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1

Joint Genome Institute (JGI) Projects at NERSC  

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

Joint Genome Institute Joint Genome Institute (JGI) Joint Genome Institute (JGI) nicole-illumina-flowcell.jpg Key Challenges: Ensuring that there is a robust computational infrastructure for managing, storing and gleaning scientific insights from the torrent of data that constantly flows from the advanced sequencing platforms at the Department of Energy Joint Genome Institute (JGI). JGI sequencing capacity exceeds 40 billion DNA base pairs per year and is growing at a rate that exceeds computer hardware improvements, with exponential increases in computation and storage needed. JGI will generate about 1 petabyte of data in their first year as a NERSC partner; this is expected to double each year. Why it Matters: JGI is the primary production sequencing facility for the DOE. By revealing the genetic blueprint and fundamental principles that

2

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.

3

DOE Joint Genome Institute: DOE JGI Announces 2011 Community Sequencing  

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

October 4, 2010 October 4, 2010 Bigger is Better: DOE JGI Announces 2011 Community Sequencing Program Portfolio The U.S. Department of Energy (DOE) Joint Genome Institute (JGI) has selected 35 new genomic sequencing projects for its 2011 Community Sequencing Program (CSP)-a targeted sampling of the planet's biodiversity-to be characterized for bioenergy and environmental applications. A sample of CSP 2011 projects *[see photo credits below] Supported by the Office of Biological and Environmental Research in the DOE Office of Science, the DOE JGI's Community Sequencing Program enables scientists from universities and national laboratories around the world to probe the hidden world of microbes and plants for innovative solutions to the nation's major challenges in energy, climate, and environment. This

4

DOE Joint Genome Institute: DOE JGI Releases Expanded Version of  

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

28, 2009 28, 2009 DOE JGI Releases Expanded Version of Phytozome.net: Clearinghouse for Comparative Plant Genomics Data WALNUT CREEK, CA-An enhanced version of Phytozome.net, a web portal for comparative plant genomics geared to advance biofuel, food, feed, and fiber research, has been released by the U.S. Department of Energy (DOE) Joint Genome Institute (JGI). Phytozome provides a central "hub" for web access to a rapidly growing number of plant genomes, and includes tools for visualization of plant genomes and associated annotations, sequence analysis, and bulk, as well as targeted, plant data retrieval. The gene families available in Phytozome, defined at several evolutionarily significant epochs, provide a framework for the transfer of functional information to important biofuel and

5

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.

6

JGI Visiting Scientist Program The DOE Joint Genome Institute Visiting Scientist Program (VSP)  

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

Visiting Scientist Program Visiting Scientist Program The DOE Joint Genome Institute Visiting Scientist Program (VSP) provides an opportunity for researchers who are seeking to build upon their line of scientific inquiry by leveraging JGI experimental, computational, and personnel resources for genomic research and sequence-based science. Projects include de novo generation of genome data, assistance in interpreting and/or building on an existing data set, or the refining of new technology (e.g., single-cell genomics; metagenomics, etc.). Length of stay depends on complexity of the project being considered and availability of data and other resources. Investigators, post docs, and graduate students participating in approved JGI User Projects are also invited to apply for on-site access to JGI

7

DOE JGI Whole Genome Shotgun Sequencing, part 1  

ScienceCinema (OSTI)

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).

Miranda Harmon-Smith

2010-09-01T23:59:59.000Z

8

JGI Genomics and Bioinformatics for Undergraduate Educators Workshop |  

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

JGI Genomics and Bioinformatics for Undergraduate Educators JGI Genomics and Bioinformatics for Undergraduate Educators Workshop JGI Genomics and Bioinformatics for Undergraduate Educators Workshop March 23, 2013 3:00PM EDT to March 26, 2013 6:00PM EDT University of California The JGI will be holding the JGI Genomics and Bioinformatics for Undergraduate Educators Workshop in conjunction with the JGI User Meeting. The workshop will take place March 23-26, 2013 at the JGI. The DOE Joint Genome Institute's Education Program is providing opportunities for colleges and universities across the country to "interpret" bacterial genomes, such as those sequenced as part of the GEBA project, for analysis. This "Interpret a GEBA Genome" Education Program makes available a selection of recently sequenced genomes

9

JGI - 2009 Genome Sequencing Targets  

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

July 2, 2008 July 2, 2008 Pine Tree, Boat-Boring Bivalve "Bugs", Duck Weed, Oil-Producing Microalgae, Stinkbird Gut, 40 Others Top DOE Joint Genome Institute 2009 Genome Sequencing Targets WALNUT CREEK, CA-In the continuing effort to tap the vast, unexplored reaches of the earth's microbial and plant domains for bioenergy and environmental applications, the DOE Joint Genome Institute (DOE JGI) has announced its latest portfolio of DNA sequencing projects that it will undertake in the coming year. The 44 projects, culled from nearly 150 proposals received through the Community Sequencing Program (CSP), represent over 60 billion nucleotides of data to be generated through this biodiversity sampling campaign-roughly the equivalent of 20 human genomes. "The scientific and technological advances enabled by the information

10

DOE Joint Genome Institute: Beyond Genomics-DOE JGI leads method  

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

September 20, 2010 September 20, 2010 Beyond Genomics-DOE JGI leads method validation effort in Metatranscriptomics Ultra-high throughput DNA sequencing platforms that allow researchers to sequence the genetic code of organisms at lightning speed for just pennies are enabling more focused genomic studies on a massive scale. One example involves the transcriptome, a tiny but complex fraction of the complete genetic sequence that is transcribed into different types of RNA molecules. These molecules provide researchers with information about what genes are turned on and off under various conditions, and what the functions of these genes are. Researchers focus on the messenger RNA (mRNA), which transfer the genetic information from the DNA to functional proteins. The bulk of cellular RNA

11

DOE Joint Genome Institute: DOE JGI Produces New QC Tool for Microbial  

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

May 24, 2010 May 24, 2010 DOE JGI Produces New QC Tool for Microbial Genomes WALNUT CREEK, CA-More than a thousand microbial genomes have been sequenced at various sequencing centers in the past 15 years to better understand their roles in tasks ranging from bioenergy to health to environmental cleanup. Conservative estimates suggest roughly 10,000 microbial genomes will be publicly available within the next two years, but genomic standards have not caught up with the technological advances that have made the sequencing process faster and cheaper. As a result, the torrent of DNA sequences being released has varying levels of quality, which impacts researchers' ability to use this information. To assist in checking the quality of the microbial genomic DNA sequences generated before they are submitted to the federally funded public archive

12

JGI CSP Delivers First Moss Genome  

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

13, 2007 13, 2007 DOE JGI Community Sequencing Program Delivers First Moss Genome WALNUT CREEK, CA--Messages from nearly a half-billion years ago, conveyed via the inventory of genes sequenced from a present-day moss, provide clues about the earliest colonization of dry land by plants. The U.S. Department of Energy Joint Genome Institute (DOE JGI) was among the leaders of an international effort uniting more than 40 institutions to complete the first genome sequencing project of a nonvascular land plant, the moss Physcomitrella patens. The team's insights into the code that enabled this seminal emergence and dominance of land by plants are published December 13 online in Science Express. Scanning electron micrograph of Physcomitrella patens gametophores (moss shoots).

13

JGI - Structural Genomics Program  

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

Structural Genomics Program Structural Genomics Program The structural characterization of proteins of unknown function can be described as structural genomics, an approach in which structure determination by X-ray crystallography supplies key functional information. This is exemplified by studies of the carboxysome. The structures of the first carboxysome shell proteins (Kerfeld et al., Science 2005) confirmed earlier hypotheses that they are indeed the basic building blocks of the carboxysome shell; the quaternary structure and the higher order assemblies of the proteins in the crystals provided insight into how they assemble into shell facets. Likewise, our structure of the carboxysome component CsoS3 revealed that it was a member of the beta-carbonic family, despite having no detectable sequence homology at the level of primary structure

14

NERSC and JGI Join Forces to Tackle Genomics HPC - NERSC Center News, Apr  

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

NERSC and JGI Join NERSC and JGI Join Forces to Tackle Genomics HPC NERSC and JGI Join Forces to Tackle Genomics HPC April 19, 2010 A torrent of data has been flowing from the advanced sequencing platforms at the Department of Energy Joint Genome Institute (JGI), among the world's leading generators of DNA sequence information for bioenergy and environmental applications. Last year, JGI generated over one trillion nucleotide letters of genetic code for its various user programs, an eight-fold increase in productivity from 2008. This year JGI expects to sequence five-times more data than the previous year, producing more than a petabyte of data. Kathy Yelick and Eddy Rubin in front of Cray XT5 supercomputer NERSC Division Director Kathy Yelick (left) and JGI Director Eddy Rubin

15

A Collection of Algal Genomes from the JGI  

SciTech Connect (OSTI)

Algae, defined as photosynthetic eukaryotes other than plants, constitute a major component of fundamental eukaryotic diversity. Acquisition of the ability to conduct oxygenic photosynthesis through endosymbiotic events has been a principal driver of eukaryotic evolution, and today algae continue to underpin aquatic food chains as primary producers. Algae play profound roles in the carbon cycle, can impose health and economic costs through toxic blooms, and are candidate sources for bio-fuels; all of these research areas are part of the mission of DOE?s Joint Genome Institute (JGI). A collection of algal projects ongoing at JGI contributes to each of these areas and illustrates analyses employed in their genome exploration.

Kuo, Alan; Grigoriev, Igor

2012-03-19T23:59:59.000Z

16

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

ScienceCinema (OSTI)

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

Rubin, Eddy

2011-06-03T23:59:59.000Z

17

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

ScienceCinema (OSTI)

The U.S. Department of Energy Joint Genome Institute (JGI) invited scientists interested in the application of genomics to bioenergy and environmental issues, as well as all current and prospective users and collaborators, to attend the annual DOE JGI Genomics of Energy & Environment Meeting held March 22-24, 2011 in Walnut Creek, Calif. The emphasis of this meeting was on the genomics of renewable energy strategies, carbon cycling, environmental gene discovery, and engineering of fuel-producing organisms. The meeting features presentations by leading scientists advancing these topics. Scott Hodges of the University of California, Santa Barbara gives a presentation on "Genomic Speciation and Adaptation in Aquilegia" at the 6th annual Genomics of Energy & Environment Meeting on March 23, 2011

Hodges, Scott [University of California, Santa Barbara

2011-06-03T23:59:59.000Z

18

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

ScienceCinema (OSTI)

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

Mavrommatis, Kostas

2011-06-08T23:59:59.000Z

19

JGI - Intro to Genomics 1  

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

An Introduction to Genomics: The Human Genome and Beyond An Introduction to Genomics: The Human Genome and Beyond 1 | 2 | 3 | 4 | Next>> What is genomics? THE HUMAN BODY consists of trillions of cells. Almost all contain an entire genome--the complete set of inherited genetic information encoded in our DNA. When humans reproduce, the parents' sperm and egg DNA combine to contribute a genome's worth of genetic information to the fertilized embryo. That same information is in each of the cells that eventually make up an organism. cell, DNA helix, and protein structure Some segments of DNA, called genes or "coding" DNA, contain the chemical recipe that determines particular traits; genetics is the study of the inheritance and function of these genes. Scientists now estimate that humans have about 30,000 genes, located along threadlike, tightly coiled

20

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

ScienceCinema (OSTI)

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

Chapman, Jarrod

2011-06-03T23:59:59.000Z

Note: This page contains sample records for the topic "genome institute jgi" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


21

Joint Genome Institute's Automation Approach and History  

SciTech Connect (OSTI)

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.

Roberts, Simon

2006-07-05T23:59:59.000Z

22

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

SciTech Connect (OSTI)

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

Tringe, Susannah [DOE JGI] [DOE JGI

2011-10-12T23:59:59.000Z

23

JGI in the News  

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

JGI in the News JGI in the News For the latest JGI News, see: http://jginews.blogspot.com/ August 20, 2008 Gut Reactions. The termite's stomach, of all things, has become the focus of large-scale scientific investigations. Could the same properties that make the termite such a costly pest help us solve global warming? (TheAtlantic.com) August 1, 2008 Termite Bellies and Biofuels. Scientist Falk Warnecke's research into termite digestion may hold solutions to our energy crisis. (Smithsonian.com) July 8, 2008 JGI's 2009 Community Sequencing Program Marks Shift from Sanger to New Platforms. For next year's CSP, which accounts for about half of JGI's sequencing activities, the institute has selected 44 projects, including genomes of eukaryotes, bacteria, and archaea, as well as metagenomic

24

JGI - FY2002 Sequencing for the DOE Microbial Genome Program  

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

2 Sequencing for the 2 Sequencing for the DOE Microbial Genome Program For status information, see the Genome Projects section. For more information about the DOE Office of Science's Microbial Genome Program, see http://microbialgenomics.energy.gov/. For more information about microbial sequencing at JGI, contact David Bruce. Eukaryotes Organism Genome Size Thalassiosira pseudonana CCMP 1335 (diatom) 32 Mb Lactic Acid Bacteria Organism Genome Size Bifidobacterium longum DJO10A 2.4 Mb Brevibacterium linens BL2 4.5 Mb Lactobacillus brevis ATCC 367 1.8 Mb Lactobacillus casei ATCC 334 2.8 Mb Lactobacillus delbrueckii ATCC BAA-365 1.6 Mb Lactobacillus gasseri ATCC 33323 1.9 Mb Lactococcus lactis subsp. cremoris SK11 2.6 Mb Leuconostoc mesenteroides ATCC 8293 2 Mb Oenococcus oeni PSU-1 1.8 Mb

25

JGI - A Genomic Encyclopedia of Bacteria and Archaea  

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

A Genomic Encyclopedia A Genomic Encyclopedia of Bacteria and Archaea (GEBA) The GEBA project is aimed at systematically filling in the gaps in sequencing along the bacterial and archaeal branches of the tree of life. Though the wide variety of microbial sequencing projects undertaken throughout the world has created a rich, diverse collection of microbial genomes, strong biases in what has been sequenced thus far are evident. This project represents the first systematic attempt to use the tree of life itself as a guide to sequencing target selection. JGI is beginning by collaborating on a pilot project with DSMZ. Why GEBA? The GEBA Pilot Project GEBA Sequencing Plans Interpret a Genome for Education Home > User Programs > A Genomic Encyclopedia of Bacteria and Archaea (GEBA)

26

JGI - FY2003 Sequencing for the DOE Microbial Genome Program  

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

3 Sequencing for the 3 Sequencing for the DOE Microbial Genome Program For status information, see the Genome Projects section. For more information about the DOE Office of Science's Microbial Genome Program, see http://microbialgenomics.energy.gov/. For more information about microbial sequencing at JGI, contact David Bruce. Eukaryotes Organism Genome Size Emiliania huxleyi 220 Mb Ostreococcus lucimarinus 9.3 Mb Monosiga brevicollis Bacteria Organism Genome Size Anabaena variabilis ATCC 29413 7 Mb Burkholderia sp. 383 8.80 Mb Burkholderia vietnamiensis G4 8.40 Mb Chlorobium aggregatum Chlorobium chlorochromatii CaD3 2.6 Mb Chlorochromatium aggregatum Lake Dagow Crocosphaera watsonii WH 8501 6.40 Mb Kineococcus radiotolerans SRS30216 4.90 Mb Methylibium petroleiphilum PM1 4.60 Mb

27

JGI - FY2005 Sequencing for the DOE Microbial Genome Program  

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

5 Sequencing for the 5 Sequencing for the DOE Microbial Genome Program For status information, see the Genome Projects section. For more information about the DOE Office of Science's Microbial Genome Program, see http://microbialgenomics.energy.gov/. For more information about microbial sequencing at JGI, contact David Bruce. Strains of Shewanella Organism Est. Genome Size Shewanella baltica OS195 5 Mb Shewanella sp. ANA-3 5 Mb Shewanella sp. MR-4 5 Mb Shewanella sp. MR-7 5 Mb Shewanella sp. W3-18-1 5 Mb Shewanella baltica OS223 5 Mb Strains of Chloroflexi Organism Est. Genome Size Chloroflexus aggregans DSM 9485 5 Mb Chloroflexus sp. Y-396-1 5 Mb Chlorothrix halophila (Candidatus) 5 Mb Herpetosiphon aurantiacus DSM 785 5 Mb Roseiflexus castenholzii HLO8 5 Mb Roseiflexus sp. strain RS-1 5 Mb

28

JGI - FY2004 Sequencing for the DOE Microbial Genome Program  

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

4 Sequencing for the 4 Sequencing for the DOE Microbial Genome Program For status information, see the Genome Projects section. For more information about the DOE Office of Science's Microbial Genome Program, see http://microbialgenomics.energy.gov/. For more information about microbial sequencing at JGI, contact David Bruce. Chlorobia (avg:~2.4Mb) Organism Genome Size Chlorobium ferrooxidans DSM 13031 2.40 Mb Chlorobium limicola DSMZ 245 2.4 Mb Chlorobium phaeobacteroides BS1 2.4 Mb Chlorobium phaeobacteroides DSM 266 2.3 Mb Pelodictyon luteolum DSMZ 273 2.3 Mb Pelodictyon phaeoclathratiforme BU-1 (DSM 5477) 2.4 Mb Prosthecochloris aestuarii DSM 271 2.4 Mb Prosthecochloris vibrioformis DSM 265 2.4 Mb Chlorobaculum parvum n/a Chloroherpeton thalassium n/a Model Syntrophic Consortium

29

JGI - FY2001 Sequencing for the DOE Microbial Genome Program  

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

1 Sequencing for the 1 Sequencing for the DOE Microbial Genome Program For status information, see the Genome Projects section. For more information about the DOE Office of Science's Microbial Genome Program, see http://microbialgenomics.energy.gov/. For more information about microbial sequencing at JGI, contact David Bruce. Organism Genome Size Burkholderia xenovorans LB400 8 Mb Chloroflexus aurantiacus J-10-fl 3 Mb Cupriavidus metallidurans CH34 6.8 Mb Cytophaga hutchinsonii ATCC 33406 4.4 Mb Desulfitobacterium halfniense DCB-2 4.7 Mb Enterococcus faecium DO 2.8 Mb Ferroplasma acidarmanus fer1 1.8 Mb Magnetococcus sp. MC-1 4.7 Mb Methanosarcina barkerii fusaro 4.8 Mb Nitrosomonas europaea ATCC 19718 2.8 Mb Nostoc punctiforme PCC 73102 9.2 Mb Novosphingobium aromaticivorans DSM 12444 4.2 Mb

30

JGI - FY2007 Sequencing for the DOE Microbial Genome Program  

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

7 Sequencing for the 7 Sequencing for the DOE Microbial Genome Program For status information, see the Genome Projects section. For more information about the DOE Office of Science's Microbial Genome Program, see http://microbialgenomics.energy.gov/. For more information about microbial sequencing at JGI, contact David Bruce. Organism(s) Est. Genome Size Acremonium alcalophilum ATCC90507 40 MB Azolla Cyanobacterium, Arthrospira maxima, and Cyanobacterium JSC-1 NA bacterioplankton pool cDNA day, night, night + DOC1, night + DOC2 NA Clostridum carboxidivorans, Clostridium sp. strains, Clostridium straminisolvens, Clostridum thermocellum LQR1 DSM2360 , Clostridium thermocellum JW20 DSM 4150 Thermoanaerobacter italicus Ab9 DSM9252, T. ethanolicus X513, T. ethanoloicus X561, T. mathrani, Thermoanaerobacterium thermosaccharaolyticum, Thermoanaerobacterium xylanolyticum LX11 DSM7097 3.5-4.0 MB

31

JGI User Meeting 2007  

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

Second Annual Second Annual DOE Joint Genome Institute User Meeting Marriott Hotel Walnut Creek, California March 28-30, 2007 The U.S. Department of Energy Joint Genome Institute (JGI) welcomed its users and collaborators, as well as prospective new users, to the second annual JGI User Meeting. This international gathering of researchers with an interest in sequence-based science offered three days of user presentations, tours, workshops, and poster sessions. This was a unique opportunity to meet fellow users and JGI staff. Sessions and posters in the fields of microbial genomics, microbial communities, eukaryotic genomics, and genome technologies were presented. ©2006-2007, The Regents of the University of California. Last updated May 9, 2007. Disclaimer | Webmaster Agenda

32

FORGING THE FUTURE OF THE DOE JGI  

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

FORGING FORGING THE FUTURE OF THE DOE JGI A 10-Year Strategic Vision U.S. Department of Energy Joint Genome Institute (JGI) September, 2012 OUR VISION The user facility pioneering functional genomics to solve the most relevant bioenergy and environmental problems A 10-Year Strategic Vision FORGING THE FUTURE OF THE DOE JGI U.S. Department of Energy Joint Genome Institute (JGI) September 2012 This document contains three sections: I. Introduction II. Background-Science Drivers III. Capabilities The Introduction provides a high level overview of the DOE Joint Genome Institute (DOE JGI) and how it plans to evolve as a genomic user facility to meet the scientific needs of energy and environmental research over the next decade. The Background-Science Driver section provides an assessment of the major scientific

33

U.S. Department of Energy Joint Genome Institute Progress Report  

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

U.S. Department of Energy Joint Genome Institute Progress Report Sequencing the world of possibilities for energy and the environment Table of Contents DOE JGI Mission ........................................................ 7 Director's Perspective.................................................... 8 DOE Mission Areas ................................................... 12 By the Numbers.......................................................... 14 User Map ............................................................ 15 Scientific Literature/Impact ................................ 16 DOE JGI Sequence Output .............................. 17 DOE JGI Team Science Realized ....................... 18 DOE JGI User Community ............................... 19 User Meeting 5 ...........................................................

34

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

ScienceCinema (OSTI)

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

Rubin, Eddy

2011-04-25T23:59:59.000Z

35

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

ScienceCinema (OSTI)

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

Aluru, Srinivas [Iowa State University

2011-06-08T23:59:59.000Z

36

JGI - DOE Mission Relevance  

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

User Programs User Programs Project Management Office Community Science Program Emerging Technologies Opportunity Program Technology Development Pilot Program Genomic Encyc. of Bacteria and Archaea MyJGI: Information for Collaborators DOE Mission Relevance CSP | Overview | How to Propose a Project | Review Process | DOE Relevance Proposal Schedule | FAQ The Department of Energy Joint Genome Institute (DOE JGI) is managed by the Department of Energy's Office of Biological and Environmental Research (OBER) to produce high-throughput DNA sequencing and analysis in support of its missions in alternative energy, global carbon cycling, and biogeochemistry. These areas mirror DOE and national priorities to develop abundant sources of clean energy, to control greenhouse gas accumulation in

37

A Taste of Algal Genomes from the Joint Genome Institute  

SciTech Connect (OSTI)

Algae play profound roles in aquatic food chains and the carbon cycle, can impose health and economic costs through toxic blooms, provide models for the study of symbiosis, 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.

Kuo, Alan; Grigoriev, Igor

2012-06-17T23:59:59.000Z

38

JGI - Scientific Posters  

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

News and Publications News and Publications News Releases Science Highlights JGI in the News Notable Scientific Publications Scientific Posters The Primer Templates and Logos Scientific Posters Note: neither these posters nor their contents may be reproduced except by permission of JGI. Illumina Production Sequencing at the DOE Joint Genome Institute - Workflow and Optimizations (Bay Area Illumina User Meeting 2011) Angela Tarver, Alison Fern, Matthew San Diego, Megan Kennedy, Matthew Zane, Christopher Daum, Christopher Hack, Eric Tang, Shweta Deshpande, Jan-Fang Cheng, Simon Roberts, Melanie Alexandre, Miranda Harmon-Smith, Susan Lucas Phylogeny and comparative genome analysis of a Basidiomycete fungi (DOE JGI User Meeting 2011) Robert W. Riley, Asaf Salamov, Igor Grigoriev, David

39

14128_JGI_CR_07:2007 JGI Progress Report  

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

JOINT JOINT GENOME INSTITUTE PROGRESS REPORT 2007 U.S. DEPARTMENT OF ENERGY On the cover: The eucalyptus tree was selected in 2007 for se- quencing by the JGI. The microbial community in the termite hindgut of Nasutitermes corniger was the subject of a study published in the November 22, 2007 edition of the journal, Nature. JGI Mission The U.S. Department of Energy Joint Genome Institute, supported by the DOE Office of Science, unites the expertise of five national laboratories-Lawrence Berkeley, Lawrence Livermore, Los Alamos, Oak Ridge, and Pacific Northwest - along with the Stanford Human Genome Center to advance genomics in support of the DOE mis- sions related to clean energy generation and environmental char- acterization and cleanup. JGI's Walnut Creek, CA, Production

40

DOE Joint Genome Institute 2008 Progress Report  

E-Print Network [OSTI]

Stanford Human Genome Center (SHGC) began collaborating withscientific goals, and the JGI SHGC kept pace, focusing on

Gilbert, David

2009-01-01T23:59:59.000Z

Note: This page contains sample records for the topic "genome institute jgi" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


41

DOE Joint Genome Institute Completes Soybean Genome- Data Released to  

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

Press Release: December 8, 2008 Press Release: December 8, 2008 DOE Joint Genome Institute Completes Soybean Genome- Data Released to Advance Biofuel, Food, & Feed Research WALNUT CREEK, CA- The U.S. Department of Energy Joint Genome Institute (DOE JGI) has released a complete draft assembly of the soybean (Glycine max) genetic code, making it widely available to the research community to advance new breeding strategies for one of the world's most valuable plant commodities. Soybean not only accounts for 70 percent of the world's edible protein, but also is an emerging feedstock for biodiesel production. Soybean is second only to corn as an agricultural commodity and is the leading U.S. agricultural export. DOE JGI's interest in sequencing the soybean centers on its use for biodiesel, a renewable, alternative fuel with the highest energy content of

42

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

ScienceCinema (OSTI)

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

Muchero, Wellington [Oak Ridge National Laboratory

2013-01-22T23:59:59.000Z

43

DOE Joint Genome Institute: New Genomic Model Defines Microbes by  

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

September 8, 2009 September 8, 2009 New Genomic Model Defines Microbes by Diet-Provides Tool for Tracking Environmental Change WALNUT CREEK, CA-In line with the U.S. Department of Energy (DOE) interest in characterizing the biotic factors involved in global carbon cycling, the DOE Joint Genome Institute (JGI) characterizes a diverse array of plants, microorganisms, and the communities in which they reside to inform options for reducing and stabilizing atmospheric greenhouse gases. Through a novel genomic approach detailed in the September 7 online edition and on the cover September 14 of the journal Proceedings of the National Academy of Sciences, an international team of scientists led by the University of New South Wales and the DOE JGI demonstrates how the microbial diversity of the oceans can be analyzed without necessarily

44

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

SciTech Connect (OSTI)

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.

Swaminathan, Kankshita [Energy Biosciences Institute

2014-03-20T23:59:59.000Z

45

OSCARS helps build new circuit for JGI-NERS  

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

Studies » OSCARS JGI Studies » OSCARS JGI About ESnet Overview ESnet Staff Governance Our Network Case Studies OSCARS Case Studies OSCARS JGI Science DMZ Case Studies Multi-facility Workflow LCLS ESnet Strategic Plan ESnet Organizational Chart ESnet History Science Requirements Careers Contact Us Technical Assistance: 1 800-33-ESnet (Inside the US) 1 800-333-7638 (Inside the US) 1 510-486-7600 (Globally) 1 510-486-7607 (Globally) Report Network Problems: trouble@es.net Provide Web Site Feedback: info@es.net OSCARS Extends JGI Network Capacity In February 2010, the Joint Genome Institute (JGI) at Lawrence Berkeley National Laboratory (Berkeley Lab) had an immediate need for increased computing resources. Meanwhile, twenty miles away the Magellan Cloud computing cluster located at National Energy Research Scientific Computing

46

JGI - Organization Structure  

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

Organization Structure Organization Structure clickable organizational chart Dan Rokhsar Genomic Technologies Department Nikos Kyrpides Jeremy Schmutz Plant Program Metagenome Program Igor Grigoriev Fungal Program LBNL Director P. Alivisatos Scientific Advisory Committee JGI Director, Eddy Rubin Deputy Director of Science Programs, Jim Bristow S. Canon NERSC JGI Support Team Ray Turner Operations Department Prokaryote Super Program Genomic Technologies Department Len Pennacchio Microbial Program Tanja Woyke Dan Rokhsar Eukaryote Super Program Susannah Tringe Chia-lin Wei Executive Management DOE JGI Director: Eddy Rubin Deputy of Science: Jim Bristow Deputy of Operations: Ray Turner Deputy of Genomic Technologies: Len Pennacchio Departments Operations Deputy of Operations Ray Turner

47

cr_14229_JGI_Primer_Fall07 :Layout 1  

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

JGI Community Sequencing JGI Community Sequencing Program (CSP) is contributing to an ambi- tious international effort to decode the genome of Eucalyptus, one of the world's most valuable fiber and paper-producing trees-with the goal to maximize its poten- tial in the burgeoning bioenergy market and for capturing excess atmospheric carbon. The scientific effort to characterize the Eucalyptus genome, uniting some two dozen institutions worldwide, is led by Alexander Myburg of the University of Pretoria (South Africa), with co-leads Dario Grattapaglia, of EMBRAPA and Catholic University of Brasília (Brazil), and Jerry Tuskan of Oak Ridge National Laboratory-JGI's Laboratory Science Program lead. The 600-million-nucleotide tree genome was selected as one of JGI's CSP FY2008 major allocations.

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

ScienceCinema (OSTI)

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

Sayre, Richard [LANL

2013-01-22T23:59:59.000Z

49

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

SciTech Connect (OSTI)

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

Chain, Patrick [DOE JGI at LANL] [DOE JGI at LANL

2011-10-13T23:59:59.000Z

50

10897_JGI_Progress_CR  

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

Progress Report 2002-2005 Progress Report 2002-2005 U.S. DEPARTMENT OF ENERGY JOINT GENOME INSTITUTE JGI's Mission To develop and exploit new sequencing and other high-throughput, genome-scale, and computational technologies as a means for discovering and charac- terizing the basic principles and relationships underly- ing the organization, function, and evolution of living systems. What is Sequencing? Just as computer software is rendered in long strings of 0s and 1s, the "software" of life is represented by a string of four chemicals, abbreviated as A, T, C, and G. To understand the software of either a computer or a living organism, we must know the order, or sequence, of these informative bits. JGI PROGRESS REPORT 2002-2005 * TABLE OF CONTENTS table of contents Director's Perspective

51

DOE JGI CSP 2012 PI Workshop  

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

Organizers Organizers Workshop Organizers Nikos Kyrpides Prokaryotic Superprogram Lead, DOE JGI Susannah Tringe Metagenomics Program Lead, DOE JGI Tanja Woyke Microbial Genomics Program Lead, DOE JGI Igor Grigoriev Fungal Genomics Program Lead, DOE JGI Participants Heike Bucking, South Dakota State University Jeff Dangl, University of North Carolina Chapel Hill Kristen DeAngelis, University of Massachusetts University of Massachusetts, University of British Columbia Jorge Rodrigues, University of Texas Louis Tisa, University of New Hampshire Christopher Schadt, ORNL Jerry Tuskan, ORNL Eoin Brodie, LBNL Brendan Bohannan, University of Oregon Angela Kent, University of Illinois Urbana-Champaign James Tiedje, Michigan State University Nikos Kyrpides, DOE JGI Susannah Tringe, DOE JGI

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DOE Joint Genome Institute: Biofuel-Producing Bacteria, Insect Gut  

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

June 29, 2009 June 29, 2009 Biofuel-Producing Bacteria, Insect Gut Microbes, ~ 70 other Projects Fill DOE Joint Genome Institute 2010 Pipeline WALNUT CREEK, CA-The U.S. Department of Energy (DOE) Joint Genome Institute (JGI) has selected 71 new genomic sequencing projects for its 2010 Community Sequencing Program (CSP)-a targeted sampling of the planet's biodiversity-to be characterized for bioenergy, climate, and environmental applications. JGI's Community Sequencing Program is the largest genomic sequencing effort in the world focused on nonmedical organisms, enabling scientists from universities and national laboratories to probe the hidden world of microbes and plants to tap nature's ingenuity for innovative solutions to the nation's major challenges in energy, climate, and environment. The

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DOE Joint Genome Institute: DNA of Uncultured Organisms Sequenced Using  

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

21, 2009 21, 2009 DNA of Uncultured Organisms Sequenced Using Novel Single-Cell Approach Download a Podcast of this Release! WALNUT CREEK, CA-Scientists from the U.S. Department of Energy (DOE) Joint Genome Institute (JGI) and the Bigelow Laboratory for Ocean Sciences have assembled high quality, contamination-free draft genomes of uncultured biodegrading microorganisms using a novel single cell genome sequencing approach. This proof of principle study, published in the April 23 edition of the journal PLoS One, offers researchers a new method to access and decipher the information embedded in genomes of interest with only minute quantities of DNA. "Most of the microbial genomes sequenced to date are derived from organisms cultured in the laboratory," said DOE JGI Director Eddy Rubin.

