in Western Colorado

    SciTech Connect (OSTI)

    Daniels Jeffrey I.,Chapman Jenny B.

    2012-01-01T23:59:59.000Z

    The Project Rulison underground nuclear test was conducted in 1969 at a depth of 8,400 ft in the Williams Fork Formation of the Piceance Basin, west-central Colorado (Figure 1). The U.S. Department of Energy Office of Legacy Management (LM) is the steward of the site. Their management is guided by data collected from past site investigations and current monitoring, and by the results of calculations of expected behavior of contaminants remaining in the deep subsurface. The purpose of this screening risk assessment is to evaluate possible health risks from current and future exposure to Rulison contaminants so the information can be factored into LM's stewardship decisions. For example, these risk assessment results can inform decisions regarding institutional controls at the site and appropriate monitoring of nearby natural-gas extraction activities. Specifically, the screening risk analysis can provide guidance for setting appropriate action levels for contaminant monitoring to ensure protection of human health.

  9. Human Genome Research: Decoding DNA

    Office of Scientific and Technical Information (OSTI)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645 3,625 1,006 492 742EnergyOn AprilAElectronic InputRudolphMATERIALSInformationUniversity)W "Up"Decoding

  10. ageing human colonic: Topics by E-print Network

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

    : 0469-9 12;5122013 Postdoctoral position for the Thalis Program Human cells Genome surveillance, Proteasome Mitochondrial metabolism Mitochondria & Lysosomes Genome 213...

  11. 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

  12. Current developments in genomics challenge the established framework of

    E-Print Network [OSTI]

    Church, George M.

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

  13. 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.

  14. 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.

  15. 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.

  16. 2015 collaborative science projects announced | EMSL

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

    call represents a unique opportunity for researchers to combine the power of genomics and molecular characterization in one research project to help advance the missions...

  17. 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.)

  18. 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...

  19. HumanMouse Gene Identification by Comparative Evidence Integration and

    E-Print Network [OSTI]

    Pavlovic, Vladimir

    The identification of genes in the human genome remains a challenge, as the actual predictions appear to disagree of genes in the human genome by using a reference, such as mouse genome. However, this comparative genome. In particular, it is not clear whether the mouse is at the correct evolutionary distance from

  20. 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

  1. Characterizing non-coding hits in genome-wide association studies using epigenetic data

    E-Print Network [OSTI]

    Sarkar, Abhishek Kulshreshtha

    2013-01-01T23:59:59.000Z

    Understanding the molecular basis of human disease is one of the greatest challenges of our time, and recent explosion in genetic and genomic datasets are finally putting it within reach. In the last ten years, genome-wide ...

  2. 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

  3. Department Human Resources Bulletin, #027, FY06, dated August 1,2006 DOC Demonstration Project Operating Procedures

    E-Print Network [OSTI]

    setting pay for Presidential Management Fellows (PMF) who are covered by the DOC Demonstration Project Resources Bulletin #027, FY06, Presidential Management Fellows Program. This bulletin provides agencieswho Committee meeting, comprised of members in organizationscovered by the DOC Demonstration Project, to permit

  4. High quality genome-scale metabolic network reconstruction of mycobacterium tuberculosis and comparison with human metabolic network: application for drug targets identification 

    E-Print Network [OSTI]

    Kalapanulak, Saowalak

    2009-01-01T23:59:59.000Z

    Mycobacterium tuberculosis (Mtb), a pathogenic bacterium, is the causative agent in the vast majority of human tuberculosis (TB) cases. Nearly one-third of the world’s population has been affected by TB and annually two ...

  5. Dr. Mae Jemison is the principal for the 100 Year Starship Project, which envisions human travel beyond our solar system

    E-Print Network [OSTI]

    Collins, Gary S.

    , such as projects using satellite technology for healthcare delivery in West Africa and solar dish Stirling engines beyond our solar system to another star within the next 100 years. Her leadership and vision provide

  6. 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

  7. Complete genome sequence of Thermomonospora curvata type strain (B9)

    SciTech Connect (OSTI)

    Chertkov, Olga [Los Alamos National Laboratory (LANL); Sikorski, Johannes [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Nolan, Matt [Joint Genome Institute, Walnut Creek, California; Lapidus, Alla L. [Joint Genome Institute, Walnut Creek, California; Lucas, Susan [Joint Genome Institute, Walnut Creek, California; Glavina Del Rio, Tijana [Joint Genome Institute, Walnut Creek, California; Tice, Hope [Joint Genome Institute, Walnut Creek, California; Cheng, Jan-Fang [Joint Genome Institute, Walnut Creek, California; Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Pitluck, Sam [Joint Genome Institute, Walnut Creek, California; Liolios, Konstantinos [Joint Genome Institute, Walnut Creek, California; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Mavromatis, K [U.S. Department of Energy, Joint Genome Institute; Mikhailova, Natalia [U.S. Department of Energy, Joint Genome Institute; Ovchinnikova, Galina [U.S. Department of Energy, Joint Genome Institute; Pati, Amrita [U.S. Department of Energy, Joint Genome Institute; Chen, Amy [Joint Genome Institute, Walnut Creek, California; Palaniappan, Krishna [Joint Genome Institute, Walnut Creek, California; Ngatchou, Olivier Duplex [HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany; Land, Miriam L [ORNL; Hauser, Loren John [ORNL; Chang, Yun-Juan [ORNL; Jeffries, Cynthia [Oak Ridge National Laboratory (ORNL); Brettin, Thomas S [ORNL; Han, Cliff [Los Alamos National Laboratory (LANL); Detter, J. Chris [Joint Genome Institute, Walnut Creek, California; Rohde, Manfred [HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany; Goker, Markus [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Woyke, Tanja [Joint Genome Institute, Walnut Creek, California; Bristow, James [Joint Genome Institute, Walnut Creek, California; Eisen, Jonathan [Joint Genome Institute, Walnut Creek, California; Markowitz, Victor [Joint Genome Institute, Walnut Creek, California; Hugenholtz, Philip [U.S. Department of Energy, Joint Genome Institute; Klenk, Hans-Peter [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Kyrpides, Nikos C [Joint Genome Institute, Walnut Creek, California

    2011-01-01T23:59:59.000Z

    Thermomonospora curvata Henssen 1957 is the type species of the genus Thermomonospora. This genus is of interest because members of this clade are sources of new antibiotics, enzymes, and products with pharmacological activity. In addition, members of this genus participate in the active degradation of cellulose. This is the first complete genome sequence of a member of the family Thermomonosporaceae. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 5,639,016 bp long genome with its 4,985 protein-coding and 76 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  8. Developmental genomics of the most dangerous animal Matthew P. Scott*

    E-Print Network [OSTI]

    Quake, Stephen R.

    Developmental genomics of the most dangerous animal Matthew P. Scott* Departments of Developmental as far and away the most dangerous animal to humans. Mos- quitoes also transmit numerous other infections

  9. An Investigation of Insulator Proteins in Mosquito Genomes

    E-Print Network [OSTI]

    Johanson, Michael

    2013-08-02T23:59:59.000Z

    of transgenes in mosquito species. The use of insulator sequences to flank transgenes may have the ability to overcome position effects caused by the genomic environment surrounding the insertion site. CTCF is a multifunctional protein, conserved from humans...

  10. Melanoma genome sequencing reveals frequent PREX2 mutations

    E-Print Network [OSTI]

    Lander, Eric S.

    Melanoma is notable for its metastatic propensity, lethality in the advanced setting and association with ultraviolet exposure early in life. To obtain a comprehensive genomic view of melanoma in humans, we sequenced the ...

  11. Role of DNA supercoiling in genome structure and regulation 

    E-Print Network [OSTI]

    Corless, Samuel

    2014-07-05T23:59:59.000Z

    A principle challenge of modern biology is to understand how the human genome is organised and regulated within a nucleus. The field of chromatin biology has made significant progress in characterising how protein and ...

  12. This projects aims at cultivating previously uncultivated microorganis...

    Office of Scientific and Technical Information (OSTI)

    Final Report Project Title: To bioethanol through genomics of microbial synergies PI: S. Epstein, Northeastern University, Boston MA Period of time report covers: 9.1.2007-0831...

  13. The Genome of the Western Clawed Frog Xenopus tropicalis

    SciTech Connect (OSTI)

    Hellsten, Uffe; Harland, Richard M.; Gilchrist, Michael J.; Hendrix, David; Jurka, Jerzy; Kapitonov, Vladimir; Ovcharenko, Ivan; Putnam, Nicholas H.; Shu, Shengqiang; Taher, Leila; Blitz, Ira L.; Blumberg, Bruce; Dichmann, Darwin S.; Dubchak, Inna; Amaya, Enrique; Detter, John C.; Fletcher, Russell; Gerhard, Daniela S.; Goodstein, David; Graves, Tina; Grigoriev, Igor V.; Grimwood, Jane; Kawashima, Takeshi; Lindquist, Erika; Lucas, Susan M.; Mead, Paul E.; Mitros, Therese; Ogino, Hajime; Ohta, Yuko; Poliakov, Alexander V.; Pollet, Nicolas; Robert, Jacques; Salamov, Asaf; Sater, Amy K.; Schmutz, Jeremy; Terry, Astrid; Vize, Peter D.; Warren, Wesley C.; Wells, Dan; Wills, Andrea; Wilson, Richard K.; Zimmerman, Lyle B.; Zorn, Aaron M.; Grainger, Robert; Grammer, Timothy; Khokha, Mustafa K.; Richardson, Paul M.; Rokhsar, Daniel S.

    2009-10-01T23:59:59.000Z

    The western clawed frog Xenopus tropicalis is an important model for vertebrate development that combines experimental advantages of the African clawed frog Xenopus laevis with more tractable genetics. Here we present a draft genome sequence assembly of X. tropicalis. This genome encodes over 20,000 protein-coding genes, including orthologs of at least 1,700 human disease genes. Over a million expressed sequence tags validated the annotation. More than one-third of the genome consists of transposable elements, with unusually prevalent DNA transposons. Like other tetrapods, the genome contains gene deserts enriched for conserved non-coding elements. The genome exhibits remarkable shared synteny with human and chicken over major parts of large chromosomes, broken by lineage-specific chromosome fusions and fissions, mainly in the mammalian lineage.

  14. Scotts Valley Energy Office and Human Capacity Building that will provide energy-efficiency services and develop sustainable renewable energy projects.

    SciTech Connect (OSTI)

    Anderson, Temashio [Scotts Valley Band of Pomo Indians

    2013-06-28T23:59:59.000Z

    The primary goal of this project is to develop a Scotts Valley Energy Development Office (SVEDO). This office will further support the mission of the Tribe's existing leadership position as the DOE Tribal Multi-County Weatherization Energy Program (TMCWEP) in creating jobs and providing tribal homes and buildings with weatherization assistance to increase energy efficiency, occupant comfort and improved indoor air quality. This office will also spearhead efforts to move the Tribe towards its further strategic energy goals of implementing renewable energy systems through specific training, resource evaluation, feasibility planning, and implementation. Human capacity building and continuing operations are two key elements of the SVEDO objectives. Therefore, the project will 1) train and employ additional Tribal members in energy efficiency, conservation and renewable resource analyses and implementation; 2) purchase materials and equipment required to implement the strategic priorities as developed by the Scotts Valley Tribe which specifically include implementing energy conservation measures and alternative energy strategies to reduce energy costs for the Tribe and its members; and 3) obtain a dedicated office and storage space for ongoing SVEDO operations.

  15. 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...

  16. 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.

  17. 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.

  18. Genome Clone Libraries and Data from the Integrated Molecular Analysis of Genomes and their Expression (I.M.A.G.E.) Consortium

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

    The I.M.A.G.E. Consortium was initiated in 1993 by four academic groups on a collaborative basis after informal discussions led to a common vision of how to achieve an important goal in the study of the human genome: the Integrated Molecular Analysis of Genomes and their Expression Consortium's primary goal is to create arrayed cDNA libraries and associated bioinformatics tools, and make them publicly available to the research community. The primary organisms of interest include intensively studied mammalian species, including human, mouse, rat and non-human primate species. The Consortium has also focused on several commonly studied model organisms; as part of this effort it has arrayed cDNAs from zebrafish, and Fugu (pufferfish) as well as Xenopus laevis and X. tropicalis (frog). Utilizing high speed robotics, over nine million individual cDNA clones have been arrayed into 384-well microtiter plates, and sufficient replicas have been created to distribute copies both to sequencing centers and to a network of five distributors located worldwide. The I.M.A.G.E. Consortium represents the world's largest public cDNA collection, and works closely with the National Institutes of Health's Mammalian Gene Collection(MGC) to help it achieve its goal of creating a full-length cDNA clone for every human and mouse gene. I.M.A.G.E. is also a member of the ORFeome Collaboration, working to generate a complete set of expression-ready open reading frame clones representing each human gene. Custom informatics tools have been developed in support of these projects to better allow the research community to select clones of interest and track and collect all data deposited into public databases about those clones and their related sequences. I.M.A.G.E. clones are publicly available, free of any royalties, and may be used by anyone agreeing with the Consortium's guidelines.

  19. 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

  20. 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

  1. 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

  2. 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

  3. 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

  4. Genetic association with overall survival of taxane-treated lung cancer patients - a genome-wide association study in human lymphoblastoid cell lines followed by a clinical association study

    E-Print Network [OSTI]

    Niu, Nifang

    Background: Taxane is one of the first line treatments of lung cancer. In order to identify novel single nucleotide polymorphisms (SNPs) that might contribute to taxane response, we performed a genome-wide association study ...

  5. 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

  6. (New hosts and vectors for genome cloning)

    SciTech Connect (OSTI)

    Not Available

    1991-01-01T23:59:59.000Z

    The main goal of our project remains the development of new bacterial hosts and vectors for the stable propagation of human DNA clones in E. coli. During the past six months of our current budget period, we have (1) continued to develop new hosts that permit the stable maintenance of unstable features of human DNA, and (2) developed a series of vectors for (a) cloning large DNA inserts, (b) assessing the frequency of human sequences that are lethal to the growth of E. coli, and (c) assessing the stability of human sequences cloned in M13 for large-scale sequencing projects.

  7. 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.

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

    E-Print Network [OSTI]

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

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

  10. 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

  11. 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

  12. Since the early 1990s a large amount of effort has focused on determining the complete genomic DNA sequence

    E-Print Network [OSTI]

    Botstein, David

    Since the early 1990s a large amount of effort has focused on determining the complete genomic DNA sequencing. From the determination of the first complete genome sequence of an organism, the bacteriophage X174 (Ref. 2), to the completion of 95% of the human genome sequence3,4, many technical advances

  13. The Trichoplax Genome and the Nature of Placozoans

    SciTech Connect (OSTI)

    Srivastava, Mansi; Begovic, Emina; Chapman, Jarrod; Putnam, Nicholas H.; Hellsten, Uffe; Kawashima, Takeshi; Kuo, Alan; Mitros, Therese; Salamov, Asaf; Carpenter, Meredith L.; Signorovitch, Ana Y.; Moreno, Maria A.; Kamm, Kai; Grimwood, Jane; Schmutz, Jeremy; Shapiro, Harris; Grigoriev, Igor V.; Buss, Leo W.; Schierwater, Bernd; Dellaporta, Stephen L.; Rokhsar, Daniel S.

    2008-08-01T23:59:59.000Z

    Placozoans are arguably the simplest free-living animals, possibly evoking an early stage in metazoan evolution, yet their biology is poorly understood. Here we report the sequencing and analysis of the {approx}98 million base pair nuclear genome of the placozoan Trichoplax adhaerens. Whole genome phylogenetic analysis suggests that placozoans belong to a 'eumetazoan' clade that includes cnidarians and bilaterians, with sponges as the earliest diverging animals. The compact genome exhibits conserved gene content, gene structure, and synteny relative to the human and other complex eumetazoan genomes. Despite the apparent cellular and organismal simplicity of Trichoplax, its genome encodes a rich array of transcription factor and signaling pathway genes that are typically associated with diverse cell types and developmental processes in eumetazoans, motivating further searches for cryptic cellular complexity and/or as yet unobserved life history stages.

  14. 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

  15. 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/

  16. Compressing and Querrying the Human Genome /

    E-Print Network [OSTI]

    Kozanitis, Christos A.

    2013-01-01T23:59:59.000Z

    Acknowledgement . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .Acknowledgements . . . . . . . . . . . . . . . . . . . . . . . . . . .1.7 Acknowledgement . . . . . . . . . . . . .

  17. History of the DOE Human Genome Program

    Office of Scientific and Technical Information (OSTI)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645 3,625 1,006 492 742EnergyOnItem Not Found Item Not Found The

  18. 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.

  19. 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.

  20. 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

  1. 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

  2. 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.

