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August 2014

JGI Newsletter The Primer Summer 2014 edition now posted [8/14]

JGI MGM workshop: September 8-12, 2014 - JGI, Walnut Creek, CA. 
The DOE JGI offers five-day workshops on Microbial Genomics and Metagenomics (MGM) that include two days of intensive seminars and three days of hands-on tutorials, including tutorials for the following tools: IMGIMG/MIMG-ERIMG-EDUVISTAGREENGENES and ARB . Registration

10th Annual DOE Joint Genome Institute Genomics of Energy & Environment Meeting (UMX). March 24-26, 2015. details upcoming.

May 2014

JGI Newsletter The Primer Spring 2014 edition now posted [5/14]

Research for Sustainable Bioenergy: Linking Genomic and Ecosystem Sciences workshop report now available.

March 2014

2013 JGI Progress Report available for download. Significant accomplishments of the past fiscal year (Oct 2012-Sept 2013), from plumbing the depths of microbial dark matter to whole genome analyses of cotton, peach, and the button mushroom are summarized in the U.S. Department of Energy Joint Genome Institute (DOE JGI) annual Progress Report.

February 2014

The DOE Joint Genome Institute (DOE JGI) Community Science Program (CSP) is now accepting Letters of Intent for large-scale sequence-based genomic science projects that address questions of relevance to DOE missions in sustainable biofuel production, global carbon cycling, and biogeochemistry.  Priority for this call will be given to projects that address the following areas of special emphasis and exploit the diversity of DOE JGI capabilities. The CSP data is immediately made publicly available, without exception.

Details of the Call can be found here.

I. Functional Genomics and Microbiomes of DOE JGI Flagship Plants
II. Probing functional diversity of microbes
III. Microbial emission and capture of greenhouse gases in terrestrial systems
IV. Discovery and expression of natural product pathways relevant to energy-related and environmental processes

Deadlines
Letters of intent (LOI) will only be accepted electronically and should be submitted at http://proposals.jgi-psf.org/.
·       LOI due: April 10, 2014 
·       Full proposals invited: April 24, 2014 
·       Full proposals due: June 5, 2014  
·       Projects begin: October 2014
Questions? Contact: Axel Visel (avisel@lbl.gov), DOE JGI Strategic Planning-Science Lead.

January 2014

JGI Newsletter The Primer Winter 2014 edition now posted [1/14]

JGI-EMSL Collaborative Science Proposals Accepted until April 7
Letters of Intent for the JGI-EMSL Collaborative Science Call may be submitted at any time via the EMSL User Portal until April 7, 2014 at 11:00 p.m. (Pacific Daylight Time).
This call represents a unique opportunity for researchers to combine the power of genomics at the Joint Genome Institute and molecular characterization at EMSL in one proposed research project. Both user facilities, which are stewarded by the Department of Energy's Office of Biological and Environmental Research, play critical roles in supporting DOE's energy, environment and basic research missions. Applications should focus on high risk/high payoff projects that can be completed in 18 months, utilize a broad range of the capabilities of each facility, and generate datasets unique to these two facilities and beyond what each could generate by itself. Applications for this joint Call will follow a proposal package, schedule, and review process that has been tailored to meet both EMSL and JGI requirements. Details regarding this year's focused topics, as well as contact information and links to the 2014 review criteria and proposal package guidance, are available at the JGI-EMSL Collaborative Science Call web page. Questions regarding EMSL's user program or specifics about the Call opportunities may be directed to the User Support Office (509-371-6003, emsl@pnnl.gov).

 

December 2013

Registration for the Ninth Annual DOE Joint Genome Institute Genomics of Energy & Environment Meeting
March 18-20, 2014 in Walnut Creek, California is now open. Speakers covering the world of possibilities in 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. Keynote speakers: Annalee Newitz, editor in chief of io9, author of the recent book, "Scatter, Adapt, Remember" and Steve Quake of Stanford University. In addition, there will be workshops and tutorials on genomic informatics, data management, and new genomic technologies.  Also, short talks will be selected from poster abstracts.

USDA and DOE Fund 7 Research Projects to Develop Plant Feedstocks for Bioenergy. The U.S. Departments of Agriculture (USDA) and Energy (DOE) today announced $8 million in research grants to develop non-food feedstocks that can be used for bioenergy. The grants are part of a broader effort by the Obama administration to develop domestic renewable energy and advanced biofuels, providing a more secure future for America’s energy needs and enhancing rural economies. See Plant Feestocks for Bioenergy site.

