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1

Joint Genome Institute (JGI) Projects at NERSC  

NLE Websites -- All DOE Office Websites (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

DOE Joint Genome Institute: JGI & NERSC Partner for GenomicHigh...  

NLE Websites -- All DOE Office Websites (Extended Search)

April 12, 2010 JGI & NERSC Partner for Genomic High-performance Computing WALNUT CREEK, CA-The Department of Energy Joint Genome Institute (JGI) and the National Energy Research...

3

Eukaryotic Genomics Data from the DOE Joint Genome Institute (JGI)  

DOE Data Explorer (OSTI)

From the JGI webportal users can choose Eukaryotic genomes from a photo list, access the JGI FTP directories to download data files, use the Tree of Life navigation tool, or choose a genome and go directly to a website specific to that one genome. The individual sites include direct access to download sequence files, BLAST, search, view and navigate the genomic annotations.

4

DOE Joint Genome Institute: DOE JGI Announces 2011 Community Sequencing  

NLE Websites -- All DOE Office Websites (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

5

DOE Joint Genome Institute: DOE JGI Releases Expanded Version of  

NLE Websites -- All DOE Office Websites (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

6

JGI Fungal Genomics Program  

E-Print Network (OSTI)

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

Grigoriev, Igor V.

2012-01-01T23:59:59.000Z

7

DOE Joint Genome Institute: 2013 DOE JGI Community Sequencing...  

NLE Websites -- All DOE Office Websites (Extended Search)

transposon mutagenesis (TnSeq), a method of generating large sets of random mutations in target DNA. These techniques will allow the DOE JGI to study in greater depth the genomes...

8

JGI Fungal Genomics Program  

E-Print Network (OSTI)

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

Grigoriev, Igor V.

2011-01-01T23:59:59.000Z

9

Microbial Genomics Data from the DOE Joint Genome Institute (JGI)  

DOE Data Explorer (OSTI)

As of March 2008, The Joint Genome Institute has released 296 Prokaryotic microbial sites, with 216 in finished status.

10

JGI Fungal Genomics Program  

SciTech Connect

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

Grigoriev, Igor V.

2011-03-14T23:59:59.000Z

11

DOE JGI Microbial Genomics & Metagenomics Workshops  

NLE Websites -- All DOE Office Websites (Extended Search)

DOE Joint Genome Institute Microbial Genomics & Metagenomics Workshops Walnut Creek, California The U.S. Department of Energy Joint Genome Institute (DOE JGI) will be offering...

12

Integrated Microbial Genomes (IMG) System from the DOE Joint Genome Institute (JGI)  

DOE Data Explorer (OSTI)

The integrated microbial genomes (IMG) system is a data management, analysis and annotation platform for all publicly available genomes. IMG contains both draft and complete JGI microbial genomes integrated with all other publicly available genomes from all three domains of life, together with a large number of plasmids and viruses. IMG provides tools and viewers for analyzing and annotating genomes, genes and functions, individually or in a comparative context. Since its first release in 2005, IMG's data content and analytical capabilities have been constantly expanded through quarterly releases. IMG is provided by the DOE-Joint Genome Institute (JGI) and is available from http://img.jgi.doe.gov. [Abstract from The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions; Victor M. Markowitz, Ernest Szeto, Krishna Palaniappan, Yuri Grechkin, Ken Chu, I-Min A. Chen, Inna Dubchak, Iain Anderson, Athanasios Lykidis, Konstantinos Mavromatis, Natalia N. Ivanova and Nikos C. Kyrpides; Nucleic Acids Research, 2008, Vol. 36. (Database Issue) See also the companion system, Integrated Microbial Genomes with Microbiome Samples.

13

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

NLE Websites -- All DOE Office Websites (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

14

DOE Joint Genome Institute: JGI's Susannah Tringe Receives Prestigious...  

NLE Websites -- All DOE Office Websites (Extended Search)

Energy (DOE) Office of Science Early Career Research Program has awarded a grant to DOE Joint Genome Institute scientist Susannah Green Tringe to conduct genomic studies of...

15

JGI - Distinguished Postdoctoral Fellow in Genomics  

NLE Websites -- All DOE Office Websites (Extended Search)

Distinguished Postdoctoral Fellow in Genomics The Department of Energy Joint Genome Institute (DOE JGI) in Walnut Creek, CA is soliciting Postdoctoral Fellows working in the...

16

DOE Joint Genome Institute: Breaking Biomass Better, DOE JGI...  

NLE Websites -- All DOE Office Websites (Extended Search)

12, 2010 Breaking Biomass Better: DOE JGI Sequences Wood Decaying Fungus to Advance Biofuels Prospects WALNUT CREEK, CA-One of the challenges in making cellulosic biofuels...

17

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

NLE Websites -- All DOE Office Websites (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

18

JGI Genomics and Bioinformatics for Undergraduate Educators Workshop |  

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

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

19

The US Department of Energy Joint Genome Institute Microbial Genome Program  

E-Print Network (OSTI)

Institute A typical genome sequencing project AssemblyInstitute A typical genome sequencing project AssemblyJGI Microbial Sequencing US DOE Joint Genome Institute JGI

Lapidus, Alla

2005-01-01T23:59:59.000Z

20

JGI - Sequencing  

NLE Websites -- All DOE Office Websites (Extended Search)

Sequencing Product Offerings Statistics Sequencing Plans Educational Resources MyJGI: Information for Collaborators The Department of Energy's Joint Genome Institute (DOE JGI)...

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

JGI - Ergonomics  

NLE Websites -- All DOE Office Websites (Extended Search)

Ergonomics at DOE JGI U.S. Department of Energy (DOE) Joint Genome Institute (JGI) Ergonomics Program aims to address ergonomics risks in the laboratories. Laboratory Ergonomics...

22

JGI - 2009 Genome Sequencing Targets  

NLE Websites -- All DOE Office Websites (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

23

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

NLE Websites -- All DOE Office Websites (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

24

JGI Partners  

NLE Websites -- All DOE Office Websites (Extended Search)

Partners The DOE Joint Genome Institute (DOE JGI) integrates the genomic capabilities of six partner institutions: Lawrence Berkeley National Laboratory, Lawrence Livermore...

25

JGI CSP Delivers First Moss Genome  

NLE Websites -- All DOE Office Websites (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).

26

Genome Improvement at JGI-HAGSC  

Science Conference Proceedings (OSTI)

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

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

2012-03-03T23:59:59.000Z

27

Genomic Sequencing of Single Bacterial Cells (2010 JGI User Meeting)  

SciTech Connect

Tanja Woyke from the DOE JGI on the "Genomic Sequencing of Single Bacterial Cells" on March 26, 2010 at the 5th Annual DOE JGI User Meeting

Woyke, Tanje

2010-03-26T23:59:59.000Z

28

JGI - The Facility  

NLE Websites -- All DOE Office Websites (Extended Search)

The Facility aerial photo of JGI The Joint Genome Institute (foreground) The U.S. Department of Energy (DOE) Joint Genome Institute (JGI) is located in the former Dow Chemical...

29

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

SciTech Connect

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

Rubin, Eddy

2010-01-25T23:59:59.000Z

30

JGI - Genomic Technologies  

NLE Websites -- All DOE Office Websites (Extended Search)

opportunities for technological access to our user services (including single cell genomics and DNA synthesis). Our Department serves at the interface between the Project...

31

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

NLE Websites -- All DOE Office Websites (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

32

JGI - Structural Genomics Program  

NLE Websites -- All DOE Office Websites (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

33

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

Science Conference Proceedings (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

2011-03-23T23:59:59.000Z

34

Genomics of Extinct and Endangered Species (2011 JGI User Meeting)  

Science Conference Proceedings (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. Stephen Shuster of Penn State University gives a presentation on "Genomics of Extinct and Endangered Species" at the 6th annual Genomics of Energy & Environment Meeting on March 23, 2011

Shuster, Stephen [Penn State University

2011-03-23T23:59:59.000Z

35

JGI - Sequencing for the DOE Genomics: GTL Program  

NLE Websites -- All DOE Office Websites (Extended Search)

Educational Resources MyJGI: Information for Collaborators Sequencing for the DOE Genomics: GTL Program For status information, see the Genome Projects section. For more...

36

Tackling the Triple-Threat Genome of Miscanthus x giganteus (2010 JGI User Meeting)  

Science Conference Proceedings (OSTI)

Steve Moose from the University of Illinois at Urbana-Champaign and the Energy Biosciences Institute on "Tackling the Triple-Threat Genome of Miscanthus x giganteus" on March 25, 2010 at the 5th Annual DOE JGI User Meeting

Moose, Steve

2010-03-25T23:59:59.000Z

37

The US Department of Energy Joint Genome Institute Microbial Genome Program  

E-Print Network (OSTI)

Community Sequencing Program (CSP). 24 proposals accepted 10http://www.jgi.doe.gov/CSP/ US DOE Joint Genome InstituteGTL) Community Sequencing Program (CSP) JGI Internal Program

Lapidus, Alla

2005-01-01T23:59:59.000Z

38

JGI - Budget  

NLE Websites -- All DOE Office Websites (Extended Search)

Operating Expenses The U.S. Department of Energy (DOE) Joint Genome Institute (JGI) is funded primarily by the DOE Office of Biological and Environmental Research, part of the DOE...

39

DOE JGI Microbial Genomics & Metagenomics Workshops  

NLE Websites -- All DOE Office Websites (Extended Search)

Organizers Workshop Organizers Nikos Kyrpides Head of the Prokaryotic Super Program, DOE JGI Kostas Mavrommatis Scientific Programs, DOE JGI Marsha Fenner Sr. Admin, Scientific...

40

DOE Joint Genome Institute: IMG ER Goes Primetime: Provides Expert...  

NLE Websites -- All DOE Office Websites (Extended Search)

that regulate our environment. Scientists at the U.S. Department of Energy (DOE) Joint Genome Institute (JGI) and the Biological Data Management and Technology Center...

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

JGI - Intro to Genomics 1  

NLE Websites -- All DOE Office Websites (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

42

JGI's Pennacchio Wins Presidential Early Career Award  

NLE Websites -- All DOE Office Websites (Extended Search)

Department of Energy Joint Genome Institute (JGI) and senior staff scientist in the Genomics Division of Lawrence Berkeley National Laboratory, is among this year's recipients of...

43

DOE JGI Microbial Genomics & Metagenomics Workshops  

NLE Websites -- All DOE Office Websites (Extended Search)

Logistics What to Bring LAPTOP COMPUTERS REQUIRED Please plan to bring your own laptop to the JGI in order to participate in the Workshop. Details regarding system requirements...

44

DOE JGI Microbial Genome Reannotation Workshop  

NLE Websites -- All DOE Office Websites (Extended Search)

Logistics What to Bring LAPTOP COMPUTERS REQUIRED Please plan to bring your own laptop to the JGI in order to participate in the Workshop. Details regarding system requirements...

45

JGI - About Us  

NLE Websites -- All DOE Office Websites (Extended Search)

of the U.S. Department of Energy (DOE) Joint Genome Institute (JGI) is to advance genomics in support of the DOE missions related to clean energy generation and environmental...

46

DOE Joint Genome Institute: Opening New Frontiers: First Volume...  

NLE Websites -- All DOE Office Websites (Extended Search)

in the spirit of his goal of providing "light to the obscure," the Department of Energy Joint Genome Institute (DOE JGI) has published the initial "volume" of the Genomic...

47

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

Science Conference Proceedings (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

2011-10-12T23:59:59.000Z

48

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

Science Conference Proceedings (OSTI)

Carl Zimmer, a reporter for the New York Times, speaks on "The Genome Beat," the opening keynote presentation at the JGI User 7th Annual Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, Calif

Zimmer, Carl [New York Times

2012-03-20T23:59:59.000Z

49

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

NLE Websites -- All DOE Office Websites (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 ...........................................................

50

DOE Joint Genome Institute: Preparing for a Thaw: How Arctic...  

NLE Websites -- All DOE Office Websites (Extended Search)

Research) To answer this question, researchers from the U.S. Department of Energy (DOE) Joint Genome Institute (JGI), the Earth Sciences Division (ESD) within Berkeley Lab, and the...

51

DOE Joint Genome Institute: Trillions Served: Massive, Complex...  

NLE Websites -- All DOE Office Websites (Extended Search)

the number of burgers served has eclipsed the billion mark, while the U.S. Department of Energy (DOE) Joint Genome Institute (JGI) will now serve up trillions of nucleotides of...

52

JGI - Undergraduate Research in Functional Genomics  

NLE Websites -- All DOE Office Websites (Extended Search)

Education Microbial Genome Analysis Microbial Functional Genomics Undergraduate Research in Microbial Functional Genomics Genomics not only can answer questions about known genes,...

53

JGI - Education  

NLE Websites -- All DOE Office Websites (Extended Search)

Education Microbial Genome Analysis Microbial Functional Genomics DOE JGI's Education Program was conceived to develop educational programs and tools, centered on large-scale DNA...

54

JGI - Careers  

NLE Websites -- All DOE Office Websites (Extended Search)

Laboratory Employment Information LLNL | LBNL Distinguished Postdoctoral Fellow in Genomics DOE JGI Visiting Scientist Program Diversity (LBNL Life Sciences and Genomics Divsions)...

55

JGI in the News  

NLE Websites -- All DOE Office Websites (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

56

Association Genetics of Populus trichocarpa or Resequencing in Populus: Towards Genome Wide Association Genetics (2011 JGI User Meeting)  

Science Conference Proceedings (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. Gerry Tuskan of Oak Ridge National Laboratory on "Resequencing in Populus: Towards Genome Wide Association Genetics" at the 6th annual Genomics of Energy & Environment Meeting on March 23, 2011

Tuskan, Gerry

2011-03-23T23:59:59.000Z

57

2009 JGI DOE User Meeting  

NLE Websites -- All DOE Office Websites (Extended Search)

Department of Energy Joint Genome Institute (JGI) Fourth Annual User Meeting Marriott Hotel in Walnut Creek, California March 25-27, 2009 The U.S. Department of Energy Joint...

58

Closing Keynote Presentation on the Genomics of Energy and the Environment (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)  

Science Conference Proceedings (OSTI)

Steve Benner, a distinguished chemist at the Foundation for Applied Molecular Evolution, Westheimer Institute of Science and Technology, provides the closing keynote address for the JGI 7th Annual Users Meeting: Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, California.

Benner, Stephen [Foundation for Applied Molecular Evolution, Westheimer Institute of Science and Technology

2012-03-22T23:59:59.000Z

59

JGI - FY2002 Sequencing for the DOE Microbial Genome Program  

NLE Websites -- All DOE Office Websites (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

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JGI - A Genomic Encyclopedia of Bacteria and Archaea  

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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)

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.


61

JGI - FY2003 Sequencing for the DOE Microbial Genome Program  

NLE Websites -- All DOE Office Websites (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

62

JGI - FY2005 Sequencing for the DOE Microbial Genome Program  

NLE Websites -- All DOE Office Websites (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

63

New Technique Improves Microbial Genome Assembly | U.S. DOE Office...  

Office of Science (SC) Website

FeedbackShare Page Click to enlarge photo. Enlarge Photo Image courtesy of DOE Joint Genome Institute (JGI), Roy Kaltschmidt DOE JGI researchers have helped develop a...

64

JGI - FY2004 Sequencing for the DOE Microbial Genome Program  

NLE Websites -- All DOE Office Websites (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

65

JGI - FY2001 Sequencing for the DOE Microbial Genome Program  

NLE Websites -- All DOE Office Websites (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

66

JGI - FY2007 Sequencing for the DOE Microbial Genome Program  

NLE Websites -- All DOE Office Websites (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

67

FORGING THE FUTURE OF THE DOE JGI  

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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

68

JGI User Meeting 2007  

NLE Websites -- All DOE Office Websites (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. ツゥ2006-2007, The Regents of the University of California. Last updated May 9, 2007. Disclaimer | Webmaster Agenda

69

DOE JGI Releases Soybean Genome Assembly  

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SoyMap team, comprising principal investigator Scott Jackson, Gary Stacey and Henry Nguyen, Jeff Doyle of Cornell University, William Beavis of the National Center for Genome...