  3. Bioinformatics and Genomics Degree Requirements Booklet

    E-Print Network [OSTI]

    dePamphilis, Claude

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

  4. 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

  5. Permanent draft genome sequence of the gliding predator Saprospira grandis strain Sa g1 (= HR1)

    SciTech Connect (OSTI)

    Mavromatis, K [U.S. Department of Energy, Joint Genome Institute; Chertkov, Olga [Los Alamos National Laboratory (LANL); Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute; Nolan, Matt [U.S. Department of Energy, Joint Genome Institute; Lucas, Susan [U.S. Department of Energy, Joint Genome Institute; Tice, Hope [U.S. Department of Energy, Joint Genome Institute; Glavina Del Rio, Tijana [U.S. Department of Energy, Joint Genome Institute; Cheng, Jan-Fang [U.S. Department of Energy, Joint Genome Institute; Han, Cliff [Los Alamos National Laboratory (LANL); Tapia, Roxanne [Los Alamos National Laboratory (LANL); Bruce, David [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Huntemann, Marcel [U.S. Department of Energy, Joint Genome Institute; Liolios, Konstantinos [U.S. Department of Energy, Joint Genome Institute; Pagani, Ioanna [U.S. Department of Energy, Joint Genome Institute; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Mikhailova, Natalia [U.S. Department of Energy, Joint Genome Institute; Pati, Amrita [U.S. Department of Energy, Joint Genome Institute; Chen, Amy [U.S. Department of Energy, Joint Genome Institute; Palaniappan, Krishna [U.S. Department of Energy, Joint Genome Institute; Land, Miriam L [ORNL; Brambilla, Evelyne-Marie [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Rohde, Manfred [HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany; Spring, Stefan [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Goker, Markus [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Bristow, James [U.S. Department of Energy, Joint Genome Institute; Eisen, Jonathan [U.S. Department of Energy, Joint Genome Institute; Markowitz, Victor [U.S. Department of Energy, Joint Genome Institute; Hugenholtz, Philip [U.S. Department of Energy, Joint Genome Institute; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute; Klenk, Hans-Peter [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute

    2012-01-01T23:59:59.000Z

    Saprospira grandis Gross et al. 1911 is a member of the Saprospiraceae, a family in the class 'Sphingobacteria' that remains poorly characterized at the genomic level. The species is known for preying on other marine bacteria via 'ixotrophy'. S. grandis strain Sa g1 was isolated from decaying crab carapace in France and was selected for genome sequencing because of its isolated location in the tree of life. Only one type strain genome has been published so far from the Saprospiraceae, while the sequence of strain Sa g1 represents the second genome to be published from a non-type strain of S. grandis. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 4,495,250 bp long Improved-High-Quality draft of the genome with its 3,536 protein-coding and 62 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  6. Degree project in Communication Systems

    E-Print Network [OSTI]

    Maguire Jr., Gerald Q.

    Degree project in Communication Systems Second level, 30.0 HEC Stockholm, Sweden E L M I R A K H O-bönor till FXML. Den föreslagna algoritmen har sedan utvärderats genom automatiserade mjukvarutester

  7. 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.

  8. Genome sequence of the brown Norway rat yields insights into mammalian evolution

    SciTech Connect (OSTI)

    Gibbs, Richard A.; Weinstock, George M.; Metzker, Michael L.; Muzny, Donna M.; Sodergren, Erica J.; Scherer, Steven; Scott, Graham; Steffen, David; Worley, Kim C.; Burch, Paula E.; Okwuonu, Geoffrey; Hines, Sandra; Lewis, Lora; DeRamo, Christine; Delgado, Oliver; Dugan-Rocha, Shannon; Miner, George; Morgan, Margaret; Hawes, Alicia; Gill, Rachel; Holt, Robert A.; Adams, Mark D.; Amanatides, Peter G.; Baden-Tillson, Holly; Barnstead, Mary; Chin, Soo; Evans, Cheryl A.; Ferriera, Steven; Fosler, Carl; Glodek, Anna; Gu, Zhiping; Jennings, Don; Kraft, Cheryl L.; Nguyen, Trixie; Pfannkoch, Cynthia M.; Sitter, Cynthia; Sutton, Granger G.; Venter, J. Craig; Woodage, Trevor; Smith, Douglas; Lee, Hong-Maei; Gustafson, Erik; Cahill, Patrick; Kana, Arnold; Doucette-Stamm, Lynn; Weinstock, Keith; Fechtel, Kim; Weiss, Robert B.; Dunn, Diane M.; Green, Eric D.; Blakesley, Robert W.; Bouffard, Gerard G.; de Jong, Pieter J.; Osoegawa, Kazutoyo; Zhu, Baoli; Marra, Marco; Schein, Jacqueline; Bosdet, Ian; Fjell, Chris; Jones, Steven; Krzywinski, Martin; Mathewson, Carrie; Siddiqui, Asim; Wye, Natasja; McPherson, John; Zhao, Shaying; Fraser, Claire M.; Shetty, Jyoti; Shatsman, Sofiya; Geer, Keita; Chen, Yixin; Abramzon, Sofyia; Nierman, William C.; Havlak, Paul H.; Chen, Rui; Durbin, K. James; Egan, Amy; Ren, Yanru; Song, Xing-Zhi; Li, Bingshan; Liu, Yue; Qin, Xiang; Cawley, Simon; Cooney, A.J.; D'Souza, Lisa M.; Martin, Kirt; Wu, Jia Qian; Gonzalez-Garay, Manuel L.; Jackson, Andrew R.; Kalafus, Kenneth J.; McLeod, Michael P.; Milosavljevic, Aleksandar; Virk, Davinder; Volkov, Andrei; Wheeler, David A.; Zhang, Zhengdong; Bailey, Jeffrey A.; Eichler, Evan E.; Tuzun, Eray; Birney, Ewan; Mongin, Emmanuel; Ureta-Vidal, Abel; Woodwark, Cara; Zdobnov, Evgeny; Bork, Peer; Suyama, Mikita; Torrents, David; Alexandersson, Marina; Trask, Barbara J.; Young, Janet M.; et al.

    2004-02-02T23:59:59.000Z

    The laboratory rat (Rattus norvegicus) is an indispensable tool in experimental medicine and drug development, having made inestimable contributions to human health. We report here the genome sequence of the Brown Norway (BN) rat strain. The sequence represents a high-quality 'draft' covering over 90 percent of the genome. The BN rat sequence is the third complete mammalian genome to be deciphered, and three-way comparisons with the human and mouse genomes resolve details of mammalian evolution. This first comprehensive analysis includes genes and proteins and their relation to human disease, repeated sequences, comparative genome-wide studies of mammalian orthologous chromosomal regions and rearrangement breakpoints, reconstruction of ancestral karyotypes and the events leading to existing species, rates of variation, and lineage-specific and lineage-independent evolutionary events such as expansion of gene families, orthology relations and protein evolution.

  9. 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 ...

  10. 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.

  11. Phytozome: a Tool for Green Plant Comparative Genomics

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

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

  12. Local chromatin structure of heterochromatin regulates repeatedDNA stability, nucleolus structure, and genome integrity

    SciTech Connect (OSTI)

    Peng, Jamy C.

    2007-05-05T23:59:59.000Z

    Heterochromatin constitutes a significant portion of the genome in higher eukaryotes; approximately 30% in Drosophila and human. Heterochromatin contains a high repeat DNA content and a low density of protein-encoding genes. In contrast, euchromatin is composed mostly of unique sequences and contains the majority of single-copy genes. Genetic and cytological studies demonstrated that heterochromatin exhibits regulatory roles in chromosome organization, centromere function and telomere protection. As an epigenetically regulated structure, heterochromatin formation is not defined by any DNA sequence consensus. Heterochromatin is characterized by its association with nucleosomes containing methylated-lysine 9 of histone H3 (H3K9me), heterochromatin protein 1 (HP1) that binds H3K9me, and Su(var)3-9, which methylates H3K9 and binds HP1. Heterochromatin formation and functions are influenced by HP1, Su(var)3-9, and the RNA interference (RNAi) pathway. My thesis project investigates how heterochromatin formation and function impact nuclear architecture, repeated DNA organization, and genome stability in Drosophila melanogaster. H3K9me-based chromatin reduces extrachromosomal DNA formation; most likely by restricting the access of repair machineries to repeated DNAs. Reducing extrachromosomal ribosomal DNA stabilizes rDNA repeats and the nucleolus structure. H3K9me-based chromatin also inhibits DNA damage in heterochromatin. Cells with compromised heterochromatin structure, due to Su(var)3-9 or dcr-2 (a component of the RNAi pathway) mutations, display severe DNA damage in heterochromatin compared to wild type. In these mutant cells, accumulated DNA damage leads to chromosomal defects such as translocations, defective DNA repair response, and activation of the G2-M DNA repair and mitotic checkpoints that ensure cellular and animal viability. My thesis research suggests that DNA replication, repair, and recombination mechanisms in heterochromatin differ from those in euchromatin. Remarkably, human euchromatin and fly heterochromatin share similar features; such as repeated DNA content, intron lengths and open reading frame sizes. Human cells likely stabilize their DNA content via mechanisms and factors similar to those in Drosophila heterochromatin. Furthermore, my thesis work raises implications for H3K9me and chromatin functions in complex-DNA genome stability, repeated DNA homogenization by molecular drive, and in genome reorganization through evolution.

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

    E-Print Network [OSTI]

    Hammerton, James

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

  14. Project Year Project Title

    E-Print Network [OSTI]

    Gray, Jeffrey J.

    Project Year 2011-2012 Project Title Using M-Health and GIS Technology in the Field to Improve-specialized, but practically useless skill. Solution One goal of this summer's Applied Geographic Information Systems in Public lessons about observational epidemiology. Technologies Used Geographic Info System (GIS), Blackboard

  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. Identifying the conserved network of cis-regulatory sites of a eukaryotic genome

    E-Print Network [OSTI]

    Babu, M. Madan

    that our algorithm should be applicable to much larger genomes, such as the human genome, without reaching algorithms inferring with the regulatory sites. That strategy depends highly on the experiments, so limita- tions in experiments are propagated to the computational methods that infer motifs from the data

  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. SHORT REVIEW Butterfly genomics eclosing

    E-Print Network [OSTI]

    Beldade, Patrícia

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

  19. Project Fact Sheet Project Update

    E-Print Network [OSTI]

    & Figures: Budget: £51,074,000 Funding Source: Capital Plan Construction Project Programme: Start on SiteProject Fact Sheet Project Update: Project Brief: The concept of the new scheme is to redevelop Gardens project http://www.imperial.ac.uk/princesgardens/ Construction Project Team: Project Facts

  20. Complete genome sequence of Calditerrivibrio nitroreducens type strain (Yu37-1T)

    SciTech Connect (OSTI)

    Pitluck, Sam [Joint Genome Institute, Walnut Creek, California; Sikorski, Johannes [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Zeytun, Ahmet [Los Alamos National Laboratory (LANL); Lapidus, Alla L. [Joint Genome Institute, Walnut Creek, California; Nolan, Matt [Joint Genome Institute, Walnut Creek, California; Lucas, Susan [Joint Genome Institute, Walnut Creek, California; Hammon, Nancy [Joint Genome Institute, Walnut Creek, California; Deshpande, Shweta [Joint Genome Institute, Walnut Creek, California; Cheng, Jan-Fang [Joint Genome Institute, Walnut Creek, California; Tapia, Roxanne [Los Alamos National Laboratory (LANL); Han, Cliff [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Liolios, Konstantinos [Joint Genome Institute, Walnut Creek, California; Pagani, Ioanna [Joint Genome Institute, Walnut Creek, California; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Mavromatis, K [U.S. Department of Energy, Joint Genome Institute; Pati, Amrita [U.S. Department of Energy, Joint Genome Institute; Chen, Amy [Joint Genome Institute, Walnut Creek, California; Palaniappan, Krishna [Joint Genome Institute, Walnut Creek, California; Hauser, Loren John [ORNL; Chang, Yun-Juan [ORNL; Jeffries, Cynthia [Oak Ridge National Laboratory (ORNL); Detter, J. Chris [Joint Genome Institute, Walnut Creek, California; Brambilla, Evelyne-Marie [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Ngatchou, Olivier Duplex [HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany; Rohde, Manfred [HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany; Spring, Stefan [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Goker, Markus [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Woyke, Tanja [Joint Genome Institute, Walnut Creek, California; Bristow, James [Joint Genome Institute, Walnut Creek, California; Eisen, Jonathan [Joint Genome Institute, Walnut Creek, California; Markowitz, Victor [Joint Genome Institute, Walnut Creek, California; Hugenholtz, Philip [U.S. Department of Energy, Joint Genome Institute; Kyrpides, Nikos C [Joint Genome Institute, Walnut Creek, California; Klenk, Hans-Peter [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Land, Miriam L [ORNL

    2011-01-01T23:59:59.000Z

    Calditerrivibrio nitroreducens Iino et al. 2008 is the type species of the genus Calditerrivibrio. The species is of interest because of its important role in the nitrate cycle as nitrate reducer and for its isolated phylogenetic position in the Tree of Life. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the third complete genome sequence of a member of the family Deferribacteraceae. The 2,216,552 bp long genome with its 2,128 protein-coding and 50 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  1. 2012 U.S. Department of Energy: Joint Genome Institute: Progress Report

    SciTech Connect (OSTI)

    Gilbert, David [DOE JGI Public Affairs Manager] [DOE JGI Public Affairs Manager

    2013-01-01T23:59:59.000Z

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

  2. Deep-sea vent -proteobacterial genomes provide insights into emergence of pathogens

    E-Print Network [OSTI]

    Reysenbach, Anna-Louise

    % of the human population is infected by Helicobacter pylori, which causes gastric ulcer and cancer (12, Helicobacter and Campylobacter species. The deep-sea vent -proteobacterial genomes encode for multiple systems

  3. Mining data from 1000 genomes to identify the causal variant in regions under positive selection

    E-Print Network [OSTI]

    Grossman, Sharon Rachel

    The human genome contains hundreds of regions in which the patterns of genetic variation indicate recent positive natural selection, yet for most of these the underlying gene and the advantageous mutation remain unknown. ...

  4. Assembly of the Candida albicans genome into sixteen supercontigs aligned on the eight chromosomes

    E-Print Network [OSTI]

    van het Hoog, Marco

    Background: The 10.9× genomic sequence of Candida albicans, the most important human fungal pathogen, was published in 2004. Assembly 19 consisted of 412 supercontigs, of which 266 were a haploid set, since this fungus is ...

  5. Project Funding

    Broader source: Energy.gov [DOE]

    Federal energy projects require funding to generate results. Carefully matching available funding options with specific project needs can make the difference between a stalled, unfunded project and a successful project generating energy and cost savings.

  6. ECRbase: Database of Evolutionary Conserved Regions, Promoters, and Transcription Factor Binding Sites in Vertebrate Genomes

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

    Loots, Gabriela G. [LLNL; Ovcharenko, I. [LLNL

    Evolutionary conservation of DNA sequences provides a tool for the identification of functional elements in genomes. This database of evolutionary conserved regions (ECRs) in vertebrate genomes features a database of syntenic blocks that recapitulate the evolution of rearrangements in vertebrates and a comprehensive collection of promoters in all vertebrate genomes generated using multiple sources of gene annotation. The database also contains a collection of annotated transcription factor binding sites (TFBSs) in evolutionary conserved and promoter elements. ECRbase currently includes human, rhesus macaque, dog, opossum, rat, mouse, chicken, frog, zebrafish, and fugu genomes. (taken from paper in Journal: Bioinformatics, November 7, 2006, pp. 122-124

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

    SciTech Connect (OSTI)

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

    2013-10-03T23:59:59.000Z

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

  8. 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

  9. 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.

  10. 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

  11. CRIS Project Internal DASNR Compliance Checklist

    E-Print Network [OSTI]

    Ghajar, Afshin J.

    CRIS Project Internal DASNR Compliance Checklist Researcher's Name: Department: Address / Phone: Project Title: Does this project involve research with: Human Subjects Yes No If yes, attach copy of IRB to Animals, Plants, or Humans Radioactive Materials or Yes No If yes, attach copy of Radiation Sa X

  12. 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

  13. 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–

  14. 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...

  15. 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...

  16. Contextual Genomics: Chris Wagner CEO cwagner@contextualgenomics.com Personalized Medicine Initiative (PMI): Rob Fraser -COO -robertfr@mail.ubc.ca

    E-Print Network [OSTI]

    Strynadka, Natalie

    Initiative (PMI): Rob Fraser - COO - robertfr@mail.ubc.ca Contextual Genomics and PMI have launched mutations and designed to improve clinical outcomes and reduce costs. The project is being managed by PMI laboratory, LifeLabs. "NationalAccessProjectForCancerTesting" Our Unique Approach PMI and Contextual Genomics

  17. A study of the necessary and optimal conditions for success in the most challenging human endeavors : modem day Manhattan Projects are needed for overcoming contemporary global challenges

    E-Print Network [OSTI]

    Chowdhury, Anando A

    2012-01-01T23:59:59.000Z

    It is possible to categorize four contemporary challenges as the greatest threats to global well-being and the persistence of humankind. These challenges are global climate and ecological change, poor human health management, ...

  18. 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...

  19. 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

  20. 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...

  1. 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

  2. LATERAL GENE TRANSFER AND THE HISTORY OF BACTERIAL GENOMES

    SciTech Connect (OSTI)

    Howard Ochman

    2006-02-22T23:59:59.000Z

    The aims of this research were to elucidate the role and extent of lateral transfer in the differentiation of bacterial strains and species, and to assess the impact of gene transfer on the evolution of bacterial genomes. The ultimate goal of the project is to examine the dynamics of a core set of protein-coding genes (i.e., those that are distributed universally among Bacteria) by developing conserved primers that would allow their amplification and sequencing in any bacterial taxa. In addition, we adopted a bioinformatic approach to elucidate the extent of lateral gene transfer in sequenced genome.

  3. 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

  4. 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

  5. Project Title:

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

    Repair flowline 61-66-SX-3 DOE Code: Project Lead: Wes Riesland NEPA COMPLIANCE SURVEY 291 Project Information Date: 31 12010 Contractor Code: Project Overview In order to...