54

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

ScienceCinema (OSTI)

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

Stevens, Rick [ANL

2011-06-08T23:59:59.000Z

55

JGI - Cheryl Kerfeld  

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

Cheryl Kerfeld Cheryl Kerfeld Kerfeld Cheryl A. Kerfeld is head of the Education Program at the DOE Joint Genome Institute. Prior to joining the JGI, she developed and directed the Undergraduate Genomics Research Initiative (doi:10.1371/journal.pbio.0050141). Cheryl is also a structural biologist; her current research involves the structural and functional characterization of bacterial microcompartments and of proteins involved in photoprotection in photosynthetic organisms. Cheryl has degrees in Biology (B.A. and Ph.D.) and English (B.A. and M.A.) and has longstanding interests in bioinformatics and research-based and interdisciplinary education. Kerfeld is also an Adjunct Professor of Plant and Microbial Biology at the University of California, Berkeley. Publications

56

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

SciTech Connect (OSTI)

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

Kyrpides, Nikos [DOE JGI] [DOE JGI

2011-10-12T23:59:59.000Z

57

DOE Joint Genome Institute: Unraveling the Threads: Simplest cotton genome  

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

December 19, 2012 December 19, 2012 Unraveling the Threads: Simplest cotton genome offers clues for fiber improvements From the stockings decorating mantles to the new outfits in display windows calling to shoppers, cotton is woven into the fabric of the holiday season. For bioenergy researchers, however, fiber composition matters more than color and texture as each cotton strand is composed of more than two dozen coils of cellulose, a target biomass for next-generation biofuels. In the December 20, 2012 edition of Nature, an international consortium of researchers from 31 institutions including a team from the U.S. Department of Energy Joint Genome Institute (DOE JGI) present a high-quality draft assembly of the simplest cotton (Gossypium raimondii) genome. Additionally,

58

DOE Joint Genome Institute: Soybean Genome Analysis Reveals Pathways for  

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

January 13, 2010 January 13, 2010 Soybean Genome Analysis Reveals Pathways for Improving Biodiesel, Disease Resistance, and Reducing Waste Runoff WALNUT CREEK, CA-Soybean, one of the most important global sources of protein and oil, is now the first legume species with a published complete draft genome sequence. The sequence and its analysis appear in the January 14 edition of the journal Nature. The research team comprised 18 institutions, including the U.S. Department of Energy Joint Genome Institute (DOE JGI), the U.S. Department of Agriculture-Agricultural Research Service (USDA-ARS), Purdue University and the University of North Carolina at Charlotte. The DOE, National Science Foundation, USDA and United Soybean Board supported the research. helix made of soybeans

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

SciTech Connect (OSTI)

The U.S. Department of Energy (DOE) Joint Genome Institute?s (JGI) Production Sequencing group is committed to the generation of high-quality genomic DNA sequence to support the DOE mission areas of renewable energy generation, global carbon management, and environmental characterization and clean-up. Within the JGI?s Production Sequencing group, the Illumina Genome Analyzer pipeline has been established as one of three sequencing platforms, along with Roche/454 and ABI/Sanger. Optimization of the Illumina pipeline has been ongoing with the aim of continual process improvement of the laboratory workflow. These process improvement projects are being led by the JGI?s Process Optimization, Sequencing Technologies, Instrumentation& Engineering, and the New Technology Production groups. Primary focus has been on improving the procedural ergonomics and the technicians? operating environment, reducing manually intensive technician operations with different tools, reducing associated production costs, and improving the overall process and generated sequence quality. The U.S. DOE JGI was established in 1997 in Walnut Creek, CA, to unite the expertise and resources of five national laboratories? Lawrence Berkeley, Lawrence Livermore, Los Alamos, Oak Ridge, and Pacific Northwest ? along with HudsonAlpha Institute for Biotechnology. JGI is operated by the University of California for the U.S. DOE.

Tarver, Angela; Fern, Alison; Diego, Matthew San; Kennedy, Megan; Zane, Matthew; Daum, Christopher; Hack, Christopher; Tang, Eric; Deshpande, Shweta; Cheng, Jan-Fang; Roberts, Simon; Alexandre, Melanie; Harmon-Smith, Miranda; Lucas, Susan

2010-06-18T23:59:59.000Z

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DOE Joint Genome Institute: Genome of Simplest Animal Reveals Ancient  

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

21, 2008 21, 2008 Genome of Simplest Animal Reveals Ancient Lineage, Confounding Array of Complex Capabilities WALNUT CREEK, CA-As Aesop said, appearances are deceiving-even in life's tiniest critters. From first detection in the 1880s, clinging to the sides of an aquarium, to its recent characterization by the U.S. Department of Energy Joint Genome Institute (DOE JGI), a simple and primitive animal, Trichoplax adhaerens, appears to harbor a far more complex suite of capabilities than meets the eye. The findings, reported in the August 21 online edition of the journal Nature, establish a group of organisms as a branching point of animal evolution and identify sets of genes, or a "parts list," employed by organisms that have evolved along particular branches.

Note: This page contains sample records for the topic "genome institute jgi" from the National Library of EnergyBeta (NLEBeta).
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61

JGI - Product Offerings  

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

Product Offerings Product Offerings Scientific Program Product Brief Description Deliverables FY14 target cycle time (median), days FY14 target cycle time (75th %), days Fungal Minimal Draft Low coverage whole genome shotgun sequencing for evaluation. May turn into a standard draft or improved standard draft. Assembly. Annotation optional (JGI portal); raw data submitted to SRA 250 400 Fungal Resequencing SNP and short indel calls, rearrangement detection, population analysis. Text file of SNPs (incl location in genome, coding/vs non, syn vs non-syn aa change etc) and structural rearrangements, alignment files, tracks for upload to genome browser and fastq files; raw data submitted to SRA 140 200 Fungal Standard Draft Whole genome shotgun sequencing. Exact scope items and quality of finished product depend on genome. Selected genomes will be improved based on feasibility and scientific merit. Assembly, annotation (JGI Portal + Genbank); raw data submitted to SRA 250 400

62

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

ScienceCinema (OSTI)

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

Mosier, Annika [Stanford University

2013-01-22T23:59:59.000Z

63

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

ScienceCinema (OSTI)

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

Glass, N Louise [UC Berkeley

2013-01-25T23:59:59.000Z

64

JGI - Sequencing Plans  

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

Sequencing Plans Sequencing Plans JGI engages users from the National Laboratory system, academic institutions, and private industry to perform sequencing projects that directly relate to the DOE Office of Biological and Environmental Research's missions in alternative energy, global carbon cycling, and bioremediation. JGI's sequencing portfolio is drawn from its user programs, including the Community Science Program and the new Bioenergy Research Centers, as well as targets chosen by DOE to meet programmatic objectives. Plans by Program and Year All projects GEBA Sequencing Plans Community Science Program FY2014 Community Sequencing Program FY2013 Community Sequencing Program FY2012 Community Sequencing Program FY2011 Community Sequencing Program FY2010 Community Sequencing Program FY2009

65

JGI - Approved CSP Projects, 2005  

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

5 5 For status information, see the Genome Projects section. Organism Proposer Affiliation Microbes Olavius algarvensis symbionts Why? Dubilier Max Planck Institute of Marine Microbiology Crenarchaeota Why? Delong MIT Marinobacter aquaeolei VT8 Why? Edwards Woods Hole Oceanographic Institution Staphylococcus aureus subsp. aureus JH1 and JH9 Why? Tomasz Rockefeller University Prochlorococcus ACM A12II Why? Chisholm MIT Rhodocyclus-like polyphosphate accum. Why? Hugenholtz JGI Rhodobacter sphaeroides ATCC17025 and ATCC17029 Why? Kaplan University of Texas, Houston Contaminated groundwater Why? Zhou ORNL Lactobacillus reuteri strains 100-23 and F275 Why? Tannock University of Otago, Dunedin, NZ Ignicoccus hospitalis KIN4/I Podar Diversa Bacillus cereus subsp. cytotoxis NVH 391-98 and

66

DOE Joint Genome Institute: Scientists Publish Complete Genetic Blueprint  

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

January 28, 2009 January 28, 2009 Scientists Publish Complete Genetic Blueprint of Key Biofuels Crop WALNUT CREEK, CA-Scientists at the U.S. Department of Energy (DOE) Joint Genome Institute (JGI) and several partner institutions have published the sequence and analysis of the complete genome of sorghum, a major food and fodder plant with high potential as a bioenergy crop. The genome data will aid scientists in optimizing sorghum and other crops not only for food and fodder use, but also for biofuels production. The comparative analysis of the sorghum genome appears in the January 29 edition of the journal Nature. Prized for its drought resistance and high productivity, sorghum is currently the second most prevalent biofuels crop in the United States, behind corn. Grain sorghum produces the same amount of ethanol per bushel

67

JGI - Contact Us  

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

Contact Us Contact Us Search for a Staff Member Enter a name, email address, or phone number for a DOE JGI staff member. (* is a wildcard.) Public and media inquiries Contact David Gilbert, Public Affairs Manager, degilbert@lbl.gov, 925-296-5643. Community Sequencing Program (CSP) questions Send email for support to jgi-jira+pmosupport@lbl.gov, or call Jim Bristow at 925-296-5609. Genome Portal questions For help with the Genome Portal tools/data or the Projects List search page, click the "comments/questions" link at the bottom of the page on those sites. General web site questions For general comments relating to this web site, send email to the webmaster. Other ways to reach us . . . by phone call 925-296-5670. . . . by driving Map with driving directions . . . by public transit

68

U.S Department of Energy Joint Genome Institute Progress Report  

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

S Department of Energy S Department of Energy Joint Genome Institute Progress Report 2009 Representatives of the four DOE JGI genome programs (plant, fungal, metagenome, and microbe) grace the cover of this annual report. Three of the organisms were among the 81 projects selected in 2009 for the 2010 Community Sequencing Program portfolio. Photo credits, clockwise from bottom left: Brachypodium distachyon by Roy Kaltschmidt, LBNL; Amanita thiersii fungus by Joe McFarland; Cow rumen metagenome by Gemma Henderson, AgResearch; Soybeans by Roy Kaltschmidt, LBNL; Zymomonas mobilis Z4 by Katherine Pappas, University of Athens U.S Department of Energy Joint Genome Institute Progress Report 2009 DOE JGI Mission . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6 Director's

69

JGI - CSP Proposal Study Panel  

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

User Programs User Programs Project Management Office Community Science Program Emerging Technologies Opportunity Program Technology Development Pilot Program Genomic Encyc. of Bacteria and Archaea MyJGI: Information for Collaborators The CSP Proposal Study Panel CSP | Overview | How to Propose a Project | Review Process | DOE Relevance Proposal Schedule | Project Management | Forms | FAQ | People and Contacts Members Nina Agabian University of California, San Francisco, http://www.ucsf.edu Chris Amemiya Benaroya Research Institute at Virginia Mason, http://www.benaroyaresearch.org Gary L. Andersen Lawrence Berkeley National Laboratory, http://www.lbl.gov Jo Ann Banks Purdue University, http://www.purdue.edu John Battista Louisiana State University, http://www.lsu.edu Fred Brockman

70

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

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

Computing Requirements Shane Canon, Rob Egan, David Goodstein Victor M Markowitz NERSC BER Requirements for 2017 September 11-12, 2012 Established in 1999, located in Walnut Creek Supported by the DOE Office of Science. Budget of ~70 Million/ yr ~ 300 Employees Mission User facility for large scale genomics to enable bioenergy & environmental research DOE Joint Genome Institute (JGI) JGI Programs Plants Fungi Microbes Metagenomes Bioenergy Carbon Cycling Biogeochemistry Mission Areas Energy and Environmental Science Experimental Data Generation Data Interpretation User Interactions Sequencing Data Distribution Assembly of Sequence Data 4 30 Tb Sequence data Science publications Annotated Datasets: Genes Assembled Datasets Integrated Datasets:

71

JGI - Emerging Technologies Opportunity Program (ETOP)  

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

Funding Opportunity: DOE JGI Emerging Technologies Opportunity Program Funding Opportunity: DOE JGI Emerging Technologies Opportunity Program (ETOP) Overview | Eligible Applicants | Anticipated Funding | Applications and Submission Information : Pre-proposals, ETOP Full Application, Proposal Review Overview The DOE JGI is a genome science user facility focused on providing scientists access to state-of-the-art large-scale genomic technologies to address important energy and environmental problems. A core philosophy of the DOE JGI is that our suite of technical and analytical capabilities needs to evolve continuously in order to maximally enable our users' science. This occurs by building new scientific capabilities at the DOE JGI itself, and by enlisting partners to develop and provide specialized and critical capabilities that complement the activities in its Walnut Creek

72

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

SciTech Connect (OSTI)

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

Dubilier, Nicole [Max Planck Institute

2014-03-19T23:59:59.000Z

73

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

SciTech Connect (OSTI)

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.

Rounsley, Steve [University of Arizona

2014-03-20T23:59:59.000Z

74

DOE JGI Releases a New Version of its Metagenome Data Management & Analysis  

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

February 7, 2008 February 7, 2008 DOE JGI Releases a New Version of its Metagenome Data Management & Analysis System WALNUT CREEK, CA--Targeting its ever-expanding user community, the U.S. Department of Energy Joint Genome Institute (DOE JGI) has released an upgraded version of the IMG/M metagenome data management and analysis system, accessible to the public at http://img.jgi.doe.gov/m. IMG/M provides tools for analyzing the functional capability of microbial communities based on their metagenome DNA sequence in the context of reference isolate genomes. The new version of IMG/M includes five additional metagenome datasets generated from microbial community samples that were the subject of recently published studies. These include the metagenomic and functional analysis of termite hindgut microbiota (Nature

75

DOE JGI CSP 2012 PI Workshop  

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

Agenda Agenda Monday, January 23 8:15am Shuttle bus departs from the Walnut Creek Marriott 8:30 Sign In and Continental Breakfast at JGI 9:00-9:15 Introductions, Workshop Overview and Goals Metagenome Program overview Susannah Tringe 9:15-9:30 JGI Prokaryotic Super Program Overview Nikos Kyrpides 9:30-9:45 JGI Microbial Program Overview Tanja Woyke 9:45-10:00 JGI Fungal Program Overview Igor Grigoriev 10:00-10:15 JGI Sequencing Technologies Feng Chen 10:15-10:30 Questions 10:30-10:45 Break 10:45-11:15 Rhizosphere Grand Challenge and CSP2012 Plant-Microbe interactions projects Susannah Tringe 11:15-11:35 CSP2012: Plant associated metagenomes--Microbial community diversity and host control of community assembly across model and emerging plant ecological genomics systems Jeff Dangl

76

DOE Joint Genome Institute: Next Gen Sequencing Technology Pinpoint  

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

February 12, 2009 February 12, 2009 Next Gen Sequencing Technology Pinpoint "On-Off Switches" in Genomes WALNUT CREEK, CA-Scientists from the U.S. Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Laboratory, and the University of California, San Diego have developed a set of molecular tools that provide important insight into the complex genomes of multicellular organisms. The strategy promises to clarify the longstanding mystery of the role played by vast stretches of DNA sequence that do not code for the functional units-genes-that nevertheless may have a powerful regulatory influence. The research is described in the 12 February edition of the journal Nature. DOE bioenergy researchers have an interest in identifying these regulatory

77

JGI Sets 'Gold Standard' for Metagenomic Data Analysis  

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

14, 2007 14, 2007 DOE JGI Sets 'Gold Standard' for Metagenomic Data Analysis WALNUT CREEK, CA--With the advent of more powerful and economical DNA sequencing technologies, gene discovery and characterization is transitioning from single-organism studies to revealing the potential biotechnology applications embedded in communities of microbial genomes, or metagenomes. The field of metagenomics is still in its infancy--the equivalent of the early days of the California Gold Rush, with labs vying to stake their claim. Amidst the prospecting, the call has been issued for methods to separate fool's gold from the real nuggets. Such a gold standard has now been provided through work led by the U.S. Department of Energy Joint Genome Institute (DOE JGI) with colleagues from Oak Ridge National Laboratory and

78

JGI - Data Management Policy, Practices & Resources  

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

Data Management Policy, Practices & Resources Data Management Policy, Practices & Resources Data Management Policy In keeping with its role as a federally-funded User Facility, it is the DOE JGI's explicit policy to make the data it produces during the conduct of user projects (primarily but not exclusively its Community Sequencing Program, CSP) available to the broad scientific community as rapidly as possible and in accordance with DOE Office of Science policies. The DOE JGI serves raw and processed data to users through its individual genome project data portals (accessed through the Project List, http://genome.jgi.doe.gov/) as well as its several comparative genomics platforms (Phytozome, MycoCosm and IMG). The DOE JGI provides permanent local archiving of these data in addition to depositing raw data,

79

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

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

MyJGISubmit ProposalsInternalEmergency InfoCareers MyJGISubmit ProposalsInternalEmergency InfoCareers JGI website People Go Genomes Project List User Programs Sequencing Informatics Systems Education News & Publications Events About Us JGI Home DOE Joint Genome Institute Latest News R. irregularis December 20, 2013 A gluttonous plant reveals how its cellular power plant devours foreign DNA. Amborella trichopoda, a sprawling shrub that grows on just a single island in the remote South Pacific, is the only plant in its family and genus. It is also one of the oldest flowering plants, having branched off from others about 200 million years ago. more... R. irregularis November 25, 2013 How Scavenging Fungi Became a Plant's Best Friend. Glomeromycota is an ancient lineage of fungi that has a symbiotic relationship with roots that

80

Genomic Encyclopedia of Fungi  

SciTech Connect (OSTI)

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.

Grigoriev, Igor

2012-08-10T23:59:59.000Z

Note: This page contains sample records for the topic "genome institute jgi" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


81

DOE Joint Genome Institute: Adaptable Button Mushroom Serves Up  

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

8, 2012 8, 2012 Adaptable Button Mushroom Serves Up Biomass-Degrading Genes Critical to Managing the Planet's Carbon Stores The button mushroom occupies a prominent place in our diet and in the grocery store where it boasts a tasty multibillion-dollar niche, while in nature, Agaricus bisporus is known to decay leaf matter on the forest floor. Now, owing to an international collaboration of two-dozen institutions led by the French National Institute for Agricultural Research (INRA) and the U.S. Department of Energy Joint Genome Institute (DOE JGI), the full repertoire of A. bisporus genes has been determined. In particular, new work shows how its genes are actually deployed not only in leaf decay but also wood decay and in the development of fruiting bodies (the above ground part of the mushroom harvested for food). The work also

82

Upgraded IMG Data Management System Released by DOE JGI to Eager User  

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

4, 2007 4, 2007 Upgraded Integrated Microbial Genomes (IMG) Data Management System Released by DOE JGI to Eager User Community WALNUT CREEK, CA--A powerful set of computational tools established to ease the visualization and exploration of genomes flooding the public domain is now available in IMG Version 2.3--the Integrated Microbial Genomes (IMG) data management system hosted by the U.S. Department of Energy Joint Genome Institute (DOE JGI). The content of IMG 2.3, upgraded with new microbial genomes from the Version 23 release of the National Center for Biotechnology Information (NCBI) Reference Sequence (RefSeq) collection, now includes fungi, protists (eukaryotic unicellular organisms), and plant genomes to enhance the breadth of comparative analysis. A new addition of particular interest to

83

Visualizing Assembling Everything (2010 JGI/ANL HPC Workshop)  

ScienceCinema (OSTI)

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

Jaffe, David; Gnerre, Sante

2011-06-08T23:59:59.000Z

84

DOE Joint Genome Institute: Making up the gut microbiome is a host-driven  

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

November 16, 2010 November 16, 2010 Making up the gut microbiome is a host-driven project Baking sourdough bread requires a starter, and so do mammalian guts, which are first colonized by microbial communities from the mother and then acquire more microbes over time. These gut microbial communities are important for maintaining health and combating disease, and it's why the Human Microbiome Project launched by the National Institutes of Health in 2008 is studying the microbial communities that populate the human body by sequencing them and assembling a reference catalog, a project that involves researchers at the U.S. Department of Energy (DOE) Joint Genome Institute (JGI). G. beringei Photo: G. beringei by rbleib While the HMP was getting off the ground, DOE JGI collaborator Howard

85

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

SciTech Connect (OSTI)

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

Matzen, Kelly [OXITEC

2014-03-19T23:59:59.000Z

86

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

SciTech Connect (OSTI)

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

Arkin, Adam [LBNL

2014-03-20T23:59:59.000Z

87

DOE Joint Genome Institute: Breaking down cellulose without blasting  

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

4, 2011 4, 2011 Breaking down cellulose without blasting lignin: "Dry rot" genome offers lessons for biofuel pretreatment WALNUT CREEK, Calif.-Feared by realtors and homeowners alike, dry rot due to the fungus Serpula lacrymans causes millions of dollars worth of damage to homes and buildings around the world. This brown rot fungus' capacity to break down the cellulose in wood led to its selection for sequencing by the U.S. Department of Energy (DOE) Joint Genome Institute (JGI) in 2007, with the goal of identifying the enzymes involved in the degradation process and using the information to improve cellulosic biofuels production. Photo: A variant of Serpula lacrymans causes dry rot. (Dave Brown via Flickr/Creative Commons Attribution 2.0) As reported online July 14 in Science Express, an international team of

88

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

ScienceCinema (OSTI)

The U.S. Department of Energy Joint Genome Institute (JGI) invited scientists interested in the application of genomics to bioenergy and environmental issues, as well as all current and prospective users and collaborators, to attend the annual DOE JGI Genomics of Energy & Environment Meeting held March 22-24, 2011 in Walnut Creek, Calif. The emphasis of this meeting was on the genomics of renewable energy strategies, carbon cycling, environmental gene discovery, and engineering of fuel-producing organisms. The meeting features presentations by leading scientists advancing these topics. Pam Silver of Harvard University gives a presentation on "Designing Biological Systems for Sustainability and Programmed Environmental Interface" at the 6th annual Genomics of Energy & Environment Meeting on March 23, 2011

Silver, Pam [Harvard University

2011-06-03T23:59:59.000Z

89

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

ScienceCinema (OSTI)

The U.S. Department of Energy Joint Genome Institute (JGI) invited scientists interested in the application of genomics to bioenergy and environmental issues, as well as all current and prospective users and collaborators, to attend the annual DOE JGI Genomics of Energy & Environment Meeting held March 22-24, 2011 in Walnut Creek, Calif. The emphasis of this meeting was on the genomics of renewable energy strategies, carbon cycling, environmental gene discovery, and engineering of fuel-producing organisms. The meeting features presentations by leading scientists advancing these topics. Rob Knight of the University of Colorado gives a presentation on "Spatially and Temporally Resolved Studies of the Human Microbiome" at the 6th annual Genomics of Energy & Environment Meeting on March 23, 2011

Knight, Rob [University of Colorado

2011-06-03T23:59:59.000Z

90

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

ScienceCinema (OSTI)

The U.S. Department of Energy Joint Genome Institute (JGI) invited scientists interested in the application of genomics to bioenergy and environmental issues, as well as all current and prospective users and collaborators, to attend the annual DOE JGI Genomics of Energy & Environment Meeting held March 22-24, 2011 in Walnut Creek, Calif. The emphasis of this meeting was on the genomics of renewable energy strategies, carbon cycling, environmental gene discovery, and engineering of fuel-producing organisms. The meeting features presentations by leading scientists advancing these topics. Berkeley Lab microbial ecologist Terry Hazen delivers a keynote on "The Gulf Oil Spill: Ecogenomics and Ecoresilience" at the 6th Genomics of Energy & Environment Meeting on March 22, 2011.

Hazen, Terry [LBNL

2011-06-03T23:59:59.000Z

91

The Physcomitrella Genome Reveals Evolutionary Insights into the Conquest of Land by Plants  

Science Journals Connector (OSTI)

...Magill, Eds. (Missouri Botanical Garden Press, St. Louis, MO, 2004 ), pp. 3 12. 39 We thank K. Zhou and S. Pitluck at DOE Joint Genome Institute (JGI) for GenBank submissions and G. Werner and his group at JGI for support of gene annotation...

Stefan A. Rensing; Daniel Lang; Andreas D. Zimmer; Astrid Terry; Asaf Salamov; Harris Shapiro; Tomoaki Nishiyama; Pierre-Franois Perroud; Erika A. Lindquist; Yasuko Kamisugi; Takako Tanahashi; Keiko Sakakibara; Tomomichi Fujita; Kazuko Oishi; Tadasu Shin-I; Yoko Kuroki; Atsushi Toyoda; Yutaka Suzuki; Shin-ichi Hashimoto; Kazuo Yamaguchi; Sumio Sugano; Yuji Kohara; Asao Fujiyama; Aldwin Anterola; Setsuyuki Aoki; Neil Ashton; W. Brad Barbazuk; Elizabeth Barker; Jeffrey L. Bennetzen; Robert Blankenship; Sung Hyun Cho; Susan K. Dutcher; Mark Estelle; Jeffrey A. Fawcett; Heidrun Gundlach; Kousuke Hanada; Alexander Heyl; Karen A. Hicks; Jon Hughes; Martin Lohr; Klaus Mayer; Alexander Melkozernov; Takashi Murata; David R. Nelson; Birgit Pils; Michael Prigge; Bernd Reiss; Tanya Renner; Stephane Rombauts; Paul J. Rushton; Anton Sanderfoot; Gabriele Schween; Shin-Han Shiu; Kurt Stueber; Frederica L. Theodoulou; Hank Tu; Yves Van de Peer; Paul J. Verrier; Elizabeth Waters; Andrew Wood; Lixing Yang; David Cove; Andrew C. Cuming; Mitsuyasu Hasebe; Susan Lucas; Brent D. Mishler; Ralf Reski; Igor V. Grigoriev; Ralph S. Quatrano; Jeffrey L. Boore

2008-01-04T23:59:59.000Z

92

JGI - Prokaryote Super Program  

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

Prokaryote Super Program Prokaryote Super Program While the sequencing and assembly strategies for the Microbial Genomics and Metagenomics Programs are quite different, the scientific goals of the two programs are very much aligned with an underlying common objective to understand the structure and function of microorganisms and microbial communities with mission relevance to the Department of Energy. To achieve this, scientists in the program are pursuing the sequencing of nucleic acids from both individual microbes and entire communities of organisms. This combined approach offers unique opportunities to the scientific community, but also requires coordinated activities between metagenomic and individual microbial genome sequence generation and data analysis. To capitalize on these emerging opportunities, JGI recently merged the two

93

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

ScienceCinema (OSTI)

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

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

2013-01-22T23:59:59.000Z

94

JGI - Scientific Posters  

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

News and Publications News and Publications News Releases Science Highlights JGI in the News Notable Scientific Publications Scientific Posters The Primer Templates and Logos Scientific Posters - Archive Note: neither these posters nor their contents may be reproduced except by permission of JGI. JGI Sequencing Projects: Statistics and Timelines (JGI User Meeting 2007) Tijana Glavina del Rio, Kerrie Barry, Lynne Goodwin, Miranda Harmon-Smith, Harris Shapiro, Susan Lucas and David Bruce. What's new in project management? A Look at the JGI Project Management Office (JGI User Meeting 2007) David Bruce, Lynne Goodwin, Kerrie Barry, Susannah Tringe, Tijana Glavina del Rio Comparison of Protocols for Isolating Large Insert Clone DNA that is Suitable for High Throughput Library Construction (JGI User Meeting 2007)

95

DOE Joint Genome Institute: Model Microbial Community for Studying  

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

October 22, 2009 October 22, 2009 Model Microbial Community for Studying Expanding Dead Zones Characterized WALNUT CREEK, CA-Among the many changes in the ocean is the expansion of oxygen-deficient or oxygen minimum zones (OMZs), also known as dead zones, which affect the processes by which carbon is captured and sequestered on the seafloor and alter the microbial activities that impact the rate and magnitude of ocean carbon sequestration. Despite the importance of these effects, very little is known about the metabolism of OMZ microbes and how they respond to environmental changes. In the Oct. 23 issue of the journal Science, researchers from the University of British Columbia and the U.S. Department of Energy Joint Genome Institute (DOE JGI) describe the metagenome of an abundant but

96

JGI Plumbs Termite Guts to Yield Novel Enzymes for Better Biofuel  

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

21, 2007 21, 2007 DOE JGI Plumbs Termite Guts to Yield Novel Enzymes for Better Biofuel Production WALNUT CREEK, CA--Termites -- notorious for their voracious appetite for wood, rendering houses to dust and causing billions of dollars in damage per year -- may provide the biochemical means to a greener biofuel future. The bellies of these tiny beasts actually harbor a gold mine of microbes that have now been tapped as a rich source of enzymes for improving the conversion of wood or waste biomass to valuable biofuels. Termites of the genus Nasutitermes. The genomic sequencing and analysis of the termite gut microbes by the U.S. Department of Energy Joint Genome Institute (DOE JGI), the California Institute of Technology, Verenium Corporation (formerly Diversa), a

97

Rob Egan JGI  

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

JGI Types of parallelism Fine grained Lots of communication syncs "Game of Life" Climate modelling Coarse grained Moderate communication few syncs ...

98

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

ScienceCinema (OSTI)

The U.S. Department of Energy Joint Genome Institute (JGI) invited scientists interested in the application of genomics to bioenergy and environmental issues, as well as all current and prospective users and collaborators, to attend the annual DOE JGI Genomics of Energy & Environment Meeting held March 22-24, 2011 in Walnut Creek, Calif. The emphasis of this meeting was on the genomics of renewable energy strategies, carbon cycling, environmental gene discovery, and engineering of fuel-producing organisms. The meeting features presentations by leading scientists advancing these topics. Peer Bork of the European Molecular Biology Laboratory on "Comparative Metagenomics of Gut and Ocean: Identification of Microbial Marker Genes for Complex Environmental Properties" at the 6th annual Genomics of Energy & Environment Meeting on March 23, 2011

Bork, Peer

2011-06-03T23:59:59.000Z

99

The Power of Teamwork: JGI Ergonomics Program  

E-Print Network [OSTI]

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

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

2007-01-01T23:59:59.000Z

100

Joint Genome Institute's Automation Approach and History  

E-Print Network [OSTI]

Joint Genome Institutes Automation Approach and Historythroughput environment; automation does not necessarilyissues Islands of Automation modular instruments with

Roberts, Simon

2006-01-01T23:59:59.000Z

Note: This page contains sample records for the topic "genome institute jgi" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


101

JGI Compute User Training  

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

JGI Compute JGI Compute User Training Series JGI Compute User Training Series homeh1 Overview NERSC and IT staff will host a series training sessions and open office hours to introduce new services and review best practices for using the Crius cluster. All sessions are hands on, so please bring your laptop. If you are or were a user of any of the following systems, Crius, Rhea, Kronos, Theia, Oceanus or Phoebe, it will be beneficial for you to attend these training sessions. And if you plan to use JGI compute resources in the future, we also encourage you to attend. It will also be an opportunity for JGI compute users to ask questions and give NERSC and IT staff feedback on your requirements. Session 3: February 24th, 2012 1:30-5pm rm 100-101 Agenda 1:30-1:45 - Intro and presentation of the transition schedule we talked

102

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

103

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

ScienceCinema (OSTI)

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

Keasling, Jay

2011-04-28T23:59:59.000Z

104

DOE Joint Genome Institute: Genes from Tiny Algae Shed Light on Big Role  

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

April 9, 2009 April 9, 2009 Genes from Tiny Algae Shed Light on Big Role Managing Carbon in World's Oceans & Coping with Environmental Change WALNUT CREEK, CA-Scientists from two-dozen research organizations led by the U.S. Department of Energy (DOE) Joint Genome Institute (JGI) and the Monterey Bay Aquarium Research Institute (MBARI) have decoded genomes of two algal strains, highlighting the genes enabling them to capture carbon and maintain its delicate balance in the oceans. These findings, from a team led by Alexandra Z. Worden of MBARI and published in the April 10 edition of the journal Science, will illuminate cellular processes related to algae-derived biofuels being pursued by DOE scientists. The study sampled two geographically diverse isolates of the photosynthetic

105

JGI - Why Sequence Poplar Leaf Rust?  