70

Genomic and Systems Biology Analyses of Social Behavior or Evolutionary Genomic Analyses of Insect Society: Eat, Drink, and Be Scary (2011 JGI User Meeting)  

Science Conference Proceedings (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. Gene Robinson of the University of Illinois on "Genomic and Systems Biology Analyses of Social Behavior" at the 6th Annual Genomics of Energy & Environment Meeting on March 23, 2011

Robinson, Gene

2011-03-23T23:59:59.000Z

71

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

Science Conference Proceedings (OSTI)

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

Goldberg, Robert [UCLA

2012-03-21T23:59:59.000Z

72

DOE Joint Genome Institute 2008 Progress Report  

Science Conference Proceedings (OSTI)

While initially a virtual institute, the driving force behind the creation of the DOE Joint Genome Institute in Walnut Creek, California in the Fall of 1999 was the Department of Energy's commitment to sequencing the human genome. With the publication in 2004 of a trio of manuscripts describing the finished 'DOE Human Chromosomes', the Institute successfully completed its human genome mission. In the time between the creation of the Department of Energy Joint Genome Institute (DOE JGI) and completion of the Human Genome Project, sequencing and its role in biology spread to fields extending far beyond what could be imagined when the Human Genome Project first began. Accordingly, the targets of the DOE JGI's sequencing activities changed, moving from a single human genome to the genomes of large numbers of microbes, plants, and other organisms, and the community of users of DOE JGI data similarly expanded and diversified. Transitioning into operating as a user facility, the DOE JGI modeled itself after other DOE user facilities, such as synchrotron light sources and supercomputer facilities, empowering the science of large numbers of investigators working in areas of relevance to energy and the environment. The JGI's approach to being a user facility is based on the concept that by focusing state-of-the-art sequencing and analysis capabilities on the best peer-reviewed ideas drawn from a broad community of scientists, the DOE JGI will effectively encourage creative approaches to DOE mission areas and produce important science. This clearly has occurred, only partially reflected in the fact that the DOE JGI has played a major role in more than 45 papers published in just the past three years alone in Nature and Science. The involvement of a large and engaged community of users working on important problems has helped maximize the impact of JGI science. A seismic technological change is presently underway at the JGI. The Sanger capillary-based sequencing process that dominated how sequencing was done in the last decade is being replaced by a variety of new processes and sequencing instruments. The JGI, with an increasing number of next-generation sequencers, whose throughput is 100- to 1,000-fold greater than the Sanger capillary-based sequencers, is increasingly focused in new directions on projects of scale and complexity not previously attempted. These new directions for the JGI come, in part, from the 2008 National Research Council report on the goals of the National Plant Genome Initiative as well as the 2007 National Research Council report on the New Science of Metagenomics. Both reports outline a crucial need for systematic large-scale surveys of the plant and microbial components of the biosphere as well as an increasing need for large-scale analysis capabilities to meet the challenge of converting sequence data into knowledge. The JGI is extensively discussed in both reports as vital to progress in these fields of major national interest. JGI's future plan for plants and microbes includes a systematic approach for investigation of these organisms at a scale requiring the special capabilities of the JGI to generate, manage, and analyze the datasets. JGI will generate and provide not only community access to these plant and microbial datasets, but also the tools for analyzing them. These activities will produce essential knowledge that will be needed if we are to be able to respond to the world's energy and environmental challenges. As the JGI Plant and Microbial programs advance, the JGI as a user facility is also evolving. The Institute has been highly successful in bending its technical and analytical skills to help users solve large complex problems of major importance, and that effort will continue unabated. The JGI will increasingly move from a central focus on 'one-off' user projects coming from small user communities to much larger scale projects driven by systematic and problem-focused approaches to selection of sequencing targets. Entire communities of scientists working in a particular field, such as feeds

Gilbert, David

2009-03-12T23:59:59.000Z

73

DOE Joint Genome Institute 2008 Progress Report  

E-Print Network (OSTI)

National Labora- tory (PNNL), and the HudsonAlpha InstituteLand JGI Paci?c Northwest National Laboratory (PNNL) Since2004, PNNL has collaborated with DOE JGI in the area of

Gilbert, David

2009-01-01T23:59:59.000Z

74

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

Science Conference Proceedings (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

2010-03-25T23:59:59.000Z

75

From Fjords to Open Seas: Ecological Genomics of Expanding Oxygen Minimum Zones (2010 JGI User Meeting)  

Science Conference Proceedings (OSTI)

Steven Hallam of the University of British Columbia talks "From Fjords to Open Seas: Ecological Genomics of Expanding Oxygen Minimum Zones" on March 24, 2010 at the 5th Annual DOE JGI User Meeting

Hallam, Steven

2010-03-24T23:59:59.000Z

76

DOE Joint Genome Institute Completes Soybean Genome- Data Released to  

NLE Websites -- All DOE Office Websites (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

77

DOE Joint Genome Institute: New Genomic Model Defines Microbes by  

NLE Websites -- All DOE Office Websites (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

78

JGI - DOE Mission Relevance  

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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

79

DOE JGI CSP 2012 PI Workshop  

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CSP 2012 PI Workshop DOE Joint Genome Institute Walnut Creek, California The DOE-JGI is organizing a two-day workshop for Principal Investigators on successful CSP 2012 proposals...

80

JGI - Scientific Posters  

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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

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

14128_JGI_CR_07:2007 JGI Progress Report  

NLE Websites -- All DOE Office Websites (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

82

doi:10.1093/nar/gkr947 The Genome Portal of the Department of Energy Joint Genome Institute  

E-Print Network (OSTI)

The Department of Energy (DOE) Joint Genome Institute (JGI) is a national user facility with massive-scale DNA sequencing and analysis capabilities dedicated to advancing genomics for bioenergy and environmental applications. Beyond generating tens of trillions of DNA bases annually, the Institute develops and maintains data management systems and specialized analytical capabilities to manage and interpret complex genomic data sets, and to enable an expanding community of users around the world to analyze these data in different contexts over the web. The JGI Genome Portal

Igor V. Grigoriev; Henrik Nordberg; Igor Shabalov; Andrea Aerts; Mike Cantor; David Goodstein; Alan Kuo; Simon Minovitsky; Roman Nikitin; Robin A. Ohm; Robert Otillar; Alex Poliakov; Igor Ratnere; Robert Riley; Tatyana Smirnova; Daniel Rokhsar; Inna Dubchak

2011-01-01T23:59:59.000Z

83

CyanoGEBA: A Better Understanding of Cynobacterial Diversity through Large-scale Genomics (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)  

Science Conference Proceedings (OSTI)

Patrick Shih, representing both the University of California, Berkeley and JGI, gives a talk titled "CyanoGEBA: A Better Understanding of Cynobacterial Diversity through Large-scale Genomics" at the JGI 7th Annual Users Meeting: Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, California.

Shih, Patrick [Kerfeld Lab, UC Berkeley and JGI

2012-03-22T23:59:59.000Z

84

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

NLE Websites -- All DOE Office Websites (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

85

Reprogramming Bacteria to Seek and Destroy Small Molecules (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)  

Science Conference Proceedings (OSTI)

Justin Gallivan, of Emory University presents a talk titled "Reprogramming Bacteria to Seek and Destroy Small Molecules" at the JGI User 7th Annual Genomics of Energy & Environment Meeting on March 21, 2012 in Walnut Creek, Calif

Gallivan, Justin [Emory University

2012-03-21T23:59:59.000Z

86

DOE Joint Genome Institute: DNA of Uncultured Organisms Sequenced Using  

NLE Websites -- All DOE Office Websites (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.

87

DOE Joint Genome Institute: Soybean Genome Analysis Reveals Pathways for  

NLE Websites -- All DOE Office Websites (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

88

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

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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,

89

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

Science Conference Proceedings (OSTI)

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

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

2013-01-01T23:59:59.000Z

90

The DOE-JGI Standard Operating Procedure for the Annotations of the Microbial Genomes  

E-Print Network (OSTI)

1:63-67 DOI:10.4056/sigs.632 The DOE-JGI Standard OperatingtRNA-Scan, RNAmmer, Rfam, IMG-ER. The DOE-JGI MicrobialAnnotation Pipeline (DOE-JGI MAP) supports gene prediction

Mavromatis, Konstantinos

2010-01-01T23:59:59.000Z

91

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

Science Conference Proceedings (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

2012-03-22T23:59:59.000Z

92

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

Science Conference Proceedings (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

93

DOE Joint Genome Institute: Genome of Simplest Animal Reveals Ancient  

NLE Websites -- All DOE Office Websites (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.

94

OSCARS helps build new circuit for JGI-NERS  

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Studies ツサ OSCARS JGI Studies ツサ 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

95

Building Communities: The Community Sequencing Program at JGI (2011 JGI User Meeting)  

Science Conference Proceedings (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. DOE JGI Deputy Director Jim Bristow gives a presentation on the Community Sequencing Program at the 6th annual Genomics of Energy and Environment Meeting on March 23, 2011

Bristow, Jim [DOE JGI Deputy Director

2011-03-23T23:59:59.000Z

96

cr_14229_JGI_Primer_Fall07 :Layout 1  

NLE Websites -- All DOE Office Websites (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 Brasテュlia (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.

97

Getting to the Root of Things: Spatiotemporal Regulatory Networks (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)  

Science Conference Proceedings (OSTI)

Siobhan Brady from University of California, Davis, gives a talk titled "tGetting to the Root of things: Spatiotemporal Regulatory Networks" at the JGI 7th Annual Users Meeting: Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, California.

Brady, Siobhan [UC Davis

2012-03-22T23:59:59.000Z

98

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

Science Conference Proceedings (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

2012-03-22T23:59:59.000Z

99

Los Alamos National Laboratory: Bioscience Division: Genome Science...  

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areas. B-6 Teams Applications Bioinformatics Computational Finishing Project Management Sequencing Technology Focus on Research Links Resources Joint Genome Institute (JGI)...

100

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

Science Conference Proceedings (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

2011-10-13T23:59:59.000Z

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.


101

JGI - Organization Structure  

NLE Websites -- All DOE Office Websites (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

102

JGI - Why Sequence Six Archaea?  

NLE Websites -- All DOE Office Websites (Extended Search)

Huber (Univ. Regensburg); Nikos Kyrpides (JGI), William Whitman (Univ. of Georgia). Genome Portal Sites: Methanoculleus marisnigri JR1 , Thermofilum pendens Hrk 5 Home >...

103

Synthetic Metagenomics: Converting digital information back to Biology (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)  

SciTech Connect

Sam Deutsch of the DOE JGI on "Synthetic Metagenomics: Converting digital information back to Biology" at the 8th Annual Genomics of Energy & Environment Meeting in Walnut Creek, Calif.

Deutsch, Sam [DOE Joint Genome Institute

2013-03-01T23:59:59.000Z

104

DOE Joint Genome Institute: Scientists Publish Complete Genetic Blueprint  

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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

105

JGI - Directions  

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Map to JGI Directions from Directions from key local start points, public transit Home > About Us > Map to JGI UC logo DOE logo Contact Us Credits Disclaimer Access...

106

10897_JGI_Progress_CR  

NLE Websites -- All DOE Office Websites (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

107

DOE JGI CSP 2012 PI Workshop  

NLE Websites -- All DOE Office Websites (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

108

JGI Computing 5-Year Strategic Plan  

DOE Green Energy (OSTI)

A broad range of scientific goals and a similarly diverse set of consumers drive the informatics requirements and computing needs of the JGI. The scope of work in this area encompasses not only the informatics and analysis pipelines in support of the PGF sequence production, but also the integration of data from a variety of sources and sophisticated large scale analyses led by investigators within JGI and driven by the user science community. In laying out a forward looking strategy, the full range of these activities need to be examined together to build a comprehensive program that will serve as a catalyst for the DOE research community. The science landscape envisioned in the overall strategic plan calls for significantly increasing the throughput of microbial genomes sequenced to cover their phylogenetic space and building a set of finished reference plant genomes to enable DOE relevant science. Additionally, the established impact of microbial communities on global energy cycles and their potential in remediation endeavors, warrant building upon JGI's established expertise in metagenomic analysis. Not only is each of these program areas relevant and exciting in their own right, but they also can and should be undertaken in a way that allows synthesis across domains (e.g. utilize knowledge from sequence of plants and the soil from which they are grown). Both dramatic increases in the scale of genomic data collection and the synergistic potential of integrating data across domains will demand new strategies in the informatics pipeline within the JGI and in the facility's approach to computational analysis and user access to the data in aggregated form. In addition to a robust and scalable informatics infrastructure, fulfilling the strategic science goals of the JGI will require ongoing investment in usability of the data, to ensure that the data collected will be used to maximal effect. It must be recognized that 'usability' will have a different appearance depending on the specific user base, and the JGI has several distinct classes of users it must enable to be successful. For some, rapid and convenient dissemination of the sequence data will be sufficient to enable their external research. For others, JGI hosted analysis tools and collaborative environments will be required to catalyze individual or team research. Finally, and significantly, there are genomic scientists within the JGI, often working closely with external collaborators, who rely on the ability to devise project-dependent and often very large scale customized analyses that result in publicly available tools. A successful strategy will require effort to satisfy each of these user classes, and careful attention to economies of software reuse and extensibility. There are only a handful of sequencing facilities worldwide that operate at the scale of the JGI's Production Genomics Facility, and these are devoted almost entirely to sequencing driven by biomedical applications. The PGF therefore fulfills a unique and vital role as a resource for genomic studies of DOE relevance. Like the other large-scale facilities, JGI has been carefully following the development of 'next-generation' sequencing technologies, and clearly must continue to refresh its instrumentation as advances are made. Critical to advances in sequencing technology are the computational infrastructure advances that are required to turn raw sequence into quality data. This is one area where JGI can leverage the broader sequencing community's investment in technology development, adopting the best practices and software for sequence processing and assembly. JGI can add unique value by further developing annotation pipelines and tools that serve to build an integrated framework where the Institute's complementary science components can be viewed in a larger 'systems' perspective than is currently possible. As technology, tools, and infrastructure advance, JGI is uniquely positioned in its ability complement core PGF expertise with a diverse set of capabilities provided by partners within the

Bader, D A; Brettin, T S; Cottingham, R W; Folta, P A; Golder, Y; Gregurick, S K; Himmel, M E; Mann, R C; Remington, K A; Slezak, T R

2008-10-01T23:59:59.000Z

109

U.S Department of Energy Joint Genome Institute Progress Report  

NLE Websites -- All DOE Office Websites (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

110

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

Science Conference Proceedings (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

2011-10-12T23:59:59.000Z

111

JGI - Cheryl Kerfeld  

NLE Websites -- All DOE Office Websites (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

112

DOE Joint Genome Institute: Next Gen Sequencing Technology Pinpoint  

NLE Websites -- All DOE Office Websites (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

113

DOE Joint Genome Institute: Adaptable Button Mushroom Serves Up  

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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

114

Science Videos from DOE's Joint Genome Institute on YouTube  

DOE Data Explorer (OSTI)

DOE's Joint Genome Institute began posting lab-produced videos on YouTube in September of 2008. Many of JGI's YouTube videos are of speakers' presentations at meetings and workshops; others may be promotional or educational in nature. They are freely available to the public for viewing and can be interactively shared or commented on. Users can subscribe and be notified when new videos are posted to their specific area of interest.

115

JGI - Directory  

NLE Websites -- All DOE Office Websites (Extended Search)

JGI Directory Search for a Staff Member The search string was empty. Please try again. Enter a name, email address, or phone number for a JGI staff member. (* is a wildcard.) Home...

116

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

SciTech Connect

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

Bermingham, Eldredge [STRI-Panama

2013-03-27T23:59:59.000Z

117

DOE Joint Genome Institute: Breaking down cellulose without blasting  

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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

118

DOE Joint Genome Institute 2008 Progress Report  

E-Print Network (OSTI)

JGI Mission Areas Bioenergy Carbon Cycling BiogeochemistryJGI User Community DOE Bioenergy Research Center Sequencinginteractions with the DOE Bioenergy Research Centers, and

Gilbert, David

2009-01-01T23:59:59.000Z

119

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

NLE Websites -- All DOE Office Websites

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

120

DOE JGI Secures Long-Term Lease on Production Genomics Facility  

NLE Websites -- All DOE Office Websites (Extended Search)

world's leading DNA sequencing centers in the DOE Joint Genome Institute," said Susan Rainey, Mayor of the City of Walnut Creek, Calif. "In our very own backyard, we can lay claim...