  6. Evolutionarily conserved sequences on human chromosome 21

    SciTech Connect (OSTI)

    Frazer, Kelly A.; Sheehan, John B.; Stokowski, Renee P.; Chen, Xiyin; Hosseini, Roya; Cheng, Jan-Fang; Fodor, Stephen P.A.; Cox, David R.; Patil, Nila

    2001-09-01T23:59:59.000Z

    Comparison of human sequences with the DNA of other mammals is an excellent means of identifying functional elements in the human genome. Here we describe the utility of high-density oligonucleotide arrays as a rapid approach for comparing human sequences with the DNA of multiple species whose sequences are not presently available. High-density arrays representing approximately 22.5 Mb of nonrepetitive human chromosome 21 sequence were synthesized and then hybridized with mouse and dog DNA to identify sequences conserved between humans and mice (human-mouse elements) and between humans and dogs (human-dog elements). Our data show that sequence comparison of multiple species provides a powerful empiric method for identifying actively conserved elements in the human genome. A large fraction of these evolutionarily conserved elements are present in regions on chromosome 21 that do not encode known genes.

  7. 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

  8. 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

  9. 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

  10. 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,

  11. 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

  12. 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

  13. 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

  14. 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

  15. 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

  16. Complete genome sequence of Intrasporangium calvumtype strain (7 KIPT)

    SciTech Connect (OSTI)

    Glavina Del Rio, Tijana [Joint Genome Institute, Walnut Creek, California; Chertkov, Olga [Los Alamos National Laboratory (LANL); Yasawong, Montri [HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany; Lucas, Susan [Joint Genome Institute, Walnut Creek, California; Deshpande, Shweta [Joint Genome Institute, Walnut Creek, California; Cheng, Jan-Fang [Joint Genome Institute, Walnut Creek, California; Detter, J. Chris [Joint Genome Institute, Walnut Creek, California; Tapia, Roxanne [Los Alamos National Laboratory (LANL); Han, Cliff [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Pitluck, Sam [Joint Genome Institute, Walnut Creek, California; Liolios, Konstantinos [Joint Genome Institute, Walnut Creek, California; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Mavromatis, K [U.S. Department of Energy, Joint Genome Institute; Pati, Amrita [U.S. Department of Energy, Joint Genome Institute; Chen, Amy [Joint Genome Institute, Walnut Creek, California; Palaniappan, Krishna [Joint Genome Institute, Walnut Creek, California; Land, Miriam L [ORNL; Hauser, Loren John [ORNL; Chang, Yun-Juan [ORNL; Jeffries, Cynthia [Oak Ridge National Laboratory (ORNL); Rohde, Manfred [HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany; Pukall, Rudiger [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Sikorski, Johannes [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Goker, Markus [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Woyke, Tanja [Joint Genome Institute, Walnut Creek, California; Bristow, James [Joint Genome Institute, Walnut Creek, California; Eisen, Jonathan [Joint Genome Institute, Walnut Creek, California; Markowitz, Victor [Joint Genome Institute, Walnut Creek, California; Hugenholtz, Philip [U.S. Department of Energy, Joint Genome Institute; Kyrpides, Nikos C [Joint Genome Institute, Walnut Creek, California; Klenk, Hans-Peter [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Lapidus, Alla L. [Joint Genome Institute, Walnut Creek, California

    2010-01-01T23:59:59.000Z

    Intrasporangium calvum Kalakoutskii et al. 1967 is the type species of the genus Intrasporangium, which belongs to the actinobacterial family Intrasporangiaceae. The species is a Gram-positive bacterium that forms a branching mycelium, which tends to break into irregular fragments. The mycelium of this strain may bear intercalary vesicles but does not contain spores. The strain described in this study is an airborne organism that was isolated from a school dining room in 1967. One particularly interesting feature of I. calvum is that the type of its menaquinone is different from all other representatives of the family Intrasporangiaceae. This is the first completed genome sequence from a member of the genus Intrasporangium and also the first sequence from the family Intrasporangiaceae. The 4,024,382 bp long genome with its 3,653 protein-coding and 57 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  17. A framework for human microbiome research

    E-Print Network [OSTI]

    Friedman, Jonathan

    A variety of microbial communities and their genes (the microbiome) exist throughout the human body, with fundamental roles in human health and disease. The National Institutes of Health (NIH)-funded Human Microbiome Project ...

  18. Project Controls

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

    1997-03-28T23:59:59.000Z

    Project controls are systems used to plan, schedule, budget, and measure the performance of a project/program. The cost estimation package is one of the documents that is used to establish the baseline for project controls. This chapter gives a brief description of project controls and the role the cost estimation package plays.

  19. 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

  20. Genome Biology 2009, 10:R25 Open Access2009Langmeadet al.Volume 10, Issue 3, Article R25Software

    E-Print Network [OSTI]

    Shafran, Izhak

    the original work is properly cited. Bowtie: short-read alignmentBowtie: a new ultrafast memory-efficient tool for the alignment of short DNA sequence reads to large genomes. Abstract Bowtie. For the human genome, Burrows-Wheeler indexing allows Bowtie to align more than 25 million reads per CPU hour

  1. Complete genome sequence of Kangiella koreensis type strain (SW-125T)

    SciTech Connect (OSTI)

    Han, Cliff [Los Alamos National Laboratory (LANL); Sikorski, Johannes [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Lapidus, Alla L. [Joint Genome Institute, Walnut Creek, California; Nolan, Matt [Joint Genome Institute, Walnut Creek, California; Glavina Del Rio, Tijana [Joint Genome Institute, Walnut Creek, California; Tice, Hope [Joint Genome Institute, Walnut Creek, California; Cheng, Jan-Fang [Joint Genome Institute, Walnut Creek, California; Lucas, Susan [Joint Genome Institute, Walnut Creek, California; Chen, Feng [Joint Genome Institute, Walnut Creek, California; Copeland, A [U.S. Department of Energy, Joint Genome Institute; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Mavromatis, K [U.S. Department of Energy, Joint Genome Institute; Ovchinnikova, Galina [U.S. Department of Energy, Joint Genome Institute; Pati, Amrita [U.S. Department of Energy, Joint Genome Institute; Bruce, David [Joint Genome Institute, Walnut Creek, California; Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Pitluck, Sam [Joint Genome Institute, Walnut Creek, California; Chen, Amy [Joint Genome Institute, Walnut Creek, California; Palaniappan, Krishna [Joint Genome Institute, Walnut Creek, California; Land, Miriam L [ORNL; Hauser, Loren John [ORNL; Chang, Yun-Juan [ORNL; Jeffries, Cynthia [Oak Ridge National Laboratory (ORNL); Chain, Patrick S. G. [Lawrence Livermore National Laboratory (LLNL); Saunders, Elizabeth H [Los Alamos National Laboratory (LANL); Brettin, Thomas S [ORNL; Goker, Markus [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Tindall, Brian [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Bristow, James [Joint Genome Institute, Walnut Creek, California; Eisen, Jonathan [Joint Genome Institute, Walnut Creek, California; Markowitz, Victor [Joint Genome Institute, Walnut Creek, California; Hugenholtz, Philip [U.S. Department of Energy, Joint Genome Institute; Kyrpides, Nikos C [Joint Genome Institute, Walnut Creek, California; Klenk, Hans-Peter [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Detter, J. Chris [Joint Genome Institute, Walnut Creek, California

    2009-11-01T23:59:59.000Z

    Kangiella koreensis (Yoon et al. 2004) is the type species of the genus and is of phylogenetic interest because of the very isolated location of the genus Kangiella in the gammaproteobac-terial order Oceanospirillales. K. koreensis SW-125T is a Gram-negative, non-motile, non-spore-forming bacterium isolated from tidal flat sediments at Daepo Beach, Yellow Sea, Ko-rea. Here we describe the features of this organism, together with the complete genome se-quence, and annotation. This is the first completed genome sequence from the genus Kangiel-la and only the fourth genome from the order Oceanospirillales. This 2,852,073 bp long sin-gle replicon genome with its 2647 protein-coding and 48 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

  2. Project Fact Sheet Project Update

    E-Print Network [OSTI]

    Project Fact Sheet Project Update: Project Brief: The works cover the refurbishment of floors 4, 5, with `wet' labs for molecular biology, materials characterisation, cell culture and flow studies, and `dry operating theatre. The Bionanotechnology Centre is one of the projects funded from the UK Government's £20

  3. Project Fact Sheet Project Brief

    E-Print Network [OSTI]

    .union.ic.ac.uk/marketing/building Construction Project Team: Project Facts & Figures: Budget: £1,400,000 Funding Source: Capital PlanProject Fact Sheet Project Brief: In the first phase of the Union Building re that it adapts to meet the needs of a changing student body. The re-development plans are grounded in a full

  4. Project Fact Sheet Project Brief

    E-Print Network [OSTI]

    Facts & Figures: Budget: £3,500,000 Funding Source: SRIF III Construction Project Programme: StartProject Fact Sheet Project Brief: This project refurbished half of the 5th and 7th floors of work includes: · Building fabric replacement and revised space planning · New mechanical and electrical

  5. Intra-species sequence comparisons for annotating genomes

    SciTech Connect (OSTI)

    Boffelli, Dario; Weer, Claire V.; Weng, Li; Lewis, Keith D.; Shoukry, Malak I.; Pachter, Lior; Keys, David N.; Rubin, Edward M.

    2004-07-15T23:59:59.000Z

    Analysis of sequence variation among members of a single species offers a potential approach to identify functional DNA elements responsible for biological features unique to that species. Due to its high rate of allelic polymorphism and ease of genetic manipulability, we chose the sea squirt, Ciona intestinalis, to explore intra-species sequence comparisons for genome annotation. A large number of C. intestinalis specimens were collected from four continents and a set of genomic intervals amplified, resequenced and analyzed to determine the mutation rates at each nucleotide in the sequence. We found that regions with low mutation rates efficiently demarcated functionally constrained sequences: these include a set of noncoding elements, which we showed in C intestinalis transgenic assays to act as tissue-specific enhancers, as well as the location of coding sequences. This illustrates that comparisons of multiple members of a species can be used for genome annotation, suggesting a path for the annotation of the sequenced genomes of organisms occupying uncharacterized phylogenetic branches of the animal kingdom and raises the possibility that the resequencing of a large number of Homo sapiens individuals might be used to annotate the human genome and identify sequences defining traits unique to our species. The sequence data from this study has been submitted to GenBank under accession nos. AY667278-AY667407.

  6. [New hosts and vectors for genome cloning]. Progress report

    SciTech Connect (OSTI)

    Not Available

    1991-12-31T23:59:59.000Z

    The main goal of our project remains the development of new bacterial hosts and vectors for the stable propagation of human DNA clones in E. coli. During the past six months of our current budget period, we have (1) continued to develop new hosts that permit the stable maintenance of unstable features of human DNA, and (2) developed a series of vectors for (a) cloning large DNA inserts, (b) assessing the frequency of human sequences that are lethal to the growth of E. coli, and (c) assessing the stability of human sequences cloned in M13 for large-scale sequencing projects.

  7. 10.1101/gr.5716607Access the most recent version at doi: 2007 17: 720-731Genome Res.

    E-Print Network [OSTI]

    Weng, Zhiping

    , Stanford, California 94305, USA; 2 Bioinformatics Program, Boston University, Boston, Massachusetts 02215, Connecticut 06520, USA; 5 Biomedical Engineering Department, Boston University, Boston, Massachusetts 02215, USA The regulation of transcriptional initiation in the human genome is a critical component of global

  8. Complete Genome Sequence of Yersinia pestis Strains Antiqua and Nepal516: Evidence of Gene Reduction in an Emerging Pathogen

    E-Print Network [OSTI]

    2006-01-01T23:59:59.000Z

    a human infection in Nepal (possibly from a 1967 outbreak ofone IS285 in CO92, KIM and Nepal but not Antiqua; and oneLoss of functional TufB in Nepal The genomes of Y. pestis

  9. Complete genome sequence of Riemerella anatipestifer type strain (BrunerT)

    SciTech Connect (OSTI)

    Mavromatis, K [U.S. Department of Energy, Joint Genome Institute; Lu, Megan [Los Alamos National Laboratory (LANL); Misra, Monica [Los Alamos National Laboratory (LANL); Lapidus, Alla L. [Joint Genome Institute, Walnut Creek, California; Nolan, Matt [Joint Genome Institute, Walnut Creek, California; Lucas, Susan [Joint Genome Institute, Walnut Creek, California; Hammon, Nancy [Joint Genome Institute, Walnut Creek, California; Deshpande, Shweta [Joint Genome Institute, Walnut Creek, California; Cheng, Jan-Fang [Joint Genome Institute, Walnut Creek, California; Tapia, Roxanne [Los Alamos National Laboratory (LANL); Han, Cliff [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Pitluck, Sam [Joint Genome Institute, Walnut Creek, California; Liolios, Konstantinos [Joint Genome Institute, Walnut Creek, California; Pagani, Ioanna [Joint Genome Institute, Walnut Creek, California; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Mikhailova, Natalia [U.S. Department of Energy, Joint Genome Institute; Pati, Amrita [U.S. Department of Energy, Joint Genome Institute; Chen, Amy [Joint Genome Institute, Walnut Creek, California; Palaniappan, Krishna [Joint Genome Institute, Walnut Creek, California; Land, Miriam L [ORNL; Hauser, Loren John [ORNL; Chang, Yun-Juan [ORNL; Jeffries, Cynthia [Oak Ridge National Laboratory (ORNL); Detter, J. Chris [Joint Genome Institute, Walnut Creek, California; Brambilla, Evelyne-Marie [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Rohde, Manfred [HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany; Goker, Markus [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Gronow, Sabine [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Woyke, Tanja [Joint Genome Institute, Walnut Creek, California; Bristow, James [Joint Genome Institute, Walnut Creek, California; Eisen, Jonathan [Joint Genome Institute, Walnut Creek, California; Markowitz, Victor [Joint Genome Institute, Walnut Creek, California; Hugenholtz, Philip [U.S. Department of Energy, Joint Genome Institute; Klenk, Hans-Peter [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Kyrpides, Nikos C [Joint Genome Institute, Walnut Creek, California

    2011-01-01T23:59:59.000Z

    Riemerella anatipestifer (Hendrickson and Hilbert 1932) Segers et al. 1993 is the type species of the genus Riemerella, which belongs to the family Flavobacteriaceae. The species is of interest because of the position of the genus in the phylogenetic tree and because of its role as a pathogen of commercially important avian species worldwide. This is the first completed genome sequence of a member of the genus Riemerella. The 2,155,121 bp long genome with its 2,001 protein-coding and 51 RNA genes consists of one circular chromosome and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  10. Non-contiguous finished genome sequence of Aminomonas paucivorans type strain (GLU-3T)

    SciTech Connect (OSTI)

    Pitluck, Sam [Joint Genome Institute, Walnut Creek, California; Yasawong, Montri [HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany; Held, Brittany [Los Alamos National Laboratory (LANL); Lapidus, Alla L. [Joint Genome Institute, Walnut Creek, California; Nolan, Matt [Joint Genome Institute, Walnut Creek, California; Copeland, A [U.S. Department of Energy, Joint Genome Institute; Lucas, Susan [Joint Genome Institute, Walnut Creek, California; Glavina Del Rio, Tijana [Joint Genome Institute, Walnut Creek, California; Tice, Hope [Joint Genome Institute, Walnut Creek, California; Cheng, Jan-Fang [Joint Genome Institute, Walnut Creek, California; Chertkov, Olga [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Tapia, Roxanne [Los Alamos National Laboratory (LANL); Han, Cliff [Los Alamos National Laboratory (LANL); Liolios, Konstantinos [Joint Genome Institute, Walnut Creek, California; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Mavromatis, K [U.S. Department of Energy, Joint Genome Institute; Ovchinnikova, Galina [U.S. Department of Energy, Joint Genome Institute; Pati, Amrita [U.S. Department of Energy, Joint Genome Institute; Chen, Amy [Joint Genome Institute, Walnut Creek, California; Palaniappan, Krishna [Joint Genome Institute, Walnut Creek, California; Land, Miriam L [ORNL; Hauser, Loren John [ORNL; Chang, Yun-Juan [ORNL; Jeffries, Cynthia [Oak Ridge National Laboratory (ORNL); Pukall, Rudiger [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Spring, Stefan [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Rohde, Manfred [HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany; Sikorski, Johannes [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Goker, Markus [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Woyke, Tanja [Joint Genome Institute, Walnut Creek, California; Bristow, James [Joint Genome Institute, Walnut Creek, California; Eisen, Jonathan [Joint Genome Institute, Walnut Creek, California; Markowitz, Victor [Joint Genome Institute, Walnut Creek, California; Hugenholtz, Philip [U.S. Department of Energy, Joint Genome Institute; Kyrpides, Nikos C [Joint Genome Institute, Walnut Creek, California; Klenk, Hans-Peter [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany

    2010-01-01T23:59:59.000Z

    Aminomonas paucivorans Baena et al. 1999 is the type species of the genus Aminomonas, which belongs to the family Synergistaceae. The species is of interest because it is an asaccharolytic chemoorganotrophic bacterium which ferments quite a number of amino acids. This is the first completed genome sequence (with one gap in a rDNA region) of a member of the genus Aminomonas and the third sequence from the family Synergistaceae. The 2,630,120 bp long genome with its 2,433 protein-coding and 61 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  11. Complete genome sequence of Paludibacter propionicigenes type strain (WB4T)