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

Poplar Leaf Rust? Poplar Leaf Rust? The Populus (poplar tree) genome has been publicly released by the JGI, and the genomes of its symbiotic fungal associates Laccaria bicolor and Glomus intraradices are near completion. As part of the development of a broader community-based Populus genomics resource, and as a means of conducting informative comparative genomics among fungi, JGI will be sequencing Melampsora larici-populina (poplar leaf rust fungus), which causes widespread economic losses in poplar plantations worldwide and is a close relative of other economically important rusts (Uredinales), including Puccinia and other cereal rusts. There is a pressing need to develop a thorough understanding of the Melampsora species that are poplar pathogens so that new control approaches

106

The JGI Metagenome Program (2009 JGI User Meeting)  

ScienceCinema (OSTI)

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

Tringe, Susannah Green

2011-04-25T23:59:59.000Z

107

DOE Joint Genome Institute. Pulp NonFiction: Fungal Analysis Reveals Clues  

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

March 22, 2012 March 22, 2012 Pulp NonFiction: Fungal Analysis Reveals Clues for Targeted Biomass Deconstruction Without fungi and microbes to break down dead trees and leaf litter in nature, the forest floor might look like a scene from TV's "Hoarders." Ceriporiopsis subvermispora mycelium on wood Photo: Scanning electron micrograph of Ceriporiopsis subvermispora mycelium on wood. (R. Blanchette, University of Minnesota) Massive-scale genome sequencing projects supported by the U.S. Department of Energy (DOE) and being carried out at the DOE Joint Genome Institute (JGI) highlight the importance of learning how the cellulose, hemicellulose and lignin that serve as a plant's infrastructure can be broken down by these forest organisms to extract needed nutrients. Among the fungi being

108

JGI - Len Pennacchio  

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

Len Pennacchio Len Pennacchio Len Pennacchio Len Pennacchio, Ph.D Deputy of Genomic Technologies, DOE Joint Genome Institute & Senior Staff Scientist, Genomic Division, Lawrence Berkeley National Laboratory Education BA in Biology, Sonoma State University; PhD in Genetics, Stanford University, Stanford, CA; Postdoctoral training, Lawrence Berkeley National Laboratory, Berkeley, CA. Awards and Honors Co-Organizer, "Advances in Genome Biology & Technology." Marco Island, FL.; Board of Directors, G Corp.; Scientific Advisory Committee Chair for the Genome Canada and the Canadian Institutes of Health Research (CIHR) Initiative for Advancing Technology Innovation through Discovery; Scientific Advisory Boards: 1) Scientific Advisor to the NHGRI Sequencing Program (2011-); 2) Ontario Institute for Cancer Research (OICR); 3) NIH

109

JGI - Jeremy Schmutz  

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

Jeremy Schmutz Jeremy Schmutz Igor Grigoriev Plant Program Lead, DOE Joint Genome Institute & HudsonAlpha Institute for Biotechnology Education BA in Biology, North Central College, Naperville, IL; BS in Computer Science, North Central College, Naperville, IL Summary Mr. Schmutz's involvement with the DOE Joint Genome Institute dates back to 1997, when he was working for the Stanford Human Genome Center, now the HudsonAlpha Institute for Biotechnology. There he constructed the pipelines for directed finishing and co-led the team that finished the DOE human chromosomes 5, 16, and 19. Prior to this he participated in the CO-OP program at Argonne National Laboratory for sequencing technology development, developing algorithms for oligo probe-based sequencing. Following the completion of the human genome project in 2003, he developed

110

The Annual DOE JGI User Meeting  

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

2010 Agenda 2010 Agenda Wednesday - Thursday - Friday Download Agenda PDF - Shuttle Schedule (between JGI & Marriott) Click here to download videos of speaker presentations! Wednesday, March 24 Registration Opens at 8:00 AM Workshops 9:00 AM - 12:00 PM: Workshops (pre-registration required) Lunch 12:00 PM - 1:00 PM: Provided for workshop participants only on this day. SESSION I 1:00 PM - 4:30 PM 1:00 PM - 1:10 PM Introduction - Eddy Rubin, JGI 1:10 PM - 1:40 PM Genomics on the Half Shell: So, What Do Oysters Have to Do with Energy? - Dennis Hedgecock, USC 1:40 PM - 2:10 PM From Fjords to Open Seas: Ecological Genomics of Expanding Oxygen Minimum Zones - Steven Hallam, Univ of British Columbia 2:10 PM - 2:40 PM Marine algal evolution, ecology and roles in global CO2 uptake - Alexandra

111

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

SciTech Connect (OSTI)

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

Hickey, Scott [UC Berkely

2014-03-19T23:59:59.000Z

112

The Annual DOE JGI User Meeting  

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

Genomics of Energy & Environment Genomics of Energy & Environment The annual DOE JGI User Meeting March 18 - 20, 2014 in Walnut Creek, California Register now for the Meeting and Workshops Register Topics include: Microbial genomics, fungal genomics, metagenomics, and plant genomics; genome editing, natural products, pathway engineering, synthetic biology, high-throughput functional genomics, and societal impact of technological advances. State-of-the-art presentations by invited speakers as well as short talks selected from poster abstracts. In addition, tutorials on genomic informatics, data management, and new genomic technologies. Keynotes: Annalee Newitz, io9 Steve Quake, Stanford University Other confirmed speakers: Martin Ackermann, ETH Zurich Luke Alphey, Oxitec Mary Berbee, University of British Columbia

113

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

SciTech Connect (OSTI)

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

Mercedes-Roca, Maria [Zamorano Panamerican Agriculture School

2014-03-19T23:59:59.000Z

114

JGI - Dan Rokhsar  

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

Dan Rokhsar Dan Rokhsar Dan Rokhsar Daniel S. Rokhsar, Ph.D Eukaryote Super Program Head, DOE Joint Genome Institute Professor of Molecular and Cell Biology, UC Berkeley Faculty Scientist, LBNL Education AB in Physics, Princeton University, NJ; MS in Theoretical Physics, Cornell University, NY; PhD in Physics, Cornell University, NY Summary Daniel Rokhsar joined the DOE Joint Genome Institute as the founding Associate Director for Computational Genomics, and led the computational efforts directed towards the sequencing, annotation, and analysis of three human chromosomes. After successful completion of the human genome project, Professor Rokhsar's group has continued to develop computational methods applicable to the diverse eukaryotic species, which they have applied and

115

Gerber-JGI  

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

NERSC for the NERSC for the Joint Genome Institute Richard Gerber NERSC User Services May 2, 2011 Joint Genome Institute, Walnut Creek, CA 2 * What is NERSC? * Computing Resources * Storage Resources * How to Get Help * Accounts and Allocations * Connecting to NERSC * Computing Environment * Compiling Code * Running Jobs Outline What is NERSC? 3 !"#$% &'% ()$% *+'% ()"% ,*'% -)"% *+'% .)/% *&'% 0/% **'% 2010 Allocations 4 * NERSC serves a large population Over 3000 users, 400 projects, 500 code instances * Focus on "unique" resources - Expert consulting and other services - High end computing systems - High end storage systems - Interface to high speed networking * Science-driven - Machines procured competitively using application benchmarks from DOE/SC

116

DOE Joint Genome Institute: Tringe on Popular Science's "Brilliant 10"  

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

6, 2011 6, 2011 Tringe on Popular Science's "Brilliant 10" List WALNUT CREEK, Calif.-Susannah Green Tringe of the DOE Joint Genome Institute (DOE JGI) has been named one of 2011's "Brilliant 10," the annual list compiled by Popular Science magazine of top young researchers. In adding her name to the list, which appears in the October issue, the magazine recognized her $2.5 million grant from the DOE Early Career Research Program to study the role of microbial communities in restored wetlands in the San Francisco Bay-Delta region of California and their impact on long-term carbon sequestration. Bigelow's Dashiell Masland working Photo: Tringe wading into the Brilliant 10 list The Popular Science Brilliant 10 recognizes scientists and researchers

117

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

ScienceCinema (OSTI)

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

Kaeppler, Shawn [University of Wisconsin, Madison

2013-01-15T23:59:59.000Z

118

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

SciTech Connect (OSTI)

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

Ronald, Pamela [UC Davis

2014-03-20T23:59:59.000Z

119

JGI - CSP Sequencing Plans for 2011  

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

1 1 For status information, see the Genome Projects section. Proposer Affiliation Project Description Algae Kerfeld, Cheryl DOE JGI Genome and Transcriptome Analyses of Two Extremely Acidophilic and One Neutrophilic Eukaryotic Algal Species with Diverse Mechanism for CO2 Acquisition Lovejoy, Connie Laval University, Canada Small planktonic single celled eukaryotes from the Arctic Ocean Plants Muehlbauer, Gary University of Minnesota Whole genome shotgun sequencing of the barley genome Vogel, John USDA-ARS Surveying natural diversity of the model grass Brachypodium distachyon Fungi de Vries, Ronald CBS-KNAW Fungal Biodiversity Centre, the Netherlands Comparative analysis of Aspergilli to facilitate novel strategies in fungal biotechnology Goodwin, Stephen Purdue University Sequencing of pathogens and extremophiles in the Dothideomycetes

120

JGI Available Software  

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

Software Software Software NERSC/JGI Supported Software in Modules NERSC is actively building a new tree of software for genepool accessible through the modules system. For software not yet migrated into modules, please see the legacy /jgi/tools installations below. Package Category Version Module Install Date Date Made Default 7zip applications/ general 9.20.1 7zip/9.20.1 2013-01-14 2013-01-14 ABYSS applications/ bioinformatics 1.3.2 Abyss/1.3.2 2012-04-03 2012-04-03 ABySS applications/ bioinformatics 1.3.4 ABySS/1.3.4 2012-11-26 2012-11-26 acml libraries/ math 5.1.0 acml/5.1.0 2012-07-07 ALE applications/ bioinformatics 20120918-2-g28da522 ALE/20120918-2-g28da522 2013-01-24 2013-01-24 ALE applications/ bioinformatics 20130717 ALE/20130717 2013-07-17 2013-07-17

Note: This page contains sample records for the topic "genome institute jgi" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


121

The Annual DOE JGI User Meeting  

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

1 Workshops 1 Workshops IMG Workshop Date: Monday, March 21 Time: 9:00 AM - 5:00 PM Location: Walnut Creek Marriott Audience: Users and potential users of the Integrated Microbial Genomes (IMG) data analysis systems. Description: 1-day workshop with hands-on tutorials on IMG. IMG-Metagenomes Workshop Date: Tuesday, March 22 Time: 9:00 AM - 12:00 PM Location: Walnut Creek Marriott Audience: Users and potential users of the Integrated Microbial Genomes (IMG) with Microbiome Samples (IMG/M) data analysis system. Description: half day workshop with hands-on tutorials on IMG/M. Mycocosm Workshop Date: Tuesday, March 22 Time: 9:00 AM - 12:00 PM Location: Walnut Creek Marriott Audience: Users and potential users of the Mycocosm fungal genomics portal. Description: The JGI Mycocosm web-portal provides data access,

122

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

ScienceCinema (OSTI)

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.

Chain, Patrick [DOE JGI

2011-04-28T23:59:59.000Z

123

DOE Joint Genome Institute: Mite-y Genomic Resources For Bioenergy Crop  

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

23, 2011 23, 2011 Mite-y Genomic Resources For Bioenergy Crop Protection WALNUT CREEK/BERKELEY, Calif.-For a pest that isn't quite the size of a comma on a keyboard, the two-spotted spider mite can do a disproportionate amount of damage. These web-spinners extract the nutrients they need from leaves of more than a thousand different plant species, including bioenergy feedstocks and food staples. The cost of chemically controlling spider mites to counteract reduced harvest yields hovers around $1 billion annually, reflecting their significant economic impact. spider mite Photo: The web-spinning two-spotted spider mite was sequenced at the DOE JGI. (M. Grbic) With a 90-million nucleotide genome, the smallest of those that belong to the group of animals with external skeletons or arthropods, the two-spotted

124

is a Bioinformatics Scientist at the Institute for Genomic  

E-Print Network [OSTI]

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

Salzberg, Steven

125

The Annual DOE JGI User Meeting  

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

Index of Past Speakers Index of Past Speakers An alphabetical list of past speakers, presenters and keynotes. A Eric Allen, University of California, San Diego (2012) Rick Amasino, University of Wisconsin (2012) Gary Andersen, LBNL (2009) Iain Anderson, JGI (2006) John Archibald, Dalhousie University (2007) Adam Arkin, LBNL (2012) Ginger Armbrust, U. Washington (2009) B Scott Baker, PNNL (2007) Jill Banfield, University Of California, Berkeley (2008) Jody Banks, Purdue University (2012) Greg Bell, DOE ESnet, LBNL (2012) Steve Benner, The Foundation For Applied Molecular Evolution (keynote 2012) Eldredge Bermingham, Smithsonian Tropical Research Institute (2012) Paul Blainey, Broad Institute (2012) Peer Bork, European Molecular Biology Laboratory (EMBL) Heidelberg (2011) Siobhan Brady, University of California, Davis (2012)

126

Genomics of Plant-based Biofuels in the Journal Nature  

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

3, 2008 3, 2008 DOE JGI Director Eddy Rubin Highlights the Genomics of Plant-based Biofuels in the Journal Nature WALNUT CREEK, CA-Genomics is accelerating improvements for converting plant biomass into biofuel-as an alternative to fossil fuel for the nation's transportation needs, reports Eddy Rubin, Director of the U.S. Department of Energy Joint Genome Institute (DOE JGI), in the August 14 edition of the journal Nature. In "Genomics of cellulosic biofuels," Rubin lays out a path forward for how emerging genomic technologies will contribute to a substantially different biofuels future as compared to the present corn-based ethanol industry-and in part mitigate the food-versus-fuel debate. The Nature Review is available for download (by subscription) at http://www.nature.com/.

127

JGI - Nikos Kyrpides  

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

Nikos Kyrpides Nikos Kyrpides Nikos Kyrpides Nikos C. Kyrpides, Ph.D Prokaryote Super Program Head Education BA in Biology, Aristotelian University of Thessaloniki, Greece; PhD in Molecular Biology and Biotechnology, University of Crete, Greece Awards and Service 2007 Outstanding Performance Award, Lawrence Berkeley National Laboratory (LBNL) Administrative Boards: Genomics Standards Consortium; Hellenic Society Mikrobiokosmos; Hellenic Society Computational Biology Scientific Advisory Boards: A Knowledge-Based Bioinformatics Framework for Microbial Pathway Genomics (MICROME); Association for Computing Machinery (ACM) Special Interest Group in Bioinformatics; Genomics and Proteomics Approaches to the Small Model Genome of Mycoplasma genitalium; Metagenomics of the Human Intestinal Tract (MetaHIT); Community Cyber-infrastructure for

128

JGI - Notable Scientific Publications  

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

Notable Scientific Publications Notable Scientific Publications May 5, 2013 Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. (Nature Methods.) We present a hierarchical genome-assembly process (HGAP) for high-quality de novo microbial genome assemblies using only a single, long-insert shotgun DNA library in conjunction with Single Molecule, Real-Time (SMRT) DNA sequencing. Our method uses the longest reads as seeds to recruit all other reads for construction of highly accurate preassembled reads through a directed acyclic graph–based consensus procedure, which we follow with assembly using off-the-shelf long-read assemblers. March 24, 2013 The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution. (Nature

129

JGI - Prokaryotic Super Program Advisory Committee Meeting  

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

Prokaryotic Super Program Advisory Committee Meeting Prokaryotic Super Program Advisory Committee Meeting Members Cameron Currie, University of Wisconsin Ed DeLong, MIT Jed Fuhrman, University of Southern California George Garrity, MSU Steve Hallam, University of British Columbia Bob Landick, Great Lakes Bioenergy Research Center Folker Meyer, Argonne National Laboratory Nancy Moran, Yale University Mary Ann Moran, University of Georgia Karen Nelson, JCVI Rich Roberts, NEB Doug Rusch, J. Craig Venter Institute Ramunas Stepanauskas, Bigelow Laboratory for Ocean Sciences Niels van der Lelie, RTI Phil Hugenholtz, University of Queensland Home > About Us > JGI Management > Prokaryotic Super Program Advisory Committee Meeting UC logo DOE logo Contact Us Credits Disclaimer Access KeysAccessibility/Section 508 ©1997-2013 The Regents of the University of California Page Last Updated

130

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

SciTech Connect (OSTI)

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

Berry, David [University of Vienna

2014-03-20T23:59:59.000Z

131

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

SciTech Connect (OSTI)

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

Coomey, Joshua [University of Massashusetts Amherst

2014-03-20T23:59:59.000Z

132

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

SciTech Connect (OSTI)

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

Sharon, Itai [UC Berkely

2014-03-20T23:59:59.000Z

133

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

ScienceCinema (OSTI)

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

Notredame, Cedric [Centre for Genomic Regulation

2011-06-08T23:59:59.000Z

134

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

ScienceCinema (OSTI)

The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding ''Research Coordination Network'' from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. Dawn Field of the NERC Centre for Ecology & Hydrology briefly introduces the GEM Catalogue, followed by Susanna Sansone of the European Bioinformatics Institute who talks about the ISA-GCDML workshop at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, Calif. on Sept. 9, 2009.

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

2011-04-29T23:59:59.000Z

135

JGI - Why Sequence Reniera?  

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

Reniera? Reniera? Reniera All animals, from the simplest invertebrates to humans, arose from a common ancestor that existed over 600 million years ago. Recent molecular phylogenetic and developmental data indicate that demosponges are part of the most ancient and basal metazoan lineage and have many hallmarks of animal development, including gastrulation and pattern formation. Sequencing the genome of the tropical demosponge Reniera will define genetic features that are unique to and shared by all animals--humans to sponges--and are likely to have been present in the genome of the very first animals. As such, this sequencing project will contribute significantly to our understanding of very early animal evolution. In addition, sponges possess commercially desirable biosynthetic

136

Genome Rearrangement and Planning Institute of Information Systems  

E-Print Network [OSTI]

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

Erdem, Esra

137

Fueling Future with Algal Genomics  

SciTech Connect (OSTI)

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.

Grigoriev, Igor

2012-07-05T23:59:59.000Z

138

JGI - Why Sequence Sorghum?  

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

Sorghum? Sorghum? One of the world's leading grain crops, sorghum is also an important model for tropical grasses of worldwide importance with a collective minimum economic impact of $69 billion U.S. per year. As a model for the tropical grasses, sorghum is a logical complement to Oryza (rice), the first monocot plant to be sequenced. Sorghum is representative of the tropical grasses in that it has "C4" photosynthesis, using a complex combination of biochemical and morphological specializations resulting in more efficient carbon assimilation at high temperatures. By contrast, rice is more representative of temperate grasses, using "C3" photosynthesis. In addition to its intrinsic value, the sorghum sequence will be a valuable reference for assembling and analyzing the fourfold larger genome of maize

139

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

ScienceCinema (OSTI)

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

DeLucia, Evan

2011-04-26T23:59:59.000Z

140

DOE Joint Genome Institute: Establishing Standard Definitions for Genome  

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

October 8, 2009 October 8, 2009 Establishing Standard Definitions for Genome Sequences Download a podcast of this release! WALNUT CREEK, CA-In 1996, researchers from major genome sequencing centers around the world convened on the island of Bermuda and defined a finished genome as a gapless sequence with a nucleotide error rate of one or less in 10,000 bases. This effectively set the quality target for the human genome effort and was quickly applied to other genome projects. If a genome sequence didn't meet this stringent criterion, it was simply considered a "draft." More than a decade later, researchers are finding that with the advent of the latest sequencing technologies the terms "draft" and "finished" are no longer sufficient to describe the varying levels of genome sequence

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141

JGI - DOE Bioenergy Research Centers  

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

DOE Bioenergy Research Centers DOE Bioenergy Research Centers DOE JGI performs sequencing on behalf of the U.S. Department of Energy Bioenergy Research Centers. The Centers are intended to accelerate basic research in the development of cellulosic ethanol and other biofuels, advancing the federal initiative that seeks to reduce U.S. gasoline consumption by 20% within 10 years through increased efficiency and diversification of clean energy sources. The three Centers are located in geographically distinct areas and use different plants both for laboratory research and for improving feedstock crops. DOE BioEnergy Science Center led by DOE's Oak Ridge National Laboratory in Oak Ridge, Tennessee. This center will focus on the resistance of plant fiber to breakdown into sugars and is studying the potential energy crops

142

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

ScienceCinema (OSTI)

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

Gokhale, Maya

2011-06-08T23:59:59.000Z

143

Complete genome sequence of Halopiger xanaduensis type strain (SH6T)  

SciTech Connect (OSTI)

Halopiger xanaduensis is the type species of the genus Halopiger and belongs to the euryarchaeal family Halobacteriaceae. H. xanaduensis strain SH-6, which is designated as the type strain, was isolated from the sediment of a salt lake in Inner Mongolia, Lake Shangmatala. Like other members of the family Halobacteriaceae, it is an extreme halophile requiring at least 2.5 M salt for growth. We report here the sequencing and annotation of the 4,355,268 bp genome, which includes one chromosome and three plasmids. This genome is part of a Joint Genome Institute (JGI) Community Sequencing Program (CSP) project to sequence diverse haloarchaeal genomes.

Anderson, Iain [U.S. Department of Energy, Joint Genome Institute; Tindall, Brian [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Rohde, Manfred [HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany; Lucas, Susan [U.S. Department of Energy, Joint Genome Institute; Han, James [U.S. Department of Energy, Joint Genome Institute; Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute; Cheng, Jan-Fang [U.S. Department of Energy, Joint Genome Institute; Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Peters, Lin [U.S. Department of Energy, Joint Genome Institute; Pati, Amrita [U.S. Department of Energy, Joint Genome Institute; Mikhailova, Natalia [U.S. Department of Energy, Joint Genome Institute; Pagani, Ioanna [U.S. Department of Energy, Joint Genome Institute; Teshima, Hazuki [Los Alamos National Laboratory (LANL); Han, Cliff [Los Alamos National Laboratory (LANL); Tapia, Roxanne [Los Alamos National Laboratory (LANL); Land, Miriam L [ORNL; Woyke, Tanja [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 [U.S. Department of Energy, Joint Genome Institute; Ivanova, N [U.S. Department of Energy, Joint Genome Institute

2012-01-01T23:59:59.000Z

144

Complete Genome Sequence of the Thermophilic Bacterium Exiguobacterium sp. AT1b  

SciTech Connect (OSTI)

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

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

2011-01-01T23:59:59.000Z

145

Complete Genome Sequence of the Thermophilic Bacterium Exiguobacterium sp. AT1b  

SciTech Connect (OSTI)

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

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

2011-01-01T23:59:59.000Z

146

Rooted in Wonder: Joint Genome Institute Study Reveals Amazing World  

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

Rooted in Wonder: Joint Genome Institute Study Reveals Amazing Rooted in Wonder: Joint Genome Institute Study Reveals Amazing World Underfoot Rooted in Wonder: Joint Genome Institute Study Reveals Amazing World Underfoot August 13, 2012 - 2:33pm Addthis By developing a better understanding of the microbes that affect the growth of other plants (crops like corn or wheat) researchers may be able to improve their growth -- or provide better care for them in times of drought. By developing a better understanding of the microbes that affect the growth of other plants (crops like corn or wheat) researchers may be able to improve their growth -- or provide better care for them in times of drought. Charles Rousseaux Charles Rousseaux Senior Writer, Office of Science What Is A Weed It's also known as a mouse-ear cress. The scientific name is Arababidopsis thaliana.

147

DOE Joint Genome Institute: Peach Genome Offers Insights into Breeding  

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

March 24, 2013 March 24, 2013 Peach Genome Offers Insights into Breeding Strategies for Biofuels Crops Rapidly growing trees like poplars and willows are candidate "biofuel crops" from which it is expected that cellulosic ethanol and higher energy content fuels can be efficiently extracted. Domesticating these crops requires a deep understanding of the physiology and genetics of trees, and scientists are turning to long-domesticated fruit trees for hints. The relationship between a peach and a poplar may not be obvious at first glance, but to botanists both trees are part of the rosid superfamily, which includes not only fruit crops like apples, strawberries, cherries, and almonds, but many other plants as well, including rose that gives the superfamily its name.

148

JGI - Why Sequence Physcomitrella patens?  

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

Physcomitrella patens? Physcomitrella patens? Physcomitrella patens The moss Physcomitrella patens is becoming widely recognized as an experimental organism of choice not only for basic molecular, cytological, and developmental questions in plant biology, but also as a key link in understanding plant evolutionary questions, especially those related to genome evolution. Physcomitrella is well placed phylogenetically to provide important comparisons with the flowering plants. In terms of evolutionary distance, Physcomitrella is to the flowering plants what Drosophila is to humans. Having the full Physcomitrella genome available will greatly inform bioinformatic comparisons and functional genomics in plants, just as the mouse, Fugu, and Drosophila genomes have informed animal biology.

149

Seventh Annual DOE Joint Genome Institute User Meeting Sponsored By  

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

Seventh Annual Seventh Annual DOE Joint Genome Institute User Meeting Sponsored By U.S. Department of Energy Office of Science March 20-22, 2012 Walnut Creek Marriott Walnut Creek, California Contents Speaker Presentations .......................................................................................................... 1 Poster Presentations ........................................................................................................... 13 Attendees ............................................................................................................................ 83 Author Index ....................................................................................................................... 89 Abstracts alphabetical by speaker

150

JGI - How to Propose a CSP Project  

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

How to Propose a CSP Project How to Propose a CSP Project CSP | Overview | How to Propose a Project | Review Process | DOE Relevance Proposal Schedule | FAQ How do I submit my proposal? Proposals for synthetic biology and small-scale microbial and metagenome projects may be submitted at any time as brief white papers and will be reviewed every six months. Deadline for submission is 60 days prior to the review. See proposal schedule for specific dates. Submit a small-scale microbial/metagenome or synthetic biology proposal For the CSP15 annual call, a letter of intent is required to submit a proposal to JGI. Submitters whose letters of intent/proposals are approved will receive further instructions via email. Submit a CSP annual proposal For the CSP15 JGI-EMSL joint call, a letter of intent is required to submit

151

JGI - Why Sequence Rhodobacter sphaeroides?  

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

Rhodobacter sphaeroides? Rhodobacter sphaeroides? How can a photosynthetic bacterium help us understand a fundamental question in evolutionary biology? The acquisition and loss of genetic information permits the adaptation of an organism to an ever-changing environment. However, this genetic flux is a double-edged sword. On the one hand, it permits the acquisition of new adaptive traits, but this process may result in the damage or loss of functioning genetic systems, with possibly dire consequences for the individual or species. How can such genomic plasticity occur without being severely disruptive to the ongoing lifestyle of an organism? One possible solution to this dilemma is the presence of genomic "safe zones," where the insertion or deletion of DNA is not disruptive to the genome at large. Such safe zones may also

152

JGI - The GEBA Pilot Project  

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

GEBA Sequencing Plans GEBA Sequencing Plans For status information, see the Genome Projects section, or go to Microbial Genomics to find the latest releases. Organism Domain Phylum Status IMG-ER NCBI PID Culture ID GOLD ID Acidimicrobium ferrooxidans DSM 10331 Bacteria Actinobacteria draft DSM 10331 Gi02326 Actinosynnema mirum 101, DSM 43827 Bacteria Actinobacteria draft 2500395345 19705 DSM 43827 Gi02064 Alicyclobacillus acidocaldarius acidocaldarius 104-IA, DSM 446 Bacteria Firmicutes draft 29405 DSM 446 Gi02324 Anaerococcus prevotii PC 1, DSM 20548 Bacteria Firmicutes draft DSM 20548 Gi02318 Atopobium parvulum IPP 1246, DSM 20469 Bacteria Actinobacteria draft 29401 DSM 20469 Gi02317 Beutenbergia cavernosa HKI 0122, DSM 12333 Bacteria Actinobacteria draft 2500395322 20827 DSM 12333 Gi02225

153

JGI - Why Sequence Contaminated Groundwater?  

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

Contaminated Groundwater? Contaminated Groundwater? Because the majority of microorganisms in nature have never been cultured, little is known about their genetic properties, biochemical functions, and metabolic characteristics. Although the sequence of the microbial community "genome" can now be determined with high-throughput sequencing technology, the complexity and magnitude of most microbial communities make meaningful data acquisition and interpretation difficult. Thus, the sequence determination of a groundwater microbial community with manageable diversity and complexity (~20 phylotypes) is a timely challenge. The samples for this project come from the Natural and Accelerated Bioremediation Research (NABIR) Field Research Center (FRC), Well FW-010. The overall objective is to provide a fundamental and comprehensive

154

JGI - Why Sequence Phytophthora capsici?  

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

Phytophthora capsici? Phytophthora capsici? Phytophthora capsici is a devastating pathogen of vegetable crops such as cucurbits (squashes, pumpkins, etc.), tomatoes, and peppers. A pathogen of national economic importance, it has recently expanded its host range to include legumes. Sequencing P. capsici will provide vegetable and Phytophthora investigators nationwide with gene models for comprehensive functional genomic studies of natural populations and rapid identification of loci underpinning developmental events, host range determinants, and virulence. Among Phytophthora species, P. capsici provides a uniquely tractable genetic model for the molecular dissection of oomycete biology, hemibiotroph-induced disease, evolution, adaptation, and virulence factors because of its sexual fecundity, its natural annual outcrossing, and the

155

JGI - Why Sequence Hyperthermophilic Archaea?  

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

Hyperthermophilic Archaea? Hyperthermophilic Archaea? The hyperthermophile genus Pyrobaculum represents a unique clade among the archaea because its cultured members respire toxic metals such as arsenic and selenium, sulfur compounds, ferric (Fe(III)) iron, nitrate, and oxygen. Pyrobaculum species are also capable of chemolithotrophic and organotrophic growth. In contrast to the emerging crenarchaeal model Sulfolobus, which is an acidophilic obligate aerobe, Pyrobaculum provides an alternative archaeal system to investigate biological processes in non-acidic, aerobic/anaerobic, high-temperature environments. This project involves sequencing multiple Pyrobaculum genomes, which will significantly advance the genus's establishment as a model system. Unfortunately, the first member of this genus to be sequenced, P. aerophilum, is not easily

156

JGI - Why Sequence the Limpet?  