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

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

NLE Websites -- All DOE Office Websites (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

122

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

Science Conference Proceedings (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

2012-03-22T23:59:59.000Z

123

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

Science Conference Proceedings (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

2012-03-22T23:59:59.000Z

124

JGI - Operations  

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Operations The Operations Department sees to it that JGI has the best possible facilities and support, ensuring that its operations are conducted in accordance with the...

125

JGI - Credits  

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Credits The following people are responsible for developing and maintaining the www.jgi.doe.gov web site: David Gilbert: manager, content development, photography Leila Hornick:...

126

DOE Joint Genome Institute: Model Microbial Community for Studying  

NLE Websites -- All DOE Office Websites (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

127

JGI - Product Offerings  

NLE Websites -- All DOE Office Websites (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

128

JGI - Directions  

NLE Websites -- All DOE Office Websites (Extended Search)

Directions Address DOE Joint Genome Institute 2800 Mitchell Drive Walnut Creek, CA 94598 From Oakland Airport Follow Airport exit signs onto AIRPORT DR. Turn RIGHT onto HEGENBERGER...

129

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

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

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

2011-01-31T23:59:59.000Z

130

JGI - Sequencing Plans  

NLE Websites -- All DOE Office Websites (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

131

JGI - Approved CSP Projects, 2005  

NLE Websites -- All DOE Office Websites (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

132

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

NLE Websites -- All DOE Office Websites (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:

133

JGI - Contact Us  

NLE Websites -- All DOE Office Websites (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

134

JGI - CSP Proposal Study Panel  

NLE Websites -- All DOE Office Websites (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

135

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

NLE Websites -- All DOE Office Websites (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

136

JGI - Emerging Technologies Opportunity Program (ETOP)  

NLE Websites -- All DOE Office Websites (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

137

JGI - Emergency Operations Information  

NLE Websites -- All DOE Office Websites (Extended Search)

Emergency Numbers In an emergency dial 9-911 from JGI, or 1-925-935-6400 to call 911 from a cell phone, or 911 from non-JGI land line. JGI Emergency Status Announcements...

138

JGI Sets 'Gold Standard' for Metagenomic Data Analysis  

NLE Websites -- All DOE Office Websites (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

139

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

NLE Websites -- All DOE Office Websites (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

140

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

NLE Websites -- All DOE Office Websites (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

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.


141

DOE JGI CSP 2012 PI Workshop  

NLE Websites -- All DOE Office Websites (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

142

New Approaches and Technologies to Sequence de novo Plant reference Genomes (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)  

SciTech Connect

Jeremy Schmutz of the HudsonAlpha Institute for Biotechnology on "New approaches and technologies to sequence de novo plant reference genomes" at the 8th Annual Genomics of Energy & Environment Meeting on March 27, 2013 in Walnut Creek, Calif.

Schmutz, Jeremy [HudsonAlpha Institute

2013-03-01T23:59:59.000Z

143

JGI - Data Management Policy, Practices & Resources  

NLE Websites -- All DOE Office Websites (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,

144

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

Science Conference Proceedings (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

2011-03-23T23:59:59.000Z

145

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

Science Conference Proceedings (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

2011-03-23T23:59:59.000Z

146

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

Science Conference Proceedings (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

2011-03-22T23:59:59.000Z

147

Improving biofuel feedstocks by modifying xylan biosynthesis (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)  

SciTech Connect

Jane Lau of the Joint BioEnergy Institute on "Improving biofuel feedstocks by modifying xylan biosynthesis" at the 8th Annual Genomics of Energy & Environment Meeting on March 28, 2013 in Walnut Creek, Calif.

Lau, Jane [JBEI

2013-03-01T23:59:59.000Z

148

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

NLE Websites -- All DOE Office Websites (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

149

Genomics Presentations from DOE JGI's Fourth Annual Sequencing, Finishing, Analysis in the Future Meeting, 2009  

DOE Data Explorer (OSTI)

表tMedicago trunculata Resequencing of 384 lines, Joann Mudge 表tPerformance Comparison of Two Genome Partitioning Platforms, Jon Armstrong 表tPrescreening Illumina Data Results in High-Quality Genome Polishing, Cliff Han 表tGenePRIMP: Improving Microbial Gene Prediction Quality, Amrita Pati 表tIMG Systems for Comparative Analysis of Microbial Genomes and Metagenomes, Victor Markowitz 表tAutomated Microbial Genome Annotation, Miriam Land 表tNew Technology Drafts: Production and Improvements, Alla Lapidus 表tHuman Microbiome Finishing, Jessica Hostetler

150

Genomics of Energy and Environment: the 7th Annual, 2012, DOE JGI User Meeting  

DOE Data Explorer (OSTI)

表tOmics in the Artic: Genome-enabled Contributions to Carbon Cycle Research in Low-Latitude Ecosystems (Stan Wullschleger)

151

DOE Joint Genome Institute 2008 Progress Report  

E-Print Network (OSTI)

into operating as a user facility, the DOE JGI modeleditself after other DOE user facilities, such as synchro-s approach to being a user facility is based on the concept

Gilbert, David

2009-01-01T23:59:59.000Z

152

DOE Systems Biology Knowledgebase (KBASE) (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)  

Science Conference Proceedings (OSTI)

Adam Arkin from Berkeley Lab on the DOE Systems Biology Knowledgebase (KBASE) at the 7th Annual Genomics of Energy & Environment Meeting on March 21, 2012 in Walnut Creek, Calif

Arkin, Adam [LBNL

2012-03-21T23:59:59.000Z

153

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

Science Conference Proceedings (OSTI)

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

Rieseberg, Loren [University of British Columbia

2012-03-21T23:59:59.000Z

154

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

Science Conference Proceedings (OSTI)

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

Schatz, Michael C [Cold Spring Harbor Laboratory

2012-03-21T23:59:59.000Z

155

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

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

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 -...

156

JGI Plumbs Termite Guts to Yield Novel Enzymes for Better Biofuel  

NLE Websites -- All DOE Office Websites (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

157

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

NLE Websites -- All DOE Office Websites (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

158

Genomics Presentations from the 8th Meeting of the Genomic Standards Consortium (2009), held at the DOE JGI (Videos)  

DOE Data Explorer (OSTI)

表tA New ARM of the GSC: the RCN4GSC, Dawn Field and Peter Sterk 表tStandards in Genomic Sciences (SIGS): An Open Access Journal of the Genomic Standards Consortium, George Garrity 表tGSC8 Opening Remarks, Dawn Fields

159

JGI - Tanja Woyke  

NLE Websites -- All DOE Office Websites (Extended Search)

Tanja Woyke Igor Grigoriev Tanja Woyke, PhD Microbial Genomics Program Lead, DOE Joint Genome Institute Education Diploma in Biology, University of California,...

160

Regulatory Networks Controlling Plant Cold Acclimation or Low Temperature Regulatory Networks Controlling Cold Acclimation in Arabidopsis (2011 JGI User Meeting)  

Science Conference Proceedings (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. Mike Thomashow of Michigan State University gives a presentation on on "Low Temperature Regulatory Networks Controlling Cold Acclimation in Arabidopsis" at the 6th annual Genomics of Energy & Environment Meeting on March 23, 2011. ォ

Thomashow, Mike

2011-03-23T23:59:59.000Z

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.


161

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

Science Conference Proceedings (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

2011-03-23T23:59:59.000Z

162

The Turn-on of LCLS: the X-Ray Free Electron Laser at SLAC ( Keynote - 2011 JGI User Meeting)  

Science Conference Proceedings (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. SLAC National Laboratory Director Persis Drell gives a keynote talk on "The Turn-on of LCLS: the X-Ray Free-Electron Laser at SLAC" at the 6th Genomics of Energy & Environment Meeting on March 22, 2011

Drell, Persis [SLAC Director

2011-03-22T23:59:59.000Z

163

JGI - Prokaryote Super Program  

NLE Websites -- All DOE Office Websites (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

164

JGI - Scientific Posters  

NLE Websites -- All DOE Office Websites (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)

165

Mechanisms of Plant-Fungi Symbiosis Characterized by DOE JGI...  

NLE Websites -- All DOE Office Websites (Extended Search)

birch, fir, and pine forests of North America and is a common symbiont of Populus, the poplar tree whose genome was determined by the JGI in 2006 The analysis of the...

166

JGI - Why Sequence Capitella?  

NLE Websites -- All DOE Office Websites (Extended Search)

intracellular injections for cell lineage tracing, and functional gene knockdowns. CSP project participants: Elaine Seaver (Univ. of Hawaii), Jeffrey Boore (JGI and UC...

167

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

DOE Green Energy (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

2010-03-24T23:59:59.000Z

168

Rhodopseudomonas palustris genome project. Final report  

DOE Green Energy (OSTI)

Rhodopseudomonas palustris is a common soil and water bacterium that makes its living by converting sunlight to cellular energy and by absorbing atmospheric carbon dioxide and converting it to biomass. This microbe can also degrade and recycle components of the woody tissues of plants, wood being the most abundant polymer on earth. Because of its intimate involvement in carbon management and recycling, R. palustris was selected by the DOE Carbon Management Program to have its genome sequenced by the Joint Genome Institute (JGI). This award provided funds for the preparation of R. palustris genomic DNA which was then supplied to the JGI in sufficient amounts to enable the complete sequencing of the R. palustris genome. The PI also supplied the JGI with technical information about the molecular biology of R. palustris.

Harwood, Caroline S.

2000-11-22T23:59:59.000Z

169

Host Genetic Control of the Microbiome in Humans and Maise or Relating Host Genetic Variation to the Microbiome (2011 JGI User Meeting)  

Science Conference Proceedings (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. Ruth Ley of Cornell University gives a presentation on "Relating Host Genetic Variation to the Microbiome" at the 6th annual Genomics of Energy & Environment Meeting on March 23, 2011.

Ley, Ruth [Cornell University

2011-03-23T23:59:59.000Z

170

JGI Compute User Training  

NLE Websites -- All DOE Office Websites (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

171

JGI - Ray Turner  

NLE Websites -- All DOE Office Websites (Extended Search)

DOE Joint Genome Institute Education Bachelor of Science Finance, University of Utah Masters of Science Financial Management, Naval Postgraduate School Awards and Service...

172

JGI - Susannah Tringe  

NLE Websites -- All DOE Office Websites (Extended Search)

Tringe Susannah Tringe Susannah Green Tringe, Ph.D Metagenome Program Lead, DOE Joint Genome Institute Education AB, Physics, Harvard University, Cambridge, MA (summa cum...

173

JGI Progress Report  

NLE Websites -- All DOE Office Websites (Extended Search)

Progress Report report cover The 2012 DOE Joint Genome Institute Progress Report, highlighting the achievements of the previous year, has been released and can be downloaded here....

174

Sequencing Technologies and Computational pipelines at the JGI  

NLE Websites -- All DOE Office Websites (Extended Search)

Sequencing Technologies and Computational pipelines at the JGI Sequencing Technologies and Computational pipelines at the JGI September 17, 2013 JGI logo 2 James Han, JGI...

175

JGI - Why Sequence Poplar Leaf Rust?  

NLE Websites -- All DOE Office Websites (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

176

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

NLE Websites -- All DOE Office Websites (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

177

Joint Genome Institute Progress Report 2002-2005  

E-Print Network (OSTI)

as a non-traditional user facility, the JGI is empoweringserve as a traditional user facility driven by DOE missionexperience running user facilities, it has become clear that

Gilbert, David

2005-01-01T23:59:59.000Z

178

DOE Joint Genome Institute 2008 Progress Report  

E-Print Network (OSTI)

Martinez, D. , et al. Genome sequencing and analysis of thegroup, the HudsonAlpha Genome Sequencing Center, will expandnext-genera- tion genome sequencing and add capabilities to

Gilbert, David

2009-01-01T23:59:59.000Z

179

JGI - Who We Are  

NLE Websites -- All DOE Office Websites (Extended Search)

in doing so enabled the DOE JGI to be the first to publish the sequence analysis of the target chromosomes 5, 16, and 19, in the journal Nature. Following this accomplishment,...

180

Joint Genome Institute Progress Report 2002-2005  

SciTech Connect

Progress report covering activities at the DOE-Joint Genome Institute in Walnut Creek, California for the period 2002-2005.

Gilbert, David

2005-10-03T23:59:59.000Z

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.


181

JGI - Len Pennacchio  

NLE Websites -- All DOE Office Websites (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

182

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

Science Conference Proceedings (OSTI)

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

Willerslev, Eske [University of Copenhagen

2012-03-21T23:59:59.000Z

183

JGI - Jeremy Schmutz  

NLE Websites -- All DOE Office Websites (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

184

The Annual DOE JGI User Meeting  

NLE Websites -- All DOE Office Websites (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

185

DOE Joint Genome Institute 2008 Progress Report  

E-Print Network (OSTI)

biofuel production. Diatom Genome Helps Explain Their Success in Capturing Carbon Diatoms, mighty microscopic algae,

Gilbert, David

2009-01-01T23:59:59.000Z

186

The Annual DOE JGI User Meeting  

NLE Websites -- All DOE Office Websites (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

187

Ocean Viruses: Tiny entities with Global Impacts ( JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)  

Science Conference Proceedings (OSTI)

Matt Sullivan from the University of Arizona on "Ocean Viruses: Tiny Entities with Global Impacts" at the 7th Annual Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, Calif.

Sullivan, Matthew B [University of Arizona

2012-03-22T23:59:59.000Z

188

Regulation of Flowering in Brachypodium distachyon (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)  

SciTech Connect

Rick Amasino of the University of Wisconsin on "Regulation of Flowering in Brachypodium distachyon" at the 8th Annual Genomics of Energy & Environment Meeting on March 27, 2013 in Walnut Creek, Calif.

Amasino, Rick [University of Wisconsin

2013-03-01T23:59:59.000Z

189

Strange Tails: Viral Discovery & Deep Sequencing (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)  

SciTech Connect

Joe DeRisi of UC San Francisco on "Strange Tails: Viral discovery & deep sequencing" at the 8th Annual Genomics of Energy & Environment Meeting on March 27, 2013 in Walnut Creek, Calif.

DeRisi, Joe [UCSF

2013-03-01T23:59:59.000Z

190

Part Mining for Synthetic Biology (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)  

SciTech Connect

Chris Voigt from MIT delivers the opening keynote on "Part Mining for Synthetic Biology" at the 8th Annual Genomics of Energy & Environment Meeting on March 26, 2013 in Walnut Creek, Calif.

Voigt, Chris [MIT

2013-03-01T23:59:59.000Z

191

PMI: Plant-Microbe Interfaces (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)  

SciTech Connect

Christopher Schadt of Oak Ridge National Laboratory on "Plant-Microbe Interactions" in the context of poplar trees at the 8th Annual Genomics of Energy & Environment Meeting on March 27, 2013 held in Walnut Creek, Calif.

Schadt, Christopher [ORNL

2013-03-01T23:59:59.000Z

192

DOE Joint Genome Institute: Establishing Standard Definitions for Genome  

NLE Websites -- All DOE Office Websites (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

193

Today, DOE's Joint Genome Institute (a  

NLE Websites -- All DOE Office Websites (Extended Search)

characterizing the basic principles and relationships underlying living systems. Social Impact: Armed with the DNA sequence of the human genome, scientists will be able to...

194

DOE Joint Genome Institute 2008 Progress Report  

E-Print Network (OSTI)

proteins for biofuel production. Trends in Mi- crobiology,could help improve biofuel production. Diatom Genome Helpsa key target. Current biofuel production meth- ods, such as

Gilbert, David

2009-01-01T23:59:59.000Z

195

DOE Joint Genome Institute 2008 Progress Report  

E-Print Network (OSTI)

Paterson, A. , et al. The Sorghum bicolor genome and thethe 730-million nucleotide Sorghum bicolor sequence, and thesoybean, eucalyp- tus, sorghum, foxtail millet, cassava,

Gilbert, David

2009-01-01T23:59:59.000Z

196

JGI - Dan Rokhsar  

NLE Websites -- All DOE Office Websites (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

197

The Genome of Selaginella: A Remnant of an Ancient Vascular Plant Lineage (JGI Seventh Annual User Meeting, 2012: Genomics of Energy and Environment)  

Science Conference Proceedings (OSTI)

Jody Banks from Purdue University on "The Genome of Selaginella, a Remnant of an Ancient Vascular Plant Lineage" at the 7th Annual Genomics of Energy & Environment Meeting on March 21, 2012 in Walnut Creek, Calif.