    SciTech Connect (OSTI)

    Gronow, Sabine [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Munk, Christine [Joint Genome Institute, Walnut Creek, California; Lapidus, Alla L. [Joint Genome Institute, Walnut Creek, California; Nolan, Matt [Joint Genome Institute, Walnut Creek, California; Lucas, Susan [Joint Genome Institute, Walnut Creek, California; Hammon, Nancy [Joint Genome Institute, Walnut Creek, California; Deshpande, Shweta [Joint Genome Institute, Walnut Creek, California; Cheng, Jan-Fang [Joint Genome Institute, Walnut Creek, California; Tapia, Roxanne [Los Alamos National Laboratory (LANL); Han, Cliff [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Pitluck, Sam [Joint Genome Institute, Walnut Creek, California; Liolios, Konstantinos [Joint Genome Institute, Walnut Creek, California; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Mavromatis, K [U.S. Department of Energy, Joint Genome Institute; Mikhailova, Natalia [U.S. Department of Energy, Joint Genome Institute; Pati, Amrita [U.S. Department of Energy, Joint Genome Institute; Chen, Amy [Joint Genome Institute, Walnut Creek, California; Palaniappan, Krishna [Joint Genome Institute, Walnut Creek, California; Land, Miriam L [ORNL; Hauser, Loren John [ORNL; Chang, Yun-Juan [ORNL; Jeffries, Cynthia [Oak Ridge National Laboratory (ORNL); Brambilla, Evelyne-Marie [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Rohde, Manfred [HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany; Goker, Markus [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Detter, J. Chris [Joint Genome Institute, Walnut Creek, California; Woyke, Tanja [Joint Genome Institute, Walnut Creek, California; Bristow, James [Joint Genome Institute, Walnut Creek, California; Eisen, Jonathan [Joint Genome Institute, Walnut Creek, California; Markowitz, Victor [Joint Genome Institute, Walnut Creek, California; Hugenholtz, Philip [U.S. Department of Energy, Joint Genome Institute; Kyrpides, Nikos C [Joint Genome Institute, Walnut Creek, California; Klenk, Hans-Peter [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany

    2011-01-01T23:59:59.000Z

    Paludibacter propionicigenes Ueki et al. 2006 is the type species of the genus Paludibacter, which belongs to the family Porphyromonadaceae. The species is of interest because of the position it occupies in the tree of life where it can be found in close proximity to members of the genus Dysgonomonas. This is the first completed genome sequence of a member of the genus Paludibacter and the third sequence from the family Porphyromonadaceae. The 3,685,504 bp long genome with its 3,054 protein-coding and 64 RNA genes consists of one circular chromosome and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  12. Complete genome sequence of Cellulophaga algicola type strain (IC166T)

    SciTech Connect (OSTI)

    Abt, Birte [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Lu, Megan [Los Alamos National Laboratory (LANL); Misra, Monica [Los Alamos National Laboratory (LANL); Han, Cliff [Los Alamos National Laboratory (LANL); Nolan, Matt [Joint Genome Institute, Walnut Creek, California; Lucas, Susan [Joint Genome Institute, Walnut Creek, California; Hammon, Nancy [Joint Genome Institute, Walnut Creek, California; Deshpande, Shweta [Joint Genome Institute, Walnut Creek, California; Cheng, Jan-Fang [Joint Genome Institute, Walnut Creek, California; Tapia, Roxanne [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Pitluck, Sam [Joint Genome Institute, Walnut Creek, California; Liolios, Konstantinos [Joint Genome Institute, Walnut Creek, California; Pagani, Ioanna [Joint Genome Institute, Walnut Creek, California; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Mavromatis, K [U.S. Department of Energy, Joint Genome Institute; Ovchinnikova, Galina [U.S. Department of Energy, Joint Genome Institute; Pati, Amrita [U.S. Department of Energy, Joint Genome Institute; Chen, Amy [Joint Genome Institute, Walnut Creek, California; Palaniappan, Krishna [Joint Genome Institute, Walnut Creek, California; Land, Miriam L [ORNL; Hauser, Loren John [ORNL; Chang, Yun-Juan [ORNL; Jeffries, Cynthia [Oak Ridge National Laboratory (ORNL); Detter, J. Chris [Joint Genome Institute, Walnut Creek, California; Brambilla, Evelyne-Marie [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Rohde, Manfred [HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany; Tindall, Brian [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Goker, Markus [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Woyke, Tanja [Joint Genome Institute, Walnut Creek, California; Bristow, James [Joint Genome Institute, Walnut Creek, California; Eisen, Jonathan [Joint Genome Institute, Walnut Creek, California; Markowitz, Victor [Joint Genome Institute, Walnut Creek, California; Hugenholtz, Philip [U.S. Department of Energy, Joint Genome Institute; Kyrpides, Nikos C [Joint Genome Institute, Walnut Creek, California; Klenk, Hans-Peter [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Lapidus, Alla L. [Joint Genome Institute, Walnut Creek, California

    2011-01-01T23:59:59.000Z

    Cellulophaga algicola Bowman 2000 belongs to the family Flavobacteriaceae within the phylum 'Bacteroidetes' and was isolated from Melosira collected from the Eastern Antarctic coastal zone. The species is of interest because its members produce a wide range of extra-cellular enzymes capable of degrading proteins and polysaccharides with temperature optima of 20-30 C. This is the first completed genome sequence of a member of the genus Cellulophaga. The 4,888,353 bp long genome with its 4,285 protein-coding and 62 RNA genes consists of one circular chromosome and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  13. Complete genome sequence of Odoribacter splanchnicus type strain (1651/6T)

    SciTech Connect (OSTI)

    Goker, Markus [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Gronow, Sabine [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Zeytun, Ahmet [Los Alamos National Laboratory (LANL); Nolan, Matt [Joint Genome Institute, Walnut Creek, California; Lucas, Susan [Joint Genome Institute, Walnut Creek, California; Lapidus, Alla L. [Joint Genome Institute, Walnut Creek, California; Hammon, Nancy [Joint Genome Institute, Walnut Creek, California; Deshpande, Shweta [Joint Genome Institute, Walnut Creek, California; Cheng, Jan-Fang [Joint Genome Institute, Walnut Creek, California; Pitluck, Sam [Joint Genome Institute, Walnut Creek, California; Liolios, Konstantinos [Joint Genome Institute, Walnut Creek, California; Pagani, Ioanna [Joint Genome Institute, Walnut Creek, California; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Mavromatis, K [U.S. Department of Energy, Joint Genome Institute; Ovchinnikova, Galina [U.S. Department of Energy, Joint Genome Institute; Pati, Amrita [U.S. Department of Energy, Joint Genome Institute; Tapia, Roxanne [Los Alamos National Laboratory (LANL); Han, Cliff [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Chen, Amy [Joint Genome Institute, Walnut Creek, California; Palaniappan, Krishna [Joint Genome Institute, Walnut Creek, California; Land, Miriam L [ORNL; Hauser, Loren John [ORNL; Jeffries, Cynthia [Oak Ridge National Laboratory (ORNL); Brambilla, Evelyne-Marie [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Rohde, Christine [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Detter, J. Chris [Joint Genome Institute, Walnut Creek, California; Woyke, Tanja [Joint Genome Institute, Walnut Creek, California; Bristow, James [Joint Genome Institute, Walnut Creek, California; Markowitz, Victor [Joint Genome Institute, Walnut Creek, California; Hugenholtz, Philip [U.S. Department of Energy, Joint Genome Institute; Eisen, Jonathan [Joint Genome Institute, Walnut Creek, California; Kyrpides, Nikos C [Joint Genome Institute, Walnut Creek, California; Klenk, Hans-Peter [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany

    2011-01-01T23:59:59.000Z

    Odoribacter splanchnicus (Werner et al. 1975) Hardham et al. 2008 is the type species of the genus Odoribacter, which belongs to the family Porphyromonadaceae in the order Bacteroidales . The species is of interest because members of the Odoribacter form an isolated cluster within the Porphyromonadaceae. This is the first completed genome sequence of a member of the genus Odoribacter and the fourth sequence from the family Porphyromonadaceae. The 4,392,288 bp long genome with its 3,672 protein-coding and 74 RNA genes and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  14. Evolution Confers Morality Department of Physics

    E-Print Network [OSTI]

    as Mass Length Time Pornography [Officialportrait] #12;Francis Collins ­ Human Genome Project Rejects

  15. 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.

  16. 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

  17. Hindawi Publishing Corporation Comparative and Functional Genomics

    E-Print Network [OSTI]

    Newcastle upon Tyne, University of

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

  18. 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

  19. 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

  20. 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.

  1. 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

  2. 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

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

    E-Print Network [OSTI]

    Wagner, Andreas

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

  4. 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

  5. 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.

  6. Genome-Wide Identification and 3D Modeling of Proteins involved in DNA Damage Recognition and Repair (Final Report)

    SciTech Connect (OSTI)

    Ruben A. Abagyan, PhD

    2004-04-15T23:59:59.000Z

    OAK-B135 DNA Damage Recognition and Repair (DDR and R) proteins play a critical role in cellular responses to low-dose radiation and are associated with cancer. the authors have performed a systematic, genome-wide computational analysis of genomic data for human genes involved in the DDR and R process. The significant achievements of this project include: (1) Construction of the computational pipeline for searching DDR and R genes, building and validation of 3D models of proteins involved in DDR and R; (2) Functional and structural annotation of the 3D models and generation of comprehensive lists of suggested knock-out mutations; (3) Important improvement of macromolecular docking technology and its application to predict the DNA-Protein complex conformation; (4) Development of a new algorithm for improved analysis of high-density oligonucleotide arrays for gene expression profiling; (5) Construction and maintenance of the DNA Damage Recognition and Repair Database; and (6) Producing 14 research papers (10 published and 4 in preparation).

  7. 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 ...

  8. 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

  9. 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):

  10. COMMENTARY Open Access Crowdfunding the Azolla fern genome project

    E-Print Network [OSTI]

    that allows the public to participate in, as well as to support and witness advancements in science. Here we for sustainable agriculture, phytoremediation and biofuel production. Azolla is more than just a fern

  11. Fungal Genomics Presentation for BETO 2015 Project Peer Review

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Home Page on Google Bookmark EERE: Alternative Fuels DataDepartment of Energy Your Density Isn't YourTransport inEnergy0.pdfTechnologies ProgramOutfittedof EnergydetailsDepartment

  12. FCTO Projects and the Materials Genome Initiative | Department of Energy

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Home Page on Google Bookmark EERE: Alternative Fuels Data Center Home Page onYouTube YouTube Note: Since the YouTube|6721 FederalTexasManager FAQS Reference Guide - AviationEnergy

  13. USDA and DOE Fund Genomics Projects For Bioenergy Fuels Research |

    Energy Savers [EERE]

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Home Page onYou are now leaving Energy.gov You are now leaving Energy.gov You are being directedAnnual Siteof Energy 2, 2015 -Helicopter AccidentSeptember 2009JulyUS-ChinaDepartmentDepartment

  14. FCTO Projects and the Materials Genome Initiative Webinar

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Home Page on Google Bookmark EERE: Alternative Fuels DataDepartment of Energy Your Density Isn't YourTransport in Representative Geologic MediaTreatment |Safeguards andBG-PLN-0036

  15. 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-

  16. 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://

  17. 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-

  18. 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

  19. 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

  20. 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

  1. 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

  2. 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

  3. Human health and wellbeing in environmental impact assessment in New South Wales, Australia: Auditing health impacts within environmental assessments of major projects

    SciTech Connect (OSTI)

    Harris, Patrick J., E-mail: patrick.harris@unsw.edu.a [Centre for Health Equity Training, Research and Evaluation, part of the UNSW, Research Centre for Primary Health Care and Equity, UNSW, Locked Mail Bag 7103, Liverpool BC, NSW 1871 (Australia); Harris, Elizabeth, E-mail: e.harris@unsw.edu.a [Centre for Health Equity Training, Research and Evaluation, part of the UNSW, Research Centre for Primary Health Care and Equity, UNSW, Locked Mail Bag 7103, Liverpool BC, NSW 1871 (Australia); Thompson, Susan, E-mail: s.thompson@unsw.edu.a [Faculty of the Built Environment, UNSW, Sydney, NSW 2052 (Australia); Harris-Roxas, Ben, E-mail: b.harris-roxas@unsw.edu.a [Centre for Health Equity Training, Research and Evaluation, part of the UNSW, Research Centre for Primary Health Care and Equity, UNSW, Locked Mail Bag 7103, Liverpool BC, NSW 1871 (Australia); Kemp, Lynn, E-mail: l.kemp@unsw.edu.a [Centre for Health Equity Training, Research and Evaluation, part of the UNSW, Research Centre for Primary Health Care and Equity, UNSW, Locked Mail Bag 7103, Liverpool BC, NSW 1871 (Australia)

    2009-09-15T23:59:59.000Z

    Internationally the inclusion of health within environmental impact assessment (EIA) has been shown to be limited. While Australian EIA documentation has not been studied empirically to date, deficiencies in practice have been documented. This research developed an audit tool to undertake a qualitative descriptive analysis of 22 Major Project EAs in New South Wales, Australia. Results showed that health and wellbeing impacts were not considered explicitly. They were, however, included indirectly in the identification of traditional public health exposures associated with the physical environment and to a lesser extent the inclusion of social and economic impacts. However, no health data was used to inform any of the assessments, there was no reference to causal pathways between exposures or determinants and physical or mental health effects, and there was no inclusion of the differential distribution of exposures or health impacts on different populations. The results add conceptually and practically to the long standing integration debate, showing that health is in a position to add value to the EIA process as an explicit part of standard environmental, social and economic considerations. However, to overcome the consistently documented barriers to integrating health in EIA, capacity must be developed amongst EIA professionals, led by the health sector, to progress health related knowledge and tools.

  4. Flash Updates of GSC projects (GSC8 Meeting)

    ScienceCinema (OSTI)

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

    2011-04-29T23:59:59.000Z

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

  5. Timeline of Events: 1991 to 2000 | Department of Energy

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

    Minister Tony Blair announce that the International Human Genome Project and Celera Genomics Corporation have completed a working draft of 95% of the human genetic structure. DOE...

  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. Complete genome sequence of Desulfomicrobium baculatum type strain (XT)

    SciTech Connect (OSTI)

    Copeland, Alex; Spring, Stefan; Goker, Markus; Schneider, Susanne; Lapidus, Alla; Glavina Del Rio, Tijana; Tice, Hope; Cheng, Jan-Fang; Lucas, Susan; Chen, Feng; Nolan, Matt; Bruce, David; Goodwin, Lynne; Pitluck, Sam; Ivanova, Natalia; Mavrommatis, Konstantinos; Ovchinnikova, Galina; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jefferies, Cynthia C; Meincke, Linda; Sims, David; Brettin, Thomas; Detter, John C; Han, Cliff; Chain, Patrick; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Klenk, Hans-Peter; Kyrpides, Nikos C; Lucas, Susan

    2009-05-20T23:59:59.000Z

    Desulfomicrobium baculatum is the type species of the genus Desulfomicrobium, which is the type genus of the family Desulfomicrobiaceae. It is of phylogenetic interest because of the isolated location of the family Desulfomicrobiaceae within the order Desulfovibrionales. D. baculatum strain XT is a Gram-negative, motile, sulfate-reducing bacterium isolated from water-saturated manganese carbonate ore. It is strictly anaerobic and does not require NaCl for growth, although NaCl concentrations up to 6percent (w/v) are tolerated. The metabolism is respiratory or fermentative. In the presence of sulfate, pyruvate and lactate are incompletely oxidized to acetate and CO2. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of a member of the deltaproteobacterial family Desulfomicrobiaceae, and this 3,942,657 bp long single replicon genome with its 3494 protein-coding and 72 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

  8. Reconstruction of a Bacterial Genome from DNA Cassettes

    SciTech Connect (OSTI)

    Christopher Dupont; John Glass; Laura Sheahan; Shibu Yooseph; Lisa Zeigler Allen; Mathangi Thiagarajan; Andrew Allen; Robert Friedman; J. Craig Venter

    2011-12-31T23:59:59.000Z

    This basic research program comprised two major areas: (1) acquisition and analysis of marine microbial metagenomic data and development of genomic analysis tools for broad, external community use; (2) development of a minimal bacterial genome. Our Marine Metagenomic Diversity effort generated and analyzed shotgun sequencing data from microbial communities sampled from over 250 sites around the world. About 40% of the 26 Gbp of sequence data has been made publicly available to date with a complete release anticipated in six months. Our results and those mining the deposited data have revealed a vast diversity of genes coding for critical metabolic processes whose phylogenetic and geographic distributions will enable a deeper understanding of carbon and nutrient cycling, microbial ecology, and rapid rate evolutionary processes such as horizontal gene transfer by viruses and plasmids. A global assembly of the generated dataset resulted in a massive set (5Gbp) of genome fragments that provide context to the majority of the generated data that originated from uncultivated organisms. Our Synthetic Biology team has made significant progress towards the goal of synthesizing a minimal mycoplasma genome that will have all of the machinery for independent life. This project, once completed, will provide fundamentally new knowledge about requirements for microbial life and help to lay a basic research foundation for developing microbiological approaches to bioenergy.

  9. Magnesium Projects

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

    cyberinfrastructure projects and will be augmented by original research in Computer Science and Software Engineering towards the creation of large, distributed, autonomic and...