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

the Limpet? the Limpet? The goal of this project is to produce, annotate, and analyze a high-quality draft genomic sequence for a gastropod mollusk, the limpet Lottia scutum. Molluscs and annelids represent two diverse animal phyla that are united (along with several other groups of unsegmented worms) within the superphylum Spiralia, sharing spiral cleavage patterns early in development that give rise to a primitively free-living larval form, the trochophore. This ancient developmental pattern has been conserved at least since the early Cambrian period--over 540 million years. While the molecular biology of early developmental patterning in other ancient groups of organisms, such as arthropods (e.g., flies, insects, crustaceans) and deuterostomes (e.g., sea urchins, ascidians, vertebrates), has been

157

JGI - CSP Sequencing Plans for 2013  

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

3 3 Proposer Affiliation Project Description Bartley, Laura University of Oklahoma Switchgrass resequencing to enhance biofuel production Bartley, Laura University of Oklahoma Panicum virgatum RNA sequencing to identify gene expression changes related to biofuel traits Blanchard, Jeffrey University of Massachusetts Microbial community dynamics in a long-term soil warming chronosequence Boeke, Jef Johns Hopkins University Synthesis of the largest yeast chromosome, chromosome IV, and the synthetic yeast genome Sc2.0 Brune, Andreas Max-Planck Institute, Marburg, Germany Metagenomics and metatranscriptomics of the gut microbiota of higher termites Constant, Philippe INRS, Canada Metagenomic and Metatranscriptomic Analysis of Soil Biogeochemical Processes Sustained by Interspecific Transfer of Molecular Hydrogen

158

The Annual DOE JGI User Meeting  

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

Hotels, Travel, Meals, etc. Hotels, Travel, Meals, etc. Venue Hotel A limited block of rooms for User Meeting attendees has been set aside at the Marriott Hotel Walnut Creek, the meeting venue, which is convenient to the Walnut Creek BART stop and about a ten-minute drive from the JGI. The room rate for this limited-room block is $117/night. Rooms in the block will be available on a first-come, first-served basis and will be held until February 24, 2014. (After this date, the discounted rate will be contingent upon room availability and the hotel's occupancy). Government ID will not be required to receive this rate; however, you will need to mention the correct reservation code (see below) when you make your reservation. Marriott Hotel 2355 North Main Street Walnut Creek, CA 94596 Phone: (925) 934-2000

159

The Scientific Foundation for Personal Genomics: Recommendations from a National Institutes of  

E-Print Network [OSTI]

The Scientific Foundation for Personal Genomics: Recommendations from a National Institutes of personal genomic tests has led to discussions about the validity and utility of such tests and the balance and the Centers for Disease Control and Prevention to review the scientific foundation for using personal genom

Church, George M.

160

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

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

DOE Joint Genome Institute DOE Joint Genome Institute Biological and Environmental Research (BER) BER Home About Research Research Abstracts Searchable Archive of BER Highlights External link Biological Systems Science Division (BSSD) Genomic Science DOE Bioenergy Research Centers Radiochemistry & Imaging Instrumentation Radiobiology: Low Dose Radiation Research DOE Human Subjects Protection Program Structural Biology DOE Joint Genome Institute Climate and Environmental Sciences Division (CESD) Facilities Science Highlights Benefits of BER Funding Opportunities Biological & Environmental Research Advisory Committee (BERAC) News & Resources Contact Information Biological and Environmental Research U.S. Department of Energy SC-23/Germantown Building 1000 Independence Ave., SW Washington, DC 20585 P: (301) 903-3251 F: (301)

Note: This page contains sample records for the topic "genome institute jgi" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


161

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

ScienceCinema (OSTI)

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

Garrity, George

2011-06-03T23:59:59.000Z

162

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

ScienceCinema (OSTI)

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

Pop, Mihai [University of Maryland

2013-01-22T23:59:59.000Z

163

Fungal Genomics Program  

SciTech Connect (OSTI)

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.

Grigoriev, Igor

2012-03-12T23:59:59.000Z

164

Diatom Genome Helps Explain Their Great Diversity and Success in Trapping  

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

5, 2008 5, 2008 Diatom Genome Helps Explain Their Great Diversity and Success in Trapping Excess Carbon in Oceans WALNUT CREEK, CA-Diatoms, mighty microscopic algae, have profound influence on climate, producing 20 percent of the oxygen we breathe by capturing atmospheric carbon and in so doing, countering the greenhouse effect. Since their evolutionary origins these photosynthetic wonders have come to acquire advantageous genes from bacterial, animal and plant ancestors enabling them to thrive in today's oceans. These findings, based on the analysis of the latest sequenced diatom genome, Phaeodactylum tricornutum, are published in 15 October edition of the journal Nature by an international team of researchers led by the U.S. Department of Energy Joint Genome Institute (DOE JGI) and the Ecole Normale Supérieure of

165

DOE Joint Genome Institute. Relative Reference: Foxtail Millet Offers Clues  

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

May 14, 2012 May 14, 2012 Relative Reference: Foxtail Millet Offers Clues for Assembling the Switchgrass Genome Arranging DNA fragments into a genome sequence that scientists can interpret is a challenge often compared to assembling a puzzle, except there is no box to provide an idea of what the picture is even supposed to be. Sometimes there's guidance in the form of other publicly-available DNA sequences from related organisms that can be used to guide the assembly process, but its usefulness depends on how closely related any two sequences are to one another. For example, a reference genome might be so distantly related from the one being assembled, it would be akin to comparing a Model-T to a contemporary hybrid car. Foxtail millet Photo: Foxtail millet (S. italica) panicle by Katrien Devos, University of

166

New Metadata Organizer Streamlines JGI Data Management  

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

Copeland, Genome Assembly group lead. "I began talking with Chris Beecroft and Alex Boyd in SDM about what tools they were using for archiving our current production data to...

167

JGI - CSP Sequencing Plans for 2014  

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

Science Program Science Program Sequencing Plans for 2014 Proposer Affiliation Project Description Banfield, Jillian UC Berkeley, LBNL Community metagenomic and transcriptomic analyses of microbial carbon turnover in grassland soil profiles under two rainfall regimes Bonito, Gregory Duke University Comparative genomics of early diverging terrestrial fungi and their bacterial endosymbionts Brem, Rachel UC Berkeley Pioneering fungal mutagenesis using Tn-seq Brutnell, Thomas Donald Danforth Plant Science Center Doubling the number of Panicoideae genome sequences Canovas, David University of Seville, Spain Global genomic consequences of the deletion of the Aspergilli non-homologous end joining DNA repair mechanism employed as a genetic tool worldwide Chen, Jay Oak Ridge National Laboratory RNA-seq-Enabled Expression Quantitative Trait Locus (eQTL) in Populus

168

DOE Joint Genome Institute: Same Fungus, Different Strains: A Comparative  

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

3, 2011 3, 2011 Same Fungus, Different Strains: A Comparative Genomics Approach for Improved "Green" Chemical Production WALNUT CREEK, Calif.-Fungi play key roles in nature and are valued for their great importance in industry. Consider citric acid, a key additive in several foods and pharmaceuticals produced on a large-scale basis for decades with the help of the filamentous fungus Aspergillus niger. While A. niger is an integral player in the carbon cycle, it possesses an arsenal of enzymes that can be deployed in breaking down plant cell walls to free up sugars that can then be fermented and distilled into biofuel, a process being optimized by U.S. Department of Energy researchers. Susannah Tringe Photo: Aspergillus niger conidiospore by Kathie T. Hodges, Cornell.

169

JGI - CSP Sequencing Plans for 2010  

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

0 0 For status information, see the Genome Projects section. Proposer Affiliation Project Description Eukaryotes Collier, Jackie Stony Brook University Four Labyrinthulomycete species Cullen, Daniel US Forest Service, Forest Products Laboratory Homkaryotic derivative of Postia placenta Cullen, Daniel US Forest Service, Forest Products Laboratory Lignin-degrading fungus Phlebiopsis gigantea Goodwin, Stephen USDA-ARS and Purdue University Dothideomycetes plant pathogens Grossniklaus, Ueli University of Zurich Apomictic plant Boechera holboellii Koppisch, Andy Los Alamos National Laboratory Colony forming microalga Botryococcus braunii var Showa Kubisiak, Thomas US Forest Service, Southern Research Station Fusiform rust fungus Cronartium quercuum f.sp. fusiforme

170

JGI - CSP Sequencing Plans for 2009  

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

9 9 For status information, see the Genome Projects section. Organism Proposer Affiliation Eukaryotes Resequencing Trichoderma reesei Why? Scott Baker Pacific Northwest National Lab Rhizopogon salebrosus (ectomycorrhizal fungus) Why? Thomas Bruns University of California, Berkeley Ceriporiopsis subvermispora (lignin-degrading fungus) Why? Daniel Cullen USDA Forest Products Laboratory Gene expression in Chlamydomonas reinhardtii Why? Maria Ghirardi Natl. Renewable Energy Lab. Paralvinella sulfincola (polychaete worm) Why? Peter Girguis Harvard Univ. Thalassiosira rotula (diatom) Why? Bethany Jenkins Univ. of Rhode Island Dendroctonus frontalis (southern pine beetle) ESTs Why? Scott Kelley San Diego State Univ. Botryococcus braunii (Oil-Producing Green Microalga) cDNA

171

JGI - CSP Sequencing Plans for 2006  

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

6 6 For status information, see the Genome Projects section. Organism Proposer Affiliation Large Eukaryotes Arabidopsis lyrata and Capsella rubella (pink shepherd's-purse) Why? Weigel Max Planck Inst. for Developmental Biology Mimulus guttatus (monkey flower) Why? Willis Duke Univ. Sorghum bicolor Why? Paterson Univ. of Georgia Small Eukaryotes Batrachochytrium dendrobatidis (frog-infecting chytrid fungus ) Why? Taylor UC Berkeley Bicyclus anynana (a butterfly) Why? Long UC Irvine Campanulales (Grammathotheca bergiana, Isotoma petraea, Lobelia anceps, L. angolenis, L. baumannii, L. cardinalis, L. erinus, L. galpinii, L. gregoriana, L. inflata, L. jasionoides, L. malowensis, L. laxa, L. linearis chloroplast, L. patula, L. siphilitica, L. spicata, L. thermalis, L. boninensis, L. morogoroensis chloroplast

172

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

ScienceCinema (OSTI)

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

Simpson, Jared [Wellcome Trust Sanger Institute

2013-01-22T23:59:59.000Z

173

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

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

DOE Joint Genome Institute DOE Joint Genome Institute Latest News R. irregularis December 20, 2013 A gluttonous plant reveals how its cellular power plant devours foreign DNA. Amborella trichopoda, a sprawling shrub that grows on just a single island in the remote South Pacific, is the only plant in its family and genus. It is also one of the oldest flowering plants, having branched off from others about 200 million years ago. more... R. irregularis November 25, 2013 How Scavenging Fungi Became a Plant's Best Friend. Glomeromycota is an ancient lineage of fungi that has a symbiotic relationship with roots that goes back nearly 420 million years to the earliest plants. More than two thirds of the world's plants depend on this soil-dwelling symbiotic fungus to survive, including critical agricultural crops such as wheat,

174

MycoCosm, an Integrated Fungal Genomics Resource  

SciTech Connect (OSTI)

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

Shabalov, Igor; Grigoriev, Igor

2012-03-16T23:59:59.000Z

175

DOE Joint Genome Institute: Sentinel of Change: Water Flea Genome to  

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

February 3, 2011 February 3, 2011 Sentinel of Change: Water Flea Genome to Improve Environmental Monitoring Capabilities WALNUT CREEK, Calif.-A tiny crustacean that has been used for decades to develop and monitor environmental regulations is the first of its kind to have its genetic code sequenced and analyzed-revealing the most gene-packed animal characterized to date. The information deciphered could help researchers develop and conduct real-time monitoring systems of the effects of environmental remediation efforts. Daphnia pulex (commonly called water flea) Photo: Dr. Jan Michels, Christian-Albrechts-University, Kiel Daphnia pulex (commonly called water flea) Considered a keystone species in freshwater ecosystems, the water flea, Daphnia pulex, is roughly the size of the equal sign on a keyboard. Its 200

176

The Annual DOE JGI User Meeting  

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

Posters and Abstracts Posters and Abstracts Abstract Guidance: Abstract submission deadline: March 3, 2014 Formatting Each abstract submission must meet the following criteria: Each abstract must be submitted as a Microsoft Word formatted document. The total length should not exceed 500 words. The Title should be clearly presented in Bold typeface at the top of the page. The Lead/First Author should appear in Bold typeface. The Presenting Author should be indicated by an asterisk (*) and a contact e-mail address provided. Affiliations (organization, city, state/country) should be provided for all authors. If multiple institutions are represented, assign each organization a superscript number. Include the authors' names with the superscript number of their affiliation, followed by a numbered list of corresponding

177

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

ScienceCinema (OSTI)

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

Stamatakis, Alexis [Technical University of Munich

2011-06-08T23:59:59.000Z

178

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

ScienceCinema (OSTI)

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

Meyer, Folker [ANL

2011-06-08T23:59:59.000Z

179

DOE Joint Genome Institute: A Microbiological "Template" for Mitigating  

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

July 1, 2011 July 1, 2011 A Microbiological "Template" for Mitigating Methane Emissions WALNUT CREEK, Calif.-Carbon dioxide may be the most name-dropped greenhouse gas, but methane is 20 times more potent. In 2009, the U.S. Environmental Protection Agency calculated that 20 percent of the nation's human-related methane emissions were attributable to livestock digestive processes. In Australia, livestock emissions account for 12 percent of the country's total greenhouse gas emissions. Wallaby Photo:Wallaby, photo by Mehgan Murphy, Smithsonian's National Zoo. To understand how methane is produced in livestock, an international team of scientists including researchers at Australia's Commonwealth Scientific and Industrial Research Organisation (CSIRO) and the DOE JGI

180

Link Alpha J  

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

BioEnergy Institute JCAP: Joint Center for Artificial Photosynthesis JDEM: The Joint Dark Energy Mission JGI: Joint Genome Institute Job Descriptions Job Hazards Analysis (JHA Help...

Note: This page contains sample records for the topic "genome institute jgi" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


181

JGI_Training_FileSystems_Feb2012.ppt  

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

Jason Jason H ick Storage Systems Group Lawrence Berkeley Na:onal Lab 10 February 2012 A N ew 2 PB G PFS fi le s ystem f or the JGI "projectb" The n ew 2 PB " projectb" fi le s ystem i s a vailable o n Phoebe n ow * Some high level specs for users * 2.8 PB * Has a "per project" non--- purged, b acked---up por:on w ith s maller quota ( 1---5 T B) * And a " per u ser" p urged, not b acked---up p or:on with l arger q uota ( 10TB) File s ystems b est p rac:ces * Unfortunately d isk i s s :ll expensive * All o f t he J GI's d ata c an not c on:nue t o b e s tored on d isk w ithin t he c urrent budget * Archive a nd d elete d ata you no longer need * Disk u sage w ill b e controlled t hrough quotas i n s ome c ases a nd purging i n o thers There a re t wo a reas o f s torage w ithin

182

Ms. Arti K. Rai, Elvin R. Latty Professor of Law Duke Law School, Duke Institute for Genome Sciences & Policy  

E-Print Network [OSTI]

Institutes of Health/Department of Energy research grant to study collaborative R&D models in genomics-2001 UNIVERSITY OF SAN DIEGO SCHOOL OF LAW Assistant Professor 1996-1997 PROGRAM IN ETHICS AND THE PROFESSIONS Foundations for Policy Development, 61 DUKE LAW JOURNAL 101 (2012)

Richardson, David

183

Genome sequence of the chemoheterotrophic soil bacterium Saccharomonospora cyanea type strain (NA-134(T))  

SciTech Connect (OSTI)

Saccharomonospora cyanea Runmao et al. 1988 is a member of the genus Saccharomonospora in the family Pseudonocardiaceae that is moderately well characterized at the genome level thus far. Members of the genus Saccharomonospora are of interest because they originate from diverse habitats, such as soil, leaf litter, manure, compost, surface of peat, moist, over-heated grain, and ocean sediment, where they probably play a role in the primary degradation of plant material by attacking hemicellulose. Species of the genus Saccharomonospora are usually Gram-positive, non-acid fast, and are classified among the actinomycetes. S. cyanea is characterized by a dark blue (= cyan blue) aerial mycelium. After S. viridis, S. azurea, and S. marina, S. cyanea is only the fourth member in the genus for which a completely sequenced (non-contiguous finished draft status) type strain genome will be published. Here we describe the features of this organism, together with the draft genome sequence, and annotation. The 5,408,301 bp long chromosome with its 5,139 protein-coding and 57 RNA genes was sequenced as part of the DOE funded Community Sequencing Program (CSP) 2010 at the Joint Genome Institute (JGI).

Meier-Kolthoff, Jan P. [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany] [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Lu, Megan [Los Alamos National Laboratory (LANL)] [Los Alamos National Laboratory (LANL); Huntemann, Marcel [U.S. Department of Energy, Joint Genome Institute] [U.S. Department of Energy, Joint Genome Institute; Lucas, Susan [U.S. Department of Energy, Joint Genome Institute] [U.S. Department of Energy, Joint Genome Institute; Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute] [U.S. Department of Energy, Joint Genome Institute; Copeland, A [U.S. Department of Energy, Joint Genome Institute] [U.S. Department of Energy, Joint Genome Institute; Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute] [U.S. Department of Energy, Joint Genome Institute; Goodwin, Lynne A. [Los Alamos National Laboratory (LANL)] [Los Alamos National Laboratory (LANL); Han, Cliff [Los Alamos National Laboratory (LANL)] [Los Alamos National Laboratory (LANL); Tapia, Roxanne [Los Alamos National Laboratory (LANL)] [Los Alamos National Laboratory (LANL); Potter, Gabriele [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany] [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Land, Miriam L [ORNL] [ORNL; Ivanova, N [U.S. Department of Energy, Joint Genome Institute] [U.S. Department of Energy, Joint Genome Institute; Rohde, Manfred [HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany] [HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany; Goker, Markus [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany] [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute] [U.S. Department of Energy, Joint Genome Institute; Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute] [U.S. Department of Energy, Joint Genome Institute; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute] [U.S. Department of Energy, Joint Genome Institute; Klenk, Hans-Peter [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany] [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany

2013-01-01T23:59:59.000Z

184

Genome sequence of the ocean sediment bacterium Saccharomonospora marina type strain (XMU15T)  

SciTech Connect (OSTI)

Saccharomonospora marina Liu et al. 2010 is a member to the genomically so far poorly characterized genus Saccharomonospora in the family Pseudonocardiaceae. Members of the genus Sacharomonospora are of interest because they originate from diverse habitats, such as leaf litter, manure, compost, surface of peat, moist, over-heated grain, and ocean sediment, where they might play a role in the primary degradation of plant material by attacking hemicellulose. Organisms belonging to the genus are usually Gram-positive staining, non-acid fast, and classify among the actinomycetes. Next to S. viridis and S. azurea, S. marina is the third member in the genus Saccharomonospora for with a completely sequenced (permanent draft status) type strain genome will be published. Here we describe the features of this organism, together with the complete genome sequence, and annotation. The 5,965,593 bp long chromosome with its 5,727 protein-coding and 57 RNA genes was sequenced as part of the DOE funded Community Sequencing Program (CSP) 2010 at the Joint Genome Institute (JGI).

Klenk, Hans-Peter [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Lu, Megan [Los Alamos National Laboratory (LANL); Lucas, Susan [U.S. Department of Energy, Joint Genome Institute; Copeland, A [U.S. Department of Energy, Joint Genome Institute; Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Han, Cliff [Los Alamos National Laboratory (LANL); Tapia, Roxanne [Los Alamos National Laboratory (LANL); Brambilla, Evelyne-Marie [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Potter, Gabriele [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Land, Miriam L [ORNL; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; 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 [U.S. Department of Energy, Joint Genome Institute; Li, Wen-Jun [Yunnan University, Kunming, China; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute; Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute

2012-01-01T23:59:59.000Z

185

Genome sequence of the soil bacterium Saccharomonospora azurea type strain (NA-128T)  

SciTech Connect (OSTI)

Saccharomonospora azurea Runmao et al. 1987 is a member to the genomically so far poorly characterized genus Saccharomonospora in the family Pseudonocardiaceae. Members of the genus Sacharomonosoras are of interest because they originate from diverse habitats, such as leaf litter, manure, compost, surface of peat, moist and over-heated grain, where they might play a role in the primary degradation of plant material by attacking hemicellulose. They are Gram-negative staining organisms classified among the usually Gram-positive actinomycetes. Next to S. viridis, S. azurea is only the second member in the genus Saccharomonospora for with a completely sequenced type strain genome will be published. Here we describe the features of this organism, together with the complete genome sequence with project status 'permanent draft', and annotation. The 4,763,832 bp long chromosome with its 4,472 protein-coding and 58 RNA genes was sequenced as part of the DOE funded Community Sequencing Program (CSP) 2010 at the Joint Genome Institute (JGI).

Klenk, Hans-Peter [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Held, Brittany [Los Alamos National Laboratory (LANL); Lucas, Susan [U.S. Department of Energy, Joint Genome Institute; Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute; Copeland, A [U.S. Department of Energy, Joint Genome Institute; Hammon, Nancy [U.S. Department of Energy, Joint Genome Institute; Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Han, Cliff [Los Alamos National Laboratory (LANL); Tapia, Roxanne [Los Alamos National Laboratory (LANL); Brambilla, Evelyne-Marie [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Potter, Gabriele [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Land, Miriam L [ORNL; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; 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 [U.S. Department of Energy, Joint Genome Institute; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute; Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute

2012-01-01T23:59:59.000Z

186

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

ScienceCinema (OSTI)

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

Knapp, Steve

2011-04-26T23:59:59.000Z

187

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

ScienceCinema (OSTI)

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

Kent, Jim [UCSC

2011-06-08T23:59:59.000Z

188

NERSC Featured Announcements  

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

Bioinformatics Computing Consultant Position Available October 31, 2011 by Katie Antypas | 0 Comments NERSC and the Joint Genome Institute (JGI) are searching for two individuals...

189

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

SciTech Connect (OSTI)

Enrichment of emulsion PCR product is the most laborious and pipette-intensive step in the 454 Titanium process, posing the biggest obstacle for production-oriented scale up. The Joint Genome Institute has developed a pair of custom-made robots based on the Microlab Star liquid handling deck manufactured by Hamilton to mediate the complexity and ergonomic demands of the 454 enrichment process. The robot includes a custom built centrifuge, magnetic deck positions, as well as heating and cooling elements. At present processing eight emulsion cup samples in a single 2.5 hour run, these robots are capable of processing up to 24 emulsion cup samples. Sample emulsions are broken using the standard 454 breaking process and transferred from a pair of 50ml conical tubes to a single 2ml tube and loaded on the robot. The robot performs the enrichment protocol and produces beads in 2ml tubes ready for counting. The robot follows the Roche 454 enrichment protocol with slight exceptions to the manner in which it resuspends beads via pipette mixing rather than vortexing and a set number of null bead removal washes. The robotic process is broken down in similar discrete steps: First Melt and Neutralization, Enrichment Primer Annealing, Enrichment Bead Incubation, Null Bead Removal, Second Melt and Neutralization and Sequencing Primer Annealing. Data indicating our improvements in enrichment efficiency and total number of bases per run will also be shown.

Hamilton, Matthew; Wilson, Steven; Bauer, Diane; Miller, Don; Duffy-Wei, Kecia; Hammon, Nancy; Lucas, Susan; Pollard, Martin; Cheng, Jan-Fang

2010-05-28T23:59:59.000Z

190

Deep-sea vent {epsilon}-proteobacterial genomes provide insights into emergence of pathogens  

Science Journals Connector (OSTI)

...21) (A. Copeland, S. Lucas, A. Lapidus, K. Barry, J. C. Detter, T. Glavina, N. Hammon, S. Israni, S. Pitluck, P. Chain et al., http://genome.jgi-psf.org) (SI Fig. 6 and Table 1). One of the keys to surviving and thriving...

Satoshi Nakagawa; Yoshihiro Takaki; Shigeru Shimamura; Anna-Louise Reysenbach; Ken Takai; Koki Horikoshi

2007-01-01T23:59:59.000Z

191

JGI - Why Sequence a Rhodocyclus-like PAO?  

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

a Rhodocyclus-like PAO? a Rhodocyclus-like PAO? Shotgun sequencing of a simple acid-mine-drainage biofilm community has recently demonstrated that, for one archaeal species population at least, individual genomes are recombinant mosaics (i.e., combinations of segments of genomes) of closely related strains. This suggests that, as in sexual organisms and contrary to current opinion, genetic exchange may be the cohesive force holding microbial species together. How, then, might microbial genomes diverge to define separate species? Since the frequency of homologous recombination decreases exponentially with genome divergence, microbial species may be naturally defined by their ability to recombine, solving a fundamental issue in biology. However, genomic mosaicism is an isolated observation in an extreme habitat that needs to be confirmed with

192

Challenges in Whole-Genome Annotation of Pyrosequenced Eukaryotic Genomes  

SciTech Connect (OSTI)

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.

Kuo, Alan; Grigoriev, Igor

2009-04-17T23:59:59.000Z

193

JGI - LSP Small-Scale Sequencing Plans for 2007  

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

Laboratory Science Program Laboratory Science Program Small-Scale Sequencing Plans For status information, see the Genome Projects section. Organism Proposer Affiliation Five Archaea (Methanohalobium evestigatum, Methanobacterium formicicum, Halococcoides, Ferroglobus placidus, and Acidianus sp. JP7) Kyrpides LBNL Aspergillus terreus EST Baker PNNL Avena Barbata ESTs Anderson BNL Burkholderia cepacia Bu72 van der Lelie BNL ChIP-enriched binding sequences Stubbs LLNL CRISPR loci of Leptospirillum Banfield Cochliobolus heterostrophus Turgeon Cornell University Columbia River Microbiota Magnuson PNNL Dehalococcoides Brodie LBNL Etolico Lagoon in Greece Kyrpides LBNL Fungal comparative genomics (Orpinomyces) Baker PNNL Hypersaline microbial mat Raymond LLNL Leonotis nepetifolia Shanklin BNL

194

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

E-Print Network [OSTI]

dc4el@u.washington.edu Samuel Pitluck DOE Joint Genome29 Pitluck, Sam ..14 Plugge,3 Sanjay Israni, 3 Sam Pitluck, 3 Miriam L. Land, 4 Frank W.

Various

2006-01-01T23:59:59.000Z

195

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

E-Print Network [OSTI]

solvents tetrachloroethene (PCE) and trichloroethene (TCE),PCBs. The genome of the PCE-dechlorinating D. ethenogenesin D. ethenogenes grown on PCE or TCE by qPCR showed high

Various

2006-01-01T23:59:59.000Z

196

GenePRIMP: A GENE PRediction IMprovement Pipeline for Prokaryotic genomes  

SciTech Connect (OSTI)

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

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

2010-04-01T23:59:59.000Z

197

JGI - Why Sequence Sea Squirt cDNA?  

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

Sea Squirt cDNA? Sea Squirt cDNA? Ascidians are invertebrate chordates, which diverged from the vertebrate lineage near the root of the chordate phylogenetic tree. Their larvae have a tadpole structure that closely resembles lower vertebrate larvae. They are, however, composed of a very small number of cells (2600 for Ciona intestinalis), have a stereotyped development due to invariant cleavage patterns, and are therefore simpler to study than vertebrate embryos. This, combined with the recent establishment of powerful functional genomics tools in the wake of the sequencing of the Ciona intestinalis genome, has led to the re-emergence of ascidians as a chordate model organism of great evolutionary and developmental significance. Ciona studies have provided crucial insights into chordate evolution and the function of families of

198

Complete genome sequence of Serratia plymuthica strain AS12  

SciTech Connect (OSTI)

A plant associated member of the family Enterobacteriaceae, Serratia plymuthica strain AS12 was isolated from rapeseed roots. It is of scientific interest due to its plant growth promoting and plant pathogen inhibiting ability. The genome of S. plymuthica AS12 comprises a 5,443,009 bp long circular chromosome, which consists of 4,952 protein-coding genes, 87 tRNA genes and 7 rRNA operons. This genome was sequenced within the 2010 DOE-JGI Community Sequencing Program (CSP2010) as part of the project entitled 'Genomics of four rapeseed plant growth promoting bacteria with antagonistic effect on plant pathogens'.

Neupane, Saraswoti [Uppsala University, Uppsala, Sweden; Finlay, Roger D. [Uppsala University, Uppsala, Sweden; Alstrom, Sadhna [Uppsala University, Uppsala, Sweden; Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute; Lucas, Susan [U.S. Department of Energy, Joint Genome Institute; Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute; Bruce, David [Los Alamos National Laboratory (LANL); Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Peters, Lin [U.S. Department of Energy, Joint Genome Institute; Ovchinnikova, Galina [U.S. Department of Energy, Joint Genome Institute; Chertkov, Olga [Los Alamos National Laboratory (LANL); Han, James [U.S. Department of Energy, Joint Genome Institute; Han, Cliff [Los Alamos National Laboratory (LANL); Tapia, Roxanne [Los Alamos National Laboratory (LANL); Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Land, Miriam L [ORNL; Hauser, Loren John [ORNL; Cheng, Jan-Fang [U.S. Department of Energy, Joint Genome Institute; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Pagani, Ioanna [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; Hogberg, Nils [Uppsala University, Uppsala, Sweden

2012-01-01T23:59:59.000Z

199

DOE Joint Genome Institute: First Wild Grass Species and Model System for  

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

February 10, 2010 February 10, 2010 First Wild Grass Species and Model System for Energy Crops Sequenced WALNUT CREEK, CA-As the U.S. Department of Energy (DOE) works toward developing sustainable sources of clean renewable energy, perennial grasses have emerged as major candidates for the commercial production of cellulosic biofuels from feedstocks. However, little is known about the specific biological traits of the grasses that might contribute to their usefulness for energy production, in part because such grasses typically have long lifecycles and possess large, complex genomes, making them difficult to study. Representative genomes for two of the three major subfamilies of grasses-those that include rice, maize, sorghum and sugar cane-have already been sequenced. Now in the February 11 edition of the journal

200

JGI - Why Sequence Euryarchaeota in Acid Mine Drainage?  

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

Euryarchaeota in Acid Mine Drainage? Euryarchaeota in Acid Mine Drainage? Acid mine drainage (AMD) is a major worldwide environmental problem associated with the mining of energy resources (coal and uranium) and metals (eg., iron and copper), thus of direct DOE relevance. The processes that underpin AMD formation can be harnessed for bioleaching and bioremediation. Many scientific and industrial groups are studying various aspects of the biogeochemistry of AMD generation. Random shotgun sequencing of an extremely acidic (pH <0.9) chemolithotrophic subsurface AMD biofilm community (from the Richmond Mine in Iron Mountain, California) recovered a genome fragment from a novel euryarchaeon, named WTF-1. This novel lineage was previously missed by common broad-specificity primers used for PCR-based surveys. Further study

Note: This page contains sample records for the topic "genome institute jgi" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


201

Institutional  

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

institutional Sign In About | Careers | Contact | Investors | bpa.gov Search Policy & Reporting Expand Policy & Reporting EE Sectors Expand EE Sectors Technology & Innovation...

202

Exploiting proteomic data for genome annotation and gene model validation in Aspergillus niger  

E-Print Network [OSTI]

strain of A.niger sequenced by DSM showed that a number ofby JGI and CBS 513.88 by DSM [24]. The JGI sequence inderived from the JGI and DSM model sets using Mascot [25].

Wright, James C.