Banks, Jody [Purdue University

2012-03-21T23:59:59.000Z

198

The Challenges and Opportunities for Extending Plant Genomics to Climate (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)  

SciTech Connect

David Weston of Oak Ridge National Laboratory on "The challenges and opportunities for extending plant genomics to climate" at the 8th Annual Genomics of Energy & Environment Meeting on March 27, 2013 in Walnut Creek, Calif.

Weston, David [ORNL

2013-03-01T23:59:59.000Z

199

Uncovering Transcriptional Circuits in Arabidoposis by Functional Genomics (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)  

SciTech Connect

Jose Pruneda-Paz of UC San Diego on "Uncovering Transcriptional Circuits in Arabidopsis by Functional Genomics" at the 8th Annual Genomics of Energy & Environment Meeting in Walnut Creek, Calif.

Pruneda-Paz, Jose [UC San Diego

2013-03-01T23:59:59.000Z

200

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

Science Conference Proceedings (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

2012-03-21T23:59:59.000Z

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.


201

DOE Joint Genome Institute: Brown Tide Culprit Sequenced: Genome...  

NLE Websites -- All DOE Office Websites (Extended Search)

Culprit Sequenced: Genome of the First of Algal Bloom Species WALNUT CREEK, Calif.- Algae play key roles in the global carbon cycle, helping sequester significant amounts of...

202

Gerber-JGI  

NLE Websites -- All DOE Office Websites (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

203

DOE Joint Genome Institute 2008 Progress Report  

E-Print Network (OSTI)

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

Gilbert, David

2009-01-01T23:59:59.000Z

204

DOE Joint Genome Institute: Spikemoss Genome Offers New Paths...  

NLE Websites -- All DOE Office Websites (Extended Search)

5, 2011 Spikemoss Genome Offers New Paths for Biofuels Research--Bridges Plant Development Gap WALNUT CREEK, Calif.- It's not quite Christmas, but the DNA sequence of a small plant...

205

Omics in the Arctic: Genome-enabled Contributions to Carbon Cycle Research in High-Latitude Ecosystems (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)  

Science Conference Proceedings (OSTI)

Stan Wullschleger of Oak Ridge National Laboratory on "Omics in the Arctic: Genome-enabled Contributions to Carbon Cycle Research in High-Latitude Ecosystems" on March 22, 2012 at the 7th Annual Genomics of Energy & Environment Meeting in Walnut Creek, California.

Wullschleger, Stan [ORNL

2012-03-22T23:59:59.000Z

206

Applications of Genome-based Science in Shaping the World's Citrus Industries (JGI Seventh Annual User Meeting, 2012: Genomics of Energy and Environment)  

Science Conference Proceedings (OSTI)

Fred Gmitter from the University of Florida on "Applications of Genome-based Science in Shaping the Future of the World's Citrus Industries" at the 7th Annual Genomics of Energy & Environment Meeting on March 21, 2012 in Walnut Creek, California.

Gmitter, Jr., Fred (University of Florida)

2012-03-21T23:59:59.000Z

207

genome109280 634..641  

NLE Websites -- All DOE Office Websites (Extended Search)

(http: www.phytozome.net), Selaginella moellendorffii (http:www. phytozome.net), Sorghum bicolor (http:genome.jgi-psf.org Sorbi1), Vitis vinifera (http:...

208

Rooted in Wonder: Joint Genome Institute Study Reveals Amazing World  

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

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.

209

JGI - CSP Sequencing Plans for 2011  

NLE Websites -- All DOE Office Websites (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

210

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

E-Print Network (OSTI)

Production Sequencing at DOE Joint Genome Institute 剖.S. Department of Energy (DOE) Joint Genome Institute痴 (DNA sequence to support the DOE mission areas of renewable

Tarver, Angela

2010-01-01T23:59:59.000Z

211

Genomics of Plant-based Biofuels in the Journal Nature  

NLE Websites -- All DOE Office Websites (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/.

212

DOE Joint Genome Institute: Peach Genome Offers Insights into Breeding  

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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.

213

The Microbial Genomics and Metagenomics (MGM) five-day  

NLE Websites -- All DOE Office Websites (Extended Search)

Microbial Genomics and Metagenomics (MGM) five-day workshop (www.jgi.doe.gov meetingsmgm) provides strong and solid training in microbial genomic and metagenomic analysis and...

214

Seventh Annual DOE Joint Genome Institute User Meeting Sponsored By  

NLE Websites -- All DOE Office Websites (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

215

The Annual DOE JGI User Meeting  

NLE Websites -- All DOE Office Websites (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,

216

JGI Available Software  

NLE Websites -- All DOE Office Websites (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

217

JGI - Chia-Lin Wei  

NLE Websites -- All DOE Office Websites (Extended Search)

Chia-Lin Wei Chia-Lin Wei Chia-Lin Wei, PhD Group Lead, Sequencing Technologies, DOE Joint Genome Institute Education B. Sc in Medical Technology, National Yang-Ming University,...

218

The Annual DOE JGI User Meeting  

NLE Websites -- All DOE Office Websites (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)

219

JGI - Why GEBA?  

NLE Websites -- All DOE Office Websites (Extended Search)

for Bacteria and Archaea | Why GEBA? | Pilot Project | Interpret a Genome Page Genome sequencing has revolutionized our understanding of microorganisms and the role they...

220

JGI - DOE Sequencing Projects  

NLE Websites -- All DOE Office Websites (Extended Search)

DOE Sequencing Projects For status information, see the Genome Projects section Organism Est. Genome Size Branchiostoma floridae (Florida lancelet) 600 Mb Chlamydomonas reinhardtii...

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

JGI - IMG-ACT  

NLE Websites -- All DOE Office Websites (Extended Search)

Education Microbial Genome Analysis Microbial Functional Genomics IMG-ACT IMG Annotation Collaboration Toolkit (IMG-ACT) is a multi-platform toolkit created to assist instructors...

222

Genomics Encyclopedia of Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB): a resource for microsymbiont genomes (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)  

SciTech Connect

Wayne Reeve of Murdoch University on "Genomics Encyclopedia of Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB): a resource for microsymbiont genomes" at the 8th Annual Genomics of Energy & Environment Meeting on March 27, 2013 in Walnut Creek, Calif.

Reeve, Wayne [Murdoch University

2013-03-01T23:59:59.000Z

223

Joint Genome Institute Progress Report 2002-2005  

E-Print Network (OSTI)

S, et al. Comparative genome sequencing of DrosophilaInternational Human Genome Sequencing Consortium. FinishingWhile NIH-funded genome sequencing activities largely

Gilbert, David

2005-01-01T23:59:59.000Z

224

JGI - Igor Grigoriev  

NLE Websites -- All DOE Office Websites (Extended Search)

dynamic nature and multi-lineage evolutionary history of diatom genomes. Nature. 2008; 456, 239-244. Martin F et al. The genome of Laccaria bicolor provides insights into...

225

JGI - Prokaryotic Super Program Advisory Committee Meeting  

NLE Websites -- All DOE Office Websites (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 ツゥ1997-2013 The Regents of the University of California Page Last Updated

226

Genomic Science Program Systems Biology for Energy and Environment  

NLE Websites -- All DOE Office Websites (Extended Search)

Major KBase Public Release Now Available 0213 More News and Announcements Reports DOE JGI Strategic Planning for the Genomic Sciences: Workshop Report 912 Plants and...

227

DOE JGI CSP 2012 PI Workshop  

NLE Websites -- All DOE Office Websites (Extended Search)

Logistics What to Bring LAPTOP COMPUTERS REQUIRED Please plan to bring your own laptop to the JGI in order to participate in the Workshop. Details regarding system requirements...

228

JGI - Technology Development Pilot Program (TDP)  

NLE Websites -- All DOE Office Websites (Extended Search)

Inquires | Proposal Review Purpose JGI's current main User Program, the Community Sequencing Program (CSP) is intended for large (terabase-) scale sequencing projects, with...

229

Metabolic Engineering of Clostridium thermocellum for Biofuel Production (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)  

SciTech Connect

Adam Guss of Oak Ridge National Lab on "Metabolic engineering of Clostridium thermocellum for biofuel production" at the 8th Annual Genomics of Energy & Environment Meeting on March 28, 2013 in Walnut Creek, Calif.

Guess, Adam [ORNL

2013-03-01T23:59:59.000Z

230

Assembly-driven metagenomics of a hypersaline microbial ecosystem (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)  

SciTech Connect

Eric Allen of Scripps and UC San Diego on "Assembly-driven metagenomics of a hypersaline microbial ecosystem" at the 8th Annual Genomics of Energy & Environment Meeting on March 27, 2013 in Walnut Creek, Calif.

Allen, Eric [Scripps and UCSD

2013-03-01T23:59:59.000Z

231

Network as Discovery Instrument: A Quick-Start Guide (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)  

SciTech Connect

Gregory Bell of Berkeley Lab on "Network as discovery instrument: a Quick-Start Guide" at the 8th Annual Genomics of Energy & Environment Meeting in Walnut Creek, Calif.

Bell, Gregory [Berkeley Lab

2013-03-01T23:59:59.000Z

232

Succession of Phylogeny and Function During Plant Litter Decomposition (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)  

SciTech Connect

Eoin Brodie of Berkeley Lab on "Succession of phylogeny and function during plant litter decomposition" at the 8th Annual Genomics of Energy & Environment Meeting on March 27, 2013 in Walnut Creek, Calif.

Brodie, Eoin [Berkeley Lab

2013-03-01T23:59:59.000Z

233

Biodiversity Monitoring Using NGS Approaches on Unusual Substrates (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)  

SciTech Connect

Tom Gilbert of the Natural History Museum of Denmark on "Biodiversity monitoring using NGS approaches on unusual substrates" at the 8th Annual Genomics of Energy & Environment Meeting in Walnut Creek, Calif.

Gilbert, Tom [National History Museum of Denmark

2013-03-01T23:59:59.000Z

234

Modulation of Root Microbiome Community Assembly by the Plant Immune Response (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)  

SciTech Connect

Sarah Lebeis of University of North Carolina on "Modulation of root microbiome community assembly by the plant immune response" at the 8th Annual Genomics of Energy & Environment Meeting on March 28, 2013 in Walnut Creek, Calif.

Lebeis, Sarah [University of North Carolina

2013-03-01T23:59:59.000Z

235

Delineating Molecular Interaction Mechanisms in an In Vitro Microbial-Pant Community (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)  

SciTech Connect

Peter Larsen of Argonne National Lab on "Delineating molecular interaction mechanisms in an in vitro microbial-plant community" at the 8th Annual Genomics of Energy & Environment Meeting in Walnut Creek, Calif.

Larsen, Peter [Argonne

2013-03-01T23:59:59.000Z

236

Genetic Regulation of Grass Biomass Accumulation and Biological Conversion Quality (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)  

SciTech Connect

Sam Hazen of the University of Massachusetts on "Genetic Regulation of Grass Biomass Accumulation and Biological Conversion Quality" at the 8th Annual Genomics of Energy & Environment Meeting on March 27, 2013 in Walnut Creek, Calif.

Hazen, Sam [University of Massachusetts

2013-03-01T23:59:59.000Z

237

TARA OCEANS: A Global Analysis of Oceanic Plankton Ecosystems (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)  

SciTech Connect

Eric Karsenti of EMBL delivers the closing keynote on "TARA OCEANS: A Global Analysis of Oceanic Plankton Ecosystems" at the 8th Annual Genomics of Energy & Environment Meeting on March 28, 2013 in Walnut Creek, Calif.

Karsenti, Eric [EMBL Heidelberg

2013-03-01T23:59:59.000Z

238

Natural variation in Brachypodium disctachyon: Deep Sequencing of Highly Diverse Natural Accessions (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)  

SciTech Connect

Sean Gordon of the USDA on "Natural variation in Brachypodium disctachyon: Deep Sequencing of Highly Diverse Natural Accessions" at the 8th Annual Genomics of Energy & Environment Meeting on March 27, 2013 in Walnut Creek, Calif.

Gordon, Sean [USDA

2013-03-01T23:59:59.000Z

239

Evolutionary Perspectives on Diversity of Lignocellulose Decay Mechanisms in Basidionycetes (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)  

Science Conference Proceedings (OSTI)

David Hibbett from Clark University on "Evolutionary Perspectives on Diversity of Lignocellulose Decay Mechanisms in Basidiomycetes" at the 7th Annual Genomics of Energy & Environment Meeting on March 21, 2012 in Walnut Creek, California.

Hibbett, David [Clark University

2012-03-21T23:59:59.000Z

240

Complete genome sequence of Staphylothermus hellenicus P8T  

SciTech Connect

Staphylothermus hellenicus belongs to the order Desulfurococcales within the archaeal phy- lum Crenarchaeota. Strain P8T is the type strain of the species and was isolated from a shal- low hydrothermal vent system at Palaeochori Bay, Milos, Greece. It is a hyperthermophilic, anaerobic heterotroph. Here we describe the features of this organism together with the com- plete genome sequence and annotation. The 1,580,347 bp genome with its 1,668 protein- coding and 48 RNA genes was sequenced as part of a DOE Joint Genome Institute (JGI) La- boratory Sequencing Program (LSP) project.

Anderson, Iain [U.S. Department of Energy, Joint Genome Institute; Wirth, Reinhard [Universitat Regensburg, Regensburg, Germany; 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; Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Davenport, Karen W. [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; Pati, Amrita [U.S. Department of Energy, Joint Genome Institute; Mikhailova, Natalia [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; 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

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

JGI - Nikos Kyrpides  

NLE Websites -- All DOE Office Websites (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

242

JGI - Why Sequence Trichoplax?  

NLE Websites -- All DOE Office Websites (Extended Search)

known animals and provide the first genomics platform in a simple multicellular system. CSP project participants: Stephen L. DellaPorta (proposer) and Leo Buss (Yale Univ.), Dan...

243

JGI - Why Sequence Prochlorococcus?  

NLE Websites -- All DOE Office Websites (Extended Search)

of this project is to understand the genomic underpinnings of the observed ecological diversity and distribution of Prochlorococcus. This unicellular cyanobacterium is an extremely...

244

Bioenergy at DOE JGI  

NLE Websites -- All DOE Office Websites (Extended Search)

Advancing Alternative Energy Sources Soybeans: Translational Genomics for Clean Energy Corn: The Leading U.S. Fuel Ethanol Crop Switchgrass: Power Grass Brachypodium: Growing...

245

JGI - Archived Press Releases  

NLE Websites -- All DOE Office Websites (Extended Search)

new genome projects, representing a cornucopia of life forms, from the important grain sorghum to catfish, crustaceans, and a host of extreme lifestyle microbes, slated for DNA...

246

JGI - Notable Scientific Publications  

NLE Websites -- All DOE Office Websites (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ツ肪ased 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

247

Complete Genome Sequence of the Thermophilic Bacterium Exiguobacterium sp. AT1b  

Science Conference Proceedings (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

248

Complete Genome Sequence of the Thermophilic Bacterium Exiguobacterium sp. AT1b  

Science Conference Proceedings (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

249

Complete genome sequence of Halopiger xanaduensis type strain (SH6T)  

SciTech Connect

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

250

Cluster Overview of Archaeal Life (COAL) from the DOE Joint Genome Institute  

DOE Data Explorer (OSTI)

COAL is an acronym for Cluster Overview of Archaeal Life. The purpose of COAL is to visualize protein orthology and to relate orthology with additional information derived from their genomes. This information includes phylogeny, ecotype, metabolism, thermal preference and aerobicity. The protein orthology networks are also subclustered, when possible, using a bipartioning approach based on spectral clustering. COAL clusters are of three types; root, stem and leaf. Enter a cluster number into the Cluster box on the Main COAL page at http://coal.jgi-psf.org/coal/ and click Update. The cluster appears as a network of nodes (proteins) connected by edges representing the orthology. Various information about the cluster will be loaded below the applet, along with information of the individual proteins. Proteins can be highlighted according to the phylogenetic placement of their genomes. Currently, there are four categories of metadata in COAL, oxygen usage (e.g. aerobe, anaerobe), Metabolism (e.g. Chemoorganoheterotroph, Chemolithoautotroph), thermal preference (e.g. hyperthermophile, mesophile) and ecotype (e.g. marine, aquatic).[Taken with liberal editing from the COAL Help page.