  10. Project Construction

    Broader source: Energy.gov [DOE]

    Integrating renewable energy into Federal new construction or major renovations requires effective structuring of the construction team and project schedule. This overview discusses key construction team considerations for renewable energy as well as timing and expectations for the construction phase. The project construction phase begins after a project is completely designed and the construction documents (100%) have been issued. Construction team skills and experience with renewable energy technologies are crucial during construction, as is how the integration of renewable energy affects the project construction schedule.

  11. Conservation of exon scrambling in human and mouse

    E-Print Network [OSTI]

    Hamilton, Monica L. (Monica Lauren)

    2012-01-01T23:59:59.000Z

    Exon scrambling is a phenomenon in which the exons of an mRNA transcript are spliced in an order inconsistent with that of the genome. In this thesis, I present a computational analysis of scrambled exons in human and ...

  12. ATGC: a database of orthologous genes from closely related prokaryotic genomes and a research platform for microevolution of prokaryotes

    SciTech Connect (OSTI)

    Novichkov, Pavel S.; Ratnere, Igor; Wolf, Yuri I.; Koonin, Eugene V.; Dubchak, Inna

    2009-07-23T23:59:59.000Z

    The database of Alignable Tight Genomic Clusters (ATGCs) consists of closely related genomes of archaea and bacteria, and is a resource for research into prokaryotic microevolution. Construction of a data set with appropriate characteristics is a major hurdle for this type of studies. With the current rate of genome sequencing, it is difficult to follow the progress of the field and to determine which of the available genome sets meet the requirements of a given research project, in particular, with respect to the minimum and maximum levels of similarity between the included genomes. Additionally, extraction of specific content, such as genomic alignments or families of orthologs, from a selected set of genomes is a complicated and time-consuming process. The database addresses these problems by providing an intuitive and efficient web interface to browse precomputed ATGCs, select appropriate ones and access ATGC-derived data such as multiple alignments of orthologous proteins, matrices of pairwise intergenomic distances based on genome-wide analysis of synonymous and nonsynonymous substitution rates and others. The ATGC database will be regularly updated following new releases of the NCBI RefSeq. The database is hosted by the Genomics Division at Lawrence Berkeley National laboratory and is publicly available at http://atgc.lbl.gov.

  13. ; 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

  14. Complete genome sequence of Dyadobacter fermentans type strain (NS114T)

    SciTech Connect (OSTI)

    Lang, Elke; Lapidus, Alla; Chertkov, Olga; Brettin, Thomas; Detter, John C.; Han, Cliff; Copeland, Alex; Glavina Del Rio, Tijana; Nolan, Matt; Chen, Feng; Lucas, Susan; Tice, Hope; Cheng, Jan-Fang; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia; Bruce, David; Goodwin, Lynne; Pitluck, Sam; Ovchinnikova, Galina; Pati, Amrita; Ivanova, Natalia; Mavromatis, Konstantinos; Chen, Amy; Chain, Patrick; Bristow, Jim; Eisen, Jonathan A.; Markowitz, Victor; Hugenholtz, Philip; Goker, Markus; Rohde, Manfred; Kyrpides, Nikos C; Klenk, Hans-Peter

    2009-05-20T23:59:59.000Z

    Dyadobacter fermentans (Chelius MK and Triplett EW, 2000) is the type species of the genus Dyadobacter. It is of phylogenetic interest because of its location in the Cytophagaceae, a very diverse family within the order 'Sphingobacteriales'. D. fermentans has a mainly respiratory metabolism, stains Gram-negative, is non-motile and oxidase and catalase positive. It is characterized by the production of cell filaments in ageing cultures, a flexirubin-like pigment and its ability to ferment glucose, which is almost unique in the aerobically living members of this taxonomically difficult family. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of the 'sphingobacterial' genus Dyadobacter, and this 6,967,790 bp long single replicon genome with its 5804 protein-coding and 50 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

  15. Complete genome sequence of Cellulophaga lytica type strain (LIM-21T)

    SciTech Connect (OSTI)

    Pati, Amrita [U.S. Department of Energy, Joint Genome Institute; Abt, Birte [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Teshima, Hazuki [Los Alamos National Laboratory (LANL); Nolan, Matt [Joint Genome Institute, Walnut Creek, California; Lapidus, Alla L. [Joint Genome Institute, Walnut Creek, California; Lucas, Susan [Joint Genome Institute, Walnut Creek, California; Hammon, Nancy [Joint Genome Institute, Walnut Creek, California; Deshpande, Shweta [Joint Genome Institute, Walnut Creek, California; Cheng, Jan-Fang [Joint Genome Institute, Walnut Creek, California; Tapia, Roxanne [Los Alamos National Laboratory (LANL); Han, Cliff [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Pitluck, Sam [Joint Genome Institute, Walnut Creek, California; Liolios, Konstantinos [Joint Genome Institute, Walnut Creek, California; Pagani, Ioanna [Joint Genome Institute, Walnut Creek, California; Mavromatis, K [U.S. Department of Energy, Joint Genome Institute; Ovchinnikova, Galina [U.S. Department of Energy, Joint Genome Institute; Chen, Amy [Joint Genome Institute, Walnut Creek, California; Palaniappan, Krishna [Joint Genome Institute, Walnut Creek, California; Land, Miriam L [ORNL; Hauser, Loren John [ORNL; Jeffries, Cynthia [Oak Ridge National Laboratory (ORNL); Detter, J. Chris [Joint Genome Institute, Walnut Creek, California; Brambilla, Evelyne-Marie [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Kannan, K. Palani [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Rohde, Manfred [HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany; Spring, Stefan [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Goker, Markus [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Woyke, Tanja [Joint Genome Institute, Walnut Creek, California; Bristow, James [Joint Genome Institute, Walnut Creek, California; Eisen, Jonathan [Joint Genome Institute, Walnut Creek, California; Markowitz, Victor [Joint Genome Institute, Walnut Creek, California; Hugenholtz, Philip [U.S. Department of Energy, Joint Genome Institute; Kyrpides, Nikos C [Joint Genome Institute, Walnut Creek, California; Klenk, Hans-Peter [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Ivanova, N [U.S. Department of Energy, Joint Genome Institute

    2011-01-01T23:59:59.000Z

    Cellulophaga lytica (Lewin 1969) Johansen et al. 1999 is the type species of the genus Cellulophaga, which belongs to the family Flavobacteriaceae within the phylum 'Bacteroidetes' and was isolated from marine beach mud in Limon, Costa Rica. The species is of biotechnological interest because its members produce a wide range of extracellular enzymes capable of degrading proteins and polysaccharides. After the genome sequence of Cellulophaga algicola this is the second completed genome sequence of a member of the genus Cellulophaga. The 3,765,936 bp long genome with its 3,303 protein-coding and 55 RNA genes consists of one circular chromosome and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  16. Non-contiguous finished genome sequence of Bacteroides coprosuis type strain (PC 139T)

    SciTech Connect (OSTI)

    Land, Miriam L [ORNL; Held, Brittany [Los Alamos National Laboratory (LANL); Gronow, Sabine [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Abt, Birte [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Lucas, Susan [Joint Genome Institute, Walnut Creek, California; Glavina Del Rio, Tijana [Joint Genome Institute, Walnut Creek, California; Nolan, Matt [Joint Genome Institute, Walnut Creek, California; Tice, Hope [Joint Genome Institute, Walnut Creek, California; Cheng, Jan-Fang [Joint Genome Institute, Walnut Creek, California; Pitluck, Sam [Joint Genome Institute, Walnut Creek, California; Liolios, Konstantinos [Joint Genome Institute, Walnut Creek, California; Pagani, Ioanna [Joint Genome Institute, Walnut Creek, California; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Mavromatis, K [U.S. Department of Energy, Joint Genome Institute; Pati, Amrita [U.S. Department of Energy, Joint Genome Institute; Tapia, Roxanne [Los Alamos National Laboratory (LANL); Han, Cliff [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Chen, Amy [Joint Genome Institute, Walnut Creek, California; Palaniappan, Krishna [Joint Genome Institute, Walnut Creek, California; Hauser, Loren John [ORNL; Brambilla, Evelyne-Marie [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Rohde, Manfred [HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany; Goker, Markus [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Detter, J. Chris [Joint Genome Institute, Walnut Creek, California; Woyke, Tanja [Joint Genome Institute, Walnut Creek, California; Bristow, James [Joint Genome Institute, Walnut Creek, California; Eisen, Jonathan [Joint Genome Institute, Walnut Creek, California; Markowitz, Victor [Joint Genome Institute, Walnut Creek, California; Hugenholtz, Philip [U.S. Department of Energy, Joint Genome Institute; Kyrpides, Nikos C [Joint Genome Institute, Walnut Creek, California; Klenk, Hans-Peter [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Lapidus, Alla L. [Joint Genome Institute, Walnut Creek, California

    2011-01-01T23:59:59.000Z

    Bacteroides coprosuis Whitehead et al. 2005 belongs to the genus Bacteroides, which is a member of the family Bacteroidaceae. Members of the genus Bacteroides in general are known as beneficial protectors of animal guts against pathogenic microorganisms, and as contributors to the degradation of complex molecules such as polysaccharides. B. coprosuis itself was isolated from a manure storage pit of a swine facility, but has not yet been found in an animal host. The species is of interest solely because of its isolated phylogenetic location. The genome of B. coprosuis is already the 5th sequenced type strain genome from the genus Bacteroides. The 2,991,798 bp long genome with its 2,461 protein-coding and 78 RNA genes and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  17. Complete genome sequence of Desulfobulbus propionicus type strain (1pr3T)

    SciTech Connect (OSTI)

    Pagani, Ioanna [Joint Genome Institute, Walnut Creek, California; Lapidus, Alla L. [Joint Genome Institute, Walnut Creek, California; Nolan, Matt [Joint Genome Institute, Walnut Creek, California; Lucas, Susan [Joint Genome Institute, Walnut Creek, California; Hammon, Nancy [Joint Genome Institute, Walnut Creek, California; Deshpande, Shweta [Joint Genome Institute, Walnut Creek, California; Cheng, Jan-Fang [Joint Genome Institute, Walnut Creek, California; Chertkov, Olga [Los Alamos National Laboratory (LANL); Davenport, Karen W. [Los Alamos National Laboratory (LANL); Tapia, Roxanne [Los Alamos National Laboratory (LANL); Han, Cliff [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Pitluck, Sam [Joint Genome Institute, Walnut Creek, California; Liolios, Konstantinos [Joint Genome Institute, Walnut Creek, California; Mavromatis, K [U.S. Department of Energy, Joint Genome Institute; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Mikhailova, Natalia [U.S. Department of Energy, Joint Genome Institute; Pati, Amrita [U.S. Department of Energy, Joint Genome Institute; Chen, Amy [Joint Genome Institute, Walnut Creek, California; Palaniappan, Krishna [Joint Genome Institute, Walnut Creek, California; Land, Miriam L [ORNL; Hauser, Loren John [ORNL; Chang, Yun-Juan [ORNL; Jeffries, Cynthia [Oak Ridge National Laboratory (ORNL); Detter, J. Chris [Joint Genome Institute, Walnut Creek, California; Brambilla, Evelyne-Marie [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Kannan, K. Palani [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Ngatchou, Olivier Duplex [HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany; Rohde, Manfred [HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany; Pukall, Rudiger [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Spring, Stefan [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Goker, Markus [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Sikorski, Johannes [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Woyke, Tanja [Joint Genome Institute, Walnut Creek, California; Bristow, James [Joint Genome Institute, Walnut Creek, California; Eisen, Jonathan [Joint Genome Institute, Walnut Creek, California; Markowitz, Victor [Joint Genome Institute, Walnut Creek, California; Hugenholtz, Philip [U.S. Department of Energy, Joint Genome Institute; Kyrpides, Nikos C [Joint Genome Institute, Walnut Creek, California; Klenk, Hans-Peter [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany

    2011-01-01T23:59:59.000Z

    Desulfobulbus propionicus Widdel 1981 is the type species of the genus Desulfobulbus, which belongs to the family Desulfobulbaceae. The species is of interest because of its great implication in the sulfur cycle in aquatic sediments, its large substrate spectrum and a broad versatility in using various fermentation pathways. The species was the first example of a pure culture known to disproportionate elemental sulfur to sulfate and sulfide. This is the first completed genome sequence of a member of the genus Desulfobulbus and the third published genome sequence from a member of the family Desulfobulbaceae. The 3,851,869 bp long genome with its 3,351 protein-coding and 57 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  18. Complete genome sequence of Syntrophothermus lipocalidus type strain (TGB-C1T)

    SciTech Connect (OSTI)

    Ngatchou, Olivier Duplex [HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany; Zhang, Xiaojing [Los Alamos National Laboratory (LANL); Lucas, Susan [Joint Genome Institute, Walnut Creek, California; Lapidus, Alla L. [Joint Genome Institute, Walnut Creek, California; Glavina Del Rio, Tijana [Joint Genome Institute, Walnut Creek, California; Nolan, Matt [Joint Genome Institute, Walnut Creek, California; Tice, Hope [Joint Genome Institute, Walnut Creek, California; Cheng, Jan-Fang [Joint Genome Institute, Walnut Creek, California; Han, Cliff [Los Alamos National Laboratory (LANL); Tapia, Roxanne [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Pitluck, Sam [Joint Genome Institute, Walnut Creek, California; Liolios, Konstantinos [Joint Genome Institute, Walnut Creek, California; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Mavromatis, K [U.S. Department of Energy, Joint Genome Institute; Mikhailova, Natalia [U.S. Department of Energy, Joint Genome Institute; Ovchinnikova, Galina [U.S. Department of Energy, Joint Genome Institute; Pati, Amrita [U.S. Department of Energy, Joint Genome Institute; Brambilla, Evelyne-Marie [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Chen, Amy [Joint Genome Institute, Walnut Creek, California; Palaniappan, Krishna [Joint Genome Institute, Walnut Creek, California; Land, Miriam L [ORNL; Hauser, Loren John [ORNL; Chang, Yun-Juan [ORNL; Jeffries, Cynthia [Oak Ridge National Laboratory (ORNL); Rohde, Manfred [HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany; Sikorski, Johannes [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Spring, Stefan [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Goker, Markus [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Detter, J. Chris [Joint Genome Institute, Walnut Creek, California; Woyke, Tanja [Joint Genome Institute, Walnut Creek, California; Bristow, James [Joint Genome Institute, Walnut Creek, California; Eisen, Jonathan [Joint Genome Institute, Walnut Creek, California; Markowitz, Victor [Joint Genome Institute, Walnut Creek, California; Held, Brittany [Los Alamos National Laboratory (LANL); Hugenholtz, Philip [U.S. Department of Energy, Joint Genome Institute; Kyrpides, Nikos C [Joint Genome Institute, Walnut Creek, California; Klenk, Hans-Peter [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany

    2010-01-01T23:59:59.000Z

    Syntrophothermus lipocalidus Sekiguchi et al. 2000 is the type species of the genus Syntrophothermus. The species is of interest because of its strictly anaerobic lifestyle, its participation in the primary step of the degradation of organic maters, and for releasing products which serve as substrates for other microorganisms. It also contributes significantly to maintain a regular pH in its environment by removing the fatty acids through -oxidation. The strain is able to metabolize isobutyrate and butyrate, which are the substrate and the product of degradation of the substrate, respectively. This is the first complete genome sequence of a member of the genus Syntrophothermus and the second in the family Syntrophomonadaceae. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2,405,559 bp long genome with its 2,385 protein-coding and 55 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  19. Complete genome sequence of Truepera radiovictrix type strain (RQ-24T)

    SciTech Connect (OSTI)

    Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Rohde, Christine [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Munk, Christine [Joint Genome Institute, Walnut Creek, California; Nolan, Matt [Joint Genome Institute, Walnut Creek, California; Lucas, Susan [Joint Genome Institute, Walnut Creek, California; Glavina Del Rio, Tijana [Joint Genome Institute, Walnut Creek, California; Tice, Hope [Joint Genome Institute, Walnut Creek, California; Deshpande, Shweta [Joint Genome Institute, Walnut Creek, California; Cheng, Jan-Fang [Joint Genome Institute, Walnut Creek, California; Tapia, Roxanne [Los Alamos National Laboratory (LANL); Han, Cliff [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Pitluck, Sam [Joint Genome Institute, Walnut Creek, California; Liolios, Konstantinos [Joint Genome Institute, Walnut Creek, California; Mavromatis, K [U.S. Department of Energy, Joint Genome Institute; Pati, Amrita [U.S. Department of Energy, Joint Genome Institute; Chen, Amy [Joint Genome Institute, Walnut Creek, California; Palaniappan, Krishna [Joint Genome Institute, Walnut Creek, California; Land, Miriam L [ORNL; Hauser, Loren John [ORNL; Chang, Yun-Juan [ORNL; Jeffries, Cynthia [Oak Ridge National Laboratory (ORNL); Brambilla, Evelyne-Marie [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Rohde, Manfred [HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany; Goker, Markus [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Tindall, Brian [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Woyke, Tanja [Joint Genome Institute, Walnut Creek, California; Bristow, James [Joint Genome Institute, Walnut Creek, California; Eisen, Jonathan [Joint Genome Institute, Walnut Creek, California; Markowitz, Victor [Joint Genome Institute, Walnut Creek, California; Hugenholtz, Philip [U.S. Department of Energy, Joint Genome Institute; Kyrpides, Nikos C [Joint Genome Institute, Walnut Creek, California; Klenk, Hans-Peter [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Lapidus, Alla L. [Joint Genome Institute, Walnut Creek, California