2014-01-01T23:59:59.000Z

203

Complete genome sequence of the plant-associated Serratia plymuthica strain AS13  

SciTech Connect (OSTI)

Serratia plymuthica AS13 is a plant-associated Gammaproteobacteria, isolated from rapeseed roots. It is of special interest because of its ability to inhibit fungal pathogens of rapeseed and to promote plant growth. The complete genome of S. plymuthica AS13 consists of a 5,442,549 bp circular chromosome. The chromosome contains 4,951 protein-coding genes, 87 tRNA genes and 7 rRNA operons. This genome was sequenced as part of the project enti- tled Genomics of four rapeseed plant growth promoting bacteria with antagonistic effect on plant pathogens within the 2010 DOE-JGI Community Sequencing Program (CSP2010).

Neupane, Saraswoti [Uppsala University, Uppsala, Sweden; Finlay, Roger D. [Uppsala University, Uppsala, Sweden; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute; Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Alstrom, Sadhna [Uppsala University, Uppsala, Sweden; Lucas, Susan [U.S. Department of Energy, Joint Genome Institute; Land, Miriam L [ORNL; Han, James [U.S. Department of Energy, Joint Genome Institute; Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute; Cheng, Jan-Fang [U.S. Department of Energy, Joint Genome Institute; Bruce, David [Los Alamos National Laboratory (LANL); Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Peters, Lin [U.S. Department of Energy, Joint Genome Institute; Ovchinnikova, Galina [U.S. Department of Energy, Joint Genome Institute; Held, Brittany [Los Alamos National Laboratory (LANL); Han, Cliff [Los Alamos National Laboratory (LANL); Detter, J C [U.S. Department of Energy, Joint Genome Institute; Tapia, Roxanne [Los Alamos National Laboratory (LANL); Hauser, Loren John [ORNL; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Pagani, Ioanna [U.S. Department of Energy, Joint Genome Institute; Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute; Klenk, Hans-Peter [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Hogberg, Nils [Uppsala University, Uppsala, Sweden

2012-01-01T23:59:59.000Z

204

JGI - Statistics  

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

Statistics Statistics FY 2014 Overall Sequencing Progress, Updated Quarterly Quarter Total Bases (trillions) Operating Hours Goal Actual Total* Actual % of Goal Goal (hours)** Actual Total Actual % Goal Q1 2014 15,000 18.827 126% 2,164 2208 102% Q2 2014 17,000 2,117 Q3 2014 18,000 2,140 Q4 2014 18,000 2,164 FY 2014 Total 68,000 18.827 28% 8,585 2208 26% * Includes Illumina HiSeq, MiSeq and PacBio sequencing platforms. ** Operating Hour target is based on 98% of the total available hours. FY 2013 Overall Sequencing Progress, Updated Quarterly Quarter Total Bases (Billions) Operating Hours Goal Actual Total* Actual % of Goal Goal (hours)** Actual Total Actual % Goal Q1 2013 15,000 20,004 133% 2,164 2,208 102%

205

Abstract IA37: Clinical genomics  

Science Journals Connector (OSTI)

...Research. 15 October 2014 meeting-abstract Clinical Genomics Clinical Genomics: Oral Presentations - Invited Abstracts Abstracts...2013; San Diego, CA Abstract IA37: Clinical genomics Katherine A. Janeway Dana-Farber Cancer Institute...

Katherine A. Janeway

2014-10-15T23:59:59.000Z

206

FUNCTIONAL GENOMICS Program of Study  

E-Print Network [OSTI]

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

Thomas, Andrew

207

Communicating Genomics:GTL  

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

Annual Annual DOE Joint Genome Institute User Meeting Sponsored By U.S. Department of Energy Office of Science March 29-April 1, 2006 Embassy Suites Hotel and DOE Joint Genome Institute Walnut Creek, California iii Contents Agenda .................................................................................................................. iv Speaker Presentations . .........................................................................................1 Abtracts in order of presentation according to agenda (p. iv) Poster Presentations ..............................................................................................9 Posters alphabetical by first author. *Presenting author. Attendees...............................................................................................................75

208

E-Print Network 3.0 - artur jgi sirje Sample Search Results  

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

Universitt Oldenburg Institut fr Physik, 26111 Oldenburg Summary: Forschungszentrum Geesthacht Seegang und Monsterwellen Rainer Reuter 7.11.2005 Dr. Artur Erbe FB Physik,...

209

Sequencing the Rice Genome  

Science Journals Connector (OSTI)

...University of Delhi and Nagendra Singh of the Indian Agricultural Research Institute) and...representing a single contig. On this point, Sasaki presented evidence from the RGP...ncgr.ac.cn/index.html Indian Rice Genome Program (University of Delhi...

Nancy A. Eckardt

210

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

E-Print Network [OSTI]

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

Kellis, Manolis

211

Complete genome sequence of the rapeseed plant-growth promoting Serratia plymuthica strain AS9  

SciTech Connect (OSTI)

Serratia plymuthica are plant-associated, plant beneficial species belonging to the family Enterobacteriaceae. The members of the genus Serratia are ubiquitous in nature and their life style varies from endophytic to free-living. S. plymuthica AS9 is of special interest for its ability to inhibit fungal pathogens of rapeseed and to promote plant growth. The genome of S. plymuthica AS9 comprises a 5,442,880 bp long circular chromosome that consists of 4,952 protein-coding genes, 87 tRNA genes and 7 rRNA operons. This genome is part of the project entitled Genomics of four rapeseed plant growth promoting bacteria with antagonistic effect on plant pathogens awarded through the 2010 DOE-JGI Community Sequencing Program (CSP2010).

Neupane, Saraswoti [Uppsala University, Uppsala, Sweden; Hogberg, Nils [Uppsala University, Uppsala, Sweden; Alstrom, Sadhna [Uppsala University, Uppsala, Sweden; Lucas, Susan [U.S. Department of Energy, Joint Genome Institute; Han, James [U.S. Department of Energy, Joint Genome Institute; Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute; Cheng, Jan-Fang [U.S. Department of Energy, Joint Genome Institute; Bruce, David [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Peters, Lin [U.S. Department of Energy, Joint Genome Institute; Ovchinnikova, Galina [U.S. Department of Energy, Joint Genome Institute; Lu, Megan [Los Alamos National Laboratory (LANL); Han, Cliff [Los Alamos National Laboratory (LANL); Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Tapia, Roxanne [Los Alamos National Laboratory (LANL); Fiebig, Anne [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Land, Miriam L [ORNL; Hauser, Loren John [ORNL; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Pagani, Ioanna [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; Finlay, Roger D. [Uppsala University, Uppsala, Sweden

2012-01-01T23:59:59.000Z

212

Hindawi Publishing Corporation Comparative and Functional Genomics  

E-Print Network [OSTI]

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

Newcastle upon Tyne, University of

213

Abstract SY36-01: Functional genomics and cancer dependencies  

Science Journals Connector (OSTI)

...CA Abstract SY36-01: Functional genomics and cancer dependencies William C. Hahn...Institute, Boston, MA. Recent advances in genomics continue to elucidate the genetic lesions...Format: William C. Hahn. Functional genomics and cancer dependencies. [abstract...

William C. Hahn

2014-10-01T23:59:59.000Z

214

Chlamydomonas reinhardtii at the Crossroads of Genomics  

Science Journals Connector (OSTI)

...55108 4 Department of Energy, Joint Genome Institute...with light as a sole energy source (photoautotrophic...production of clean, solar-generated energy in the form of H2, and...59). Ongoing genome projects offer the scientific...

Arthur R. Grossman; Elizabeth E. Harris; Charles Hauser; Paul A. Lefebvre; Diego Martinez; Dan Rokhsar; Jeff Shrager; Carolyn D. Silflow; David Stern; Olivier Vallon; Zhaoduo Zhang

2003-12-01T23:59:59.000Z

215

THE CAMPAIGN FOR UC SANTA CRUZ THE GENOMICS  

E-Print Network [OSTI]

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

California at Santa Cruz, University of

216

Terragenome: International Soil Metagenome Sequencing Consortium (GSC8 Meeting)  

ScienceCinema (OSTI)

The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding "Research Coordination Network" from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. Janet Jansson of the Lawrence Berkeley National Laboratory discusses the Terragenome Initiative at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, Calif. on Sept. 9, 2009

Jansson, Janet [LBNL

2011-04-29T23:59:59.000Z

217

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

ScienceCinema (OSTI)

The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding "Research Coordination Network" from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. Jeroen Raes of the University of Brussels discusses the Tara-Oceans expedition at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, Calif. on Sept. 9, 2009

Raes, Jeroen [University of Brussels

2011-04-28T23:59:59.000Z

218

Systems Biology Knowledgebase (GSC8 Meeting)  

ScienceCinema (OSTI)

The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding "Research Coordination Network" from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. Robert W. Cottingham of Oak Ridge National Laboratory discusses the DOE KnowledgeBase at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, Calif. on Sept. 9, 2009.

Cottingham, Robert W [ORNL

2011-04-29T23:59:59.000Z

219

The Biocurator Society (GSC8 Meeting)  

ScienceCinema (OSTI)

The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding "Research Coordination Network" from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. Pascal Gaudet of Northwestern University talks about "The Biocurator Society" at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, Calif. on Sept. 11, 2009

Gaudet, Pascal [Northwestern University

2011-04-28T23:59:59.000Z

220

Towards a Consensus Annotation System (GSC8 Meeting)  

ScienceCinema (OSTI)

The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding "Research Coordination Network" from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. "Comparing Annotations: Towards Consensus Annotation" at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, Calif. on Sept. 10, 2009

White, Owen [University of Maryland

2011-04-28T23:59:59.000Z

Note: This page contains sample records for the topic "genome institute jgi" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


221

From genome to proteome: developing expression clone resources for the human genome  

E-Print Network [OSTI]

From genome to proteome: developing expression clone resources for the human genome Gary Temple1 Mammalian Gene Collection, National Human Genome Research Institute and 2 National Center for Biotechnology human genome sequence, it has become possible and highly productive to compare the sequences of m

222

Finding Fingerprints of Selection in Poplar Genomes  

SciTech Connect (OSTI)

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

Tuskan, Gerald

2014-10-02T23:59:59.000Z

223

Finding Fingerprints of Selection in Poplar Genomes  

ScienceCinema (OSTI)

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

Tuskan, Gerald

2014-10-28T23:59:59.000Z

224

Meeting report The changing face of genomics  

E-Print Network [OSTI]

this technology into studying transcriptional regulator binding in the human genome, with applicationsMeeting report The changing face of genomics Manolis Kellis Address: The Broad Institute AGBT / AMS meeting on Advances in Genome Biology & Technology Marco Island, Florida, USA, February 4

Kellis, Manolis

225

Flash Updates of GSC projects (GSC8 Meeting)  

ScienceCinema (OSTI)

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.

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

2011-04-29T23:59:59.000Z

226

Communicating Genomics:GTL  

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

DOE Joint Genome Institute User Meeting Sponsored By U.S. Department of Energy Office of Science March 24-26, 2010 Walnut Creek Marriott Walnut Creek, California iii Contents Speaker Presentations ......................................................................................... 1 Poster Presentations........................................................................................... 11 Attendees............................................................................................................. 67 Author Index ...................................................................................................... 75 iv Posters alphabetical by first author. *Presenting author 1 Speaker Presentations Abstracts alphabetical by speaker

227

Structural Genomics  

Science Journals Connector (OSTI)

Structural Genomics ... Structural genomics is the field of science focused on the systematic determination of the three-dimensional structure of the proteins encoded into genomes. ... Structural genomics is spreading the philosophy of high throughput in all fields of science and making available new tools to speed up research procedures. ...

Ivano Bertini

2003-03-01T23:59:59.000Z

228

Discovering Geometric Patterns in Genomic Data Wenxuan Gao  

E-Print Network [OSTI]

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

Grossman, Robert

229

JGI - CSP Proposal Schedule  

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

Proposal Schedule Proposal Schedule CSP | Overview | How to Propose a Project | Review Process | DOE Relevance Proposal Schedule | FAQ Small-scale Microbial/Metagenome Proposals - reviewed twice yearly Small-scale proposals for specific types of microbial and metagenome projects are accepted on a continuous basis and will be reviewed twice a year. Letters of intent are not required. Deadline for submission is 60 days prior to the review date. Next review dates (submission deadline in parentheses): January 2014 (Nov 22, 2013) July 2014 (May 23, 2014) Submit small-scale microbial/metagenome proposals anytime using the Work Initiation Process (WIP) interface. Synthetic Biology proposals Synthetic biology proposals are accepted on a continuous basis and will be reviewed twice a year. Letters of intent are not required. Deadline for

230

JGI - News Releases  

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

News Releases News Releases December 20, 2013 A gluttonous plant reveals how its cellular power plant devours foreign DNA. Amborella trichopoda, a sprawling shrub that grows on just a single island in the remote South Pacific, is the only plant in its family and genus. It is also one of the oldest flowering plants, having branched off from others about 200 million years ago. November 25, 2013 How Scavenging Fungi Became a Plant's Best Friend. Glomeromycota is an ancient lineage of fungi that has a symbiotic relationship with roots that goes back nearly 420 million years to the earliest plants. More than two thirds of the world's plants depend on this soil-dwelling symbiotic fungus to survive, including critical agricultural crops such as wheat, cassava, and rice. November 22, 2013

231

JGI - Why Sequence Mycosphaerella?  

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

Mycosphaerella? Mycosphaerella? Mycosphaerella is one of the largest genera of plant pathogenic fungi, having more than 1,000 named species, many of which cause economically important diseases in temperate and tropical crops. A few species of Mycosphaerella cause disease in humans and other vertebrates, so the genus is of interest both for human and plant health. Two species will be sequenced: M. graminicola (asexual stage: Septoria tritici), the cause of Septoria tritici blotch, one of the most common and important diseases of wheat worldwide; and M. fijiensis, the cause of black sigatoka, the most economically significant disease in banana plants. Losses caused by M. graminicola cost United States wheat growers more than $275 million every year. The estimated annual cost of fungicides applied against Septoria

232

JGI Digital Scavenger Hunt  

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

1) Log on to Genepool (ssh -Y genepool.nersc.gov) 2) Load the JAMO (dev) module (module load jamodev) 3) Run the following sequence of commands and answer the questions:...

233

2013 REU Program in Computational Neuropsychiatric Genomics research experiences for undergraduates  

E-Print Network [OSTI]

2013 REU Program in Computational Neuropsychiatric Genomics research experiences for undergraduates University of Illinois at Chicago University of Haifa Harvard Medical School IGSB Institute for Genomics & Systems Biology #12;2013 REU Program in Computational Neuropsychiatric Genomics research experiences

Kemner, Ken

234

2015 REU Program in Computational Neuropsychiatric Genomics research experiences for undergraduates  

E-Print Network [OSTI]

2015 REU Program in Computational Neuropsychiatric Genomics research experiences for undergraduates Harvard Medical School ! IGSB Institute for Genomics & Systems Biology www.contechicago.org #12;2015 REU Program in Computational Neuropsychiatric Genomics research experiences for undergraduates The Conte

Kemner, Ken

235

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

236

Flexibility and Symmetry of Prokaryotic Genome Rearrangement Reveal Lineage-Associated Core-Gene-Defined Genome Organizational Frameworks  

Science Journals Connector (OSTI)

...big.ac.cn . a CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, Peoples Republic of China b College of Computer Science, Sichuan University, Chengdu, Peoples Republic...

Yu Kang; Chaohao Gu; Lina Yuan; Yue Wang; Yanmin Zhu; Xinna Li; Qibin Luo; Jingfa Xiao; Daquan Jiang; Minping Qian; Aftab Ahmed Khan; Fei Chen; Zhang Zhang; Jun Yu

2014-12-01T23:59:59.000Z

237

Ancient genomics  

Science Journals Connector (OSTI)

...2015 review-article PART IV: ANCIENT GENOMICS 1001 70 198 Discussion meeting issue...author and source are credited. Ancient genomics Clio Der Sarkissian Morten E. Allentoft...field of aDNA has entered the new era of genomics and has provided valuable information...

2015-01-01T23:59:59.000Z

238

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

ScienceCinema (OSTI)

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

Koren, Sergey [University of Maryland

2013-01-22T23:59:59.000Z

239

GenePRIMP: A GENE PRediction IMprovement Pipeline for Prokaryotic genomes  

E-Print Network [OSTI]

PRediction IMprovement Pipeline for Amrita Pati 1 , NataliaGene Prediction IMprovement Pipeline, http://geneprimp.jgi-based post-processing pipeline that identifies erroneously

Pati, Amrita

2012-01-01T23:59:59.000Z

240

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

E-Print Network [OSTI]

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

Utrecht, Universiteit

Note: This page contains sample records for the topic "genome institute jgi" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


241

Institutional INSTITUTIONAL DATA BOOK  

E-Print Network [OSTI]

that institutions provide for their learning and personal development. The University of Minnesota is an equal ORGANIZATIONAL STRUCTURE UMM Organizational Chart as of August 2009

Minnesota, University of

242

Genome Engineering  

SciTech Connect (OSTI)

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

Voytas, Dan [University of Minnesota

2014-03-20T23:59:59.000Z

243

Comparative genomics and genome evolution in yeasts  

Science Journals Connector (OSTI)

...Sternberg and Janet Thornton Comparative genomics and genome evolution in yeasts Kenneth...powerful model system for comparative genomics research. The availability of multiple...cerevisiae |evolution|bioinformatics|genomics| 1. Introduction The rationale put...

2006-01-01T23:59:59.000Z

244

Engineering Institute  

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

Institute Engineering Institute Engineering dynamics that include flight, vibration isolation for precision manufacturing, earthquake engineering, blast loading, signal processing,...

245

Whole-genome sequencing and intensive analysis of the undomesticated soybean (Glycine soja Sieb. and Zucc.) genome  

Science Journals Connector (OSTI)

...MPS technologies, the reliability of the de novo...DOE-JGI, for further analysis. MAQ...2 3 Repeat sequence analysis. We downloaded...high-density picolitre20 reactors. Nature 437:376-380...package for phylogenetic analysis by maximum likelihood...

Moon Young Kim; Sunghoon Lee; Kyujung Van; Tae-Hyung Kim; Soon-Chun Jeong; Ik-Young Choi; Dae-Soo Kim; Yong-Seok Lee; Daeui Park; Jianxin Ma; Woo-Yeon Kim; Byoung-Chul Kim; Sungjin Park; Kyung-A Lee; Dong Hyun Kim; Kil Hyun Kim; Jin Hee Shin; Young Eun Jang; Kyung Do Kim; Wei Xian Liu; Tanapon Chaisan; Yang Jae Kang; Yeong-Ho Lee; Kook-Hyung Kim; Jung-Kyung Moon; Jeremy Schmutz; Scott A. Jackson; Jong Bhak; Suk-Ha Lee

2010-01-01T23:59:59.000Z

246

Reconstructing large regions of an ancestral mammalian genome in silico  

E-Print Network [OSTI]

of California, Santa Cruz, California 95064, USA; 2 National Human Genome Research Institute, National.ucsc.edu/ancestors.] Following completion of the human genome sequence, there is now considerable interest in obtaining a more comprehensive understanding of its evolution (International Human Genome Sequencing Consortium [IHGSC] 2001

Miller, Webb

247

Potential of metabolomics as a functional genomics tool  

E-Print Network [OSTI]

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

Wurtele, Eve Syrkin

248

Genome Biology 2004, 5:R92 commentreviewsreportsdepositedresearchrefereedresearchinteractionsinformation  

E-Print Network [OSTI]

Federal Institute of Technology (ETH), Zurich. Colab, ETH, Zurich 8092, Switzerland. Seminar for Statistics, ETH, Zurich 8092, Switzerland. §Institute for Plant Sciences and Functional Genomics Center Zurich, ETH, Zurich 8092, Switzerland. ¶Computer Engineering and Networks Laboratory, ETH, Zurich 8092

Zitzler, Eckart

249

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

ScienceCinema (OSTI)

The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding Research Coordination Network from the National Science Foundation and was held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. Pelin Yilmaz of the Max Planck Institute-Bremen talks about the MIENS specification and Eugene Kolker of Seattle Children's Hospital discusses the GSC's non-for-profit at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, Calif. on Sept. 9, 2009

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

2011-04-29T23:59:59.000Z

250

Enhancing a Genome Database Using the XSB Tabled Logic Programming System  

E-Print Network [OSTI]

goal of the Human Genome Project 1] is to construct detailed physical maps of the human genome implementationof laboratory information systems developed at the Center for Genome Research in the Whitehead Research at the Whitehead Institute in MIT is engaged in several large-scale genome mapping projects

Davulcu, Hasan

251

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

E-Print Network [OSTI]

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

Levin, Judith G.

252

Comparative Microbial Genomics group CenterforBiologicalSequenceanalysisDepartmentofSystemsBiology,TechnicalUniversityofDenmark  

E-Print Network [OSTI]

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

Ussery, David W.

253

Fungal Genomics Program  

E-Print Network [OSTI]

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

Grigoriev, Igor

2012-01-01T23:59:59.000Z

254

NMR and Structural Genomics  

Science Journals Connector (OSTI)

NMR and Structural Genomics ... The role of NMR in structural genomics is outlined, with particular emphasis on using protein domains as targets. ... Targets in Structural Genomics ...

David Staunton; Jo Owen; Iain D. Campbell

2002-12-07T23:59:59.000Z

255

DOE Joint Genome Institute 2008 Progress Report  

E-Print Network [OSTI]

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

Gilbert, David

2009-01-01T23:59:59.000Z

256

DOE Joint Genome Institute 2008 Progress Report  

E-Print Network [OSTI]

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

Gilbert, David

2009-01-01T23:59:59.000Z

257

DOE Joint Genome Institute 2008 Progress Report  

E-Print Network [OSTI]

energy strategies, biomass conversion to biofuels, environ-the efficiency of the conversion of biomass to fuels. JGImore economi- cal conversion of biomass from such feedstocks

Gilbert, David

2009-01-01T23:59:59.000Z

258

DOE Joint Genome Institute 2008 Progress Report  

E-Print Network [OSTI]

producing microbial subsamples highly enriched for organisms that could metabo- lize methane, methanol,

Gilbert, David

2009-01-01T23:59:59.000Z

259

DOE Joint Genome Institute 2008 Progress Report  

E-Print Network [OSTI]

hemicellulose and lignin. Bio- fuels researchers are ableatmosphere when burned, but bio- fuels only release carbonenvironmentally sustainable bio- fuel crop than corn and

Gilbert, David

2009-01-01T23:59:59.000Z

260

DOE Joint Genome Institute 2008 Progress Report  

E-Print Network [OSTI]

possible to produce ethanol from cellulose on an industrialof breaking down cellulose into ethanol, considered by someof cellulosic ethanol, carbohydrate polymers (cellulose and

Gilbert, David

2009-01-01T23:59:59.000Z

Note: This page contains sample records for the topic "genome institute jgi" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


261

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

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

The sequencing of the first tree genome, that of Populus, was a project initiated by the Office of Biological and Environmental Research in DOEs 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.

International Populus Genome Consortium (IPGC)

262

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

ScienceCinema (OSTI)

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

Canon, Shane [LBNL

2013-01-22T23:59:59.000Z

263

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

SciTech Connect (OSTI)

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.

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

2009-09-09T23:59:59.000Z

264

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

ScienceCinema (OSTI)

The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding "Research Coordination Network" from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. Bob Vaughan of EMBL on submitting MIGS/MIMS/MIENS information to EMBL-EBI's system, followed by a brief talk from Jon Kaye of the Gordon and Betty Moore Foundation on standards and the foundation's sequencing pipelines at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, Calif. on Sept. 9, 2009

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

2011-04-29T23:59:59.000Z

265

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

ScienceCinema (OSTI)

The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding Research Coordination Network from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. Dawn Field of the NERC Centre for Ecology and Hydrology briefly describes RCN4GSC and Peter Sterk of the NERC Centre for Ecology and Hydrology follows with a talk on curation of MIGS-compliant data at the Genomic Standards Consortium 8th meeting at the DOE JGI in Walnut Creek, Calif. on Sept. 9, 2009.

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

2011-04-29T23:59:59.000Z

266

cv15866_JGI_PR_CR:JGI Progress Report  

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

E E J G I - p o w e r i n g a s u s t a i n a b l e f u t u r e w i t h t h e s c i e n c e w e n e e d f o r b i o f u e l s , e n v i r o n m e n t a l c l e a n u p , a n d c a r b o n c a p t u r e . 2 0 0 8 P r o g r e s s R e p o r t J o i n t G e n o m e I n s t i t u t e U . S . D E P A R T M E N T O F E N E R G Y T h e c o v e r d e p i c t s v a r i o u s D O E m i s s i o n - r e l e v a n t g e n o m e s e q u e n c i n g t a r g e t s o f t h e D O E J o i n t G e n o m e I n s t i t u t e . D O E J G I M i s s i o n T h e U . S . D e p a r t m e n t o f E n e r g y J o i n t G e n o m e I n s t i - t u t e , s u p p o r t e d b y t h e D O E O f f i c e o f S c i e n c e , u n i t e s t h e e x p e r t i s e o f f i v e n a t i o n a l l a b o r a t o r i e s - L a w r e n c e B e r k e l e y , L a w r e n c e L i v e r m o r e , L o s A l a m o s , O a k R i d g e , a n d P a c i f i c N o r t h w e s t - a l o n g w i t h t h e H u d s o n A l p h a I n s t i t u t e f o r B i o t e c h n o l o g y t o a d v a n c e g e n o m i c s i n s u p p o r t o f t h e D O E m i s s i o n s r e l a t e d t o b i o e n e r g y , c a r b o n c y c l i n g , a n d b i o g e o c h e m i s t r y . J G I , l o c a t e d i n W a l n u t C r e e k , C a l i f o r n i a , p r o v i d e s i n t e g r a t e d

267

UCSC cancer genomics browser.  

Science Journals Connector (OSTI)

...Chicago, IL Abstract 5087: UCSC Cancer Genomics Browser 2.0 Jingchun Zhu 1 Brian Craft...and analyze that data. The UCSC Cancer Genomics Browser (https://genome-cancer...enhances the interpretability of the cancer genomics information. UCSC Cancer Genomics Browser...

J Zhu; JZ Sanborn; T Wang; F Hsu; S Benz; C Szeto; L Esserman; D Haussler

2009-01-15T23:59:59.000Z

268

JGI - Len Pennacchio - Select Publications  

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

Len Pennacchio - Select Publications Len Pennacchio - Select Publications Graduate Studies Pennacchio, L. A., Lehesjoki, A.-E., Stone, N. E., Willour, V., Virtaneva, K., Miao, J., D'Amato, E., Ramirez, L., Faham, M., Koskiniemi, M., Warrington, J., Norio, R., A., de la Chapelle, A., Cox, D. R. and Myers, R. M. 1996. Mutations in the gene encoding cystatin B in Progressive Myoclonus Epilepsy (EPM1). Science 271(5256): 1731-1734. Virtaneva, K., D'Amato, E., Miao, J., Koskiniemi, M., Norio, R., Avanzini, G., Franceschetti, S., Michelucci, R., Tassinari, C. A., Omer, S., Pennacchio, L. A., Myers, R. M., Dieguez-Lucena, J. L., Krahe, R., de la Chapelle, A., and Lehesjoki, A.-E. 1997. Unstable minisatellite expansion causing recessive myoclonus epilepsy (EPM1). Nature Genetics 15(4): 393-396. Pennacchio, L. A., Bouley, D. M., Higgins, K. M., Scott, M. P., Noebels, J.

269

JGI - Why Sequence Alvinella pompejana?  

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

Pompeii Worm? Pompeii Worm? Alvinella pompeiiana One of the most thermophilic eukaryotes, Alvinella pompejana, the Pompeii worm, is a resident of the Pacific deep-sea hydrothermal vent area. These worms reside on black smoker chimneys 2500 meters under the ocean surface where they experience (1) the highest temperatures and temperature gradients known for any eukaryote (20-80°C), (2) a toxic soup of heavy metals, and (3) very low pH. Thus their environment is perhaps the most extreme known for any eukaryote. This project unites cDNA sequencing, which is crucial for genetic and protein analysis, with macromolecular structure determination by x-ray crystallography, solution small-angle x-ray scattering, and electron microscopy. Proteins from thermophilic sources, currently limited to unicellular bacteria and archaea, have proven to be

270

JGI - Why Sequence Trichoderma virens?  

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

Trichoderma virens? Trichoderma virens? Trichoderma virens is a haploid, filamentous hyphomycete (a subclass of fungi). As strains of T. virens are used to protect many crops from a variety of pathogens, this species is a model system for elucidating the mechanisms of biological control. Mechanisms being investigated include mycoparasitism and antibiosis (direct interaction with the pathogen), induction of host plant resistance, metabolism of pathogen germination stimulants released by seeds, and increased tolerance to stress by enhancing plant growth (indirect effects). Since this fungus is present in most soils throughout the world, isolates affect ecosystem health and productivity. This occurs both through interactions with pathogens and through induced changes in plant chemistry, which influence growth and

271

JGI - Why Sequence Xanthoria parietina?  

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

Xanthoria parietina? Xanthoria parietina? photo of lichen The lichen-forming fungus Xanthoria parietina would be the first lichen fungus to be sequenced. A lichen is an association between a fungus (usually an ascomycete) and either a microalga or a cyanobacterium, or both. Lichens are widely regarded as the classic example of a mutualistic symbiosis. Lichens grow in soil-less habitats such as on rocks or tree bark, or on poorly developed soils. Although these habitats occur in all terrestrial biomes, they are particularly abundant at high latitudes in the Subarctic, Arctic, and Antarctic, where lichens are of great ecological importance and where global warming and climate change pose a special threat. There are approximately 13,500 species of lichen-forming fungi, each producing a distinct lichen association (i.e., a "lichen species").

272

JGI - Why Sequence Karenia brevis?  

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

Karenia brevis? Karenia brevis? Karenia brevis (Davis) Hanson and Moestrup is a unicellular dinoflagellate protist that causes harmful algal blooms that occur annually in the Gulf of Mexico. These "red tides" cause extensive marine animal mortalities and human illness through the production of highly potent neurotoxins known as brevetoxins. Insight into the molecular mechanisms that control the growth and persistence of K. brevis blooms is critical to understanding the formation of harmful algal blooms and is a prerequisite for the development of control strategies. Karenia species (and other fucoxanthin-containing dinoflagellates) also occupy a critical position among algae with regard to plastid (photosynthetic organelle) evolution. These taxa have undergone a

273

JGI Lab Ergo Products Catalog  

E-Print Network [OSTI]

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

Alexandre, Melanie

2010-01-01T23:59:59.000Z

274

Genomic analysis of the uncultivated marine crenarchaeote Cenarchaeum symbiosum  

Science Journals Connector (OSTI)

...Celine Brochier, Asuncion Martinez, Tsultrim Palden, Tracy Mincer, Matthew Sullivan, Maureen Coleman, Jarod Chapman, Sam Pitluck, Chris Detter, Krishna Palaniappan, and the Joint Genome Institute staff for computational and technical assistance. J...

Steven J. Hallam; Konstantinos T. Konstantinidis; Nik Putnam; Christa Schleper; Yoh-ichi Watanabe; Junichi Sugahara; Christina Preston; Jos de la Torre; Paul M. Richardson; Edward F. DeLong

2006-01-01T23:59:59.000Z

275

A Celebration of The Genome, 1953-2003  

Office of Scientific and Technical Information (OSTI)

Celebration of The Genome, 1953-2003 This April Join the National Institutes of Health and the Department of Energy in a month-long series of scientific, educational, cultural and...

276

Operational streamlining in a high-throughput genome sequencing center  

E-Print Network [OSTI]

Advances in medicine rely on accurate data that is rapidly provided. It is therefore critical for the Genome Sequencing platform of the Broad Institute of MIT and Harvard to continually strive to reduce cost, improve ...