251

JGI - Project List  

NLE Websites -- All DOE Office Websites (Extended Search)

ID NCBI taxonomy ID Show projects from: all ARRA BRC-BESC BRC-GLBRC BRC-JBEI BRC-Multi CSP CSP-ICBG CSP-LD DD Director's Science DOE Legacy DOEM FGP GEBA Genomic Tech Grand...

252

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

NLE Websites -- All DOE Office Websites (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)

253

Competitiveness of Second Generation Biofuel Feedstocks: Role of Technology and Policy (2010 JGI User Meeting)  

SciTech Connect

Madhu Khanna from the University of Illinois at Urbana-Champaign and the Energy Biosciences Institute on "Competitiveness of Second Generation Biofuel Feedstocks: Role of Technology and Policy" on March 25, 2010 at the 5th Annual DOE JGI User Meeting

Khanna, Madhu

2010-03-26T23:59:59.000Z

254

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

Science Conference Proceedings (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

2010-03-25T23:59:59.000Z

255

Interactive Data Map from JGI's Microbial Earth Project  

DOE Data Explorer (OSTI)

The Microbial Earth Project's interactive data map is a graphical representation of the NCBI taxonomy tree for 7623 type strains from DSMZ culture collection. Each leaf represents a type strain. Colors denote stains with or without genome projects (red vs green). Internal nodes (transparent) denote higher taxonomic ranks. Branch lengths are not meaningful. A selection of named taxonomic groups are shown in yellow. Note the highly uneven coverage of the type strain material by genome sequencing projects. For example, groups such as the families Halobacteriaceae and Coriobacteriaceae are well represented by sequencing projects whereas other groups such as the genera Streptomyces and Pseudomonas are largely untouched. The figure was generated by mapping NCBI taxonomic information to DSMZ type strains. Information about genome projects was obtained from the GOLD database. The Guess visualization program was used for rendering with the 'gem' layout. [Copied from http://genome.jgi-psf.org/programs/bacteria-archaea/MEP/index.jsf

256

JGI - Why Sequence Reniera?  

NLE Websites -- All DOE Office Websites (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

257

DOE Joint Genome Institute: Exploring Standards to Advance Microbial...  

NLE Websites -- All DOE Office Websites (Extended Search)

July 9, 2009 Exploring Standards to Advance Microbial Genomics WALNUT CREEK, CA-Microbes contribute to manifold human endeavors ranging from bioenergy to agriculture to medicine....

258

DOE Joint Genome Institute: Up from the Depths: How Bacteria...  

NLE Websites -- All DOE Office Websites (Extended Search)

to verify the predominant bacterial lineages capable of trapping carbon in this deep underwater region. "This study represents a pristine example for the use of single cell genome...

259

JGI - Why Sequence Sorghum?  

NLE Websites -- All DOE Office Websites (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

260

JGI - DOE Bioenergy Research Centers  

NLE Websites -- All DOE Office Websites (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

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

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

NLE Websites -- All DOE Office Websites (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

262

DOE JGI Microbial Genomics & Metagenomics Workshops  

NLE Websites -- All DOE Office Websites (Extended Search)

next generation sequencing platforms. Therefore, assembly is a common step in analysis pipelines, since it can increase sequence length and reduce complexity via clustering....

263

DOE JGI Microbial Genome Reannotation Workshop  

NLE Websites -- All DOE Office Websites (Extended Search)

approach In each step below we will be discussing: Alternative methods used Proposed pipeline Implementation of confidence levels for feature prediction Benchmarking (when needed)...

264

JGI - Undergraduate Research in Microbial Genome Analysis  

NLE Websites -- All DOE Office Websites (Extended Search)

(Western New England University), Robert Ramirez (San Francisco State University), Peter Novick (Queensborough Community College), Dawn Holmes (Western New England...

265

DOE JGI Announces 2008 Genome Sequencing Targets  

NLE Websites -- All DOE Office Websites (Extended Search)

It is envisioned that pearl millet would be useful as a supplement or replacement for corn in ethanol plants in regions that suffer from drought and low-fertility soils. The...

266

JGI - Why Sequence Phycomyces blakesleeanus?  

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of Phycomyces' precisely regulated responses. The full description of a zygomycete genome will provide key information about the evolution of fungal genomes. fungus with...

267

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

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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.

268

12572_JGI_Progress_released:12572_JGI_Progress  

NLE Websites -- All DOE Office Websites (Extended Search)

activities. David Jaffe Broad Institute Bill Pearson University of Virginia Steve Lincoln Affymetrix Toby Bloom Broad Institute Peter Cartwright SRI International Steve...

269

OSCARS Case Study  

NLE Websites -- All DOE Office Websites (Extended Search)

Feedback: info@es.net OSCARS Case Study OSCARS Virtual Circuits Extend JGI Network Capacity The Challenge In February 2010, the Joint Genome Institute (JGI) at Lawrence Berkeley...

270

JGI - Why Sequence Physcomitrella patens?  

NLE Websites -- All DOE Office Websites (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.

271

JGI - The GEBA Pilot Project  

NLE Websites -- All DOE Office Websites (Extended Search)

This amount of sequencing is not beyond the capabilities of the current capacity of major genome sequencing centers. However, though the sequencing itself is within current...

272

JGI - Why Sequence Amphipod Crustaceans?  

NLE Websites -- All DOE Office Websites (Extended Search)

Amphipod Crustaceans? This project comprises preliminary directed genome and EST sequencing of two species of amphipod crustaceans. Parhyale hawaiensis is becoming an established...

273

JGI - Why Sequence Campanulale Chloroplasts?  

NLE Websites -- All DOE Office Websites (Extended Search)

yet to elucidate the underlying molecular bases for exceptional instability in organelle genome evolution. This project aims to do just that through targeted sequencing of...

274

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

NLE Websites -- All DOE Office Websites (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,

275

JGI - How to Propose a CSP Project  

NLE Websites -- All DOE Office Websites (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

276

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

Science Conference Proceedings (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

2011-10-13T23:59:59.000Z

277

Sequencing Single Cell Microbial Genomes with Microfluidic Amplifications Tools (MICW - Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)  

Science Conference Proceedings (OSTI)

Stanford University's Steve Quake on "Sequencing Single Cell Microbial Genomes with Microfluidic Amplification Tools" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

Quake, Steve [University of Stanford

2011-10-12T23:59:59.000Z

278

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

NLE Websites -- All DOE Office Websites (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

279

JGI - Why Sequence Rhodobacter sphaeroides?  

NLE Websites -- All DOE Office Websites (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

280

JGI - The GEBA Pilot Project  

NLE Websites -- All DOE Office Websites (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

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

JGI - Why Sequence Contaminated Groundwater?  

NLE Websites -- All DOE Office Websites (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

282

JGI - Why Sequence Phytophthora capsici?  

NLE Websites -- All DOE Office Websites (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

283

Soybean Rust, A Rising Star in Phytopathology  

E-Print Network (OSTI)

by Christine Stone Genome Sequencing Project Funded by theUS DOE Joint Genome Institute Sequencing at JGI Library (DOE Joint Genome Institute Fosmid sequencing Random fosmids

Posada-Buitrago, Martha Lucia

2005-01-01T23:59:59.000Z

284

JGI - CSP Sequencing Plans for 2013  

NLE Websites -- All DOE Office Websites (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

285

JGI - Why Sequence the Limpet?  

NLE Websites -- All DOE Office Websites (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

286

JGI - Why Sequence Hyperthermophilic Archaea?  

NLE Websites -- All DOE Office Websites (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

287

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

NLE Websites -- All DOE Office Websites (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

288

The Fast Changing Landscape of Sequencing Technologies and Their Impact on Microbial Genome Assemblies and Annotation  

SciTech Connect

Background: The emergence of next generation sequencing (NGS) has provided the means for rapid and high throughput sequencing and data generation at low cost, while concomitantly creating a new set of challenges. The number of available assembled microbial genomes continues to grow rapidly and their quality reflects the quality of the sequencing technology used, but also of the analysis software employed for assembly and annotation. Methodology/Principal Findings: In this work, we have explored the quality of the microbial draft genomes across various sequencing technologies. We have compared the draft and finished assemblies of 133 microbial genomes sequenced at the Department of Energy-Joint Genome Institute and finished at the Los Alamos National Laboratory using a variety of combinations of sequencing technologies, reflecting the transition of the institute from Sanger-based sequencing platforms to NGS platforms. The quality of the public assemblies and of the associated gene annotations was evaluated using various metrics. Results obtained with the different sequencing technologies, as well as their effects on downstream processes, were analyzed. Our results demonstrate that the Illumina HiSeq 2000 sequencing system, the primary sequencing technology currently used for de novo genome sequencing and assembly at JGI, has various advantages in terms of total sequence throughput and cost, but it also introduces challenges for the downstream analyses. In all cases assembly results although on average are of high quality, need to be viewed critically and consider sources of errors in them prior to analysis. Conclusion: These data follow the evolution of microbial sequencing and downstream processing at the JGI from draft genome sequences with large gaps corresponding to missing genes of significant biological role to assemblies with multiple small gaps (Illumina) and finally to assemblies that generate almost complete genomes (Illumina+PacBio).

Mavromatis, K [U.S. Department of Energy, Joint Genome Institute; Land, Miriam L [ORNL; Brettin, Thomas S [ORNL; Quest, Daniel J [ORNL; Copeland, A [U.S. Department of Energy, Joint Genome Institute; Clum, Alicia [U.S. Department of Energy, Joint Genome Institute; Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute; Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute; Klenk, Hans-Peter [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Cottingham, Robert W [ORNL; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute

2012-01-01T23:59:59.000Z

289

JGI - Why Sequence the Monkey Flower?  

NLE Websites -- All DOE Office Websites (Extended Search)

of the genomes of M. guttatus, M. nasutus, M. lewisii, and M. cardinalis. The Mimulus genome sequence will complete the genomics toolkit. CSP project participants: John H....

290

Diatom Genome Helps Explain Their Great Diversity and Success in Trapping  

NLE Websites -- All DOE Office Websites (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 Supテゥrieure of

291

The Annual DOE JGI User Meeting  

NLE Websites -- All DOE Office Websites (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

292

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

E-Print Network (OSTI)

relatives for genome sequencing (A. lyrata and CapsellaThis is our rationale for genome sequencing of a free-livingof de Novo Genome Sequencing with 454 Technology Stephen

Various

2006-01-01T23:59:59.000Z

293

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

Science Conference Proceedings (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

2011-10-13T23:59:59.000Z

294

High Performance Computational Biology: A Distributed computing Perspective (2010 JGI/ANL HPC Workshop)  

SciTech Connect

David Konerding from Google, Inc. gives a presentation on "High Performance Computational Biology: A Distributed Computing Perspective" at the JGI/Argonne HPC Workshop on January 26, 2010.

Konerding, David [Google, Inc

2010-01-26T23:59:59.000Z

295

JGI - FY2006 Sequencing for the DOE Microbial Genome Program  

NLE Websites -- All DOE Office Websites (Extended Search)

pickettii 12J 3.5 MB Rice endophyte metagenome 100 MB Schizophyllum commune 38 MB Shewanella halifaxensis HAW-EB4 5 MB Shewanella pealeana ATCC 700345 5 MB Shewanella sediminis...

296

JGI - Green Alga Genome Project Catalogs Carbon Capture Machinery  

NLE Websites -- All DOE Office Websites (Extended Search)

opportunities for improving efficiencies for this conversion process and ultimately biofuels production. "Chlamy's code helps us describe the ancient ancestor of plants and...

297

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

E-Print Network (OSTI)

of Roche 454 Titanium Emulsion PCR at the DOE Joint GenomeEnrichment of emulsion PCR product is the most laborious andand 2X Enrichment Emulsion PCR Emulsion Breaking Enhancing

Hamilton, Matthew

2010-01-01T23:59:59.000Z

298

JGI - Why Sequence Antarctic Marine Bacterioplankton?  

NLE Websites -- All DOE Office Websites (Extended Search)

gene content, but they are significant in terms of gene modification. The goal of this CSP project is to generate genome sequence data for Antarctic marine bacterioplankton...

299

JGI - Why Sequence Seed Plant Mitochondria?  

NLE Websites -- All DOE Office Websites (Extended Search)

properties of plant mtDNAs have now been revealed that comprehensive comparative genome sequencing is imperative. This work will provide a much deeper and richer...

300

Genomics, Gene Expression and Other Studies in Soybean Rust  

E-Print Network (OSTI)

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

Posada-Buitrago, Martha Lucia

2005-01-01T23:59:59.000Z

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

JGI - Why Sequence a Korarchaeota Community?  

NLE Websites -- All DOE Office Websites (Extended Search)

This sequencing project presents the ideal opportunity to use high-throughput DNA sequencing to gain a genome-level description of the Korarchaeota as well as the microbial...

302

The Annual DOE JGI User Meeting  

NLE Websites -- All DOE Office Websites (Extended Search)

in Basidiomycetes David Hibbett, Clark University 10:30 AM - 11:00 AM Using Genomics to Dissect Seed Development Robert Goldberg, UCLA 11:00 AM - 11:30 AM The Sunflower...

303

The Annual DOE JGI User Meeting  

NLE Websites -- All DOE Office Websites (Extended Search)

Times science writer Carl Zimmer delivering the opening keynote at the 7th Annual Genomics of Energy & Environment Meeting on March 20, 2012 in Walnut Creek, Calif. Watch more...

304

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

NLE Websites -- All DOE Office Websites (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

305

Berkeley Lab A to Z Index: J  

NLE Websites -- All DOE Office Websites (Extended Search)

JBEI: Joint BioEnergy Institute JCAP: Joint Center for Artificial Photosynthesis JDEM: The Joint Dark Energy Mission JGI: Department of Energy Joint Genome Institute JHA...

306

JGI - CSP Sequencing Plans for 2014  

NLE Websites -- All DOE Office Websites (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

307

JGI - Science Talks at the Lesher  

NLE Websites -- All DOE Office Websites (Extended Search)

fossil fuels on global climate change. KTVU Channel 2 Health and Science Editor John Fowler will moderate a panel consisting of Joint BioEnergy Institute CEO Jay Keasling, Joint...

308

Algal Functional Annotation Tool from the DOE-UCLA Institute for Genomics and Proteomics  

DOE Data Explorer (OSTI)

The Algal Functional Annotation Tool is a bioinformatics resource to visualize pathway maps, identify enriched biological terms, or convert gene identifiers to elucidate biological function in silico. These types of analysis have been catered to support lists of gene identifiers, such as those coming from transcriptome gene expression analysis. By analyzing the functional annotation of an interesting set of genes, common biological motifs may be elucidated and a first-pass analysis can point further research in the right direction. Currently, the following databases have been parsed, processed, and added to the tool:

  • Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathways Database
  • MetaCyc Encyclopedia of Metabolic Pathways
  • Panther Pathways Database
  • Reactome Pathways Database
  • Gene Ontology
  • MapMan Ontology
  • KOG (Eukaryotic Clusters of Orthologous Groups)
  • Pfam
  • InterPro

Lopez, David

309

JGI - CSP Sequencing Plans for 2006  

NLE Websites -- All DOE Office Websites (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

310

JGI - CSP Sequencing Plans for 2010  

NLE Websites -- All DOE Office Websites (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

311

JGI - CSP Sequencing Plans for 2009  

NLE Websites -- All DOE Office Websites (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

312

High Performance Computing for Sequence Analysis (2010 JGI/ANL HPC Workshop)  

SciTech Connect

Chris Oehmen of the Pacific Northwest National Laboratory gives a presentation on "High Performance Computing for Sequence Analysis" at the JGI/Argonne HPC Workshop on January 25, 2010.

Oehmen, Chris [PNNL

2010-01-25T23:59:59.000Z

313

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

Science Conference Proceedings (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

314

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

SciTech Connect

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

315

The Annual DOE JGI User Meeting  

NLE Websites -- All DOE Office Websites (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

316

Additional national laboratories  

NLE Websites -- All DOE Office Websites (Extended Search)

(Idaho Falls, ID) JGI Joint Genome Institute (Walnut Creek, CA) KCP - ALBQ Kansas City Plant (Albuquerque, NM) KCP Kansas City Plant (Kansas City, MO) LIGO Hanford...