    2011-01-01T23:59:59.000Z

    Truepera radiovictrix Albuquerque et al. 2005 is the type species of the genus Truepera within the phylum Deinococcus/Thermus. T. radiovictrix is of special interest not only because of its isolated phylogenetic location in the order Deinococcales, but also because of its ability to grow under multiple extreme conditions in alkaline, moderately saline, and high temperature habitats. Of particular interest is the fact that, T. radiovictrix is also remarkably resistant to ionizing radiation, a feature it shares with members of the genus Deinococcus. This is the first completed genome sequence of a member of the family Trueperaceae and the fourth type strain genome sequence from a member of the order Deinococcales. The 3,260,398 bp long genome with its 2,994 protein-coding and 52 RNA genes consists of one circular chromosome and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  20. Complete genome sequence of Bacteroides helcogenes type strain (P 36-108T)

    SciTech Connect (OSTI)

    Pati, Amrita [U.S. Department of Energy, Joint Genome Institute; Gronow, Sabine [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Zeytun, Ahmet [Los Alamos National Laboratory (LANL); Lapidus, Alla L. [Joint Genome Institute, Walnut Creek, California; Nolan, Matt [Joint Genome Institute, Walnut Creek, California; Hammon, Nancy [Joint Genome Institute, Walnut Creek, California; Deshpande, Shweta [Joint Genome Institute, Walnut Creek, California; Cheng, Jan-Fang [Joint Genome Institute, Walnut Creek, California; Tapia, Roxanne [Los Alamos National Laboratory (LANL); Han, Cliff [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Pitluck, Sam [Joint Genome Institute, Walnut Creek, California; Liolios, Konstantinos [Joint Genome Institute, Walnut Creek, California; Pagani, Ioanna [Joint Genome Institute, Walnut Creek, California; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Mavromatis, K [U.S. Department of Energy, Joint Genome Institute; Chen, Amy [Joint Genome Institute, Walnut Creek, California; Palaniappan, Krishna [Joint Genome Institute, Walnut Creek, California; Land, Miriam L [ORNL; Hauser, Loren John [ORNL; Chang, Yun-Juan [ORNL; Jeffries, Cynthia [Oak Ridge National Laboratory (ORNL); Detter, J. Chris [Joint Genome Institute, Walnut Creek, California; Brambilla, Evelyne-Marie [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Rohde, Manfred [HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany; Goker, Markus [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Woyke, Tanja [Joint Genome Institute, Walnut Creek, California; Bristow, James [Joint Genome Institute, Walnut Creek, California; Eisen, Jonathan [Joint Genome Institute, Walnut Creek, California; Markowitz, Victor [Joint Genome Institute, Walnut Creek, California; Hugenholtz, Philip [U.S. Department of Energy, Joint Genome Institute; Kyrpides, Nikos C [Joint Genome Institute, Walnut Creek, California; Klenk, Hans-Peter [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Lucas, Susan [Joint Genome Institute, Walnut Creek, California

    2011-01-01T23:59:59.000Z

    Bacteroides helcogenes Benno et al. 1983 is of interest because of its isolated phylogenetic location and, although it has been found in pig feces and is known to be pathogenic for pigs, occurrence of this bacterium is rare and it does not cause significant damage in intensive animal husbandry. The genome of B. helcogenes P 36-108T is already the fifth completed and published type strain genome from the genus Bacteroides in the family Bacteroidaceae. The 3,998,906 bp long genome with its 3,353 protein-coding and 83 RNA genes consists of one circular chromosome and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  1. 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

  2. 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...

  3. 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...

  4. 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...

  5. 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.

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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

  11. Distinct changes of genomic biases in nucleotide substitution at the time of mammalian radiation

    E-Print Network [OSTI]

    Peter F. Arndt; Dmitri A. Petrov; Terence Hwa

    2003-07-01T23:59:59.000Z

    Differences in the regional substitution patterns in the human genome created patterns of large-scale variation of base composition known as genomic isochores. To gain insight into the origin of the genomic isochores we develop a maximum likelihood approach to determine the history of substitution patterns in the human genome. This approach utilizes the vast amount of repetitive sequence deposited in the human genome over the past ~250 MYR. Using this approach we estimate the frequencies of seven types of substitutions: the four transversions, two transitions, and the methyl-assisted transition of cytosine in CpG. Comparing substitutional patterns in repetitive elements of various ages, we reconstruct the history of the base-substitutional process in the different isochores for the past 250 Myr. At around 90 Myr ago (around the time of the mammalian radiation), we find an abrupt 4- to 8-fold increase of the cytosine transition rate in CpG pairs compared to that of the reptilian ancestor. Further analysis of nucleotide substitutions in regions with different GC-content reveals concurrent changes in the substitutional patterns. While the substitutional pattern was dependent on the regional GC-content in such ways that it preserved the regional GC-content before the mammalian radiation, it lost this dependence afterwards. The substitutional pattern changed from an isochore-preserving to an isochore-degrading one. We conclude that isochores have been established before the radiation of the eutherian mammals and have been subject to the process of homogenization since then.

  12. Hanford Environmental Dose Reconstruction Project

    SciTech Connect (OSTI)

    Finch, S.M.; McMakin, A.H. (comps.)

    1991-01-01T23:59:59.000Z

    The objective of the Hanford Environmental Dose Reconstruction Project is to estimate the radiation doses that individuals and populations could have received from nuclear operations at Hanford since 1944. The project is divided into the following technical tasks. These tasks correspond to the path radionuclides followed, from release to impact on humans (dose estimates): Source terms; environmental transport environmental monitoring data; demographics, agriculture, food habits; environmental pathways and dose estimates.

  13. Genome Stability of Lyme Disease Spirochetes: Comparative Genomics of Borrelia burgdorferi Plasmids

    SciTech Connect (OSTI)

    Casjens S. R.; Dunn J.; Mongodin, E. F.; Qiu, W.-G.; Luft, B. J.; Schutzer, S. E.; Gilcrease, E. B.; Huang, W. M.; Vujadinovic, M.; Aron, J. K.; Vargas, L. C.; Freeman, S.; Radune, D.; Weidman, J. F.; Dimitrov, G. I.; Khouri, H. M.; Sosa, J. E.; Halpin, R. A.; Fraser, C. M.

    2012-03-14T23:59:59.000Z

    Lyme disease is the most common tick-borne human illness in North America. In order to understand the molecular pathogenesis, natural diversity, population structure and epizootic spread of the North American Lyme agent, Borrelia burgdorferi sensu stricto, a much better understanding of the natural diversity of its genome will be required. Towards this end we present a comparative analysis of the nucleotide sequences of the numerous plasmids of B. burgdorferi isolates B31, N40, JD1 and 297. These strains were chosen because they include the three most commonly studied laboratory strains, and because they represent different major genetic lineages and so are informative regarding the genetic diversity and evolution of this organism. A unique feature of Borrelia genomes is that they carry a large number of linear and circular plasmids, and this work shows that strains N40, JD1, 297 and B31 carry related but non-identical sets of 16, 20, 19 and 21 plasmids, respectively, that comprise 33-40% of their genomes. We deduce that there are at least 28 plasmid compatibility types among the four strains. The B. burgdorferi {approx}900 Kbp linear chromosomes are evolutionarily exceptionally stable, except for a short {le}20 Kbp plasmid-like section at the right end. A few of the plasmids, including the linear lp54 and circular cp26, are also very stable. We show here that the other plasmids, especially the linear ones, are considerably more variable. Nearly all of the linear plasmids have undergone one or more substantial inter-plasmid rearrangements since their last common ancestor. In spite of these rearrangements and differences in plasmid contents, the overall gene complement of the different isolates has remained relatively constant.

  14. Genome Biology 2004, 6:302 commentreviewsreportsdepositedresearchinteractionsinformationrefereedresearch

    E-Print Network [OSTI]

    Gent, Universiteit

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

  15. 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

  16. 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

  17. 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

  18. 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

  19. 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

  20. 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

  1. 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

  2. DATA QUALITY IN GENOME DATABASES (Research Paper)

    E-Print Network [OSTI]

    Weske, Mathias

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

  3. 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

  4. 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

  5. 10.1101/gr.7080508Access the most recent version at doi: published online Feb 7, 2008;Genome Res.

    E-Print Network [OSTI]

    Weng, Zhiping

    IP-chip experiment. Mixtures of human genomic DNA and "spike-ins" comprised of nearly 100 human sequences at variousIP-chip experiments using P of variability in ChIP-chip experiments using predefined DNA targets David S. Johnson,1,24 Wei Li,2,24,25 D

  6. Human Dimensions of Wildlife Research Norman Dandy

    E-Print Network [OSTI]

    Human Dimensions of Wildlife Research Norman Dandy Social & Economic Research Group #12;Wildlife) · Human-dimensions of species management (HDSM) Research Projects #12;Collaborative Frameworks for Land of woodland landscapes ­ discussion groups, · Choice experiments, · Fellowships / Placements, · Newsletters

  7. Integrated Genome-Based Studies of Shewanella Echophysiology

    SciTech Connect (OSTI)

    Margrethe H. Serres

    2012-06-29T23:59:59.000Z

    Shewanella oneidensis MR-1 is a motile, facultative {gamma}-Proteobacterium with remarkable respiratory versatility; it can utilize a range of organic and inorganic compounds as terminal electronacceptors for anaerobic metabolism. The ability to effectively reduce nitrate, S0, polyvalent metals andradionuclides has established MR-1 as an important model dissimilatory metal-reducing microorganism for genome-based investigations of biogeochemical transformation of metals and radionuclides that are of concern to the U.S. Department of Energy (DOE) sites nationwide. Metal-reducing bacteria such as Shewanella also have a highly developed capacity for extracellular transfer of respiratory electrons to solid phase Fe and Mn oxides as well as directly to anode surfaces in microbial fuel cells. More broadly, Shewanellae are recognized free-living microorganisms and members of microbial communities involved in the decomposition of organic matter and the cycling of elements in aquatic and sedimentary systems. To function and compete in environments that are subject to spatial and temporal environmental change, Shewanella must be able to sense and respond to such changes and therefore require relatively robust sensing and regulation systems. The overall goal of this project is to apply the tools of genomics, leveraging the availability of genome sequence for 18 additional strains of Shewanella, to better understand the ecophysiology and speciation of respiratory-versatile members of this important genus. To understand these systems we propose to use genome-based approaches to investigate Shewanella as a system of integrated networks; first describing key cellular subsystems - those involved in signal transduction, regulation, and metabolism - then building towards understanding the function of whole cells and, eventually, cells within populations. As a general approach, this project will employ complimentary "top-down" - bioinformatics-based genome functional predictions, high-throughput expression analyses, and functional genomics approaches to uncover key genes as well as metabolic and regulatory networks. The "bottom-up" component employs more traditional approaches including genetics, physiology and biochemistry to test or verify predictions. This information will ultimately be linked to analyses of signal transduction and transcriptional regulatory systems and used to develop a linked model that will contribute to understanding the ecophysiology of Shewanella in redox stratified environments. A central component of this effort is the development of a data and knowledge integration environment that will allow investigators to query across the individual research domains, link to analysis applications, visualize data in a cell systems context, and produce new knowledge, while minimizing the effort, time and complexity to participating institutions.

  8. Mechanisms of Low Dose Radio-Suppression of Genomic Instability

    SciTech Connect (OSTI)

    Engelward, Bevin P

    2009-09-16T23:59:59.000Z

    The major goal of this project is to contribute toward the elucidation of the impact of long term low dose radiation on genomic stability. We have created and characterized novel technologies for delivering long term low dose radiation to animals, and we have studied genomic stability by applying cutting edge molecular analysis technologies. Remarkably, we have found that a dose rate that is 300X higher than background radiation does not lead to any detectable genomic damage, nor is there any significant change in gene expression for genes pertinent to the DNA damage response. These results point to the critical importance of dose rate, rather than just total dose, when evaluating public health risks and when creating regulatory guidelines. In addition to these studies, we have also further developed a mouse model for quantifying cells that have undergone a large scale DNA sequence rearrangement via homologous recombination, and we have applied these mice in studies of both low dose radiation and space radiation. In addition to more traditional approaches for assessing genomic stability, we have also explored radiation and possible beneficial effects (adaptive response), long term effects (persistent effects) and effects on communication among cells (bystander effects), both in vitro and in vivo. In terms of the adaptive response, we have not observed any significant induction of an adaptive response following long term low dose radiation in vivo, delivered at 300X background. In terms of persistent and bystander effects, we have revealed evidence of a bystander effect in vivo and with researchers at and demonstrated for the first time the molecular mechanism by which cells “remember” radiation exposure. Understanding the underlying molecular mechanisms by which radiation can induce genomic instability is fundamental to our ability to assess the biological impact of low dose radiation. Finally, in a parallel set of studies we have explored the effects of heavy iron particle radiation on large scale sequence rearrangements and we have discovered tissue specific differences in sensitivity to homologous recombination. DOE support has given rise to critical new knowledge about the biological impact of low dose rate radiation and about the underlying mechanisms that govern genomic stability in response to radiation exposure. This work has spurred interest in radiation among MIT scientists, and has fostered ongoing research projects that will continue to contribute toward our understanding of the biological effects of low dose radiation exposure.

  9. Human Health Science Building Geothermal Heat Pumps

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

    HUMAN HEALTH SCIENCE BLDG GEO HEAT PUMP SYSTEMS Principal Investigator Source Heat Pumps Demo Projects May 20, 2010 This presentation does not contain any proprietary confidential,...

  10. Project Manager

    Broader source: Energy.gov [DOE]

    A successful candidate in this position will serve as a project manager in the Fuel Cell Technologies Office in the DOE-EERE Office of Transportation responsible for a wide variety of highly...

  11. RENOTER Project

    Broader source: Energy.gov [DOE]

    Overview of French project on thermoelectric waste heat recovery for cars and trucks with focus on cheap, available, efficient, and sustainable TE materials, as well as efficient material integration and production process.

  12. 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

  13. 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

  14. 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

  15. 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.

  16. Functional Area Assessments Project Charter Workstream Name Functional Area Assessments

    E-Print Network [OSTI]

    Sheridan, Jennifer

    with Huron on detailed project plan. Subject Experts Subject Expert Role Functional leadership Administrative1 of 2 Functional Area Assessments ­ Project Charter Workstream Name Functional Area Assessments - Internal Budgeting - Human Resources These diagnostics will be performed using interviews, surveys, data

  17. Hanford Environmental Dose Reconstruction Project

    SciTech Connect (OSTI)

    Finch, S.M.; McMakin, A.H. (comps.)

    1992-06-01T23:59:59.000Z

    The objective of the Hanford Environmental Dose Reconstruction Project is to estimate the radiation doses that individuals and populations could have received from nuclear operations at Hanford since 1944. The project is being managed and conducted by the Battelle Pacific Northwest Laboratories under contract with the Centers for Disease Control. The independent Technical Steering Panel (TSP) provides technical direction. The project is divided into the following technical tasks. These tasks correspond to the path radionuclides followed, from release to impact on humans (dose estimates): source terms; environmental transport; environmental monitoring data; demography, food consumption, and agriculture; environmental pathways and dose estimates.

  18. Kinetics of Facultative Heterochromatin and Polycomb Group Protein Association with the Herpes Simplex Viral Genome during

    E-Print Network [OSTI]

    Knipe, David M.

    Simplex Viral Genome during Establishment of Latent Infection Anna R. Cliffe,a* Donald M. Coen,b and David Center, University of North Carolina, Chapel Hill, North Carolina, USA. ABSTRACT The herpes simplex virus during latent infection of neurons. IMPORTANCE The human pathogen herpes simplex virus (HSV) hides

  19. 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

  20. Construction of an integrated database to support genomic sequence analysis

    SciTech Connect (OSTI)

    Gilbert, W.; Overbeek, R.

    1994-11-01T23:59:59.000Z

    The central goal of this project is to develop an integrated database to support comparative analysis of genomes including DNA sequence data, protein sequence data, gene expression data and metabolism data. In developing the logic-based system GenoBase, a broader integration of available data was achieved due to assistance from collaborators. Current goals are to easily include new forms of data as they become available and to easily navigate through the ensemble of objects described within the database. This report comments on progress made in these areas.

  1. HUMAN RESOURCES SIMON FRASER UNIVERSITY

    E-Print Network [OSTI]

    ) by coordinating budget submissions, estimating and preparing cost projections, liaising with PurchasingHUMAN RESOURCES SIMON FRASER UNIVERSITY ADMINISTRATIVE & PROFESSIONAL JOB DESCRIPTION Position of the position in one or two sentences. Manages the Department's operating, capital, temporary instruction

  2. Independence) PROJECT TITLE: Clinton Community Human Service...

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

    or proposed DOE legislation. Rational for detennination: The Iowa Office of Energy Independence proposes to provide 250,454 of SEP funds to the Area Substance Abuse...

  3. Cloudnet Project

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

    Hogan, Robin

    Cloudnet is a research project supported by the European Commission. This project aims to use data obtained quasi-continuously for the development and implementation of cloud remote sensing synergy algorithms. The use of active instruments (lidar and radar) results in detailed vertical profiles of important cloud parameters which cannot be derived from current satellite sensing techniques. A network of three already existing cloud remote sensing stations (CRS-stations) will be operated for a two year period, activities will be co-ordinated, data formats harmonised and analysis of the data performed to evaluate the representation of clouds in four major european weather forecast models.