Person, Kerry P. (Kerry Patrick)

2006-01-01T23:59:59.000Z

277

Genomic Potential of Marinobacter aquaeolei, a Biogeochemical Opportunitroph  

Science Journals Connector (OSTI)

...51). They rapidly exploit nutrient patches and die or become dormant after substrate...annotated by the Joint Genome Institute pipeline using three gene finders, Critica (version...yellow, replication, recombination, and repair; purple, general function prediction...

Esther Singer; Eric A. Webb; William C. Nelson; John F. Heidelberg; Natalia Ivanova; Amrita Pati; Katrina J. Edwards

2011-02-18T23:59:59.000Z

278

Landscape evolutionary genomics  

Science Journals Connector (OSTI)

...1001 60 70 129 Landscape evolutionary genomics David B. Lowry * * davidbryantlowry...com University Program in Genetics and Genomics, , Box 3565 Duke University Medical...genetics|adaptation|landscape ecology|genomics|natural selection|GIS| 1. Introduction...

2010-01-01T23:59:59.000Z

279

The Human Genome From human genome to other  

E-Print Network [OSTI]

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

Linial, Michal

280

Our Collaborators  

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

Collaborators Collaborators The following organizations are our collaborators. Baylor College of Medicine The Baylor College of Medicine is the only private medical school in the greater Southwest. Baylor is among the top 20 of the 125 U.S. medical schools in federal research funding. DOE Joint Genome Institute The Joint Genome Institute (JGI) established in 1996, is a consortium of scientists, engineers and support staff from the U.S. Department of Energy's Lawrence Berkeley, Lawrence Livermore, and Los Alamos National Laboratories. The JGI has assumed a significant role in the effort to determine the 3 billion letters ("base pairs") worth of genetic text that make up the human genome. Hospital for Sick Children The Hospital for Sick Children is a health care community dedicated to

Note: This page contains sample records for the topic "genome institute jgi" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


281

Microsoft PowerPoint - Microbial Genome and Metagenome Analysis Case Study (NERSC Workshop - May 7-8, 2009).ppt [Compatibility  

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

Genome & Genome & Metagenome Analysis: Computational Challenges Natalia N. Ivanova * Nikos C. Kyrpides * Victor M. Markowitz ** * Genome Biology Program, Joint Genome Institute ** Lawrence Berkeley National Lab Microbial genome & metagenome analysis General aims Understand microbial life Apply to agriculture, bioremediation, biofuels, human health Specific aims include Specific aims include Predict biochemistry & physiology of organisms based on genome sequence Explain known biochemical & physiological properties Metabolic reconstruction * Ivanova & Lykidis (2009) Metabolic reconstruction. Encyclopedia of Microbiology, Elsevier: 607-621. 2 Genome sequence data size Now ~1,400 microbial genomes = 5.5 mil genes ~ 100 metagenomes samples

282

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

E-Print Network [OSTI]

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

Weber, David J.

283

Integrating population genetics and conservation biology in the era of genomics  

Science Journals Connector (OSTI)

...and conservation biology in the era of genomics N. Joop Ouborg * * j.ouborg@science...Department of Molecular Ecology and Ecological Genomics, Institute for Water and Wetland Research...genetics is evolving into conservation genomics, while at the same time basic and applied...

2010-01-01T23:59:59.000Z

284

Bionimbus: a cloud for managing, analyzing and sharing large genomics datasets  

E-Print Network [OSTI]

of the software infrastructure required. Results Bionimbus is used by a variety of projects to process genomicsBionimbus: a cloud for managing, analyzing and sharing large genomics datasets Allison P Heath,1 Megan E McNerney,1,2 Kevin P White,1,3,4 Robert L Grossman1,3,5 1 Institute for Genomics and Systems

Grossman, Robert

285

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

SciTech Connect (OSTI)

Thermodesulfobacterium geofontis OPF15T was isolated from Obsidian Pool, Yellowstone National Park and grows optimally at 83 oC. The OPF15T genome was finished at the Joint Genome Institute and the 1.6 Mb sequence has been annotated and deposited for future genomic studies aimed at understanding microbial processes and nutrient cycles in high-temperature environments.

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

2013-01-01T23:59:59.000Z

286

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

E-Print Network [OSTI]

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

Arnold, Jonathan

287

Engineering Institute  

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

Engineering Institute Engineering Institute Engineering Institute Engineering dynamics that include flight, vibration isolation for precision manufacturing, earthquake engineering, blast loading, signal processing, and experimental model analysis. Contact Leader, LANL Charles Farrar Email Leader, UCSD Michael Todd Email LANL Program Administrator Jutta Kayser (505) 663-5649 Email Collaboration for conducting mission-driven, multidisciplinary engineering research and recruiting, revitalization, and retention of current & future staff The Engineering Institute is a collaboration between LANL and the University of California at San Diego (UCSD) Jacobs School of Engineering, whose mission is to develop a comprehensive approach for conducting mission-driven, multidisciplinary engineering research

288

Personal Genomics, Personalized Medicine,  

E-Print Network [OSTI]

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

Napp, Nils

289

Institutional Controls  

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

Institutional Controls Institutional Controls Many major Federal laws (e.g., Atomic Energy Act (AEA), Resource Conservation Recovery Act (RCRA), Comprehensive Environmental Response, Compensation and Liability Act (CERCLA)), Executive Orders, regulations and various other drivers influence the use of institutional controls at DOE sites. Some drivers directly authorize or require the use of institutional controls, while others do not. DOE also uses institutional controls when no specific statutory requirement exists to supplement active remediation, pollution control, public and resource protection, and physical security, or to bolster the integrity of engineered remedies. DOE and its predecessor agencies have conducted activities for over 50 years, using land ownership and access control, environmental monitoring and surveillance, and other tools to support protection efforts at operational and inactive facilities, including radioactive waste burial grounds.

290

Complete genome sequence of Methanoculleus marisnigri type strain JR1  

SciTech Connect (OSTI)

Methanoculleus marisnigri Romesser et al. 1981 is a methanogen belonging to the order Methanomicrobiales within the archaeal phylum Euryarchaeota. The type strain, JR1, was isolated from anoxic sediments of the Black Sea. M. marisnigri is of phylogenetic interest because at the time the sequencing project began only one genome had previously been sequenced from the order Methanomicrobiales. We report here the complete genome sequence of M. marisnigri type strain JR1 and its annotation. This is part of a Joint Genome Institute 2006 Community Sequencing Program to sequence genomes of diverse Archaea.

Anderson, Iain [U.S. Department of Energy, Joint Genome Institute; Sieprawska-Lupa, Magdalena [University of Georgia, Athens, GA; Goltsman, Eugene [U.S. Department of Energy, Joint Genome Institute; Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute; Copeland, A [U.S. Department of Energy, Joint Genome Institute; Glavina Del Rio, Tijana [U.S. Department of Energy, Joint Genome Institute; Tice, Hope [U.S. Department of Energy, Joint Genome Institute; Dalin, Eileen [U.S. Department of Energy, Joint Genome Institute; Barry, Kerrie [U.S. Department of Energy, Joint Genome Institute; Saunders, Elizabeth H [Los Alamos National Laboratory (LANL); Han, Cliff [Los Alamos National Laboratory (LANL); Brettin, Tom [Los Alamos National Laboratory (LANL); Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Bruce, David [Los Alamos National Laboratory (LANL); Mikhailova, Natalia [U.S. Department of Energy, Joint Genome Institute; Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Hauser, Loren John [ORNL; Land, Miriam L [ORNL; Lucas, Susan [U.S. Department of Energy, Joint Genome Institute; Richardson, P M [U.S. Department of Energy, Joint Genome Institute; Whitman, W. B. [University of Georgia, Athens, GA; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute

2009-01-01T23:59:59.000Z

291

Complete genome sequence of Methanocorpusculum labreanum type strain Z  

SciTech Connect (OSTI)

Methanocorpusculum labreanum is a methanogen belonging to the order Methanomicrobiales within the archaeal phylum Euryarchaeota. The type strain Z was isolated from surface sediments of Tar Pit Lake in the La Brea Tar Pits in Los Angeles, California. M. labreanum is of phylogenetic interest because at the time the sequencing project began only one genome had previously been sequenced from the order Methanomicrobiales. We report here the complete genome sequence of M. labreanum type strain Z and its annotation. This is part of a 2006 Joint Genome Institute Community Sequencing Program project to sequence genomes of diverse Archaea.

Anderson, Iain [U.S. Department of Energy, Joint Genome Institute; Sieprawska-Lupa, Magdalena [University of Georgia, Athens, GA; Goltsman, Eugene [U.S. Department of Energy, Joint Genome Institute; Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute; Copeland, A [U.S. Department of Energy, Joint Genome Institute; Glavina Del Rio, Tijana [U.S. Department of Energy, Joint Genome Institute; Tice, Hope [U.S. Department of Energy, Joint Genome Institute; Dalin, Eileen [U.S. Department of Energy, Joint Genome Institute; Barry, Kerrie [U.S. Department of Energy, Joint Genome Institute; Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Hauser, Loren John [ORNL; Land, Miriam L [ORNL; Lucas, Susan [U.S. Department of Energy, Joint Genome Institute; Richardson, P M [U.S. Department of Energy, Joint Genome Institute; Whitman, W. B. [University of Georgia, Athens, GA; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute

2009-01-01T23:59:59.000Z

292

released  

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

Arctic Arctic algae, a cereal crop whose genetic code is nearly equivalent to sequencing two full human genomes, and microbial communities in deep- sea hydrothermal vents are among the 35 projects selected by the U.S. Department of Energy (DOE) Joint Genome Institute (JGI) for its 2011 Community Sequencing Program (CSP) to be character- ized for bioenergy and environ- mental applications. Enabling scientists from universities and national labo- ratories around the world to probe the hidden world of microbes and plants to meet the DOE missions of bioenergy, carbon cycling and biogeo- chemistry, this year's CSP portfolio is composed mostly of large-scale projects, which DOE JGI Director Eddy Rubin said was in keeping with the facility's mission of large-scale genomics and analysis. "Advances in sequencing technologies are really chang- ing the landscape and have dramatically

293

Hamilton Eye Institute Neuroscience Institute  

E-Print Network [OSTI]

Care Neonatology & Maternal Fetal Pediatric Heart Institute Steve J. Schwab, MD Musculoskeletal A New of Radiology · Mari Assumes Leadership of OB/GYN city attractioNs Levitt Shell Revived Feature Vision

Cui, Yan

294

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

ScienceCinema (OSTI)

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

Tringe, Susannah

2013-05-29T23:59:59.000Z

295

Quantum Institute  

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

Quantum Institute Quantum Institute Quantum Institute A new research frontier awaits! Our door is open and we thrive on mutually beneficial partnerships, collaborations that drive innovations and new technologies. Contact Leader Malcolm Boshier (505) 665-8892 Email Two of LANL's most successful quantum technology initiatives: quantum cryptography and the race for quantum computer The area of quantum information, science, and technology is rapidly evolving, with important applications in the areas of quantum cryptography, quantum computing, quantum metrology, and advanced quantum-based sensors, some of which are directly relevant to the Laboratory's national security mission. Mission Foster a vigorous intellectual environment at LANL Define and develop strategic thrusts Target and pursue funding opportunities

296

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

ScienceCinema (OSTI)

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

Chin, Francis [University of Hong Kong

2013-01-22T23:59:59.000Z

297

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

ScienceCinema (OSTI)

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

Dehal, Paramvir [LBNL

2013-01-22T23:59:59.000Z

298

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

ScienceCinema (OSTI)

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

White, Owen [University of Maryland

2013-01-22T23:59:59.000Z

299

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

ScienceCinema (OSTI)

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

Rusch, Doug [J. Craig Venter Institute

2013-01-22T23:59:59.000Z

300

The genomics of adaptation  

Science Journals Connector (OSTI)

...introduction Special feature 1001 70 197 198 The genomics of adaptation Jacek Radwan 1 * Wieslaw...One contribution to a Special Feature Genomics of adaptation. The amount and nature...aspects of the broad field of adaptation genomics. This introductory article sets up a...

2012-01-01T23:59:59.000Z

Note: This page contains sample records for the topic "genome institute jgi" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


301

Genomics of human longevity  

Science Journals Connector (OSTI)

...the original work is properly cited. Genomics of human longevity P. E. Slagboom 1...progress. human longevity|longevity genomics|epigenetics and ageing| 1. Introduction...Innovation Oriented Research Programme on Genomics (SenterNovem; IGE01014 and IGE5007...

2011-01-01T23:59:59.000Z

302

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

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

Biological Biological Systems Science Division (BSSD) » Genomic Science Biological and Environmental Research (BER) BER Home About Research Research Abstracts Searchable Archive of BER Highlights External link Biological Systems Science Division (BSSD) Genomic Science DOE Bioenergy Research Centers Radiochemistry & Imaging Instrumentation Radiobiology: Low Dose Radiation Research DOE Human Subjects Protection Program Structural Biology DOE Joint Genome Institute Climate and Environmental Sciences Division (CESD) Facilities Science Highlights Benefits of BER Funding Opportunities Biological & Environmental Research Advisory Committee (BERAC) News & Resources Contact Information Biological and Environmental Research U.S. Department of Energy SC-23/Germantown Building

303

Complete genome sequence of Ferroglobus placidus AEDII12DO  

SciTech Connect (OSTI)

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

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

2011-01-01T23:59:59.000Z

304

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 Genomics and Systems Biology Los Alamos scientists perform research in functional genomics and structural genomics, and applications for such work cover diverse fields such as energy, agriculture, and environmental cleanup. Get Expertise Babetta Marrone Biofuels Program Manager Email Cheryl Kuske DOE BER Biological System Science Division Program Manager Email Chris Detter Emerging Threats Program Manager: Email Rebecca McDonald Bioscience Communications Email "We were asked to build a rocket ship," said developer Joel Berendzen, "but instead we built a 10,000 mph motorcycle." - Sequedex team LANL leads the world in computational finishing of microbial genomes Protein research Read caption + In 2013, Los Alamos scientist Richard Sayre and his team genetically

305

Querying genomic databases  

SciTech Connect (OSTI)

A natural-language interface has been developed that retrieves genomic information by using a simple subset of English. The interface spares the biologist from the task of learning database-specific query languages and computer programming. Currently, the interface deals with the E. coli genome. It can, however, be readily extended and shows promise as a means of easy access to other sequenced genomic databases as well.

Baehr, A.; Hagstrom, R.; Joerg, D.; Overbeek, R.

1991-09-01T23:59:59.000Z

306

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

307

Genome Science/Technologies  

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

Science & Innovation » Science & Innovation » Science & Engineering Capabilities » Bioscience: Bioenergy, Biosecurity, and Health » Environmental Microbiology » Genome Genome Science/Technologies Los Alamos using cutting-edge sequencing, finishing, and analysis, impact valuable genomic data. Get Expertise Cheryl Kuske DOE BER Biological System Science Division Program Manager Email Srinivas Iyer Bioscience Group Leader Email Momchilo Vuyisich Bioenergy and Biomedical Sciences Email Rebecca McDonald Bioscience Communications Email State-of-the art technology and extensive genomics expertise Protein research Read caption + Los Alamos National Laboratory graduate student, Patricia Langan, changes the properties of a green fluorescent protein in order to create new fluorescent protein variants.

308

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.

309

Genome-Scale Identification of Membrane-Associated Human mRNAs  

E-Print Network [OSTI]

-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America, 5 of medicine. Plasma membrane proteins and secreted signaling proteins are candidate targets for monoclonal

Botstein, David

310

California Institute of Technology  

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

California Institute of Technology o Ivan Celanovic, Principal Research Scientist, Massachusetts Institute of Technology o Geoffrey Kinsey, Director, Photovoltaic...

311

Complete Genome Sequence of the Thermophilic, Piezophilic, Heterotrophic Bacterium Marinitoga piezophila KA3  

SciTech Connect (OSTI)

Marinitoga piezophila KA3 is a thermophilic, anaerobic, chemoorganotrophic, sulfur-reducing bacterium isolated from the Grandbonum deep-sea hydrothermal vent site at the East Pacific Rise (13 degrees N, 2,630-m depth). The genome of M. piezophila KA3 comprises a 2,231,407-bp circular chromosome and a 13,386-bp circular plasmid. This genome was sequenced within Department of Energy Joint Genome Institute CSP 2010.

Lucas, Susan [U.S. Department of Energy, Joint Genome Institute; Han, James [U.S. Department of Energy, Joint Genome Institute; Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute; Cheng, Jan-Fang [U.S. Department of Energy, Joint Genome Institute; Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Peters, Lin [U.S. Department of Energy, Joint Genome Institute; Mikhailova, Natalia [U.S. Department of Energy, Joint Genome Institute; Teshima, Hazuki [Los Alamos National Laboratory (LANL); Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Han, Cliff [Los Alamos National Laboratory (LANL); Tapia, Roxanne [Los Alamos National Laboratory (LANL); Land, Miriam L [ORNL; Hauser, Loren John [ORNL; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Pagani, Ioanna [U.S. Department of Energy, Joint Genome Institute; Vannier, Pauline [Ifremer, Plouzane, France; Oger, Phil [University of Lyon, France; Bartlett, Douglas [University of California, San Diego & La Jolla; Noll, Kenneth M [University of Connecticut, Storrs; Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute; Jebbar, Mohamed [Ifremer, Plouzane, France

2012-01-01T23:59:59.000Z

312

Genomic analysis of mouse tumorigenesis  

E-Print Network [OSTI]

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 ...

Tam, Mandy Chi-Mun

2006-01-01T23:59:59.000Z

313

Genomics of isolation in hybrids  

Science Journals Connector (OSTI)

...edited by Patrik Nosil and Jeffrey L. Feder Genomics of isolation in hybrids Zachariah Gompert...limitations to the study of the speciation genomics. Further progress in understanding the genomics of speciation will require large-scale...

2012-01-01T23:59:59.000Z

314

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

ScienceCinema (OSTI)

George Weinstock, associate director at the Genome Institute at Washington University, delivered the opening keynote "Towards the Perfect Genome Sequence" at the 2012 Sequencing, Finishing, Analysis in the Future Meeting held June 5-7, 2012 in Santa Fe, New Mexico.

Weinstock, George [Washington University

2013-03-22T23:59:59.000Z

315

Institute of Design Institute of Design  

E-Print Network [OSTI]

Institute of Design Institute of Design 350 N. LaSalle St. Chicago, IL 60610 312.595.4900 design The Institute of Design has continuously explored emerg- ing ideas about how design interacts with society languages and use of new media and material. The school was renamed the Institute of Design (ID) in 1944

Heller, Barbara

316

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

ScienceCinema (OSTI)

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

Goll, Johannes [JCVI

2013-01-22T23:59:59.000Z

317

Population genomics of wild and laboratory zebrafish (Danio rerio)  

E-Print Network [OSTI]

, Bangladesh, Department of Zoology, Tribhuvan University, Kathmandu, Nepal, §§Wellcome Trust Sanger Institute zebrafish (Danio rerio) populations occurring in Nepal, India, and Bangladesh, and we genetically compared natural populations of tradi- tional laboratory models, for which a wide array of genomic resources

Bernatchez, Louis

318

Reverse Methanogenesis: Testing the Hypothesis with Environmental Genomics  

Science Journals Connector (OSTI)

...technical assistance, and the pilots of the ROV Tiburon and the captain and crew of the R/V Western Flyer. We also thank S. Pitluck and the Joint Genome Institute staff for technical assistance, and W. Ussler and D. Graham, who provided insight and commentary...

Steven J. Hallam; Nik Putnam; Christina M. Preston; John C. Detter; Daniel Rokhsar; Paul M. Richardson; Edward F. DeLong

2004-09-03T23:59:59.000Z

319

Fuzzy Genome Sequence Assembly for Single and Environmental Genomes  

E-Print Network [OSTI]

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

Nicolescu, Monica

320

COMPUTATIONAL GENOMICS: MAPPING, COMPARISON, AND ANNOTATION OF GENOMES  

E-Print Network [OSTI]

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

Batzoglou, Serafim

Note: This page contains sample records for the topic "genome institute jgi" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


321

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

322

Human Genome Program  

SciTech Connect (OSTI)

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.

Not Available

1993-01-01T23:59:59.000Z

323

Genomics and Malaria Control  

Science Journals Connector (OSTI)

...-targeted and human-targeted approaches but in reality, malaria results from three intimately interacting organisms (Figure 1). Fortunately, genomics-based approaches to malaria offer the strategic advantage of considering all three participants through integrative data sets, allowing us to identify... The genomic sequences of the malarial vector, parasite, and host the three components of the malarial transmission system have been known for at least two years. It may be possible to counter the disease by harnessing this genomic information to launch a strategic attack on the parasite during vulnerable stages of its life cycle.

Vernick K.D.; Waters A.P.

2004-10-28T23:59:59.000Z

324

The Center for integrative genomics  

E-Print Network [OSTI]

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

Kaessmann, Henrik

325

Genome mining for methanobactins  

Science Journals Connector (OSTI)

Methanotrophic bacteria have potential as a biological methane sink, and methanobactins are a set of peptides important in regulating this activity. A genome mining study highlights genes involved in methanobactin production, but also suggests that not all methanotrophs have them.

Grace E Kenney; Amy C Rosenzweig

2013-02-26T23:59:59.000Z

326

Annotating individual human genomes  

Science Journals Connector (OSTI)

Advances in DNA sequencing technologies have made it possible to rapidly, accurately and affordably sequence entire individual human genomes. As impressive as this ability seems, however, it will not likely amount to much if one cannot extract meaningful information from individual sequence data. Annotating variations within individual genomes and providing information about their biological or phenotypic impact will thus be crucially important in moving individual sequencing projects forward, especially in the context of the clinical use of sequence information. In this paper we consider the various ways in which one might annotate individual sequence variations and point out limitations in the available methods for doing so. It is arguable that, in the foreseeable future, DNA sequencing of individual genomes will become routine for clinical, research, forensic, and personal purposes. We therefore also consider directions and areas for further research in annotating genomic variants.

Ali Torkamani; Ashley A. Scott-Van Zeeland; Eric J. Topol; Nicholas J. Schork

2011-01-01T23:59:59.000Z

327

Genomic library construction  

SciTech Connect (OSTI)

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.

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

2011-07-26T23:59:59.000Z

328

Institute of Design Institute of Design  

E-Print Network [OSTI]

Institute of Design Institute of Design 350 N. LaSalle St. Chicago, IL 60610 312.595.4900 main 312.595.4906 graduate study information 312.595.4901 fax design@id.iit.edu www.id.iit.edu Dean: Patrick F. Whitney The Institute of Design (ID) is defined by a legacy of experimentation joined with unique academic programs

Heller, Barbara

329

Nucleomorph genomes: structure, function, origin and evolution  

E-Print Network [OSTI]

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

Archibald, John

330

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

Energy Savers [EERE]

like corn or wheat) researchers may be able to improve their growth -- or provide better care for them in times of drought. By developing a better understanding of the microbes...

331

Southern Research Institute Visit  

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

initiates collaboration between Southern Research Institute(SRI) and LSU CAMD hosted visitors from the Southern Research Institute in Birmingham, Alabama, and researchers from LSU...

332

DOE Drives Big Data Push  

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

2 Volume 9 Issue 2 2 Volume 9 Issue 2 From YAGS to Planetary Biology . . . . . . . . . . . . . . . 2 DOE Drives Big Data Push . . . . . . . . . . . . . . . . . . . . 3 Sweating Small Scale Genomics . . . . . . . . . . . . . . . 6 The Future of the DOE JGI . . . . . . . . . . . . . . . . . . . . 7 Save the Date for Meeting 8 . . . . . . . . . . . . . . . . . . . 8 also in this issue With a record 488 genomics researchers and bioinformaticians sitting in the Marriott Walnut Creek ballroom, New York Times science writer Carl Zimmer opened the DOE Joint Genome Institute's 7th Annual Genomics of Energy & Environment Meeting on March 20, 2012. Sharing his thoughts about being "On the Genome Beat," he informed the audience that he was worn down by seeing news about scientists successfully sequencing yet another genome sequence, and that "maybe some genomes shouldn't be written about." Zimmer's words engaged the audience in a discussion that

333

Bioinformatics and Genomics Degree Requirements Booklet  

E-Print Network [OSTI]

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

dePamphilis, Claude

334

Petroleum Institute Scholarly Publications  

E-Print Network [OSTI]

Abu Dhabi The Petroleum Institute Scholarly Publications January 1st ­ December 31st 2007 #12;The Petroleum Institute Scholarly Publications January 1st ­ December 31st 2007 v #12;- 2 - Scholarly Publications 2007 | The Petroleum Institute #12;- 3 - Scholarly Publications 2007 | The Petroleum Institute

335

Petroleum Institute Scholarly Publications  

E-Print Network [OSTI]

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

336

Genomics and plant cells: application of genomics strategies to Arabidopsis cell biology  

Science Journals Connector (OSTI)

29 June 2002 research-article Genomics and plant cells: application of genomics strategies to Arabidopsis cell biology Michael...the way we conduct plant science. Arabidopsis Genomics Functional Genomics Cell Biology| Genomics and...

2002-01-01T23:59:59.000Z

337

Institut National des Tlcommunications Advanced Telecommunications Research Institute  

E-Print Network [OSTI]

Institut National des Télécommunications Advanced Telecommunications Research Institute Rapport de

Ray, Thomas S.

338

Wellcome Trust Sanger Institute HUMAN GENETICS DATA SECURITY POLICY  

E-Print Network [OSTI]

procedures 1. Data category - All projects involving human genetics data must be assigned to one of the four. Level 2: Standard (genomic data with relatively limited demographic/phenotypic information) We expect1 Wellcome Trust Sanger Institute HUMAN GENETICS DATA SECURITY POLICY February 2011 Although almost

Maizels, Rick

339

Genomics of cellulolytic bacteria  

Science Journals Connector (OSTI)

The heterogeneous plant biomass is efficiently decomposed by the interplay of a great number of different enzymes. The enzyme systems in cellulolytic bacteria have been investigated by sequencing and bioinformatic analysis of genomes from plant biomass degrading microorganisms with valuable insights into the variety of the involved enzymes. This broadened our understanding of the biochemical mechanisms of plant polymer degradation and made the enzymes applicable for modern biotechnology. A list of the truly cellulolytic bacteria described and the available genomic information was examined for proteins with cellulolytic and hemicellulolytic capability. The importance of the isolation, characterization and genomic sequencing of cellulolytic microorganisms and their usage for sustainable energy production from biomass and other residues, is emphasized.

Daniela E Koeck; Alexander Pechtl; Vladimir V Zverlov; Wolfgang H Schwarz

2014-01-01T23:59:59.000Z

340

JGI - Why Sequence Bacillus cereus strains?  

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

Bacillus Cereus strains? Bacillus Cereus strains? The Bacillus cereus group is now attracting the greatest interest among researchers working on bacilli and other gram-positive bacteria. One of the fundamental and practical questions being asked is how the ecological adaptation of these bacteria results in pathogens for animals and insects (like B. anthracis or some B. thuringiensis lines). This has inspired intensive phylogenetic studies, revealing the epidemic structure of this bacterial population. B. cereus includes strains that are presumably innocuous (some strains are used as animal probiotics) and strains that have caused food poisoning, either emetic or diarrheic. All emetic strains, as well as B. anthracis, seem to represent a single clone, but at the moment, diarrheic strains cannot be easily discriminated from one other.

Note: This page contains sample records for the topic "genome institute jgi" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


341

JGI - Why Sequence O. algarvensis Symbionts?  

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

Olavius algarvensis Symbionts? Olavius algarvensis Symbionts? In contrast to many other marine invertebrates that generally harbor only a single bacterial symbiont, gutless oligochaetes are unique in having established highly specific and stable associations with multiple endosymbiotic species. These small worms have completely reduced their digestive and excretory systems and live in obligate symbiosis with phylogenetically diverse co-occurring bacterial symbionts. This project will address the diversity and functional roles of symbiotic bacteria in the gutless marine oligochaete Olavius algarvensis through comparative metagenomics. These worms harbor a microbial community of five co-occurring symbionts with very different metabolic pathways and evolutionary origins. In addition to the interactions of the symbionts with their hosts, these

342

The Power of Teamwork: JGI Ergonomics Program  

E-Print Network [OSTI]

Communication and Education Stretch Posters Potty TrainingCommunication/Education Group Meetings Posters Weekly Ergo

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

2007-01-01T23:59:59.000Z

343

The rice genome project in?Japan  

Science Journals Connector (OSTI)

The rice genome project in Japan Takuji Sasaki Rice Genome Research Program, National...Kannondai 2-chome, Tsukuba, Ibaraki 305, Japan Since 1991, the Rice Genome Research Program in Japan has carried out rice genomics, such as large-scale...

Takuji Sasaki

1998-01-01T23:59:59.000Z

344

Mammalian comparative genomics and epigenomics  

E-Print Network [OSTI]

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 ...

Mikkelsen, Tarjei Sigurd, 1978-

2009-01-01T23:59:59.000Z

345

Genomic Sciences | Clean Energy | ORNL  

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

the fundamental principles that control complex biological systems important to clean energy and environmental applications. Multidisciplinary genomic science research and...

346

Challenges in global genomics education  

Science Journals Connector (OSTI)

Abstract In spite of high expectations for the integration of genomics into medicine, it is not clear that health providers are competent to appropriately use new genomic approaches. The issue is further complicated by differences across the globe in terms of educational systems, access to genomic technologies, and priorities in health care. In this commentary we will review some of the major challenges in educating the health provider workforce about genomic medicine.

Ashwini de Abrew; Vajira H.W. Dissanayake; Bruce R. Korf

2014-01-01T23:59:59.000Z

347

Refining Restriction Enzyme Genome Maps  

Science Journals Connector (OSTI)

A genome map is an ordering of a set of clones according to their believed position on a DNA string. Simple heuristics for genome map assembly based on single restriction enzyme with complete digestion data can lead to inaccuracies and ambiguities. This ... Keywords: constraint query languages, genome mapping, set constraints

Peter Z. Revesz

1998-01-01T23:59:59.000Z

348

SHORT REVIEW Butterfly genomics eclosing  

E-Print Network [OSTI]

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

Beldade, Patrícia

349

Genomics in the ecological arena  

Science Journals Connector (OSTI)

...meeting-report Meeting reports 1001 60 69 70 129 Genomics in the ecological arena Luisa Orsini...Dame, IN 46556, USA 4 The Center for Genomics and Bioinformatics, Indiana University...emerging model system in environmental genomics. Daphnia has been a model species in...

2011-01-01T23:59:59.000Z

350

International milk genomics consortium  

E-Print Network [OSTI]

University, Wooster, OH 44691, USA c University of Idaho, Moscow, ID 83844, USA d University of Colorado. The general goals of the Milk Genomics Consortium are to link the scientific community through milk and geno value of milk's components is known (German, Dillard, & Ward, 2002). The scientific challenge, therefore

Rocke, David M.

351

Genomics ace quits Japan  

Science Journals Connector (OSTI)

... end he was preparing to leave for the University of Chicago in Illinois, frustrated by Japan's lack of support for genomics and doubtful that the country would ever take a ... He is one of the country's best-funded researchers and has led some of Japan's biggest science projects. In addition, he is a successful biotechnology entrepreneur, having ...

David Cyranoski

2012-02-01T23:59:59.000Z

352

Petroleum Institute Scholarly Publications  

E-Print Network [OSTI]

Abu Dhabi The Petroleum Institute Scholarly Publications 2008 #12.. AAkkgguunn Petroleum Engineering SS.. MMoorraadd Petroleum Geosciences RR.. NNuunnnn &&SS indicate Petroleum Institute faculty who are attached to the program shown. Every effort has been made

353

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

E-Print Network [OSTI]

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

2014-01-01T23:59:59.000Z

354

The Institute of Petroleum  

E-Print Network [OSTI]

The Institute of Petroleum Engineering The Institute of Petroleum Engineering (IPE) is a world leading, specialised centre in research, training and teaching, with the largest petroleum engineering and teaching. Our vision is to be the international institute of choice for research and teaching in petroleum

Painter, Kevin

355

The National Cancer Institute,  

E-Print Network [OSTI]

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

356

institution Service Fin  

E-Print Network [OSTI]

with the up eed to have: eferred institut mary DUNS nu me, title, and em enter the infor ded verificatio st universit earching on th e n institution is r "List of Comp ent, or search for the institut thorized. Not Listed? ted, it may still uctions with th n or entity can HScompliant F o determine if i cies

Hutcheon, James M.