317

Genomics, Gene Expression and Other Studies in Soybean Rust  

E-Print Network (OSTI)

by Christine Stone GENOME SEQUENCING PROJECT PhakopsoraUS DOE Joint Genome Institute DNA sequencing process LibraryUS DOE Joint Genome Institute DNA sequencing process Rolling

Posada-Buitrago, Martha Lucia

2005-01-01T23:59:59.000Z

318

JGI_Training_FileSystems_Feb2012.ppt  

NLE Websites -- All DOE Office Websites (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

319

GenePRIMP: A GENE PRediction IMprovement Pipeline for Prokaryotic genomes  

Science Conference Proceedings (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

320

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

Science Conference Proceedings (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

2010-03-25T23:59:59.000Z

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.


321

Complete genome sequence of Serratia plymuthica strain AS12  

SciTech Connect

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

322

Evolutionary Genomics of Life in (and from) the Sea  

E-Print Network (OSTI)

or by JGI痴 鼎ommunity Sequencing Program (CSP; http://www.jgi.doe.gov/CSP/index.html).The CSP accepts proposals annually and evaluates them

Boore, Jeffrey L.

2009-01-01T23:59:59.000Z

323

JGI - Why Sequence a Frog-Killing Fungus  

NLE Websites -- All DOE Office Websites (Extended Search)

studies of its pathogenicity and its epidemiology. Scientifically, obtaining the genome of B. dendrobatidis is particularly important because it will be one of the first...

324

ZipperDB: Predictions of Fibril-forming Segments within Proteins Identified by the 3D Profile Method (from the UCLA-DOE Institute for Genomics and Proteomics)  

DOE Data Explorer (OSTI)

ZipperDB contains predictions of fibril-forming segments within proteins identified by the 3D Profile Method. The UCLA-DOE Institute for Genomics and Proteomics has analyzed over 20,000 putative protein sequences for segments with high fibrillation propensity that could form a "steric zipper"two self-complementary beta sheets, giving rise to the spine of an amyloid fibril. The approach is unique in that structural information is used to evaluate the likelihood that a particular sequence can form fibrils. [copied with edits from http://www.doe-mbi.ucla.edu/]. In addition to searching the database, academic and non-profit users may also submit their protein sequences to the database.

Goldschmidt, L.; Teng, P.K.; Riek, R.; Eisenberg, D.

325

JGI - Why Sequence a Rhodocyclus-like PAO?  

NLE Websites -- All DOE Office Websites (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

326

JGI - Lean and Mean Biomass-Degrading Fungus  

NLE Websites -- All DOE Office Websites (Extended Search)

Production WALNUT CREEK, CA-The bane of military quartermasters may soon be a boon to biofuels producers. The genome analysis of a champion biomass-degrading fungus has revealed a...

327

JGI - LSP Small-Scale Sequencing Plans for 2007  

NLE Websites -- All DOE Office Websites (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

328

Application of High Performance Computing to the DOE Joint Genomic...  

NLE Websites -- All DOE Office Websites (Extended Search)

Application of High Performance Computing to the DOE Joint Genomic Institute's Data Challenges January 25-26, 2010 DOE Joint Genome Institute, Walnut Creek, CA USA -by invitation...

329

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

Science Conference Proceedings (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

330

NERSC and JGI Join Forces to Tackle Genomics HPC - NERSC Center...  

NLE Websites -- All DOE Office Websites (Extended Search)

a successful track-record in providing these kinds of services they don't have the steep learning curve to climb." "This is a great partnership because data-centric computing is...

331

JGI - Why Sequence Sea Squirt cDNA?  

NLE Websites -- All DOE Office Websites (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

332

Overview of IMG Challenges (MICW - Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)  

Science Conference Proceedings (OSTI)

DOE JGI's Victor Markowitz gives an overview of IMG challenges at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

Markowitz, Victor [JGI

2011-10-12T23:59:59.000Z

333

Incorporating Genomics and Bioinformatics across the Life Sciences Curriculum  

Science Conference Proceedings (OSTI)

Undergraduate life sciences education needs an overhaul, as clearly described in the National Research Council of the National Academies publication BIO 2010: Transforming Undergraduate Education for Future Research Biologists. Among BIO 2010's top recommendations is the need to involve students in working with real data and tools that reflect the nature of life sciences research in the 21st century. Education research studies support the importance of utilizing primary literature, designing and implementing experiments, and analyzing results in the context of a bona fide scientific question in cultivating the analytical skills necessary to become a scientist. Incorporating these basic scientific methodologies in undergraduate education leads to increased undergraduate and post-graduate retention in the sciences. Toward this end, many undergraduate teaching organizations offer training and suggestions for faculty to update and improve their teaching approaches to help students learn as scientists, through design and discovery (e.g., Council of Undergraduate Research [www.cur.org] and Project Kaleidoscope [www.pkal.org]). With the advent of genome sequencing and bioinformatics, many scientists now formulate biological questions and interpret research results in the context of genomic information. Just as the use of bioinformatic tools and databases changed the way scientists investigate problems, it must change how scientists teach to create new opportunities for students to gain experiences reflecting the influence of genomics, proteomics, and bioinformatics on modern life sciences research. Educators have responded by incorporating bioinformatics into diverse life science curricula. While these published exercises in, and guidelines for, bioinformatics curricula are helpful and inspirational, faculty new to the area of bioinformatics inevitably need training in the theoretical underpinnings of the algorithms. Moreover, effectively integrating bioinformatics into courses or independent research projects requires infrastructure for organizing and assessing student work. Here, we present a new platform for faculty to keep current with the rapidly changing field of bioinformatics, the Integrated Microbial Genomes Annotation Collaboration Toolkit (IMG-ACT). It was developed by instructors from both research-intensive and predominately undergraduate institutions in collaboration with the Department of Energy-Joint Genome Institute (DOE-JGI) as a means to innovate and update undergraduate education and faculty development. The IMG-ACT program provides a cadre of tools, including access to a clearinghouse of genome sequences, bioinformatics databases, data storage, instructor course management, and student notebooks for organizing the results of their bioinformatic investigations. In the process, IMG-ACT makes it feasible to provide undergraduate research opportunities to a greater number and diversity of students, in contrast to the traditional mentor-to-student apprenticeship model for undergraduate research, which can be too expensive and time-consuming to provide for every undergraduate. The IMG-ACT serves as the hub for the network of faculty and students that use the system for microbial genome analysis. Open access of the IMG-ACT infrastructure to participating schools ensures that all types of higher education institutions can utilize it. With the infrastructure in place, faculty can focus their efforts on the pedagogy of bioinformatics, involvement of students in research, and use of this tool for their own research agenda. What the original faculty members of the IMG-ACT development team present here is an overview of how the IMG-ACT program has affected our development in terms of teaching and research with the hopes that it will inspire more faculty to get involved.

Ditty, Jayna L.; Kvaal, Christopher A.; Goodner, Brad; Freyermuth, Sharyn K.; Bailey, Cheryl; Britton, Robert A.; Gordon, Stuart G.; Heinhorst, Sabine; Reed, Kelynne; Xu, Zhaohui; Sanders-Lorenz, Erin R.; Axen, Seth; Kim, Edwin; Johns, Mitrick; Scott, Kathleen; Kerfeld, Cheryl A.

2011-08-01T23:59:59.000Z

334

Communicating Genomics:GTL  

NLE Websites -- All DOE Office Websites (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

335

JGI - Why Sequence Euryarchaeota in Acid Mine Drainage?  

NLE Websites -- All DOE Office Websites (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

336

Retrotransposition of gene transcripts leads to structural variation in mammalian genomes  

E-Print Network (OSTI)

for Broad Institute Genome Sequencing and Analysis Programsequenced by the Mouse Genome Sequencing Consortium [49] andto the Chimp Genome Sequencing Consortium 2.1/panTro2

2013-01-01T23:59:59.000Z

337

Environmental genomics reveals a single species ecosystem deep within the Earth  

E-Print Network (OSTI)

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

Chivian, Dylan

2008-01-01T23:59:59.000Z

338

JGI - Statistics  

NLE Websites -- All DOE Office Websites (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%

339

JGI - Events  

NLE Websites -- All DOE Office Websites (Extended Search)

http:bit.lyfIVE9w The Future of Fuel: Local Solutions to Global Energy Challenges Home > Events UC logo DOE logo Contact Us Credits Disclaimer Access Keys 1997-2013 The...

340

Genomic Advances to Improve Biomass for Biofuels (Genomics and Bioenergy)  

DOE Green Energy (OSTI)

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

Rokhsar, Daniel

2008-02-11T23:59:59.000Z

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.


341

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

Science Conference Proceedings (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

342

CI Announces Globus Genomics | Argonne National Laboratory  

NLE Websites -- All DOE Office Websites (Extended Search)

CI Announces Globus Genomics April 9, 2013 Tweet EmailPrint The ArgonneUniversity of Chicago Computation Institute has announced a new sequencing analysis service called Globus...

343

Engineering Institute  

NLE Websites -- All DOE Office Websites (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

344

Personnel | VIMSS - Virtual Institute for Microbial Stress and...  

NLE Websites -- All DOE Office Websites (Extended Search)

National Laboratory Email: KKeller@lbl.gov Phil Hugenholtz Microbial Ecology Program DOE Joint Genome Institute 2800 Mitchell Drive Bldg 400-404 Walnut Creek, CA 94598 USA...

345

Institutional Controls  

NLE Websites -- All DOE Office Websites (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.

346

Communicating Genomics:GTL  

NLE Websites -- All DOE Office Websites (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

347

DOE Joint Genome Institute 2008 Progress Report  

E-Print Network (OSTI)

soon be, targets of keen interest in the biofuels researchtarget. Current biofuel production meth- ods, such as corn-to-ethanol, are a valuable BIOFUELS

Gilbert, David

2009-01-01T23:59:59.000Z

348

DOE Joint Genome Institute 2008 Progress Report  

E-Print Network (OSTI)

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

Gilbert, David

2009-01-01T23:59:59.000Z

349

DOE Joint Genome Institute 2008 Progress Report  

E-Print Network (OSTI)

ries Oak Ri a ato nt o DO me e DOE l labor amos, onAlph ar tio teg ac ana hem dP or B DOE m ogeoc ides in tional achesmanufacturer, or otherwise, does not necessarily constitute

Gilbert, David

2009-01-01T23:59:59.000Z

350

DOE Joint Genome Institute 2008 Progress Report  

E-Print Network (OSTI)

are potential raw materials for production of biofuels. TheRaw plant material, or dedicated bioenergy crops, can provide the starting point for mak- ing biofuels.

Gilbert, David

2009-01-01T23:59:59.000Z

351

Functional Genomics | VIMSS - Virtual Institute for Microbial...  

NLE Websites -- All DOE Office Websites (Extended Search)

Cloning of Identified Pathways Cloning of Identified Pathways Diversa Corporation will apply a combination of advanced technologies, including large DNA insert cloning, biopanning,...

352

DOE Joint Genome Institute 2008 Progress Report  

E-Print Network (OSTI)

B: Glossary Appendix C: CSP Sequencing Plans for 2009Community Sequencing Program (CSP). He is also responsibleand im- plemented the CSP which provides large- scale DNA

Gilbert, David

2009-01-01T23:59:59.000Z

353

DOE Joint Genome Institute 2008 Progress Report  

E-Print Network (OSTI)

Thermoacidophilic proteins for biofuel production. Trends inthat could help improve biofuel production. Diatom Genomedoc/200809/termites) Biofuel痴 Holy Grail: Shipworms? (

Gilbert, David

2009-01-01T23:59:59.000Z

354

DOE Joint Genome Institute: Genome Signatures Enable Tracking...  

NLE Websites -- All DOE Office Websites (Extended Search)

into how photosynthetic organisms can be engineered to do what we want, such as make biofuels or other products, rather than what they typically do, which is grow and make...

355

Scalability of Comparative Analysis, Novel Algorithms and Tools (MICW - Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)  

Science Conference Proceedings (OSTI)

DOE JGI's Kostas Mavrommatis, chair of the Scalability of Comparative Analysis, Novel Algorithms and Tools panel, at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

Mavrommatis, Kostas [JGI

2011-10-12T23:59:59.000Z

356

Comparative genomics of the pathogenic ciliate Ichthyophthirius multifiliis, its free-living relatives and a host species provide insights into adoption of a parasitic lifestyle and prospects for disease control  

E-Print Network (OSTI)

divergent eukaryote. BMC Genomics 2004, 5: 79. 118. Peixotoet al. : Comparative genomics of the pathogenic ciliateand Environmental Genomics, J Craig Venter Institute, 9704

2011-01-01T23:59:59.000Z

357

Quantum Institute  

NLE Websites -- All DOE Office Websites (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

358

Why sequence diatom transcriptome and genome?  

NLE Websites -- All DOE Office Websites (Extended Search)

found in both freshwater and marine ecosystems. They fix as much as 40 percent of the global ocean carbon. The DOE JGI has sequenced two diatoms: Thalassiosira pseudonanana and...

359

The Phaeodactylum genome reveals the evolutionary history of diatom genomes  

E-Print Network (OSTI)

ツィr Meereswissenschaften, 24105 Kiel, Germany. 24 Department of Botany, University of British Columbia, 3529-6270 University Boulevard, Vancouver, British Columbia V6T 1Z4, Canada. 25 School of Chemistry and Biochemistry annotated using the JGI annotation pipeline, which combines several gene prediction, annotation and analysis

Badger, Jonathan

360

Low Dose Radiation Research Program: Genomic Instability and...  

NLE Websites -- All DOE Office Websites (Extended Search)

Genomic Instability and Low Dose Low Dose Rate Radiation. Authors: Lei Huang, Suzanne Grim, William F. Morgan Institutions: University of Maryland. Humans will always receive...

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

Molluscan Evolutionary Genomics  

E-Print Network (OSTI)

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

Simison, W. Brian

2010-01-01T23:59:59.000Z

362

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

Science Conference Proceedings (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

2011-10-13T23:59:59.000Z

363

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

364

Institutional 2-cells and Grothendieck institutions  

E-Print Network (OSTI)

. of Computer Science, University of Bremen, Germany Abstract. We propose to use Grothendieck institutions based specification, you want to prove a theorem, and hence want to see a list of its possible translations (along (co)comorphisms) into tool-supported institutions. Now even with a small diagram of institutions, the list can become quite

Mossakowski, Till - Deutschen Forschungszentrum fテシr Kテシnstliche Intelligenz & Fachbereich 3

365

Molluscan Evolutionary Genomics  

E-Print Network (OSTI)

Today痴 high-throughput genome sequencing centers lack thecomplete nuclear genome sequencing, with several mollusksparticipation. The cost of genome sequencing is still very

Simison, W. Brian

2010-01-01T23:59:59.000Z

366

Argonne Accelerator Institute  

NLE Websites -- All DOE Office Websites (Extended Search)

Argonne Accelerator Institute: Mission The mission of the Argonne Accelerator Institute is centered upon the following related goals: Locate next generation accelerator facilities...

367

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

DOE Data Explorer (OSTI)

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

368

Petroleum Institute Scholarly Publications  

E-Print Network (OSTI)

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

369

Deinococcus geothermalis: The Pool of Extreme Radiation Resistance Genes Shrinks  

E-Print Network (OSTI)

MD KM. Other: JGI Genome- sequencing project coordinator:was selected for genome sequencing by BER (http://the impetus for whole-genome sequencing of D. geothermalis

Makarova, Kira S.

2008-01-01T23:59:59.000Z

370

Operations capability improvement of a molecular biology laboratory in a high throughput genome sequencing center  

E-Print Network (OSTI)

The Broad Institute is a research collaboration of MIT, Harvard University and affiliated hospitals, and the Whitehead Institute for Biomedical Research. Its scientific mission is to "(1) create tools for genomic medicine ...

Vokoun, Matthew R. (Matthew Richard)

2005-01-01T23:59:59.000Z

371

Instituting an institute: go for it!  

Science Conference Proceedings (OSTI)

The University of New Hampshire set out to inaugurate a Faculty Instructional Technology Summer Institute (FITSI) addressing the pedagogical principles that support the successful integration of instructional technology into teaching and learning. After ... Keywords: design, educational technology, faculty development, institute, instructional technology, training

Michael Giordano; Laurel Warren Trufant

2002-11-01T23:59:59.000Z

372

JGI - Why Sequence Mycosphaerella?  

NLE Websites -- All DOE Office Websites (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

373

JGI - CSP FAQs  

NLE Websites -- All DOE Office Websites (Extended Search)

CSP Frequently Asked Questions CSP | Overview | How to Propose a Project | Review Process | DOE Relevance Proposal Schedule | FAQ What can I get from the CSP program? The...