  4. Bonus Organisms in High-Throughput Eukaryotic Whole-Genome Shorgun Assembly

    SciTech Connect (OSTI)

    Pangilinan, Jasmyn; Shapiro, Harris; Tu, Hank; Platt, Darren

    2006-02-06T23:59:59.000Z

    The DOE Joint Genome Institute has sequenced over 50 eukaryotic genomes, ranging in size from 15 MB to 1.6 GB, over a wide range of organism types. In the course of doing so, it has become clear that a substantial fraction of these data sets contains bonus organisms, usually prokaryotes, in addition to the desired genome. While some of these additional organisms are extraneous contamination, they are sometimes symbionts, and so can be of biological interest. Therefore, it is desirable to assemble the bonus organisms along with the main genome. This transforms the problem into one of metagenomic assembly, which is considerably more challenging than traditional whole-genome shotgun (WGS) assembly. The different organisms will usually be present at different sequence depths, which is difficult to handle in most WGS assemblers. In addition, with multiple distinct genomes present, chimerism can produce cross-organism combinations. Finally, there is no guarantee that only a single bonus organism will be present. For example, one JGI project contained at least two different prokaryotic contaminants, plus a 145 KB plasmid of unknown origin. We have developed techniques to routinely identify and handle such bonus organisms in a high-throughput sequencing environment. Approaches include screening and partitioning the unassembled data, and iterative subassemblies. These methods are applicable not only to bonus organisms, but also to desired components such as organelles. These procedures have the additional benefit of identifying, and allowing for the removal of, cloning artifacts such as E.coli and spurious vector inclusions.

  5. 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 &...

  6. Structural Genomics and Drug Discovery for Infectious Diseases

    SciTech Connect (OSTI)

    Anderson, W.F.

    2010-09-03T23:59:59.000Z

    The application of structural genomics methods and approaches to proteins from organisms causing infectious diseases is making available the three dimensional structures of many proteins that are potential drug targets and laying the groundwork for structure aided drug discovery efforts. There are a number of structural genomics projects with a focus on pathogens that have been initiated worldwide. The Center for Structural Genomics of Infectious Diseases (CSGID) was recently established to apply state-of-the-art high throughput structural biology technologies to the characterization of proteins from the National Institute for Allergy and Infectious Diseases (NIAID) category A-C pathogens and organisms causing emerging, or re-emerging infectious diseases. The target selection process emphasizes potential biomedical benefits. Selected proteins include known drug targets and their homologs, essential enzymes, virulence factors and vaccine candidates. The Center also provides a structure determination service for the infectious disease scientific community. The ultimate goal is to generate a library of structures that are available to the scientific community and can serve as a starting point for further research and structure aided drug discovery for infectious diseases. To achieve this goal, the CSGID will determine protein crystal structures of 400 proteins and protein-ligand complexes using proven, rapid, highly integrated, and cost-effective methods for such determination, primarily by X-ray crystallography. High throughput crystallographic structure determination is greatly aided by frequent, convenient access to high-performance beamlines at third-generation synchrotron X-ray sources.

  7. Spent Nuclear Fuel project, project management plan

    SciTech Connect (OSTI)

    Fuquay, B.J.

    1995-10-25T23:59:59.000Z

    The Hanford Spent Nuclear Fuel Project has been established to safely store spent nuclear fuel at the Hanford Site. This Project Management Plan sets forth the management basis for the Spent Nuclear Fuel Project. The plan applies to all fabrication and construction projects, operation of the Spent Nuclear Fuel Project facilities, and necessary engineering and management functions within the scope of the project

  8. ERIS Project 

    E-Print Network [OSTI]

    Hunter, Philip

    repositories. If these (generally) smaller institutions wished to continue to have access to these hosted repository spaces after the end of the project, it was proposed that these repository-lite services would be administered by the SDLC (the Scottish Digital...

  9. Stories of Discovery & Innovation: From Human Genome to Materials "Genome"

    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 OurTheBrookhavenMassachusetts RegionsPaulShades of Perfection inSpiro DSquaring the|

  10. 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

  11. Complete genome sequence of Bacteroides salanitronis type strain (BL78T)

    SciTech Connect (OSTI)

    Gronow, Sabine [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Held, Brittany [Los Alamos National Laboratory (LANL); Lucas, Susan [Joint Genome Institute, Walnut Creek, California; Lapidus, Alla L. [Joint Genome Institute, Walnut Creek, California; Glavina Del Rio, Tijana [Joint Genome Institute, Walnut Creek, California; Nolan, Matt [Joint Genome Institute, Walnut Creek, California; Tice, Hope [Joint Genome Institute, Walnut Creek, California; Deshpande, Shweta [Joint Genome Institute, Walnut Creek, California; Cheng, Jan-Fang [Joint Genome Institute, Walnut Creek, California; Pitluck, Sam [Joint Genome Institute, Walnut Creek, California; Liolios, Konstantinos [Joint Genome Institute, Walnut Creek, California; Pagani, Ioanna [Joint Genome Institute, Walnut Creek, California; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Mavromatis, K [U.S. Department of Energy, Joint Genome Institute; Pati, Amrita [U.S. Department of Energy, Joint Genome Institute; Tapia, Roxanne [Los Alamos National Laboratory (LANL); Han, Cliff [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Chen, Amy [Joint Genome Institute, Walnut Creek, California; Palaniappan, Krishna [Joint Genome Institute, Walnut Creek, California; Land, Miriam L [ORNL; Hauser, Loren John [ORNL; Chang, Yun-Juan [ORNL; Jeffries, Cynthia [Oak Ridge National Laboratory (ORNL); Brambilla, Evelyne-Marie [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Rohde, Manfred [HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany; Goker, Markus [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Detter, J. Chris [Joint Genome Institute, Walnut Creek, California; Woyke, Tanja [Joint Genome Institute, Walnut Creek, California; Bristow, James [Joint Genome Institute, Walnut Creek, California; Markowitz, Victor [Joint Genome Institute, Walnut Creek, California; Hugenholtz, Philip [U.S. Department of Energy, Joint Genome Institute; Kyrpides, Nikos C [Joint Genome Institute, Walnut Creek, California; Klenk, Hans-Peter [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Eisen, Jonathan [Joint Genome Institute, Walnut Creek, California

    2011-01-01T23:59:59.000Z

    Bacteroides salanitronis Lan et al. 2006 is a species of the genus Bacteroides, which belongs to the family Bacteroidaceae. The species is of interest because it was isolated from the gut of a chicken and the growing awareness that the anaerobic microflora of the cecum is of benefit for the host and may impact poultry farming. The 4,308,663 bp long genome consists of a 4.24 Mbp chromosome and three plasmids (6 kbp, 19 kbp, 40 kbp) containing 3,737 protein-coding and 101 RNA genes and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  12. Complete genome sequence of the melanogenic marine bacterium Marinomonas mediterranea type strain (MMB-1T)

    SciTech Connect (OSTI)

    Lucas-Elio, Patricia [University of Murcia, Murcia, Spain; Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute; Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Nolan, Matt [U.S. Department of Energy, Joint Genome Institute; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute; Detter, J C [U.S. Department of Energy, Joint Genome Institute; Copeland, A [U.S. Department of Energy, Joint Genome Institute; Teshima, Hazuki [Los Alamos National Laboratory (LANL); Bruce, David [Los Alamos National Laboratory (LANL); Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Tapia, Roxanne [Los Alamos National Laboratory (LANL); Han, Cliff [Los Alamos National Laboratory (LANL); Land, Miriam L [ORNL; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Mikhailova, Natalia [U.S. Department of Energy, Joint Genome Institute; Johnston, Andrew W. B. [University of East Anglia, Norwich, United Kingdom; Sanchez-Amat, Antonio [University of Murcia, Murcia, Spain

    2012-01-01T23:59:59.000Z

    Marinomonas mediterranea MMB-1 T Solano & Sanchez-Amat 1999 belongs to the family Oceanospirillaceae within the phylum Proteobacteria. This species is of interest because it is the only species described in the genus Marinomonas to date that can synthesize melanin pigments, which is mediated by the activity of a tyrosinase. M. mediterranea expresses other oxidases of biotechnological interest, such as a multicopper oxidase with laccase activity and a novel L-lysine-epsilon-oxidase. The 4,684,316 bp long genome harbors 4,228 proteincoding genes and 98 RNA genes and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  13. Update on human genome completion and annotations: Protein information

    E-Print Network [OSTI]

    and Daniel W. Nebert2 * 1 Director of PIR, Department of Biochemistry & Molecular Biology, Georgetown revised form): 11th January 2004 Abstract The Protein Information Resource (PIR) recently joinedProt--the Universal Protein Resource--which now unifies the PIR, Swiss-Prot and TrEMBL databases. The PIRSF (Super

  14. Genetical genomic determinants of alcohol consumption in rats and humans

    E-Print Network [OSTI]

    2009-01-01T23:59:59.000Z

    total of 31,379 (quality controltotal was divided by 30 to obtain the daily average. Quality Control

  15. Stories of Discovery & Innovation: From Human Genome to Materials...

    Office of Science (SC) Website

    of Discovery & Innovation, was supported in part by the Center for Electrical Energy Storage, an EFRC led by Michael Thackeray at Argonne National Laboratory. Last modified: 4...

  16. Human Genome News: Workshop on sequencing by hybridization

    SciTech Connect (OSTI)

    Not Available

    1994-01-01T23:59:59.000Z

    A brief description of the Second International Workshop on Sequencing by Hybridization as held in Woodlands, Texas October 28--30, 1993 is provided in this report. Highlights of sessions entitled Chemistry and Analogs, Engineering and Automation, Hybridization Data and Theory and Informatics are given.

  17. Comparative genomics of the neglected human malaria parasite Plasmodium vivax

    E-Print Network [OSTI]

    Cai, Long

    , Taco W. A. Kooij18 , Michael Korsinczky9,19 , Esmeralda V.-S. Meyer20 , Vish Nene4,5 , Ian Paulsen1

  18. Published 12 March 2014 1 Human Genome Variation

    E-Print Network [OSTI]

    Cai, Long

    dissemination of accepted papers to Nature Publishing Group's wide readership and beyond is achieved through a programme of continuous online publication. Published manuscripts are enhanced by innovative web Word Limit Tables/ Figures References Article Studies that are of high scientific quality

  19. 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.

  20. 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

  1. 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

  2. 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

  3. Project Fact Sheet Project Brief

    E-Print Network [OSTI]

    Name: Centre for Assisted Robotic Surgery Number: BESS1002b Project Champion: Professor Guang-Zong Yang of the refurbishment is to renew and expand the laboratory space for Robotic Assisted Surgery at the South Kensington Campus as par to the Hamlyn Centre for Robotic Surgery. The overall programme incorpo- rates both core

  4. 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

  5. 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

  6. 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

  7. 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

  8. Enabling sample tracking in and reducing variability in DNA library construction

    E-Print Network [OSTI]

    Penake, David A. (David Allen)

    2006-01-01T23:59:59.000Z

    The Broad Institute is a world leader in genomic sequencing. The Institute gained prominence during the Human Genome Project and has continued to be the nation's leading public laboratory for genomic sequencing projects. ...

  9. 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

  10. 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

  11. 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

  12. 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

  13. 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

  14. 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

  15. 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-

  16. 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

  17. 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

  18. 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

  19. Complete genome sequence of Isosphaera pallida type strain (IS1BT)

    SciTech Connect (OSTI)

    Goker, Markus [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Cleland, David M [ORNL; Saunders, Elizabeth H [Los Alamos National Laboratory (LANL); Lapidus, Alla L. [Joint Genome Institute, Walnut Creek, California; Nolan, Matt [Joint Genome Institute, Walnut Creek, California; Lucas, Susan [Joint Genome Institute, Walnut Creek, California; Hammon, Nancy [Joint Genome Institute, Walnut Creek, California; Deshpande, Shweta [Joint Genome Institute, Walnut Creek, California; Cheng, Jan-Fang [Joint Genome Institute, Walnut Creek, California; Tapia, Roxanne [Los Alamos National Laboratory (LANL); Han, Cliff [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Pitluck, Sam [Joint Genome Institute, Walnut Creek, California; Liolios, Konstantinos [Joint Genome Institute, Walnut Creek, California; Pagani, Ioanna [Joint Genome Institute, Walnut Creek, California; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Mavromatis, K [U.S. Department of Energy, Joint Genome Institute; Pati, Amrita [U.S. Department of Energy, Joint Genome Institute; Chen, Amy [Joint Genome Institute, Walnut Creek, California; Palaniappan, Krishna [Joint Genome Institute, Walnut Creek, California; Land, Miriam L [ORNL; Hauser, Loren John [ORNL; Chang, Yun-Juan [ORNL; Jeffries, Cynthia [Oak Ridge National Laboratory (ORNL); Detter, J. Chris [Joint Genome Institute, Walnut Creek, California; Beck, Brian [ATCC - American Type Culture Collection; Woyke, Tanja [Joint Genome Institute, Walnut Creek, California; Bristow, James [Joint Genome Institute, Walnut Creek, California; Eisen, Jonathan [Joint Genome Institute, Walnut Creek, California; Markowitz, Victor [Joint Genome Institute, Walnut Creek, California; Hugenholtz, Philip [U.S. Department of Energy, Joint Genome Institute; Kyrpides, Nikos C [Joint Genome Institute, Walnut Creek, California; Klenk, Hans-Peter [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany

    2011-01-01T23:59:59.000Z

    Isosphaera pallida (ex Woronichin 1927) Giovannoni et al. 1995 is the type species of the genus Isosphaera. The species is of interest because it was the first heterotrophic bacterium known to be phototactic, and it occupies an isolated phylogenetic position within the Planctomycetaceae. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first complete genome sequence of a member of the genus Isosphaera and the third of a member of the family Planctomycetaceae. The 5,472,964 bp long chromosome and the 56,340 bp long plasmid with a total of 3,763 protein-coding and 60 RNA genes are part of the Genomic Encyclopedia of Bacteria and Archaea project.

  20. Complete genome sequence of Desulfarculus baarsii type strain (2st14T)

    SciTech Connect (OSTI)

    Sun, Christine [University of California, Berkeley; Spring, Stefan [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Lapidus, Alla L. [Joint Genome Institute, Walnut Creek, California; Davenport, Karen W. [Los Alamos National Laboratory (LANL); Glavina Del Rio, Tijana [Joint Genome Institute, Walnut Creek, California; Tice, Hope [Joint Genome Institute, Walnut Creek, California; Nolan, Matt [Joint Genome Institute, Walnut Creek, California; Copeland, A [U.S. Department of Energy, Joint Genome Institute; Cheng, Jan-Fang [Joint Genome Institute, Walnut Creek, California; Lucas, Susan [Joint Genome Institute, Walnut Creek, California; Tapia, Roxanne [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Pitluck, Sam [Joint Genome Institute, Walnut Creek, California; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Pagani, Ioanna [Joint Genome Institute, Walnut Creek, California; Mavromatis, K [U.S. Department of Energy, Joint Genome Institute; Ovchinnikova, Galina [U.S. Department of Energy, Joint Genome Institute; Pati, Amrita [U.S. Department of Energy, Joint Genome Institute; Chen, Amy [Joint Genome Institute, Walnut Creek, California; Palaniappan, Krishna [Joint Genome Institute, Walnut Creek, California; Hauser, Loren John [ORNL; Chang, Yun-Juan [ORNL; Jeffries, Cynthia [Oak Ridge National Laboratory (ORNL); Detter, J. Chris [Joint Genome Institute, Walnut Creek, California; Han, Cliff [Los Alamos National Laboratory (LANL); Rohde, Manfred [HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany; Brambilla, Evelyne-Marie [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Goker, Markus [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Woyke, Tanja [Joint Genome Institute, Walnut Creek, California; Bristow, James [Joint Genome Institute, Walnut Creek, California; Eisen, Jonathan [Joint Genome Institute, Walnut Creek, California; Markowitz, Victor [Joint Genome Institute, Walnut Creek, California; Hugenholtz, Philip [U.S. Department of Energy, Joint Genome Institute; Kyrpides, Nikos C [Joint Genome Institute, Walnut Creek, California; Klenk, Hans-Peter [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Land, Miriam L [ORNL

    2010-01-01T23:59:59.000Z

    Desulfarculus baarsii (Widdel 1981) Kuever et al. 2006 is the type and only species of the genus Desulfarculus, which represents the family Desulfarculaceae and the order Desulfarculales. This species is a mesophilic sulfate-reducing bacterium with the capability to oxidize acetate and fatty acids of up to 18 carbon atoms completely to CO2. The acetyl-CoA/CODH (Wood-Ljungdahl) pathway is used by this species for the complete oxidation of carbon sources and autotrophic growth on formate. The type strain 2st14T was isolated from a ditch sediment collected near the University of Konstanz, Germany. This is the first completed genome sequence of a member of the order Desulfarculales. The 3,655,731 bp long single replicon genome with its 3,303 protein-coding and 52 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  1. Complete genome sequence of Marivirga tractuosa type strain (H-43T)

    SciTech Connect (OSTI)