357

Policy for Institutional Consultants  

Science Journals Connector (OSTI)

Policy for Institutional Consultants ... The Association of Consulting Chemists and Chemical Engineers, therefore, offers "A Statement of Research Policy Suggested for Inclusion in Research Policies of Educational Institutions" which is the result of a study of a cross section of institutional policies now in ... ...

1946-06-10T23:59:59.000Z

358

OIL & GAS INSTITUTE Introduction  

E-Print Network [OSTI]

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

Mottram, Nigel

359

INSTITUTE OF BIOMEDICAL ENGINEERING  

E-Print Network [OSTI]

INSTITUTE OF BIOMEDICAL ENGINEERING Innovation,Translation, Impact University College London Gower Street London WC1E 6BT UK www.ibme.ucl.ac.uk DesignbyHype!hype.co.uk UCL Institute of Biomedical Engineering #12;Innovating MedTech The Institute of Biomedical Engineering (IBME) provides a much-needed focus

Saunders, Mark

360

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

SciTech Connect (OSTI)

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

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

2012-03-13T23:59:59.000Z

Note: This page contains sample records for the topic "genome institute jgi" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


361

Fast and sensitive multiple alignment of large genomic sequences  

E-Print Network [OSTI]

in Bioinformatics and Genome Research, Universitt Bielefeld, Postfach 100131, 33501 Bielefeld, Germany and 4University of Gttingen, Institute of Microbiology and Genetics, Goldschmidtstr. 1, 37077 Gttingen, Germany Email: Michael Brudno* - brudno... , Blankespoor CM, Wang ZE, Miller W, Rubin EM, Frazer KA: Identification of a coordinate regulator of interleukins 4, 13, and 5 by cross-species sequence comparisons. Science 2000, 288(5463):136-140. 14. Gttgens B, Barton LM, Gilbert JGR, Bench AJ, Sanchez MJ...

Brudno, Michael; Chapman, Michael A; Gottgens, Berthold; Batzoglou, Serafim; Morgenstern, Burkhard

2003-12-23T23:59:59.000Z

362

Genomics Division Home  

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

PIs PIs Mark Biggin Jim Bristow Jan-Fang Cheng Inna Dubchak Suzanna Lewis Chris Mungall Len Pennacchio Eddy Rubin Axel Visel Divisional Information Support Staff Seminars Diversity Directory Contact Us The characterization and analysis of genome sequences from such diverse organisms as humans to the most primitive soil microbe represent a watershed opportunity for biology. The Genomics Division is taking advantage of this wealth of new information. While it is well known that DNA encodes the basic blue print of life, it is not known how best to interpret most of this information. To address this question, laboratories within the division are developing computational, biochemical, genetic, and imaging methods to decipher the complex sequence motifs that control RNA transcription, DNA replication, and chromosome structure. The Division is

363

Institutional Change for Sustainability | Department of Energy  

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

Institutional Change for Sustainability Institutional Change for Sustainability Institutional Change Continuous Improvement Cycle Institutional Change Continuous Improvement Cycle...

364

Complete genome sequence of Kribbella flavida type strain (IFO 14399T)  

SciTech Connect (OSTI)

The genus Kribbella consists of 15 species, with Kribbella flavida (Park et al. 1999) as the type species. The name Kribbella was formed from the acronym of the Korea Research Institute of Bioscience and Biotechnology, KRIBB. Strains of the various Kribbella species were originally isolated from soil, potato, alum slate mine, patinas of catacombs or from horse racecourses. Here we describe the features of K. flavida together with the complete genome sequence and annotation. In addition to the 5.3 Mbp genome of Nocardioides sp. JS614, this is only the second completed genome sequence of the family Nocardioidaceae. The 7,579,488 bp long genome with its 7,086 protein-coding and 60 RNA genes and is part of the Genomic Encyc-lopedia of Bacteria and Archaea project.

Pukall, Rudiger [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute; Glavina Del Rio, Tijana [U.S. Department of Energy, Joint Genome Institute; Copeland, A [U.S. Department of Energy, Joint Genome Institute; Tice, Hope [U.S. Department of Energy, Joint Genome Institute; Cheng, Jan-Fang [U.S. Department of Energy, Joint Genome Institute; Lucas, Susan [U.S. Department of Energy, Joint Genome Institute; Chen, Feng [U.S. Department of Energy, Joint Genome Institute; Nolan, Matt [U.S. Department of Energy, Joint Genome Institute; LaButti, Kurt [U.S. Department of Energy, Joint Genome Institute; Pati, Amrita [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; Mikhailova, Natalia [U.S. Department of Energy, Joint Genome Institute; Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Bruce, David [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Land, Miriam L [ORNL; Hauser, Loren John [ORNL; Chang, Yun-Juan [ORNL; Jeffries, Cynthia [Oak Ridge National Laboratory (ORNL); Chen, Amy [U.S. Department of Energy, Joint Genome Institute; Palaniappan, Krishna [U.S. Department of Energy, Joint Genome Institute; Chain, Patrick S. G. [Lawrence Livermore National Laboratory (LLNL); Rohde, Manfred [HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany; Goker, Markus [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; 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

2010-01-01T23:59:59.000Z

365

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

SciTech Connect (OSTI)

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

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

2011-01-01T23:59:59.000Z

366

Abstract A33: Exploring pediatric cancer genomics with the UCSC Cancer Genomics Browser  

Science Journals Connector (OSTI)

...October 2014 meeting-abstract Pediatric Cancer Genomics and Epigenomics Pediatric Cancer Genomics and Epigenomics: Poster Presentations - Proffered...Abstract A33: Exploring pediatric cancer genomics with the UCSC Cancer Genomics Browser Melissa...

Melissa Cline; Olena Morozova; Teresa Swatloski; Brian Craft; Mary Goldman; David Haussler; Jingchun Zhu

2014-10-15T23:59:59.000Z

367

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

E-Print Network [OSTI]

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...

Chen, Huaming

2012-06-07T23:59:59.000Z

368

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

E-Print Network [OSTI]

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

Rennes, Université de

369

GenomeCons: a web server for manipulating multiple genome sequence alignments and their consensus sequences  

Science Journals Connector (OSTI)

......December 2014 brief-report Applications Note GenomeCons: a web server for manipulating multiple genome sequence alignments and...molecular biological processes. In this study, we developed a web server, GenomeCons, for manipulating multiple genome sequence......

Tetsuya Sato; Mikita Suyama

2014-12-01T23:59:59.000Z

370

Original article Neisseria Base: a comparative genomics  

E-Print Network [OSTI]

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

Jordan, King

371

A Novel Approach for Comparative Genomics  

E-Print Network [OSTI]

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

Paris-Sud XI, Université de

372

Single Cell Whole Genome Amplification  

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

Single Cell Whole Genome Amplification Single Cell Whole Genome Amplification of Uncultivated Organisms Mircea Podar , Martin Keller , and Philip Hugenholtz (* ü ) Abstract Whole genome amplification of single cells is emerging as a powerful technique for accessing the genomes of individual members of microbial communi- ties without the complication of identifying the source of sequence data posed by shotgun sequencing of environmental samples (metagenomics). This method holds particular promise for the molecular unveiling of uncultivated organisms that com- prise the bulk of the microbial diversity and functionality on our planet. 1 Introduction Over the last two decades, it has become increasingly apparent that microbial diversity

373

Genomics: Encyclopaedia of humble DNA  

Science Journals Connector (OSTI)

... ENCODE Project Consortium shows through the analysis of 1% of the human genome that the humble, unpretentious non-gene sequences have essential regulatory roles (Fig. 1). ...

John M. Greally

2007-06-13T23:59:59.000Z

374

Evolutionary Genomics of Prokaryotic Viruses.  

E-Print Network [OSTI]

??Evolutionary history of biological entities is recorded within their nucleic acid sequences and can (sometimes) be deciphered by thorough genomic analysis. In this study we (more)

Krupovic, Mart

2010-01-01T23:59:59.000Z

375

Computational genomics on the grid.  

E-Print Network [OSTI]

??The post-genomic era is characterized by large amount of data available from sequencing projects. The large size of biological datasets, inherent complexity of biological problems (more)

Chen, Chunxi.

2008-01-01T23:59:59.000Z

376

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

E-Print Network [OSTI]

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

Gent, Universiteit

377

The human genome project  

SciTech Connect (OSTI)

The Human Genome Project will obtain high-resolution genetic and physical maps of each human chromosome and, somewhat later, of the complete nucleotide sequence of the deoxyribonucleic acid (DNA) in a human cell. The talk will begin with an extended introduction to explain the Project to nonbiologists and to show that map construction and sequence determination require extensive computation in order to determine the correct order of the mapped entities and to provide estimates of uncertainty. Computational analysis of the sequence data will become an increasingly important part of the project, and some computational challenges are described. 5 refs.

Bell, G.I.

1991-06-01T23:59:59.000Z

378

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

ScienceCinema (OSTI)

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

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

2011-04-28T23:59:59.000Z

379

Institute for Advanced Studies  

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

Institute for Advanced Studies Institute for Advanced Studies Institute for Advanced Studies NMC leverages the strengths of three research universities to build joint programs, develop strategic partnerships, provide common organization and facilities. Contact Leader TBD LANL Program Administrator Pam Hundley (505) 663-5453 Email Building regional partnerships in education, leveraging strengths of three research universities The Institute for Advanced Studies (IAS) works with the three New Mexico research universities (University of New Mexico, New Mexico Tech, and New Mexico State University) to develop research and educational collaborations and partnerships. To facilitate interactions between the universities and LANL, the three New Mexico schools established the New Mexico Consortium (NMC), a nonprofit

380

INSTITUTE COLLOQUIA AND SEMINARS  

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

National Laboratory, Berkeley, California Production of Transactinide Elements in Cold Fusion Reactions at LBNL February 20 Mr. Thomas Henry, Cyclotron Institute, Texas A&M...

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381

Graduate Studies - Cyclotron Institute  

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

the Department of Chemistry, but may elect to work with any Institute faculty research advisor, irrespective of that advisor's departmental affiliation. Research programs at the...

382

Michigan Institute Science and  

E-Print Network [OSTI]

Michigan Institute for Plasma Science and Engineering Seminar Onset of Fast Magnetic Reconnection's magnetosphere, and solar flares. These observations place strong constraints on theory, which must explain

Shyy, Wei

383

Michigan Institute Plasma Science  

E-Print Network [OSTI]

Michigan Institute Plasma Science and Engineering Seminar Neutral Atom Imaging of the Terrestrial re- search includes ion heating in the solar corona, electric double layers, magne- tosphere neutral

Shyy, Wei

384

INSTITUTE OF COMPUTER SCIENCE  

E-Print Network [OSTI]

Institute of Computer Science, Academy of Sciences of the Czech Republic. Pod vodrenskou v 2, 182 07 Prague 8, Czech Republic. phone: (+420)266052083...

385

The Norwegian Polar Institute  

Science Journals Connector (OSTI)

... ON March 1, the Norwegian Polar Institute (Norsk Polarinstitutt) was established in Oslo in order to continue and expand the activity of ...

1948-06-19T23:59:59.000Z

386

Commitment Institutional Change Principle  

Broader source: Energy.gov [DOE]

Commitment can be a crucial element that helps Federal agencies inject and emphasize sustainability in their organizational culture. Institutions and people change when they have made definite...

387

Research - Cyclotron Institute  

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

Overview Viewing gamma ray spectra. The Institute research program focuses on the atomic nucleus, a many-body system of strongly interacting constituents bound together by the...

388

Massachusetts Institute of Technology  

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

132011 Teppei Katori, MIT 1 Teppei Katori for MiniBooNE collaboration Massachusetts Institute of Technology Short baseline neutrino workshop, Fermilab, Batavia, IL, May 13, 2011...

389

Genome Majority Vote (GMV), Version 0.x  

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

Genome Majority Vote (GMV), Version 0.x Genome Majority Vote (GMV), Version 0.x The pipeline runs PRODIGAL gene predictions on all genomes, runs pan-reciprocal BLAST, and...

390

The function of genomes in bioenergetic organelles  

Science Journals Connector (OSTI)

...1998 The organelle genome database project (GOBASE). Nucleic...The mito- chondrial genome of Arabidopsis is composed...native and immigrant information. Trends Plant Sci...Microbial genes in the human genome: lateral transfer...

2003-01-01T23:59:59.000Z

391

Trichoderma: the genomics of opportunistic success  

E-Print Network [OSTI]

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,

Druzhinina, Irina S.

2011-01-01T23:59:59.000Z

392

Cancer genomics and the TCGA project  

Science Journals Connector (OSTI)

...Research September 15, 2011 meeting-abstract Cancer Genomics Cancer Genomics: Poster Presentations - Proffered Abstracts Abstracts...San Francisco, CA Abstract A39: The UCSC Cancer Genomics Browser Brian Craft 1 Kyle Ellrott 1 Mary Goldman...

David Haussler

2010-10-01T23:59:59.000Z

393

From Integrative Genomics to Therapeutic Targets  

Science Journals Connector (OSTI)

...Research. 15 June 2013 review-article Reviews From Integrative Genomics to Therapeutic Targets Rachael Natrajan Paul Wilkerson Corresponding...conventional pathology with genomic profiling and functional genomics have begun to enhance our understanding of the genetic basis...

Rachael Natrajan and Paul Wilkerson

2013-06-15T23:59:59.000Z

394

Cultivation and Genomic, Nutritional, and Lipid Biomarker Characterization of Roseiflexus Strains Closely Related to Predominant In Situ Populations Inhabiting Yellowstone Hot Spring Microbial Mats  

Science Journals Connector (OSTI)

...microbial genomes (IMG) annotation pipeline of the Joint Genome Institute...separated into apolar (containing wax esters) and polar fractions...and alcohols that comprise the wax esters (see reference 44 for...are dominated by C30 to C36 wax esters, including n/iso...

Marcel T. J. van der Meer; Christian G. Klatt; Jason Wood; Donald A. Bryant; Mary M. Bateson; Laurens Lammerts; Stefan Schouten; Jaap S. Sinninghe Damst; Michael T. Madigan; David M. Ward

2010-04-02T23:59:59.000Z

395

10XXX_Primer_v2i2  

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

BDMTC), BDMTC), is accessible to the public at http://img.jgi.doe.gov/. Nikos Kyrpides of JGI's Microbial Genome Analysis Program (MGAP) provided scientific leadership and overall coordination for the IMG project. MGAP manages the Senior management representatives from five national laboratories- Lawrence Berkeley, Lawrence Livermore, Los Alamos, Pacific Northwest, and Oak Ridge-convened on March 2 at the JGI Production Genomics Facility to discuss the Memorandum of Understanding gov- erning the ongoing operations of the JGI. Ari Patrinos, Associate Director for Environmental and Biological Research of the DOE Office of Science, also joined the day-long discussion organ- ized by ORNL Director and former LLNL Deputy Director Jeff Wadsworth. "The bottom line was a major endorsement for JGI's accomplish-

396

VIRAL EVOLUTION Genomic surveillance elucidates  

E-Print Network [OSTI]

VIRAL EVOLUTION Genomic surveillance elucidates Ebola virus origin and transmission during the 2014,12,13 � Robert F. Garry,8 � S. Humarr Khan,3 � Pardis C. Sabeti1,2 � In its largest outbreak, Ebola virus disease is spreading through Guinea, Liberia, Sierra Leone, and Nigeria. We sequenced 99 Ebola virus genomes from 78

Napp, Nils

397

Genome in a Bottle Consortium Work Plan  

E-Print Network [OSTI]

lines for whole genome RMs and design synthetic DNA constructs that could will be a set of well-characterized whole genome and synthetic DNA RMs along

398

C3Bio.org - Tags: Genomics  

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

.jpeg, .jpe, .bmp, .tif, .tiff, .png, .gif) Submit You are here: Home Tags Genomics All Categories Tags: Genomics More tags Categories All Categories 2 Resources 2...

399

Human Genome Research: Decoding DNA  

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

Human Genome Research: Decoding DNA Human Genome Research: Decoding DNA Resources with Additional Information Charles DeLisi As head of DOE's Office of Health and Environmental Research, Charles DeLisi played a pivotal role in proposing and initiating the Human Genome Program in 1986. The U.S. Department of Energy (DOE) has historically been active in supporting human genome research. On September 10, 2003, Secretary of Energy Spencer Abraham presented the Secretary's Gold Award to Aristides Patrinos and Francis Collins for their leadership of the government's Human Genome Project. At DOE's Office of Science, Dr. Patrinos is the Associate Director for Biological and Environmental Research. He has been a researcher at the department's Oak Ridge National Laboratory and Brookhaven National Laboratory.

400

COUNTRY INSTITUTION SIGNING DATE  

E-Print Network [OSTI]

COUNTRY INSTITUTION SIGNING DATE /RENEWAL WEB SITE ALBANIA University of Tirana 11.12.2001 www /RENEWAL WEB SITE FINLAND JAMK University of Applied Sciences 29.10.2009 www.jamk.fi/ FRANCE ?cole INSTITUTION SIGNING DATE /RENEWAL WEB SITE MACEDONIA St. Cyril and Methodius" University of Skopje 11

Di Pillo, Gianni

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401

Nuclear Energy Institutes  

Science Journals Connector (OSTI)

Nuclear Energy Institutes ... The Atomic Energy Commission and the American Society for Engineering Education offer their nuclear energy courses for engineering and science teachers again in the summer of 1960. ... At least 160 college and university teachers will study nuclear science in the seven institutes scheduled. ...

1960-01-11T23:59:59.000Z

402

National Institutes of Health National Institute of Mental Health  

E-Print Network [OSTI]

National Institutes of Health National Institute of Mental Health Department of Health and HumanNational Institute of Mental Health Division of Intramural Research Programs http://intramural.nimh.nih.gov/ [NIMH of Fellowship Training] National Institutes of Health National Institute of Mental Health Department of Health

Baker, Chris I.

403

Draft Genome Sequence  

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

Draft Draft Genome Sequence of Serratia sp. Strain ATCC 39006, a Model Bacterium for Analysis of the Biosynthesis and Regulation of Prodigiosin, a Carbapenem, and Gas Vesicles Peter C. Fineran, a Marina C. Iglesias Cans, a Joshua P. Ramsay, b Nabil M. Wilf, b Desiree Cossyleon, a Matthew B. McNeil, a Neil R. Williamson, b Rita E. Monson, b S. Anette Becher, c Jo-Ann L. Stanton, d Kim Brügger, e Steven D. Brown, f George P. C. Salmond b Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand a ; Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom b ; AgResearch Ltd., Invermay Agricultural Centre, Mosgiel, New Zealand c ; Department of Anatomy, University of Otago, Dunedin, New Zealand d ; EASIH, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom e ; Biosciences Division, Oak Ridge National Laboratory, Oak Ridge,

404

Optimized detection of sequence variation in heterozygous genomes using DNA microarrays with  

E-Print Network [OSTI]

. The optimized design and experimental parameters determined in this study should guide DNA microarray designs Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544; c Center is almost 20 years old. A variety of improvements in probe design and experimental conditions have brought

Botstein, David

405

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

Science Journals Connector (OSTI)

Department of Chemical and Biomolecular Engineering, Department of Biochemistry, Departments of Chemistry and Bioengineering, Institute for Genomic Biology, University of Illinois at Urbana?Champaign, Urbana, Illinois 61801, United States ... We then showed the application of RAGE for improved acetic acid tolerance, a key trait for microbial production of chemicals and fuels. ...

Tong Si; Yunzi Luo; Zehua Bao; Huimin Zhao

2014-04-23T23:59:59.000Z

406

Glass Sponges and Bilaterian Animals Share Derived Mitochondrial Genomic Features: A Common Ancestry or Parallel Evolution?  

E-Print Network [OSTI]

Glass Sponges and Bilaterian Animals Share Derived Mitochondrial Genomic Features: A Common Oceanographic Institution, Fort Pierce, Florida Glass sponges (Hexactinellida) are a group of deep-water benthic glass sponges and bilaterian animals, including an Arg / Ser change in the genetic code

Lavrov, Dennis V.

407

Funding Opportunities | U.S. DOE Office of Science (SC)  

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

Opportunities Opportunities Funding Opportunities Grants & Contracts Support Award Search Find Funding Early Career Research Program Contact Information Office of Science U.S. Department of Energy 1000 Independence Ave., SW Washington, DC 20585 P: (202) 586-5430 JGI Illumina Genome Sequencers BNL Joint Genome Institute genome sequencers. Lawrence Berkeley National Laboratory Print Text Size: A A A RSS Feeds FeedbackShare Page The Office of Science issues two types of funding announcements: Funding Opportunity Announcements (FOAs), which may be open to one or more institution types (please read the eligibility requirements in a given FOA for details); and DOE National Laboratory Announcements, which are open only to DOE Laboratories. FOAs and DOE National Laboratory Announcements may be issued either as

408

A gluttonous plant reveals how its cellular power plant devours foreign DNA  

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

December 20, 2013 December 20, 2013 A gluttonous plant reveals how its cellular power plant devours foreign DNA Amborella trichopoda, a sprawling shrub that grows on just a single island in the remote South Pacific, is the only plant in its family and genus. It is also one of the oldest flowering plants, having branched off from others about 200 million years ago. Now, researchers from Indiana University, with the U.S. Department of Energy Joint Genome Institute (DOE JGI), Penn State University, and the Institute of Research for Development in New Caledonia, have determined a remarkable expansion of the genome of the plant's critical energy-generating structures. Its mitochondria, the plant's energy-producing organelles, in an epic demonstration of horizontal gene transfer, have acquired six genome equivalents of foreign DNA -- one from a

409

Argonne Accelerator Institute  

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

AAI Home AAI Home Welcome Accelerators at Argonne Mission Organization History Document Collection Conferences & Workshops Beams and Applications Seminar Argonne-Fermilab Collaboration Lee Teng Scholarship Program Useful Links Organization The Argonne Accelerator Institute is a matrixed organization. Its members and fellows reside in programmatic Argonne divisions. The Institute reports to the Associate Laboratory Director for Photon Science), and the administrative functions of the Institute are within the PSC directorate. Director: Rodney Gerig Associate Director: Hendrik Weerts ( Director of High Energy Physics Division) Associate Director: Sasha Zholents (Director of Accelerator Systems Division) Associate Director: Robert Janssens ( Director of Argonne Physics Division)

410

Argonne Accelerator Institute  

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

Useful Links Useful Links Argonne National Laboratory Accelerator Sites Conferences Advanced Photon Source (APS) Argonne Wakefield Accelerator (AWA) Argonne Tandem Linear Accelerator System (ATLAS) High Energy Physics Division RIA (????) Link to JACoW (Joint Accelerator Conferences Website) Fermi National Accelerator Laboratory Fermilab-Argonne Collaboration Accelerator Physics Center Workshops Other Accelerator Institutes Energy Recovering Linacs Center for Advance Studies of Accelerators (Jefferson Labs) Center for Beam Physics (LBNL) Accelerator Test Facility (BNL) The Cockcroft Institute (Daresbury, UK) John Adams Institute (Rutherford, UK) ERL2009 to be held at Cornell ERL2007 ERL2005 DOE Laboratory with Accelerators Fermilab Stanford Linear Accelerator Center Brookhaven National Laboratory

411

Human genome. 1993 Program report  

SciTech Connect (OSTI)

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.

Not Available

1994-03-01T23:59:59.000Z

412

Assignment of Orthologous Genes via Genome Rearrangement  

E-Print Network [OSTI]

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

Lonardi, Stefano

413

Shotgun coverage of human genome computing  

E-Print Network [OSTI]

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

Eddy, Sean

414

Course Information IB 364: Human Genome and  

E-Print Network [OSTI]

Course Information IB 364: Human Genome and Bioinformatics On this page: � Course Description � Technical Support Course Description Highlights advances in understanding the human genome, utilizing the human genome, applying bioinformatics to the genome, and realizing its potential to understand human

Kent, Angela

415

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

416

Genomics and ornithology Scott V. Edwards  

E-Print Network [OSTI]

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

Edwards, Scott

417

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

E-Print Network [OSTI]

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

Levin, Judith G.

418

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

E-Print Network [OSTI]

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

Levin, Judith G.

419

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

E-Print Network [OSTI]

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

Wagner, Andreas

420

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

E-Print Network [OSTI]

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

Dolbow, John

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421

Joint Theory Institute  

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

Program General Info Program General Info Registration Info Directions to Argonne Dynamics of Symmetry Breaking A Workshop sponsored by the ANL/UChicago Joint Theory Institute April 13-17, 2009 Argonne National Laboratory, IL The Joint Theory Institute (JTI) is a multi-disciplinary research institution jointly supported at the University of Chicago and Argonne National Laboratory to enhance collaborative research between both institutions in the broad area of theory. This year JTI sponsors a workshop the aim of which is to explore the dynamics of symmetry breaking in a broad range of systems from nuclear physics to string theory, using theoretical insights such as Dyson-Schwinger equations formalism, gauge/gravity duality and lattice QCD. We will focus on systems which exhibit dynamical symmetry breaking and will cover topics essential for understanding nonperturbative QCD and physics of quark-gluon plasma.

422

Petroleum Institute Scholarly Publications  

E-Print Network [OSTI]

Abu Dhabi The Petroleum Institute Scholarly Publications 2009 #12 Mechanical Engineering HHaaddii BBeellhhaajj Petroleum Engineering SSaaddoooonn MMoorraadd Petroleum LLaannggiillllee Advanced University Placement Editors' notes: Names in bold in citations indicate Petroleum

423

Critical Materials Institute  

ScienceCinema (OSTI)

Ames Laboratory Director Alex King talks about the goals of the Critical Materials Institute in diversifying the supply of critical materials, developing substitute materials, developing tools and techniques for recycling critical materials, and forecasting materials needs to avoid future shortages.

Alex King

2013-06-05T23:59:59.000Z

424

INSTITUTE COLLOQUIA AND SEMINARS  

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

April 16 M. Sanchez-Vega and V. E. Jacob, Cyclotron Institute, Texas A&M University Test of the Unitarity of the CKM Matrix via Superallowed + decay. April 23 Dr. Subrata...

425

Low Dose Radiation Research Program: Induction of Genomic Instability in  

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

Induction of Genomic Instability in vivo by Low Doses of 137Cs y Induction of Genomic Instability in vivo by Low Doses of 137Cs y rays, Authors: K. Rithidech1, E.B. Whorton2, M. Tungjai1, E. Ar-Bab1, S.R. Simon1, M. Tawde3 and C.W. Anderson3. Institutions: 1Pathology Department, Stony Brook University, NY 11794-8691, USA, 2University of Texas Medical Branch at Galveston, TX 77550-1047,3Biology Department, Brookhaven National Laboratory, Upton, NY 11973-5000. Information on potential health hazards of radiation at doses below or equal to the level traditionally requiring human radiation protection (less than or equal to 10 cGy) is currently lacking. It is therefore important to characterize early and subsequent in vivo biological response induced by low doses of ionizing radiation because such data should provide information that can help determine whether radiation at this dose level

426

Comparative Genomics of Gossypium spp. through GBS and Candidate Genes Delving into the Controlling Factors behind Photoperiodic Flowering  

E-Print Network [OSTI]

COMPARATIVE GENOMICS OF GOSSYPIUM SPP. THROUGH GBS AND CANDIDATE GENES ? DELVING INTO THE CONTROLLING FACTORS BEHIND PHOTOPERIODIC FLOWERING A Dissertation by CARLA JO LOGAN YOUNG Submitted to the Office of Graduate Studies of Texas A.../Deletion Polymorphism IPGB Institute for Plant Genomics and Biotechnology Ka Non-synonymous Nucleotide Substitution Rate kb Kilobase(s) kDa KiloDalton Ks Synonymous Nucleotide Substitution Rate LD Long Day LD Linkage Disequilibrium MAS Marker Assisted...

Young, Carla Jo Logan

2013-08-09T23:59:59.000Z

427

Determine Institutional Change Sustainability Goals | Department...  

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

Determine Institutional Change Sustainability Goals Determine Institutional Change Sustainability Goals Institutional Change Continuous Improvement Cycle The first step in the...

428

Institutional Change for Sustainability Contacts | Department...  

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

Institutional Change for Sustainability Contacts Institutional Change for Sustainability Contacts For more information about institutional change for sustainability, contact: Jerry...

429

Institutional Change Process for Sustainability  

Broader source: Energy.gov [DOE]

For establishing institutional change in a Federal agency to achieve sustainability or other energy efficiency goals, follow the five-step institutional change process. In accordance with the...

430

Strategies for Achieving Institutional Change  

Broader source: Energy.gov [DOE]

Many strategiesincluding those derived from Institutional Change Principlesmay be used to effect institutional change in support of energy and sustainability objectives.

431

10.1101/gr.133330.111Access the most recent version at doi: published online March 27, 2012Genome Res.  

E-Print Network [OSTI]

Kingdom; 5 Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland; 6 Functional Genomics Center, ETH and University of Zurich, 8057 Zurich, Switzerland; 7 Laval of Science, University of Zurich, 8057 Zurich, Switzerland; 10 Institute of Pharmaceutical Sciences, ETH

Miska, Eric

432

Abstract A33: Exploring pediatric cancer genomics with the UCSC Cancer Genomics Browser  

Science Journals Connector (OSTI)

...University of California, Santa Cruz, CA. The UCSC Cancer Genomics Browser (https://genome-cancer.ucsc.edu) is a set of web-based tools to display, investigate and analyze cancer genomics data and associated clinical data. Experimental quantities...

Melissa Cline; Olena Morozova; Teresa Swatloski; Brian Craft; Mary Goldman; David Haussler; Jingchun Zhu

2014-10-15T23:59:59.000Z

433

Microbial Dark Matter & Beyond  

SciTech Connect (OSTI)

Eddy Rubin, DOE JGI Director, at the 9th Annual Genomics of Energy & Environment Meeting on March 19, 2014 in Walnut Creek, Calif. The talk is related to a study published in the journal Science

Rubin, Eddy [DOE JGI Director

2014-03-19T23:59:59.000Z

434

Towards a standards-compliant genomic and metagenomic publication record  

SciTech Connect (OSTI)

Increasingly we are aware as a community of the growing need to manage the avalanche of genomic and metagenomic data, in addition to related data types like ribosomal RNA and barcode sequences, in a way that tightly integrates contextual data with traditional literature in a machine-readable way. It is for this reason that the Genomic Standards Consortium (GSC) formed in 2005. Here we suggest that we move beyond the development of standards and tackle standards-compliance and improved data capture at the level of the scientific publication. We are supported in this goal by the fact that the scientific community is in the midst of a publishing revolution. This revolution is marked by a growing shift away from a traditional dichotomy between 'journal articles' and 'database entries' and an increasing adoption of hybrid models of collecting and disseminating scientific information. With respect to genomes and metagenomes and related data types, we feel the scientific community would be best served by the immediate launch of a central repository of short, highly structured 'Genome Notes' that must be standards-compliant. This could be done in the context of an existing journal, but we also suggest the more radical solution of launching a new journal. Such a journal could be designed to cater to a wide range of standards-related content types that are not currently centralized in the published literature. It could also support the demand for centralizing aspects of the 'gray literature' (documents developed by institutions or communities) such as the call by the GSCl for a central repository of Standard Operating Procedures describing the genomic annotation pipelines of the major sequencing centers. We argue that such an 'eJournal', published under the Open Access paradigm by the GSC, could be an attractive publishing forum for a broader range of standardization initiatives within, and beyond, the GSC and thereby fill an unoccupied yet increasingly important niche within the current research landscape.