374

JGI - Why Sequence Catfish?  

NLE Websites -- All DOE Office Websites (Extended Search)

potentailly responsible for differences in important traits between the two species. CSP project participants: John Liu (proposer, Auburn Univ.), Sylvie Quiniou and Geoffrey...

375

JGI - Why Sequence Crenarchaeota?  

NLE Websites -- All DOE Office Websites (Extended Search)

'metagenomic' data, to better characterize the naturally occurring microbial world. CSP project participants: Edward F. DeLong (proposer, M.I.T.), Steve Hallam (postdoc,...

376

JGI - CSP Overview  

NLE Websites -- All DOE Office Websites (Extended Search)

Overview of the Community Science Program CSP | Overview | How to Propose a Project | Review Process | DOE Relevance Proposal Schedule | FAQ What is the Community Science Program?...

377

JGI - Why Sequence Dipterans?  

NLE Websites -- All DOE Office Websites (Extended Search)

of development that will greatly advance our understanding of the natural world. CSP project participants: Michael Eisen (proposer, LBNL and Univ. of California, Berkeley),...

378

JGI - Why Sequence Triphysaria?  

NLE Websites -- All DOE Office Websites (Extended Search)

opportunity to dissect the genetic components mediating plant-plant signaling. CSP project participants: John I. Yoder (UC Davis). Home > Sequencing > Why Sequence Them?...

379

JGI - Community Science Program  

NLE Websites -- All DOE Office Websites (Extended Search)

For all other project types, a letter of intent is required to submit a proposal to the CSP. Submitters whose letters of intentproposals are approved will receive further...

380

JGI - CSP Proposal Schedule  

NLE Websites -- All DOE Office Websites (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

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.


381

JGI - News Releases  

NLE Websites -- All DOE Office Websites (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

382

JGI - Jim Bristow  

NLE Websites -- All DOE Office Websites (Extended Search)

Honors Magna Cum Laude, Harvard Medical School (1981); inaugural Fellow of the American Heart Association (2002); American Board of Pediatrics Cardiology Sub-board (2001-2008)....

383

JGI - Eddy Rubin  

NLE Websites -- All DOE Office Websites (Extended Search)

from Middlebury College, the University of Rochester Dean's Award, the Netherlands Heart Association Declaration of Esteem, the American Heart Association Established...

384

JGI - Why Sequence Piromyces?  

NLE Websites -- All DOE Office Websites (Extended Search)

and grow as commensal organisms in the gut of a variety of herbivores. These obligate anaerobic chytrid symbionts play a key role in the digestion of plant cell wall material...

385

Rob Egan JGI  

NLE Websites -- All DOE Office Websites (Extended Search)

in jgitoolsbin) Profiling & performance analysis sar sysstats java -jar jgitoolsmiscsoftwarekSarDEFAULTkSar.jar -input cmd:'ssh -C genepool ssh...

386

JGI - All Sequencing Projects  

NLE Websites -- All DOE Office Websites (Extended Search)

microbial communities from multiple species of wood-boring bivalves. Girguis, Peter Harvard University Linking mantle to microbe: a community-wide effort to ally...

387

20844_JGI_20110308_CR  

NLE Websites -- All DOE Office Websites (Extended Search)

model system for long-term observation and process-oriented studies of OMZ phenotypes. Production and Partial Characterization of a Novel Thermostable Xylanase by Newly Isolated...

388

JGI - Participatory Ergonomics  

NLE Websites -- All DOE Office Websites (Extended Search)

Participatory Ergonomics Have you heard the saying "Mother knows best"? Well, when it comes to ergonomics in the workplace the saying should be "Employees know best." An...

389

JGI User Meeting 2008  

NLE Websites -- All DOE Office Websites (Extended Search)

capacity again this year. Featured Topics: The Helios Project Biomass Feedstocks, Sorghum, Miscanthus, Poplar Metabolism, Eucalyptus, Plant Cell Wall Synthesis, Arabidopsis...

390

JGI - Current Sequencing Technology  

NLE Websites -- All DOE Office Websites (Extended Search)

The Illumina platform takes a sequencing-by-synthesis approach and involves bridge PCR along with reversible dye terminators. The PacBio platform relies on single-molecule...

391

JGI - Educational Links  

NLE Websites -- All DOE Office Websites (Extended Search)

shotgun sequencing. Home > Sequencing > Education > Sanger Sequencing Archive UC logo DOE logo Contact Us Credits Disclaimer Access Keys 1997-2013 The Regents of the...

392

Using Partial Genomic Fosmid Libraries for Sequencing Complete Organellar Genomes  

E-Print Network (OSTI)

than total nuclear genome sequencing, making broaderavailable organellar genome sequencing methods, especiallyenables plastid genome sequencing from both parasitic and

McNeal, Joel R.; Leebens-Mack, James H.; Arumuganathan, K.; Kuehl, Jennifer V.; Boore, Jeffrey L.; dePamphilis, Claude W.

2005-01-01T23:59:59.000Z

393

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

394

Institute /or ADVANCED STUDY  

E-Print Network (OSTI)

, and Stochasticity , David W. McLaughlin, Courant Institute; Waves in Random Media, George Papanicolaou, Stanford Their Properties from Nodes or Nodal Lines, Joyce McLaughlin, Rensselaer Polytechnic Institute; the graduate

395

Genomics and Systems Biology  

NLE Websites -- All DOE Office Websites (Extended Search)

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

396

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

DOE Green Energy (OSTI)

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

Rokhsar, Daniel

2008-02-11T23:59:59.000Z

397

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

NLE Websites -- All DOE Office Websites (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

398

Institute for Advanced Studies  

NLE Websites -- All DOE Office Websites (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

399

INSTITUTE OF COMPUTER SCIENCE  

E-Print Network (OSTI)

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

400

Argonne Accelerator Institute  

NLE Websites -- All DOE Office Websites (Extended Search)

ICFA Beam Dynamics Mini-Workshop on DeflectingCrabbing Cavity Applications in Accelerators April 21-23, 2010, Cockcroft Institute, Daresbury Laboratory, Warrington, UK Sixth...

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.


401

Argonne Accelerator Institute  

NLE Websites -- All DOE Office Websites (Extended Search)

Fermilab Collaboration Lee Teng Scholarship Program Useful Links Argonne Accelerator Institute: For Industrial Collaborators -- Working with Argonne This link is addressed to...

402

"The Encyclopedia of Systems Biology and OMICS" and "The ISA Infrastructure for Multi-omics Data" (GSC8 Meeting)  

Science Conference Proceedings (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. Eugene Kolker from Seattle Children's Hospital briefly discusses "The Encyclopedia of Systems Biology and OMICS," followed by Susanna Sansone from the EBI on "The ISA Infrastructure for multi-omics data" at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, Calif. on Sept. 11, 2009.

Kolker, Eugene (Seattle Children's Hospital); Susanna Sansone (EBI)

2011-09-11T23:59:59.000Z

403

DOE Joint Genome Institute: Formidable Fungal Force Counters...  

NLE Websites -- All DOE Office Websites (Extended Search)

applications, fungi provide a source of enzymes to catalyze such processes as generating biofuels from plant biomass. One large fungal group with such enzymes are the rust plant...

404

DOE Joint Genome Institute: DNA Sequencing Reveals Complex Microbial...  

NLE Websites -- All DOE Office Websites (Extended Search)

operates at higher than normal temperatures to help degrade terephthalate (TA) wastewater that results from the production of a raw chemical used to make many plastic...

405

Joint Genome Institute Progress Report 2002-2005  

E-Print Network (OSTI)

processes, and alternative energy production. Faster andin the areas of alternative energy production, car- bonsequestration, and alternative energy production. invaluable

Gilbert, David

2005-01-01T23:59:59.000Z

406

DOE Joint Genome Institute: Tracking the Remnants of the Carbon...  

NLE Websites -- All DOE Office Websites (Extended Search)

Tracking the Remnants of the Carbon Cycle: How an Ancestral Fungus May Have Influenced Coal Formation For want of a nail, the nursery rhyme goes, a kingdom was lost. A similar,...

407

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

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

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...

408

U.S. Department of Energy Joint Genome Institute  

NLE Websites -- All DOE Office Websites (Extended Search)

areas indicate regions with more chlorophyll, while the blue regions designate xylem tissues involved in transporting water and nutrients. (Image by BESC researcher Shi-You...

409

DOE Joint Genome Institute: Rot's Unique Wood Degrading Machinery...  

NLE Websites -- All DOE Office Websites (Extended Search)

February 5, 2009 Rot's Unique Wood Degrading Machinery to be Harnessed for Better Biofuels Production WALNUT CREEK, CA-An international team led by scientists from the U.S....

410

The DOE Joint Genome Institute Expands Capabilities via New Partnershi...  

NLE Websites -- All DOE Office Websites (Extended Search)

Expands Capabilities via New Partnerships With the publication last year of its strategic plan, "Forging the Future - A Ten-Year Strategic Vision" the U.S. Department of...

411

DOE Joint Genome Institute: Tiny Algae Shed Light on Photosynthesis...  

NLE Websites -- All DOE Office Websites (Extended Search)

children learn is the recipe for photosynthesis, combining carbon dioxide, water and solar energy to produce organic compounds. Many of the world's most important...

412

Joint Genome Institute Progress Report 2002-2005  

E-Print Network (OSTI)

APPENDIX B: 2005 & 2006 CSP DNA Sequencing Projects cont.+ Appendix B: 2005 and 2006 CSP DNA Sequencing Projects + +Community Sequencing Program (CSP) Traditionally, beyond its

Gilbert, David

2005-01-01T23:59:59.000Z

413

Essays on Institutions and Innovation  

E-Print Network (OSTI)

Organizational Structure of the National Institutes of HealthOrganizational Structure of the National Institutes of Health,

Hegde, Deepak

2010-01-01T23:59:59.000Z

414

INSTITUTES OF Registration  

E-Print Network (OSTI)

to the scheduled course. Sign up for: Date Laboratory Safety at the National Institutes of Health HIV Health and Safety Office of Research Services National Institutes of Health Tel: 301-496-3353 http of Occupational Health and Safety to provide annual refresher training for research laboratory personnel who may

Bandettini, Peter A.

415

Complete genome sequence of Methanoculleus marisnigri type strain JR1  

SciTech Connect

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

416

Complete genome sequence of Methanocorpusculum labreanum type strain Z  

Science Conference Proceedings (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

417

Classification Training Institute Catalog | Department of Energy  

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

Classification Training Institute Catalog Classification Training Institute Catalog Enforcement Guidance Oversight Reporting Classification Classification Training Institute...

418

Our Collaborators  

NLE Websites -- All DOE Office Websites (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

419

Argonne Accelerator Institute  

NLE Websites -- All DOE Office Websites (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

420

Argonne Accelerator Institute  

NLE Websites -- All DOE Office Websites (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)

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.


421

NATIONAL INSTITUTES OF HEALTH | National Cancer Institute LABORATORY OF PATHOLOGY  

E-Print Network (OSTI)

NATIONAL INSTITUTES OF HEALTH | National Cancer Institute LABORATORY OF PATHOLOGY National Cancer Institute (NCI) The Laboratory of Pathology, based in the NCI, provides clinical service in anatomic-scientists DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Cancer Institute, Center

422

Joint Theory Institute  

NLE Websites -- All DOE Office Websites (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.

423

Institute of Metals Lecture  

Science Conference Proceedings (OSTI)

We will show that with the study of "Quantum Aerosols" we can gain insight into ... Dr. Yacaman has been a researcher of the Institute of Physics of UNAM, where...

424

EMPLOYERS STRATEGIES Correctional institutions  

E-Print Network (OSTI)

agencies Advocacy groups Federal, state and local government United Way agencies/local branches of national agencies Environmental advocacy groups Environmental periodicals Federal government Regional, stateEMPLOYERS STRATEGIES Correctional institutions Court systems Federal, state and local government

Escher, Christine

425

Summer Institute - Testimonials  

Science Conference Proceedings (OSTI)

... working with them, even if it was such a short time, and touring the institution ... With good luck, I will bring some of my students to tour this facility next ...

2012-12-28T23:59:59.000Z

426

CGAL: computing genome assembly likelihoods  

E-Print Network (OSTI)

SM, Lei M, Li J, et al: Genome sequencing in microfabricatedDe novo bacterial genome sequencing: millions of very shortGenome assembly, evaluation, likelihood, sequencing.

Rahman, Atif; Pachter, Lior

2013-01-01T23:59:59.000Z

427

Genomics and the human genome project: implications for psychiatry  

E-Print Network (OSTI)

and psychosis: a convergent functional genomics approach.Physiology & Genomics, 4, 8391. O LIPHANT , A. , B ARKER ,2004), 16(4), 294300 Genomics and the Human Genome Project:

Kelsoe, J R

2004-01-01T23:59:59.000Z

428

LANL Institutes - Institute of Geophysics and Planetary Physics  

NLE Websites -- All DOE Office Websites (Extended Search)

NEWS LIBRARY JOBS SITE MAP Emergency Maps Organization Goals Phone Search Science > LANL Institutes > Institute of Geophysics and Planetary Physics National Security Education...

429

Comparative genomic workflow  

E-Print Network (OSTI)

his article describes a workflow for identifying conserved patterns in noncoding regions of vertebrate genomes, with an intention of investigating possible functions of the conserved regions. The annotations of genomes are ...

Rajapakse, Jagath

430

Genome in a Bottle Consortium  

Science Conference Proceedings (OSTI)

Genome in a Bottle Consortium. Summary: NIST has organized the "Genome in a Bottle Consortium" to develop the reference ...

2013-03-15T23:59:59.000Z

431

Joint Institutes | ornl.gov  

NLE Websites -- All DOE Office Websites (Extended Search)

Joint Institutes SHARE Joint Institutes ORNL, in partnership with the Science Alliance of the University of Tennessee, Knoxville, has a number of cooperative ventures in science...

432

Argonne Accelerator Institute  

NLE Websites -- All DOE Office Websites (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

433

Argonne Accelerator Institute  

NLE Websites -- All DOE Office Websites (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)

434

The Rational Design of Security Institutions: Effects of Institutional Design on Institutional Performance .  

E-Print Network (OSTI)

??Based on the assumption that security institutions are designed rationally, I study the variations in design schemes and their possible effects on institutional performance. Military (more)

Tandon, Aakriti A.

2012-01-01T23:59:59.000Z

435

Stockholm Environment Institute (SEI) | Open Energy Information  

Open Energy Info (EERE)

Stockholm Environment Institute (SEI) (Redirected from Stockholm Environment Institute) Jump to: navigation, search Logo: Stockholm Environment Institute Name Stockholm Environment...

436

Institutional Research & Development | National Nuclear Security...  

National Nuclear Security Administration (NNSA)

& Technology Programs > Office of Advanced Simulation and Computing and Institutional R&D Programs > Institutional Research & Development Institutional Research & Development...

437

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

NLE Websites -- All DOE Office Websites (Extended Search)

Biological Biological Systems Science Division (BSSD) ツサ 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

438

Complete genome sequence of Ferroglobus placidus AEDII12DO  

Science Conference Proceedings (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

439

released  

NLE Websites -- All DOE Office Websites (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

440

Genome Bioinformatics Data from the University of California at Santa Cruz  

DOE Data Explorer (OSTI)

In addition to the sponsors listed in this citation, many additional institutions and individuals provided support and contributed data to this collection. A full listing is available on the website at http://genome.ucsc.edu/goldenPath/credits.html.

Consortium, ENCODE [Encyclopedia of DNA Elements

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.


441

Transportation Institutional Plan  

SciTech Connect

This Institutional Plan is divided into three chapters. Chapter 1 provides background information, discusses the purposes of the Plan and the policy guidance for establishing the transportation system, and describes the projected system and the plans for its integrated development. Chapter 2 discusses the major participants who must interact to build the system. Chapter 3 suggests mechanisms for interaction that will foster wide participation in program planning and implementation and provides a framework for managing and resolving the issues related to development and operation of the transportation system. A list of acronyms and a glossary are included for the reader's convenience. Also included in this Plan are four appendices. Of particular importance is Appendix A, which includes detailed discussion of specific transportation issues. Appendices B, C, and D provide supporting material to assist the reader in understanding the roles of the involved institutions.