November 2013

Plant Feedstock Genomics for Bioenergy. DOE and USDA announce funding call. Close: Feb 25, 2014; Pre-applications Due 12/19/2013 [11/13]

New Calls for Proposals and Latest News from the DOE Joint Genome Institute

June 2013

Summer 2013 edition of JGI newsletter The Primer now available

April 2013

DOE Announces Five-Year Renewal of Funding for Bioenergy Research Centers. Centers will receive $25 million per year for innovative biofuel research. [4/4/13]

Each of the three Bioenergy Research Centers also provided releases.

February 2013

First Major KBase Public Release is Now Available

The February 2013 Developer's Release includes the most complete yet set of services, as well as better user documentation, and a wider set of web-based and downloadable products. There are several ways to try out the KBase software:

  • The Downloads page offers a Mac disk image (DMG), which you can install and launch as an application. It provides a KBase programming and execution environment complete with client libraries and command-line executables for the available KBase services. An Ubuntu Linux disk image is also available.
  • Alternatively, IRIS allows users to run the KBase command-line scripts from a web-based interface without downloading any software. Tutorials for many of these command-line scripts are available on our website.
  • KBase is actively developing graphical user interfaces that will make KBase more accessible to non-programmers. Some of these are linked from the KBase Labs page.

The DOE Joint Genome Institute Community Sequencing Program (CSP) is now accepting letters of intent (LOI) for large-scale sequence-based genomic science projects that address questions in alternative fuels, global carbon cycling, and biogeochemistry. For more details and to submit an LOI by the April 8, 2013 DEADLINE, go to http://bit.ly/JGI-CSP14. Areas of emphasis:

  • DOE JGI Plant Flagship Genomes of special interest as biofuel feedstocks or as comparators that provide insight into feedstock evolution and phenotype. Projects may fall into the following four categories:  Gene Atlas & ENCODE-like projects; Large-scale resequencing projects; De novo sequencing of flagship comparators) Plant microbiomes
  • Probing functional diversity of microbes
  • Microbial emission and capture of greenhouse gases in terrestrial systems
  • Exploratory Collaborations between the EMSL and the DOE JGI
  • DNA Synthesis

DOE GSP Funding Call: Systems Biology Enabled Research on the Role of Microbial Communities in Carbon Cycling [02/13]

Call for Exploratory Collaborations between the Environmental Molecular Sciences Laboratory and Joint Genome Institute Letters of Intent Accepted February 11 - April 8, 2013 [02/13]


January 2013

8th Annual DOE Joint Genome Institute Genomics of Energy & Environment Meeting: March 26-28, 2013 in Walnut Creek, California.
http://bit.ly/JGI-Meeting
This international gathering offers invited presentations and poster sessions.  Short talks will be chosen from submitted abstracts.
Selected Topics:

  • DNA Synthesis & Synthetic Biology
  • Application of Single-Cell Genomics in Microbial Ecology & Bioprospecting
  • Genomic Analysis of Biofuel Traits in Biomass Feedstocks
  • High-Performance Computing for Next Generation Sequencing Applications
  • Biodiversity Surveying
  • Functional Metagenomics
  • Metaproteomics of Marine Bacterial Symbionts
  • Massive-Scale Data Transfer
  • Analyses of Root-Nodulating Bacteria, and more.

November 2012

Plant Feedstock Genomics for Bioenergy. DOE and USDA announce funding call. Close: Feb 25, 2013; Pre-applications Due 12/18/2012 [11/12]

July 2012

Summer 2012 edition of JGI newsletter The Primer now available

May 2012

KBase User Interface launches alpha release

EMSL User Meeting will be held August 14-15, 2012, in Richland, WA

Spring 2012 edition of JGI newsletter The Primer now available

March 2012

DOE JGI Community Sequencing Program The US Department of Energy Joint Genome Institute (DOE JGI) Community Sequencing Program (CSP) is now accepting letters of intent for large-scale sequence-based genomic science projects that address questions of relevance to DOE missions in alternative fuels, global carbon cycling, and biogeochemistry. Details at http://1.usa.gov/JGI-CSP13

Letters of intent will only be accepted electronically and should be submitted at http://bit.ly/CSP-Proposals between now and April 12, 2012.  Applicants will be advised whether to prepare a full proposal within two weeks, and full proposals will be due June 13.  Proposals will be independently peer-reviewed and ranked.  Final decisions based on ranking will be made by JGI senior management with final approval given by DOE program management.   For questions about the appropriateness of projects, program specifics or application process, please contact Jim Bristow (jbristow@lbl.gov). 