    Pagani, Ioanna [Joint Genome Institute, Walnut Creek, California; Chertkov, Olga [Los Alamos National Laboratory (LANL); Lapidus, Alla L. [Joint Genome Institute, Walnut Creek, California; Lucas, Susan [Joint Genome Institute, Walnut Creek, California; Glavina Del Rio, Tijana [Joint Genome Institute, Walnut Creek, California; Tice, Hope [Joint Genome Institute, Walnut Creek, California; Copeland, A [U.S. Department of Energy, Joint Genome Institute; Cheng, Jan-Fang [Joint Genome Institute, Walnut Creek, California; Nolan, Matt [Joint Genome Institute, Walnut Creek, California; Saunders, Elizabeth H [Los Alamos National Laboratory (LANL); Pitluck, Sam [Joint Genome Institute, Walnut Creek, California; Held, Brittany [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Liolios, Konstantinos [Joint Genome Institute, Walnut Creek, California; Ovchinnikova, Galina [U.S. Department of Energy, Joint Genome Institute; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Mavromatis, K [U.S. Department of Energy, Joint Genome Institute; Pati, Amrita [U.S. Department of Energy, Joint Genome Institute; Chen, Amy [Joint Genome Institute, Walnut Creek, California; Palaniappan, Krishna [Joint Genome Institute, Walnut Creek, California; Land, Miriam L [ORNL; Hauser, Loren John [ORNL; Jeffries, Cynthia [Oak Ridge National Laboratory (ORNL); Detter, J. Chris [Joint Genome Institute, Walnut Creek, California; Han, Cliff [Los Alamos National Laboratory (LANL); Tapia, Roxanne [Los Alamos National Laboratory (LANL); Ngatchou, Olivier Duplex [HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany; Rohde, Manfred [HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany; Goker, Markus [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Spring, Stefan [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Sikorski, Johannes [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Woyke, Tanja [Joint Genome Institute, Walnut Creek, California; Bristow, James [Joint Genome Institute, Walnut Creek, California; Eisen, Jonathan [Joint Genome Institute, Walnut Creek, California; Markowitz, Victor [Joint Genome Institute, Walnut Creek, California; Hugenholtz, Philip [U.S. Department of Energy, Joint Genome Institute; Klenk, Hans-Peter [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Kyrpides, Nikos C [Joint Genome Institute, Walnut Creek, California

    2011-01-01T23:59:59.000Z

    Marivirga tractuosa (Lewin 1969) Nedashkovskaya et al. 2010 is the type species of the genus Marivirga, which belongs to the family Flammeovirgaceae. Members of this genus are of interest because of their gliding motility. The species is of interest because representative strains show resistance to several antibiotics, including gentamicin, kanamycin, neomycin, polymixin and streptomycin. This is the first complete genome sequence of a member of the family Flammeovirgaceae. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 4,511,574 bp long chromosome and the 4,916 bp plasmid with their 3,808 protein-coding and 49 RNA genes are a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  2. 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.

  3. PROJECT SUMMARY

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

    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 742Energy ChinaofSchaeferAprilOverviewEfficiencyofHSSPIAProperty Management PlanPROJECT SUMMARY 1

  4. Hallmark Project

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

    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 742Energy ChinaofSchaefer To: CongestionDevelopmentHEADQUARTERSOutreachApril 23, 2013Project

  5. Project Management

    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)IntegratedSpeedingTechnical News,Program DirectionProject ATHENA creates

  6. Project Overview

    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)IntegratedSpeedingTechnical News,Program DirectionProject ATHENAManagement

  7. Projects | 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. DOE Office of Science (SC)IntegratedSpeedingTechnical News,Program DirectionProject ATHENAManagementIn ThisPages

  8. Project Gnome

    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 Possible forPortsmouth/Paducah47,193.70 Hg MercuryProject Final Report: HPC-Colony IIProject Gnome

  9. Project Title

    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 Possible forPortsmouth/Paducah47,193.70 Hg MercuryProject FinalFluids |Storage Research and

  10. NEPA COMPLIANCE SURVEY Project Information Project Title:

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

    Boxes Date: Nov. 11 , 2010 DOE Code: 6740.010.00000 Contractor Code: 8067-451 Project Lead: Anthony Bowler Project Overview 1. Brief project description include anything that...

  11. 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

  12. 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...

  13. 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...

  14. 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....

  15. 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...

  16. 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).

  17. 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).

  18. 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).

  19. 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...

  20. 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...

  1. 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...

  2. 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...

  3. 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...

  4. 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...

  5. 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...

  6. 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...

  7. 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:...

  8. 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.

  9. 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

  10. 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

  11. 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

  12. 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

  13. 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).

  14. 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.

  15. Digital Apollo: Human and Machine in Spaceflight

    E-Print Network [OSTI]

    Digital Apollo: Human and Machine in Spaceflight David A. Mindell The MIT Press Cambridge of America. Library of Congress Cataloging-in-Publication Data Mindell, David A. Digital Apollo : human-0-262-13497-2 (hardcover : alk. paper) 1. Human-machine systems. 2. Project Apollo (U.S.)--History. 3. Astronautics

  16. 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.

  17. WebMGA: a Customizable Web Server for Fast Metagenomic Sequence Analysis

    E-Print Network [OSTI]

    Wu, Sitao; Zhu, Zhengwei; Fu, Liming; Niu, Beifang; Li, Weizhong

    2011-01-01T23:59:59.000Z

    Massive microbial sequence project proposed. Science 2007,alignment of short DNA sequences to the human genome. Genomeserver for fast metagenomic sequence analysis. BMC Genomics

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

    SciTech Connect (OSTI)

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

    2011-01-31T23:59:59.000Z

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

  19. Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay

    E-Print Network [OSTI]

    Kheradpour, Pouya

    Genome-wide chromatin annotations have permitted the mapping of putative regulatory elements across multiple human cell types. However, their experimental dissection by directed regulatory motif disruption has remained ...

  20. An HMM-based boundary-flexible model of human haplotype variation

    E-Print Network [OSTI]

    Sheffi, Jonathan, 1981-

    2004-01-01T23:59:59.000Z

    The construction of a meaningful and detailed description of haplotype variation holds the promise for more powerful genetic association studies. The segmentation of the human genome into blocks of limited haplotype diversity ...

  1. 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,

  2. Complete genome sequence of Hydrogenobacter thermophilus type strain (TK-6T)

    SciTech Connect (OSTI)

    Zeytun, Ahmet [Los Alamos National Laboratory (LANL); Sikorski, Johannes [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Nolan, Matt [Joint Genome Institute, Walnut Creek, California; Lapidus, Alla L. [Joint Genome Institute, Walnut Creek, California; Lucas, Susan [Joint Genome Institute, Walnut Creek, California; Han, James [Joint Genome Institute; Tice, Hope [Joint Genome Institute, Walnut Creek, California; Cheng, Jan-Fang [Joint Genome Institute, Walnut Creek, California; Tapia, Roxanne [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Pitluck, Sam [Joint Genome Institute, Walnut Creek, California; Liolios, Konstantinos [Joint Genome Institute, Walnut Creek, California; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Mavromatis, K [U.S. Department of Energy, Joint Genome Institute; Mikhailova, Natalia [U.S. Department of Energy, Joint Genome Institute; Ovchinnikova, Galina [U.S. Department of Energy, Joint Genome Institute; Pati, Amrita [U.S. Department of Energy, Joint Genome Institute; Chen, Amy [Joint Genome Institute, Walnut Creek, California; Palaniappan, Krishna [Joint Genome Institute, Walnut Creek, California; Ngatchou, Olivier Duplex [HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany; Land, Miriam L [ORNL; Hauser, Loren John [ORNL; Chang, Yun-Juan [ORNL; Jeffries, Cynthia [Oak Ridge National Laboratory (ORNL); Han, Cliff [Los Alamos National Laboratory (LANL); Detter, J. Chris [Joint Genome Institute, Walnut Creek, California; Ubler, Susanne [Universitat Regensburg, Regensburg, Germany; Rohde, Manfred [HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany; Tindall, Brian [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Wirth, Reinhard [Universitat Regensburg, Regensburg, Germany; Woyke, Tanja [Joint Genome Institute, Walnut Creek, California; Bristow, James [Joint Genome Institute, Walnut Creek, California; Eisen, Jonathan [Joint Genome Institute, Walnut Creek, California; Markowitz, Victor [Joint Genome Institute, Walnut Creek, California; Hugenholtz, Philip [U.S. Department of Energy, Joint Genome Institute; Klenk, Hans-Peter [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Kyrpides, Nikos C [Joint Genome Institute, Walnut Creek, California

    2011-01-01T23:59:59.000Z

    Hydrogenobacter thermophilus Kawasumi et al. 1984 is the type species of the genus Hydrogenobacter. H. thermophilus was the first obligate autotrophic organism reported among aerobic hydrogen-oxidizing bacteria. Strain TK-6T is of interest because of the unusually efficient hydrogen-oxidizing ability of this strain, which results in a faster generation time compared to other autotrophs. It is also able to grow anaerobically using nitrate as an electron acceptor when molecular hydrogen is used as the energy source, and able to aerobically fix CO2 via the reductive tricarboxylic acid cycle. This is the fifth completed genome sequence in the family Aquificaceae, and the second genome sequence determined from a strain derived from the original isolate. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 1,742,932 bp long genome with its 1,899 protein-coding and 49 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  3. Minipig and beagle animal model genomes aid species selection in pharmaceutical discovery and development

    SciTech Connect (OSTI)

    Vamathevan, Jessica J., E-mail: jessica.j.vamathevan@gsk.com [Computational Biology, Quantitative Sciences, GlaxoSmithKline, Stevenage (United Kingdom); Hall, Matthew D.; Hasan, Samiul; Woollard, Peter M. [Computational Biology, Quantitative Sciences, GlaxoSmithKline, Stevenage (United Kingdom); Xu, Meng; Yang, Yulan; Li, Xin; Wang, Xiaoli [BGI-Shenzen, Shenzhen (China); Kenny, Steve [Safety Assessment, PTS, GlaxoSmithKline, Ware (United Kingdom); Brown, James R. [Computational Biology, Quantitative Sciences, GlaxoSmithKline, Collegeville, PA (United States); Huxley-Jones, Julie [UK Platform Technology Sciences (PTS) Operations and Planning, PTS, GlaxoSmithKline, Stevenage (United Kingdom); Lyon, Jon; Haselden, John [Safety Assessment, PTS, GlaxoSmithKline, Ware (United Kingdom); Min, Jiumeng [BGI-Shenzen, Shenzhen (China); Sanseau, Philippe [Computational Biology, Quantitative Sciences, GlaxoSmithKline, Stevenage (United Kingdom)

    2013-07-15T23:59:59.000Z

    Improving drug attrition remains a challenge in pharmaceutical discovery and development. A major cause of early attrition is the demonstration of safety signals which can negate any therapeutic index previously established. Safety attrition needs to be put in context of clinical translation (i.e. human relevance) and is negatively impacted by differences between animal models and human. In order to minimize such an impact, an earlier assessment of pharmacological target homology across animal model species will enhance understanding of the context of animal safety signals and aid species selection during later regulatory toxicology studies. Here we sequenced the genomes of the Sus scrofa Göttingen minipig and the Canis familiaris beagle, two widely used animal species in regulatory safety studies. Comparative analyses of these new genomes with other key model organisms, namely mouse, rat, cynomolgus macaque, rhesus macaque, two related breeds (S. scrofa Duroc and C. familiaris boxer) and human reveal considerable variation in gene content. Key genes in toxicology and metabolism studies, such as the UGT2 family, CYP2D6, and SLCO1A2, displayed unique duplication patterns. Comparisons of 317 known human drug targets revealed surprising variation such as species-specific positive selection, duplication and higher occurrences of pseudogenized targets in beagle (41 genes) relative to minipig (19 genes). These data will facilitate the more effective use of animals in biomedical research. - Highlights: • Genomes of the minipig and beagle dog, two species used in pharmaceutical studies. • First systematic comparative genome analysis of human and six experimental animals. • Key drug toxicology genes display unique duplication patterns across species. • Comparison of 317 drug targets show species-specific evolutionary patterns.

  4. 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.

  5. The Human Dimension in Chinese Defense Science, Technology, and Innovation: An Overview

    E-Print Network [OSTI]

    CHEUNG, Tai Ming

    2015-01-01T23:59:59.000Z

    cutting-edge research to leaders intervening to support the development of favored projects, the human factor

  6. Project Management Lessons Learned

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

    2008-08-05T23:59:59.000Z

    The guide supports DOE O 413.3A, Program and Project Management for the Acquisition of Capital Assets, and aids the federal project directors and integrated project teams in the execution of projects.

  7. [New hosts and vectors for genome cloning]. Progress report, 1990--1991

    SciTech Connect (OSTI)

    Not Available

    1991-12-31T23:59:59.000Z

    The main goal of our project remains the development of new bacterial hosts and vectors for the stable propagation of human DNA clones in E. coli. During the past six months of our current budget period, we have (1) continued to develop new hosts that permit the stable maintenance of unstable features of human DNA, and (2) developed a series of vectors for (a) cloning large DNA inserts, (b) assessing the frequency of human sequences that are lethal to the growth of E. coli, and (c) assessing the stability of human sequences cloned in M13 for large-scale sequencing projects.

  8. Protection of Human Research Subjects

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

    2015-07-20T23:59:59.000Z

    Changes are made to harmonize the definitions in this Order with those in the Federal regulations for the protection of human subjects (10 CFR Part 745), specifically, splitting the definition "human subject research" into "research" and "human subject," and adopting, verbatim, the definitions of "research" and "human subject" from 10 CFR Part 745 and adding the definition of "generalizable," since the determination of whether a project is "research" in 10 CFR Part 745 hinges on whether the work being conducted is generalizable. Small corrections and updates have been made to the references, links, and organization titles.

  9. Spring Creek Project for Ideas, Nature, and the Written Word Call for Nominations: Graduate Student Research and Writing Retreat

    E-Print Network [OSTI]

    Grünwald, Niklaus J.

    Spring Creek Project for Ideas, Nature, and the Written Word Call for Nominations: Graduate Student on a collaborative project or two graduate students who each have individual projects are invited to nominate graduate students in the humanities or environmental sciences

  10. Livingston Solar Canopy Project The Project

    E-Print Network [OSTI]

    Delgado, Mauricio

    ,000 high efficiency solar panels on canopy structures over two major surface parking areasLivingston Solar Canopy Project The Project: This project entails the installation of more than 40. In conjunction with the existing 1.4 megawatt solar energy facility on this campus, this project will generate

  11. Information Visualization Graduate Project (Group Project)

    E-Print Network [OSTI]

    Rusu, Adrian

    Information Visualization Fall 2011 Graduate Project (Group Project) (100 points total) Handed out:59PM Research Article due by online submission on Sunday, December 11, 2011, 11:59PM Project Demo due last week of classes The idea of the project is to take the knowledge and background that you

  12. 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.

  13. 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.

  14. 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.

  15. 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

  16. 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

  17. 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

  18. 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

  19. 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

  20. 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

  1. 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

  2. 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

  3. 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

  4. Highly conserved gene order and numerous novel repetitive elements in genomic regions linked to wing pattern variation in Heliconius butterflies

    E-Print Network [OSTI]

    Papa, Riccardo; Morrison, Clayton M.; Walters, James R.; Counterman, Brian A.; Chen, Rui; Halder, Georg; Ferguson, Laura; Chamberlain, Nicola; ffrench-Constant, Richard; Kapan, Durrell D.; Jiggins, Chris D.; Reed, Robert D.; McMillan, William O.

    2008-07-22T23:59:59.000Z

    and Human Genetics, Baylor College of Medicine, Houston, USA, 8Human Genome Sequencing Center, Baylor College of Medicine, Houston, USA, 9Department of Biochemistry and Molecular Biology, University of Texas – M.D. Anderson Cancer Center, Houston, USA, 10...) and contained many repeats (Table 1). Although all three major classes of transposable elements (DNA transposons, LTR, and non- Fine-scale synteny and sequence conservation between H. erato and H. melpomeneigure 3 Fine-scale synteny and sequence conservation...

  5. Groundwater Resources Assessment under the Pressures of Humanity

    E-Print Network [OSTI]

    1 GRAPHIC GRAPHIC Groundwater Resources Assessment under the Pressures of Humanity and Climate Changes Aframeworkdocument GRAPHICSeriesN°2 .................. #12;2 Groundwater Resources Assessment groundwater management considering projected climate change and linked human effects. GRAPHIC provides

  6. 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

  7. 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

  8. 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.

  9. 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.

  10. METLIN: MS/MS metabolite data from the MAGGIE Project

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

    METLIN is a metabolite database for metabolomics containing over 50,000 structures, it also represents a data management system designed to assist in a broad array of metabolite research and metabolite identification by providing public access to its repository of current and comprehensive MS/MS metabolite data. An annotated list of known metabolites and their mass, chemical formula, and structure are available on the METLIN website. Each metabolite is conveniently linked to outside resources such as the the Kyoto Encyclopedia of Genes and Genomes (KEGG) for further reference and inquiry. MS/MS data is also available on many of the metabolites. The list is expanding continuously as more metabolite information is being deposited and discovered. [from http://metlin.scripps.edu/] Metlin is a component of the MAGGIE Project. MAGGIE is funded by the DOE Genomics: GTL and is an acronym for "Molecular Assemblies, Genes, and Genomics Integrated Efficiently."

  11. 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 ...

  12. 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.

  13. 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.

  14. 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

  15. 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.

  16. 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 ...

  17. 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

  18. 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 ...

  19. 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, ...

  20. Prokaryotic Genomes from Microbes Online Database

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

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

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