1986-08-01T23:59:59.000Z

442

An integrative approach for genomic island prediction in Prokaryotic genomes  

Science Conference Proceedings (OSTI)

A genomic island (GI) is a segment of genomic sequence that is horizontally transferred from other genomes. The detection of genomic islands is extremely important to the medical research. Most of current computational approaches that use sequence composition ... Keywords: gene information, genomic islands, intergenic distance, sequence composition

Han Wang; John Fazekas; Matthew Booth; Qi Liu; Dongsheng Che

2011-05-01T23:59:59.000Z

443

Genomics and Systems Biology  

NLE Websites -- All DOE Office Websites (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

444

BMC Genomics BioMed Central  

E-Print Network (OSTI)

Software Genome Annotation Transfer Utility (GATU): rapid annotation of viral genomes using a closely related reference genome

Vasily Tcherepanov; Angelika Ehlers; Chris Upton

2006-01-01T23:59:59.000Z

445

Scaling MG-RAST to Terabases (MICW - Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)  

Science Conference Proceedings (OSTI)

Argonne National Lab's Narayan Desai on "Scaling MG-RAST to Terabases" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

Desai, Narayan [ANL

2011-10-12T23:59:59.000Z

446

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

Science Conference Proceedings (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

2011-10-13T23:59:59.000Z

447

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

Science Conference Proceedings (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

2011-10-12T23:59:59.000Z

448

A Collaborative Ecosystem Model for Metagenomics Data Preservation (MICW - Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)  

Science Conference Proceedings (OSTI)

EMBL-EBI's Guy Cochrane on "A Collaborative Ecosystem Model for Metagenomics Data Preservation" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

Cochrane, Guy [EMBL-EBI

2011-10-12T23:59:59.000Z

449

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

Science Conference Proceedings (OSTI)

University of Hong Kong's Francis Chin on "Meta-ュ?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

2011-10-13T23:59:59.000Z

450

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

Science Conference Proceedings (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

2011-10-12T23:59:59.000Z

451

Genome Science/Technologies  

NLE Websites -- All DOE Office Websites (Extended Search)

Science & Innovation ツサ Science & Innovation ツサ Science & Engineering Capabilities ツサ Bioscience: Bioenergy, Biosecurity, and Health ツサ Environmental Microbiology ツサ 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.

452

Genome Science/Technologies  

NLE Websites -- All DOE Office Websites (Extended Search)

Momchilo Vuyisich Bioenergy and Biomedical Sciences Email Rebecca McDonald Bioscience Communications Email State-of-the art technology and extensive genomics expertise Protein...

453

Genome Sequence Databases (Overview): Sequencing and Assembly  

E-Print Network (OSTI)

complete microbial genome sequencing (you get what you payet al. (2005). Genome sequencing in open microfabricatedof problem solving in genome sequencing. Genome Research 8,

Lapidus, Alla L.

2009-01-01T23:59:59.000Z

454

Genome Analysis and Systems Modeling Group  

NLE Websites -- All DOE Office Websites (Extended Search)

(Microbial Genomes) Pipeline, Comprehensive Genome Analysis Pipeline Genome Channel, Java applet for the comprehensive sequence-based view of genomes. Grail, a tool for the...

455

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

456

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

Science Conference Proceedings (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

2012-06-01T23:59:59.000Z

457

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

Science Conference Proceedings (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

458

Argonne Accelerator Institute  

NLE Websites -- All DOE Office Websites (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

459

List of all HEP Institutions  

NLE Websites -- All DOE Office Websites (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.

460

Spectrogram analysis of genomes  

Science Conference Proceedings (OSTI)

We perform frequency-domain analysis in the genomes of various organisms using tricolor spectrograms, identifying several types of distinct visual patterns characterizing specific DNA regions. We relate patterns and their frequency characteristics to ... Keywords: DNA spectrograms, frequency-domain analysis, genome analysis

David Sussillo; Anshul Kundaje; Dimitris Anastassiou

2004-01-01T23:59:59.000Z

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.


461

Legume Crop Genomics  

Science Conference Proceedings (OSTI)

This book will present this technical theme in a manner that should help many readers answer the question, "What is genomics?" And finally, this book should help readers formulate an opinion on the question, "Why is genomic research needed?" Legume Crop Ge

462

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

463

Enhancer Identification through Comparative Genomics  

E-Print Network (OSTI)

through Comparative Genomics Axel Visel, James Bristow andWalnut Creek, CA 94598 USA. Genomics Division, MS 84-171,Len A. Pennacchio, Genomics Division, One Cyclotron Road, MS

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

2006-01-01T23:59:59.000Z

464

Three New Manufacturing Innovation Institutes  

Science Conference Proceedings (OSTI)

... $200 million across five Federal agencies Defense, Energy, Commerce, NASA ... a pilot institute headquartered in Youngstown, Ohio, the President ...

465

cv15866_JGI_PR_CR:JGI Progress Report  

NLE Websites -- All DOE Office Websites (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

466

Genome Properties Database  

DOE Data Explorer (OSTI)

The Genome Properties system consists of a suite of "Properties" which are carefully defined attributes of prokaryotic organisms whose status can be described by numerical values or controlled vocabulary terms for individual completely sequenced genomes. Evaluation of these properties may take place via manual curation or by computer algorithms (numerical calculations or rules-based assignment of controlled vocabulary terms). The Genome Properties system has been designed to capture the widest possible range of attributes and currently encompasses taxonomic terms, genometric calculations, metabolic pathways, systems of interacting macromolecular components and quantitative and descriptive experimental observations (phenotypes) from the literature. Wherever possible, Genome Properties are linked to traceable lines of evidence and links are provided to data for any genes which are part of this evidence. The primary source of evidence linking genes to properties is homology modelling using Hidden Markov Models (HMMs) from the TIGRFAMs and Pfam databases. (Taken from the Genome Properties Home Page)(Specialized Interface)

Haft, Daniel H.; Selengut, Jeremy D.; Brinkac, Lauren M.; Zafar, Nikhat; White, Owen

467

Draft Transportation Institutional Plan  

SciTech Connect

The Department of Energy recognizes that the success of its program to develop and implement a national system for nuclear waste management and disposal depends on broad-based public understanding and acceptance. While each program element has its particular sensitivity, the transportation of the waste may potentially affect the greatest number of people, and accordingly is highly visible and potentially issue-laden. Therefore, the Office of Civilian Radioactive Waste Management has developed this Transportation Institutional Plan to lay the foundation for interaction among all interested parties for the purpose of identifying and resolving issues of concern. The Plan is divided into four chapters. Chapter 1 provides bachground information and discusses the purpose of the Plan and the policy guidance for establishing the transportation system. Chapter 2 introduces the major participants who must interact to build both the system itself and the consensus philosophy that is essential for effective operations. Chapter 3 suggests mechanisms for interaction that will ensure wide participation in program planning and implementation. And, finally, Chapter 4 suggests a framework for managing and resolving the issues related to development and operation of the transportation system. A list of acronyms and a glossary are included for the reader's convenience. The Plan's appendices provide supporting material to assist the reader in understanding the roles of the involved institutions. 4 figs., 1 tab.

1985-09-01T23:59:59.000Z

468

Analyzing genomic data: understanding the genome  

Science Conference Proceedings (OSTI)

The effort that led to the sequencing of the human genome ushered life sciences into a new era. One of the largest international scientific endeavors of the time delivered the genetic makeup of our species to the research community. Further international ... Keywords: Algorithmic Development, Biological Data Mining, Data Mining Software Tools

Xos M. Fern疣dez-Su疵ez

2012-03-01T23:59:59.000Z

469

Why improve the pipeline for comparative transcriptomics?  

NLE Websites -- All DOE Office Websites (Extended Search)

Plans Educational Resources MyJGI: Information for Collaborators Why improve the pipeline for comparative transcriptomics? The genomes of several brown rot and white rot fungi...

470

JGI - Why Sequence Karenia brevis?  

NLE Websites -- All DOE Office Websites (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

471

JGI - Why Sequence Staph. Aureus?  

NLE Websites -- All DOE Office Websites (Extended Search)

resistance to vancomycin, an antimicrobial agent most frequently used against it. CSP project participants: Alexander Tomasz (proposer and PI, Rockefeller Univ.) and Eugene...

472

JGI - Why Sequence Spironucleus vortens?  

NLE Websites -- All DOE Office Websites (Extended Search)

expedite future proteomic and functional analysis of diverse free-living eukaryotes. CSP project participants: W. Zacheus Cande (proposer, Univ. of California, Berkeley). Home...

473

JGI - Why Sequence Sporobolomyces roseus?  

NLE Websites -- All DOE Office Websites (Extended Search)

salmonicolor should allow researchers to find new introns with identifiable sources. CSP project participants: Kenneth H. Wolfe (proposer, Trinity College, Dublin), Michael...

474

JGI - Why Sequence Selaginella moellendorffii?  

NLE Websites -- All DOE Office Websites (Extended Search)

will help to define an ancient core of genes that are common to all vascular plants. CSP project participants: Jo Ann Banks (proposer), Clint Chapple, Scott Jackson, Joe Ogas,...

475

JGI - Why Sequence Marinobacter aquaeolei?  

NLE Websites -- All DOE Office Websites (Extended Search)

benefits a broad community of microbiologists, oceanographers, and biogeochemists. CSP project participants: Katrina Edwards (proposer), Mitchell Sogin (proposer), and Ashita...

476

JGI - Why Sequence the Leech?  

NLE Websites -- All DOE Office Websites (Extended Search)

cloning of conserved and novel genes and the deep annotation of animal gene families. CSP project participants: David Weisblat (proposer, Univ. of California, Berkeley), Jeffrey...

477

JGI - Len Pennacchio - Select Publications  

NLE Websites -- All DOE Office Websites (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.

478

JGI - Why Sequence Alvinella pompejana?  

NLE Websites -- All DOE Office Websites (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ツー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

479

JGI - Why Sequence Trichoderma virens?  

NLE Websites -- All DOE Office Websites (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

480

JGI - Why Sequence Xanthoria parietina?  

NLE Websites -- All DOE Office Websites (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").

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.


481

JGI - Why Sequence Cichlid Fish?  

NLE Websites -- All DOE Office Websites (Extended Search)

Cichlid Fish? photo of chichlid fish The sequencing of several Lake Malawi cichlid fish will contribute to major advances in our understanding of evolution in Lake Malawi cichlids....

482

JGI - Why Sequence Mycosphaerella fijiensis?  

NLE Websites -- All DOE Office Websites (Extended Search)

in sugar beet, soybean, tobacco, and many other crops of great importance to U.S. and global agriculture. This sequencing project will help scientists to understand processes...

483

JGI Lab Ergo Products Catalog  

E-Print Network (OSTI)

4 Jartubes with just one hand. No Openers (Jar and Packaging)Dycem Multi-Purpose Jar Openers http://www.amazon.com/

Alexandre, Melanie

2010-01-01T23:59:59.000Z

484

JGI - Why Sequence a Butterfly?  

NLE Websites -- All DOE Office Websites (Extended Search)

(Leiden Univ., The Netherlands), Antonia Monteiro (Univ. at Buffalo). Home > Sequencing > Why Sequence Them? > Why Sequence a Butterfly? UC logo DOE logo Contact Us Credits...

485

JGI - Why Sequence Polynucleobacter Species?  

NLE Websites -- All DOE Office Websites (Extended Search)

Free-Living and Endosymbiotic Polynucleobacter Species? The Polynucleobacter group (Betaproteobacteria, Burkholderiaceae) is of enormous environmental relevance in freshwater...

486

Argonne Accelerator Institute  

NLE Websites -- All DOE Office Websites (Extended Search)

The Argonne Accelerator History Document Collection The Argonne Accelerator History Document Collection The Argonne Accelerator Institute (AAI) has established a special collection of archived documents which describe notable Argonne accelerator work of the past 50 years. A list of such Argonne Accelerator Projects is given below. Each project is described briefly, with links to archived documents in this collection. This collection includes important Argonne accelerator documents which may have become difficult to locate, as well as ones which have broad scope. In keeping with its historical purpose, this collection only covers work done 10 or more years ago. Many of the listed documents are available online. We hope to make more of them available online in the future. [For several of the projects, interesting additional online documents can be found by

487

Argonne Accelerator Institute  

NLE Websites -- All DOE Office Websites (Extended Search)

Welcome Welcome 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. I invite you to look around the content of this web site. Accelerators at Argonne describes our rich heritage in this field, particularly with respect to the development and support of user facilities. Initiatives describes the things we are hoping to do, and Research & Development discusses our research portfolio. If you are a graduate or undergraduate student wishing to pursue a career in accelerator science or technology, please see Educational

488

Argonne Accelerator Institute  

NLE Websites -- All DOE Office Websites (Extended Search)

ZGS -- Zero Gradient Synchrotron (operation: 1963 - 1979) ZGS -- Zero Gradient Synchrotron (operation: 1963 - 1979) The ZGS was a 12 GeV weak-focusing proton synchrotron. It was the first high energy physics accelerator located between the U.S. coasts. The ZGS was also the first synchrotron to accelerate spin polarized protons and the first to use H-minus injection. Other noteworthy features of the ZGS program were the large number of university-based users and the pioneering development of large superconducting magnets for bubble chambers and beam transport. References - Document Access Guide History of the ZGS, Argonne, 1979, American Institute of Physics, AIP Conference Proceedings No. 60 (1980). (Located in the Argonne Research Library) High Energy Physics at Argonne National Laboratory, A. Crewe, R.

489

Institutional analysis for energy policy  

SciTech Connect

This report summarizes principles, techniques, and other information for doing institutional analyses in the area of energy policy. The report was prepared to support DOE's Regional Issues Identification and Assessment (RIIA) program. RIIA identifies environmental, health, safety, socioeconomic, and institutional issues that could accompany hypothetical future scenarios for energy consumption and production on a regional basis. Chapter 1 provides some theoretical grounding in institutional analysis. Chapter 2 provides information on constructing institutional maps of the processes for bringing on line energy technologies and facilities contemplated in RIIA scenarios. Chapter 3 assesses the institutional constraints, opportunities, and impacts that affect whether these technologies and facilities would in fact be developed. Chapters 4 and 5 show how institutional analysis can support use of exercises such as RIIA in planning institutional change and making energy policy choices.

Morris, F.A.; Cole, R.J.

1980-07-01T23:59:59.000Z

490

DOE Solar Decathlon: New York Institute of Technology: Instituting  

NLE Websites -- All DOE Office Websites (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

491

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

492

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

493

Stockholm Environment Institute (SEI) | Open Energy Information  

Open Energy Info (EERE)

Stockholm Environment Institute (SEI) Jump to: navigation, search Logo: Stockholm Environment Institute Name Stockholm Environment Institute Address Kraftriket 2B, SE-106 91 Place...

494

JIBS | Joint Institute for Biological Sciences | ORNL  

NLE Websites -- All DOE Office Websites (Extended Search)

Joint Institute for Biological Sciences SHARE Joint Institute for Biological Sciences The Joint Institute of ORNL and the University of Tennessee has a single mission: to enable...

495

Form:Research Institution | Open Energy Information  

Open Energy Info (EERE)

Research 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...

496

Honda Research Institute | Open Energy Information  

Open Energy Info (EERE)

Name Honda Research Institute Place Mountain View, California Sector Biofuels, Solar Product California-based research institute of Honda. The institute conducts research into...

497

Structural Genomics | Biosciences Division  

NLE Websites -- All DOE Office Websites (Extended Search)

Chart Site Index Inside BIO BIO Safety About Argonne Midwest Center for Structural Genomics Andrzej Joachimiak Director Bldg: 202. Room: Q 118 E-mail: andrzejj@anl.gov Phone:...

498

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

E-Print Network (OSTI)

annotation and comparative genomics. Database (Oxford) 2009,et al. : Comparative genomics of the core and accessoryComparative genomics of the core and accessory genomes of 48

2013-01-01T23:59:59.000Z

499

WIPP - Passive Institutional Controls (PICs)  

NLE Websites -- All DOE Office Websites (Extended Search)

Energy has developed a program for the development of Passive Institutional Controls to alert future generations to the potential hazards of intersecting the Waste Isolation Pilot...

500

Institutional Plan FY 2003 - 2007  

E-Print Network (OSTI)

III. LABORATORY STRATEGIC PLAN DOE Program Focus on ResultsInstitutional Plan addresses the strategic goals of DOE andbelow does not support those elements of the strategic plan

Chartock, Michael; Hansen, Todd

2002-01-01T23:59:59.000Z