Fenner, Marsha W; Garrity, George M.; Field, Dawn; Kyrpides, Nikos; Hirschman, Lynette; San-sone, Susanna-Assunta; Anguiloi, Samuel; Cole, James R.; Glockner, Frank Oliver; Kolker, Eugene; Kowaluchuk, George; Moran, Mary Ann; Ussery, Dave; White, Owen

2008-04-01T23:59:59.000Z

435

National Institute of Agricultural Botany  

Science Journals Connector (OSTI)

... D. M. Wills, directed attention to the value of the Institute's system of substations. By means of this organization the Institute is able to make recommendations to farmers ... and Scarborough. There are at present two defective links in the Institute's chain of substationsthe Fens and Walesand the Institute hopes that these defects will shortly be remedied ...

1937-11-13T23:59:59.000Z

436

INSTITUTE ON ASSETS & SOCIAL POLICY  

E-Print Network [OSTI]

INSTITUTE ON ASSETS & SOCIAL POLICY LIVING LONGER ON LESS IN MASSACHUSETTS: THE NEW ECONOMIC (IN)SECURITY OF SENIORS Tatjana Meschede Laura Sullivan Thomas Shapiro #12;About the Institute on Assets and Social Policy The Institute on Assets and Social Policy (IASP), a research institute at the Heller School for Social Policy

Snider, Barry B.

437

Argonne Accelerator Institute  

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

Mission Mission The mission of the Argonne Accelerator Institute is centered upon the following related goals: Locate next generation accelerator facilities in Northern Illinois Advance accelerator technology Oversee a selected, strategic, lab-wide, and acclaimed accelerator R&D portfolio In order to accomplish the above goals, the institute has established five objectives. These are coupled to programmatic objectives, and are dependent on each other, but they serve to identify important areas for the institute to focus its activities. Educate the "next generation" of accelerator physicists and engineers Work with area Universities to establish Joint Appointments and Adjunct Professorships Identify students Provide research opportunities at Argonne Work with the US Particle Accelerator School

438

MEETING: Chlamydomonas Annotation Jamboree - October 2003  

SciTech Connect (OSTI)

Shotgun sequencing of the nuclear genome of Chlamydomonas reinhardtii (Chlamydomonas throughout) was performed at an approximate 10X coverage by JGI. Roughly half of the genome is now contained on 26 scaffolds, all of which are at least 1.6 Mb, and the coverage of the genome is ~95%. There are now over 200,000 cDNA sequence reads that we have generated as part of the Chlamydomonas genome project (Grossman, 2003; Shrager et al., 2003; Grossman et al. 2007; Merchant et al., 2007); other sequences have also been generated by the Kasuza sequence group (Asamizu et al., 1999; Asamizu et al., 2000) or individual laboratories that have focused on specific genes. Shrager et al. (2003) placed the reads into distinct contigs (an assemblage of reads with overlapping nucleotide sequences), and contigs that group together as part of the same genes have been designated ACEs (assembly of contigs generated from EST information). All of the reads have also been mapped to the Chlamydomonas nuclear genome and the cDNAs and their corresponding genomic sequences have been reassembled, and the resulting assemblage is called an ACEG (an Assembly of contiguous EST sequences supported by genomic sequence) (Jain et al., 2007). Most of the unique genes or ACEGs are also represented by gene models that have been generated by the Joint Genome Institute (JGI, Walnut Creek, CA). These gene models have been placed onto the DNA scaffolds and are presented as a track on the Chlamydomonas genome browser associated with the genome portal (http://genome.jgi-psf.org/Chlre3/Chlre3.home.html). Ultimately, the meeting grant awarded by DOE has helped enormously in the development of an annotation pipeline (a set of guidelines used in the annotation of genes) and resulted in high quality annotation of over 4,000 genes; the annotators were from both Europe and the USA. Some of the people who led the annotation initiative were Arthur Grossman, Olivier Vallon, and Sabeeha Merchant (with many individual annotators from Europe and the USA). Olivier Vallon has been most active in continued input of annotation information.

Grossman, Arthur R

2007-04-13T23:59:59.000Z

439

Argonne Accelerator Institute  

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

AAI Home AAI Home Welcome Accelerators at Argonne Mission Organization History Document Collection Conferences & Workshops Beams and Applications Seminar Argonne-Fermilab Collaboration Lee Teng Scholarship Program Useful Links Argonne Accelerator Institute In 2006, Argonne Laboratory Director Robert Rosner formed the AAI as a focal point for accelerator initiatives. The institute works to utilize Argonne's extensive accelerator resources, to enhance existing facilities, to determine the future of accelerator development and construction, and to oversee a dynamic and acclaimed accelerator physics portfolio. More Information for: Members * Students Industrial Collaborators - Working with Argonne Link to: Accelerators for America's Future Upcoming Events and News 4th International Particle Accelerator Conference (IPAC'13)

440

Institut Farman 6eme Journe  

E-Print Network [OSTI]

Institut Farman 6eme Journée Institut Farman Jeudi 22 Novembre 2012 FR3311 CNRS www.farman.ens-cachan.fr #12;Institut Farman Les projets Farman ont donné lieu depuis 2007 à 28 projets dont 10 en cours ASTECH (2 thèses en co-direction LMT/SATIE) #12;Institut Farman L'Institut Farman c'est aussi : Equipex

Note: This page contains sample records for the topic "genome institute jgi" from the National Library of EnergyBeta (NLEBeta).
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441

PanFunPro: Bacterial Pan-Genome Analysis Based on the Functional Profiles (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)  

ScienceCinema (OSTI)

Julien Tremblay from DOE JGI presents "Evaluation of Multiplexed 16S rRNA Microbial Population Surveys Using Illumina MiSeq Platorm" at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

Lukjancenko, Oksana [Technical University of Denmark

2013-01-25T23:59:59.000Z

442

Human Genome Education Program  

SciTech Connect (OSTI)

The funds from the DOE Human Genome Program, for the project period 2/1/96 through 1/31/98, have provided major support for the curriculum development and field testing efforts for two high school level instructional units: Unit 1, ''Exploring Genetic Conditions: Genes, Culture and Choices''; and Unit 2, ''DNA Snapshots: Peaking at Your DNA''. In the original proposal, they requested DOE support for the partial salary and benefits of a Field Test Coordinator position to: (1) complete the field testing and revision of two high school curriculum units, and (2) initiate the education of teachers using these units. During the project period of this two-year DOE grant, a part-time Field-Test Coordinator was hired (Ms. Geraldine Horsma) and significant progress has been made in both of the original proposal objectives. Field testing for Unit 1 has occurred in over 12 schools (local and non-local sites with diverse student populations). Field testing for Unit 2 has occurred in over 15 schools (local and non-local sites) and will continue in 12-15 schools during the 96-97 school year. For both curricula, field-test sites and site teachers were selected for their interest in genetics education and in hands-on science education. Many of the site teachers had no previous experience with HGEP or the unit under development. Both of these first-year biology curriculum units, which contain genetics, biotechnology, societal, ethical and cultural issues related to HGP, are being implemented in many local and non-local schools (SF Bay Area, Southern California, Nebraska, Hawaii, and Texas) and in programs for teachers. These units will reach over 10,000 students in the SF Bay Area and continues to receive support from local corporate and private philanthropic organizations. Although HGEP unit development is nearing completion for both units, data is still being gathered and analyzed on unit effectiveness and student learning. The final field testing result from this analysis will contribute to the final revisions of each unit during the second-year of this grant.

Richard Myers; Lane Conn

2000-05-01T23:59:59.000Z

443

Enhancer Identification through Comparative Genomics  

SciTech Connect (OSTI)

With the availability of genomic sequence from numerousvertebrates, a paradigm shift has occurred in the identification ofdistant-acting gene regulatory elements. In contrast to traditionalgene-centric studies in which investigators randomly scanned genomicfragments that flank genes of interest in functional assays, the modernapproach begins electronically with publicly available comparativesequence datasets that provide investigators with prioritized lists ofputative functional sequences based on their evolutionary conservation.However, although a large number of tools and resources are nowavailable, application of comparative genomic approaches remains far fromtrivial. In particular, it requires users to dynamically consider thespecies and methods for comparison depending on the specific biologicalquestion under investigation. While there is currently no single generalrule to this end, it is clear that when applied appropriately,comparative genomic approaches exponentially increase our power ingenerating biological hypotheses for subsequent experimentaltesting.

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

2006-10-01T23:59:59.000Z

444

Perimeter Institute Cosmic Acceleration  

E-Print Network [OSTI]

Wayne Hu Perimeter Institute April 2010 Cosmic Acceleration Dark Energy v. Modified Gravity #12;Outline · Dark Energy vs Modified Gravity · Three Regimes of Modified Gravity · Worked (Toy) Models: f 1998 Discovery #12;Mercury or Pluto? General relativity says Gravity = Geometry And Geometry = Matter-Energy

Hu, Wayne

445

Cancer Research Beckman Institute  

E-Print Network [OSTI]

Cancer Research Beckman Institute FOR ADVANCED SCIENCE AND TECHNOLOGY #12;T The medical and scientific worlds have known for many years that in order to truly understand and treat cancer, the fight has and cancerous tumors have to first be visualized at the smallest scales possible, and then treated in the most

Illinois at Urbana-Champaign, University of

446

Michigan Institute Science and  

E-Print Network [OSTI]

Michigan Institute for Plasma Science and Engineering Seminar Universal Magnetic Structures Prof. Mark Moldwin Dept. of Atmospheric, Oceanic and Space Sciences University of Michigan Thursday, 19 Nov and provide examples on how thinking about discrete structures can add to our understanding of the solar

Shyy, Wei

447

Genomics, Intellectual Disability, and Autism  

Science Journals Connector (OSTI)

To the Editor: Mefford et al. (Feb. 23 issue) provide an excellent review of the genomic factors in autism but do not mention that the quantitative contribution of the enumerated genetic factors to the rates of autism is small, as compared with the contribution of nongenomic (i.e. environmental)... To the Editor: Mefford et al. (Feb. 23 issue)1 provide an excellent review of the genomic factors in autism but do not mention that the quantitative contribution of the enumerated genetic factors to the rates of autism is small, as compared with the ...

2012-06-07T23:59:59.000Z

448

Genomics, Health Care, and Society  

Science Journals Connector (OSTI)

To the Editor: Hudson, in her otherwise comprehensive review article on genomic medicine (Sept. 15 issue), did not mention the issue of reimbursement and the role of payers such as the Centers for Medicare and Medicaid Services. In my outpatient clinic, many patients decline testing for a BRCA... To the Editor: Hudson, in her otherwise comprehensive review article on genomic medicine (Sept. 15 issue),1 did not mention the issue of reimbursement and the role of payers such as the Centers for Medicare and Medicaid Services. In my outpatient clinic, ...

2011-12-15T23:59:59.000Z

449

; Evolution of genes and genomes on the Drosophila phylogeny  

E-Print Network [OSTI]

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

Kellis, Manolis

450

Kin selection, genomics and caste-antagonistic pleiotropy  

Science Journals Connector (OSTI)

...Special feature 1001 14 70 Kin selection, genomics and caste-antagonistic pleiotropy David...evolution of social behaviours. The genomics revolution now provides the opportunity...Outlook: kin selection and social insect genomics The revolution in social insect genomics...

2013-01-01T23:59:59.000Z

451

Genome and proteome annotation: organization, interpretation and integration  

Science Journals Connector (OSTI)

...In addition, the Human Genome Variation Society aims...of genomic variation information. With this in mind...variation within the human genome. The elucidation of...beginning of the 1000 genomes project (Siva 2008) aims to...

2009-01-01T23:59:59.000Z

452

Strategies and tools for whole genome alignments  

SciTech Connect (OSTI)

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

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

2002-11-25T23:59:59.000Z

453

A Gene Map of the Human Genome  

Science Journals Connector (OSTI)

...sanger.ac.uk/ Stanford Human Genome Center http://www-shgc.stanford.edu/ Wellcome Trust Centre for Human...sanger.ac.ukl Stanford Human Genome Center http://www-shgc.stanford.edu/ Wellcome Trust Centre for Human Genetics http...

G. D. Schuler; M. S. Boguski; E. A. Stewart; L. D. Stein; G. Gyapay; K. Rice; R. E. White; P. Rodriguez-Tom; A. Aggarwal; E. Bajorek; S. Bentolila; B. B. Birren; A. Butler; A. B. Castle; N. Chiannilkulchai; A. Chu; C. Clee; S. Cowles; P. J. R. Day; T. Dibling; N. Drouot; I. Dunham; S. Duprat; C. East; C. Edwards; J.-B. Fan; N. Fang; C. Fizames; C. Garrett; L. Green; D. Hadley; M. Harris; P. Harrison; S. Brady; A. Hicks; E. Holloway; L. Hui; S. Hussain; C. Louis-Dit-Sully; J. Ma; A. MacGilvery; C. Mader; A. Maratukulam; T. C. Matise; K. B. McKusick; J. Morissette; A. Mungall; D. Muselet; H. C. Nusbaum; D. C. Page; A. Peck; S. Perkins; M. Piercy; F. Qin; J. Quackenbush; S. Ranby; T. Reif; S. Rozen; C. Sanders; X. She; J. Silva; D. K. Slonim; C. Soderlund; W.-L. Sun; P. Tabar; T. Thangarajah; N. Vega-Czarny; D. Vollrath; S. Voyticky; T. Wilmer; X. Wu; M. D. Adams; C. Auffray; N. A. R. Walter; R. Brandon; A. Dehejia; P. N. Goodfellow; R. Houlgatte; J. R. Hudson Jr.; S. E. Ide; K. R. Iorio; W. Y. Lee; N. Seki; T. Nagase; K. Ishikawa; N. Nomura; C. Phillips; M. H. Polymeropoulos; M. Sandusky; K. Schmitt; R. Berry; K. Swanson; R. Torres; J. C. Venter; J. M. Sikela; J. S. Beckmann; J. Weissenbach; R. M. Myers; D. R. Cox; M. R. James; D. Bentley; P. Deloukas; E. S. Lander; T. J. Hudson

1996-10-25T23:59:59.000Z

454

Unlocking the Secrets of the Genome  

E-Print Network [OSTI]

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

Celniker, Susan E.

455

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

E-Print Network [OSTI]

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

Purugganan, Michael D.

456

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

E-Print Network [OSTI]

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

Sloman, Aaron

457

Whole-genome shotgun assembly and comparison of human genome assemblies  

E-Print Network [OSTI]

Whole-genome shotgun assembly and comparison of human genome assemblies Sorin Istraila , Granger G a whole-genome shotgun assembly (called WGSA) of the human genome generated at Celera in 2001. The Celera. With the nearly complete human DNA sequence [National Center for Biotechnology Information (NCBI) Build 34] now

Shatkay, Hagit

458

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

E-Print Network [OSTI]

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

Goldschmidt, Christina

459

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

E-Print Network [OSTI]

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

Paris-Sud XI, Université de

460

FCTO Projects and the Materials Genome Initiative  

Broader source: Energy.gov [DOE]

Download presentation slides from the DOE Fuel Cell Technologies Office webinar, Materials Genome Initiative, held on December 2, 2014.

Note: This page contains sample records for the topic "genome institute jgi" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


461

GDB - Human Genome Database final report  

SciTech Connect (OSTI)

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

Talbot, C. Conover, Jr.

2002-01-08T23:59:59.000Z

462

Institution Name Institution Name Address Place Zip Notes Website Region  

Open Energy Info (EERE)

Institute for the Built Environment CSU Institute for the Built Institute for the Built Environment CSU Institute for the Built Environment Oval Drive Fort Collins Colorado http www ibe colostate edu Rockies Area Colorado Renewable Energy Collaboratory Colorado Renewable Energy Collaboratory th Street Suite Denver Colorado http www coloradocollaboratory org Rockies Area Colorado School of Mines Colorado Energy Research Institute Colorado School of Mines Colorado Energy Research Institute Illinois Street Golden Colorado http www ceri mines org Rockies Area Denver University International Institute for Environment and Enterprise Denver University International Institute for Environment and Enterprise S University Blvd Denver Colorado http www du edu enviro Research htm Rockies Area EverSealed Windows Inc EverSealed Windows Inc Interlocken Drive Evergreen

463

Analysis of Lake Washington Microbes Shows the Power of Metagenomic  

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

8, 2008 8, 2008 Analysis of Lake Washington Microbes Shows the Power of Metagenomic Approaches WALNUT CREEK, CA-Today's powerful sequencing machines can rapidly read the genomes of entire communities of microbes, but the challenge is to extract meaningful information from the jumbled reams of data. In a paper appearing in Nature Biotechnology August 17, a collaboration headed by researchers at the University of Washington and the U.S. Department of Energy Joint Genome Institute (DOE JGI) describes a novel approach for extracting single genomes and discerning specific microbial capabilities from mixed community ("metagenomic") sequence data. Methylamine-enriched community of Lake Washington Methylamine-enriched community of Lake Washington sediment featuring

464

DATA QUALITY IN GENOME DATABASES (Research Paper)  

E-Print Network [OSTI]

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

Weske, Mathias

465

Genome Biology 2005, 6:312 commentreviewsreportsdepositedresearchinteractionsinformationrefereedresearch  

E-Print Network [OSTI]

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

Kellis, Manolis

466

Genome Biology 2006, 7:320 commentreviewsreportsdepositedresearchinteractionsinformationrefereedresearch  

E-Print Network [OSTI]

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

Pritham, Ellen J.

467

Genome Biology 2004, 6:302 commentreviewsreportsdepositedresearchinteractionsinformationrefereedresearch  

E-Print Network [OSTI]

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

Gent, Universiteit

468

Inferring Ancestral Chloroplast Genomes with Inverted Repeat  

E-Print Network [OSTI]

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

Tang, Jijun

469

Genome Biology 2007, 8:R34 commentreviewsreportsdepositedresearchrefereedresearchinteractionsinformation  

E-Print Network [OSTI]

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

Shneiderman, Ben

470

Computational Approaches Towards Human Genome Annotation  

E-Print Network [OSTI]

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

Singh, Jaswinder Pal

471

Experimental genomics of fitness in yeast  

Science Journals Connector (OSTI)

...Review articles 1001 70 129 Experimental genomics of fitness in yeast Graham Bell * * graham...084533 ) Liti, G. , 2009 Population genomics of domestic and wild yeasts. Nature...1126/science.1091317 ) Experimental genomics of fitness in yeast. | The set of single-gene...

2010-01-01T23:59:59.000Z

472

Rice functional genomics research in China  

Science Journals Connector (OSTI)

...compiled by Zhu Chen Rice functional genomics research in China Bin Han 1 7 * Yongbiao...People's Republic of China Rice functional genomics is a scientific approach that seeks to...facilitated research in rice functional genomics in China. The Ministry of Science and...

2007-01-01T23:59:59.000Z

473

Pairwise Comparison Between Genomic Sequences and  

E-Print Network [OSTI]

COM­ BAT is applied to comparative analysis between yeast genomes, and between the human genomePairwise Comparison Between Genomic Sequences and Optical­maps by Bing Sun A dissertation submitted a research problem and the need of persistence to accomplish a goal. He introduced the CAPO project to me

Mohri, Mehryar

474

Pairwise Comparison Between Genomic Sequences and  

E-Print Network [OSTI]

. In experiments COM- BAT is applied to comparative analysis between yeast genomes, and between the human genomePairwise Comparison Between Genomic Sequences and Optical-maps by Bing Sun A dissertation submitted a research problem and the need of persistence to accomplish a goal. He introduced the CAPO project to me

Mohri, Mehryar

475

SCIENCE, POLITICS. AND THE HUMAN GENOM  

E-Print Network [OSTI]

/ Robert Cook-Deegan. p. cm. Includes bibliographical references. 1. Human Genome Project. 2. Human geneSCIENCE, POLITICS. AND THE HUMAN GENOM A scrupulous . . . narrative of the genesis and opening- DEEGAN #12;#12;#12;#12;The GENE WARS Science, Politics, and theHuman Genome ROBERT COOK-DEEGAN W - W

Richardson, David

476

Genomic Comparisons of Humans and Chimpanzees  

E-Print Network [OSTI]

Genomic Comparisons of Humans and Chimpanzees Ajit Varki1 and David L. Nelson2 1 Glycobiology to human evolution, development, and disease. Sequence differences from the human genome were confirmed in the sidebar Online Sources of Information Regarding the Chimpanzee Genome. At the outset, we also emphasize

477

Genomics-based drug discovery venture  

Science Journals Connector (OSTI)

Genomics-based drug discovery venture ... The Cambridge, Mass.-based company calls its DiscoverEase program "functional genomics"designed to isolate and rapidly determine not only genes but also the related functions of critical proteins. ... Other genomics programs sequence vast amounts of human genetic information. ...

ANN THAYER

1996-10-07T23:59:59.000Z

478

Genomics Rises To Drug Discovery Challenge  

Science Journals Connector (OSTI)

Genomics Rises To Drug Discovery Challenge ... Functional genomics and functional proteomics provide a set of powerful tools to help identify novel cellular targets ... With pharmaceutical companies and biotechnology firms always looking for ways to discover new medicines more quickly and more efficiently, they are increasingly turning to new genomics and proteomics technologies to speed things along. ...

STU BORMAN

1999-04-19T23:59:59.000Z

479

UNL Core for Applied Genomics and Ecology  

E-Print Network [OSTI]

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

Farritor, Shane

480

Bridging mycorrhizal genomics, metagenomics and forest ecology  

E-Print Network [OSTI]

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

Pringle, Anne

Note: This page contains sample records for the topic "genome institute jgi" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
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We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


481

One day seminar: Genetics and Genomics of  

E-Print Network [OSTI]

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

Brierley, Andrew

482

Fraud strikes top genome lab  

SciTech Connect (OSTI)

Francis Collins, head of NIH`s Human Genome Project has informed colleagues that a junior researcher in his lab facke data in five papers co-authored by Collins. This article describes the whole scenario, how it was discovered, and what the reprocussions are.

Marshall, E.

1996-11-08T23:59:59.000Z

483

Nuclear Organization and Genome Function  

E-Print Network [OSTI]

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

Corces, Victor G.

484

List of all HEP Institutions  

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

Top 500 Top 500 HEP and Astrophysics Institutions by Country This document lists the 500 major high-energy physics and astrophysics institutions, sorted by country. Each listing will show a [SPIRES Entry] which gives the full address and phone/fax/url of the institution in addition to links to papers in HEP and people in HEPNAMES. The [Home page], where known, takes you directly to the departmental home page. Alternatively try our INSTITUTIONS search page. This list of the top 500 institutions is chosen by the number of papers from each institution in the past 5 years. Click here for the full list of HEP institutions. Please send any comments, corrections, updates or information on new institutions to: inst@slac.stanford.edu. Last modified at 17:12:32 on 06/30/04.

485

BEEKEEPING INSTITUTE Young Harris College  

E-Print Network [OSTI]

2008 BEEKEEPING INSTITUTE May 15-17 Young Harris College Young Harris, Georgia #12;Young Harris, section comb honey, mead, and beekeeping gadgets. We urge students to participate in the Institute Honey

Delaplane, Keith S.

486

Nitrogen fixation island and rhizosphere competence traits in the genome of root-associated Pseudomonas stutzeri A1501  

Science Journals Connector (OSTI)

...Yuetan Dou Ming Chen Shuzhen Ping Junping Peng Wei Lu Wei Zhang...Claudine Elmerich Min Lin Qi Jin *Biotechnology Research Institute...Microbiol 4 : 824 841 . 29 Xi J ( 2000 ) Hyperproduction of polyesters consisting...USA 103 : 9584 9589 . 43 Jin Q ( 2002 ) Genome sequence of...

Yongliang Yan; Jian Yang; Yuetan Dou; Ming Chen; Shuzhen Ping; Junping Peng; Wei Lu; Wei Zhang; Ziying Yao; Hongquan Li; Wei Liu; Sheng He; Lizhao Geng; Xiaobing Zhang; Fan Yang; Haiying Yu; Yuhua Zhan; Danhua Li; Zhanglin Lin; Yiping Wang; Claudine Elmerich; Min Lin; Qi Jin

2008-01-01T23:59:59.000Z

487

The ecoresponsive genome of Daphnia pulex  

SciTech Connect (OSTI)

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.

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; Kltz, 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

488

PRITZKER INSTITUTE FOR BIOMEDICAL SCIENCE  

E-Print Network [OSTI]

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

Heller, Barbara

489

Development of stable lines of transgenic zebrafish (Danio rerio) to investigate genomic instability  

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

stable lines of transgenic zebrafish (Danio rerio) to stable lines of transgenic zebrafish (Danio rerio) to investigate genomic instability Lahcen Jaafar 1 , Wendy W. Kuhne 2 , Xiayang Xie 3 , Xuan Zheng 1,4 , Jeffrey S. Mumm 3 , and William S. Dynan 1 1 Institute of Molecular Medicine and Genetics, Georgia Health Sciences University, Georgia 30912, USA, 2 Savannah River National Laboratory, Aiken SC 29808, 3 Department of Cellular Biology and Anatomy, Georgia Health Sciences University, Georgia 30912, USA, 4 Genetic Diagnosis Center, Zhongnan Hospital of Wuhan University, Wuhan, China The goal of our project is to investigate low-dose radiation induced-genomic instability. We describe the development of a whole-vertebrate model bearing a reporter transgene that is designed to indicate the presence of genome instability by somatic homologous

490

Complete genome sequence of the sulfate-reducing firmicute Desulfotomaculum ruminis type strain (DLT)  

SciTech Connect (OSTI)

Desulfotomaculum ruminis Campbell and Postgate 1965 is a member of the large genus Desulfotomaculum which contains 30 species and is contained in the family Peptococcaceae. This species is of interest because it represents one of the few sulfate- reducing bacteria that have been isolated from the rumen. Here we describe the features of D. ruminis together with the complete genome sequence and annotation. The 3,969,014 bp long chromosome with a total of 3,901 protein-coding and 85 RNA genes is the second completed genome sequence of a type strain of the genus Desulfotomaculum to be pub- lished, and was sequenced as part of the DOE Joint Genome Institute Community Sequencing Program 2009.

Spring, Stefan [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Visser, Michael [Wageningen University and Research Centre, The Netherlands; Lu, Megan [Los Alamos National Laboratory (LANL); Copeland, A [U.S. Department of Energy, Joint Genome Institute; Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute; Lucas, Susan [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); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Land, Miriam L [ORNL; Hauser, Loren John [ORNL; Larimer, Frank W [ORNL; 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 [U.S. Department of Energy, Joint Genome Institute; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute; Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute; Schaap, Peter J [Wageningen University and Research Centre, The Netherlands; Plugge, Caroline M. [Wageningen University and Research Centre, The Netherlands; Muyzer, Gerard [Universitate Amsterdam; Kuever, Jan [Bremen Institute for Materials Testing, Bremen, Germany; Pereira, Ines A. C. [Universidade Nova de Lisboa, Oeiras, Portugal; Parshina, Sofiya N. [Russian Academy of Sciences, Moscow; Bernier-Latmani, Rizlan [Ecole Polytechnique Federale de Lausanne, Switzerland; Stams, Alfons J. M. [Wageningen University and Research Centre, The Netherlands; Klenk, Hans-Peter [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany

2012-01-01T23:59:59.000Z

491

Insights from Human/Mouse genome comparisons  

SciTech Connect (OSTI)

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

Pennacchio, Len A.

2003-03-30T23:59:59.000Z

492

Form:Research Institution | Open Energy Information  

Open Energy Info (EERE)

Institution Jump to: navigation, search Add a Research or Development Institution Input your research or development institution name below to add to the registry. If your research...

493

Argonne Accelerator Institute  

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

Fermilab Collaboration Fermilab Collaboration Lee Teng Scholarship Program Useful Links The Argonne Accelerator Institute Historical Document Collection Document Access Guide The documents in this collection are held in several repositories, some of which have restricted access. This guide explains the different types of access, and specifies the access levels for each repository. Repositories Name Access Argonne National Laboratory Document Open Access Argonne Research Library Hard Copy Only Beam Dynamics Newsletter Open Access DOE Information Bridge Open Access IEEE Xplore Library Subscription Required JACoW Open Access Journal of Applied Physics Subscription Required Nuclear Instruments & Methods in Physics Research, Section A Subscription Required Physical Review A Subscription Required

494

Standards for a new genomic era  

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

Science paper include David Bruce, Phil Hugenholtz, Nikos Kyrpides, Alla Lapidus, Sam Pitluck, and Jeremy Schmutz. Other collaborating institutions are the Sanger Institute and...

495

DOE Solar Decathlon: New York Institute of Technology: Instituting  

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

New York Institute of Technology's solar house in its permanent location at the U.S. Merchant Marine Academy. New York Institute of Technology's solar house in its permanent location at the U.S. Merchant Marine Academy. Enlarge image Green Machine/Blue Space relies on a hydrogen fuel cell to convert and store energy collected by the house's photovoltaic system. (Courtesy of Kevin Rodgers/U.S. Merchant Marine Academy) Who: New York Institute of Technology What: Green Machine/ Blue Space Where: U.S. Merchant Marine Academy 300 Steamboat Road Kings Point, NY 11024 Map This House Public tours: Not available Solar Decathlon 2005 New York Institute of Technology: Instituting Technology New York Institute of Technology partnered with the U.S. Merchant Marine Academy to develop a solar-powered house for the U.S. Department of Energy Solar Decathlon 2005. The house, called Green Machine/Blue Space, was

496

Institution Name Institution Name Address Place Zip Notes Website Region  

Open Energy Info (EERE)

Institution Name Institution Name Address Place Zip Notes Website Region Institution Name Institution Name Address Place Zip Notes Website Region ARCH Venture Partners Texas ARCH Venture Partners Texas Bridgepoint Parkway Bldg Suite Austin Texas http www archventure com Texas Area ARCH Venture Partners Washington ARCH Venture Partners Washington Second Avenue Suite Seattle Washington http www archventure com Pacific Northwest Area African Wind Energy Association South Africa African Wind Energy Association South Africa South Africa http www afriwea org en south africa htm Alternative Energy Institute Alternative Energy Institute russell long blvd Canyon Texas http www windenergy org Texas Area Applied Process Engineering Laboratory Applied Process Engineering Laboratory Hills Street Suite Richland Washington http www apel org

497

Tokyo Institute of Technology Tokyo Institute of Technology  

E-Print Network [OSTI]

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

Shimodaira, Hidetoshi

498

Minority Educational Institution Student Partnership Program...  

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

Development Minority Educational Institution Student Partnership Program (MEISPP) Minority Educational Institution Student Partnership Program (MEISPP) Our Minority Educational...

499

Plumbing Manufacturer's Institute Ex Parte Communication Regarding...  

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

Plumbing Manufacturer's Institute Ex Parte Communication Regarding Showerheads Plumbing Manufacturer's Institute Ex Parte Communication Regarding Showerheads Letter to Department...

500

Partnering Institution Name Partnering Institution Name Place Type  

Open Energy Info (EERE)

Partnering Institution Name Partnering Institution Name Place Type Partnering Institution Name Partnering Institution Name Place Type of Partnership Partner Center Partner Year Partner Description Link Technologies Technologies North Lexington Massachusetts Incubator National Center for Photovoltaics M M St Paul Minnesota CRADA http www nrel gov pv pv manufacturing html A O Smith A O Smith Milwaukee Wisconsin Test Evaluation Partner Electricity Resources Building Systems Integration A123Systems A123Systems Watertown Massachusetts CRADA Transportation Technologies and Systems http www nrel gov news press html AAON AAON Tulsa Oklahoma Test Evaluation Partner Electricity Resources Building Systems Integration AQUA Products AQUA Products Prosperity South Carolina Test Evaluation Partner Electricity Resources Building Systems Integration