February 2012

2012 Genomic Science Awardee Meeting X abstracts available.

January 2012

Winter 2012 edition of the JGI newsletter The Primer is now available

December 2011

The U.S. Department of Energy Joint Genome Institute (DOE JGI) is offering several five-day workshops on Microbial Genomics and Metagenomics during 2012. Each workshop presents the same agenda and content and includes two days of intensive seminars and three days of hands-on tutorials for the following tools: IMG, IMG/M, IMG-ER, IMG-EDU, VISTA, GREENGENES and ARB. Our goal is to provide you with training in microbial genomic and metagenomic analysis and demonstrate how the cutting-edge science and technology of DOE JGI can enhance your research. Information and Registration

November 2011

Plant Feedstock Genomics for Bioenergy: A Joint Research Funding Opportunity Announcement SC_FOA_0000598. The U.S. Department of Energy's Office of Science, Office of Biological and Environmental Research (BER), and the U.S. Department of Agriculture (USDA), National Institute of Food and Agriculture (NIFA), hereby announce their interest in receiving applications for genomics based research that will lead to the improved use of biomass and plant feedstocks for the production of fuels such as ethanol or renewable chemical feedstocks. Specifically, applications are sought for fundamental research on plants that will improve biomass characteristics, biomass yield, or sustainability. Systems biology approaches to identify genetic indicators enabling plants to be efficiently bred or manipulated, or research to predict phenotype from underlying genotype that could lead to improved feedstock characterization and sustainability are also encouraged.
Pre-Application Due Date: December 16, 2011, 4:30 p.m. Eastern Time
(Pre-applications are Required)
Application Due Date: February 24, 2012, 11:59 p.m. Eastern Time
Applications must be submitted through Grants.gov to be considered for award.

2012 Genomic Science Meeting The Department of Energy Office of Biological and Environmental Research 2012 Genomic Science Annual Contractor-Grantee Meeting will be held February 26-29, 2012 , at the Bethesda North Marriott Hotel and Conference Center. Abstract deadline December 15, 2011. Attendance by invitation only.

October 2011

Registration is now live for the 2012 DOE Joint Genome Institute (JGI) Genomics of Energy & Environmental Meeting 7, March 20-22, 2012, Walnut Creek, California. Information and Registration

Fall 2011 edition of the JGI newsletter The Primer is now available

September 2011

Microbial Genome Analysis Workshop for Undergraduate Educators. On January 19-20, the U.S. Department of Energy (DOE) Joint Genome Institute (JGI) Education Program will be hosting its Sixth Annual Workshop in Microbial Genome Analysis for Undergraduate Educators. To read more about the Undergraduate Research in Microbial Genome Analysis program at the DOE JGI, please visit http://www.jgi.doe.gov/education/genomeannotation.html. The deadline to apply to join the program for the 2012-2013 academic year is November 18. There is a limited amount of NSF funding to support participation.

August 2011

DOE and USDA Fund Ten New Projects for Biomass Genomics Research. See website and press release.

July 2011

BSSD Director Position Announced. The Department of Energy, Office of Science, Office of Biological and Environmental Research, Biological Systems Sciences Division (BSSD), is seeking a motivated and highly qualified individual to serve as the Director.  For detailed information about the position, check the USAJobs website.

National Laboratories and Universities Team up to Build a Community Systems Biology Knowledgebase. In July 2011, DOE announced the selection of a collaboration of top scientists from across the Nation to lead development of a computer-based Systems Biology Knowledgebase. Leading the collaboration will be principal investigator Adam Arkin of Lawrence Berkeley National Laboratory (LBNL), with co-principal investigators Rick Stevens of Argonne National Laboratory (ANL), Robert Cottingham of Oak Ridge National Laboratory (ORNL), and Sergei Maslov of Brookhaven National Laboratory. Also participating as investigators in the multi-institutional program are Pamela Ronald of the University of California, Davis; Matthew DeJongh of Hope College in Michigan; Gary Olsen of the University of Illinois at Urbana-Champaign; Doreen Ware of the Cold Spring Harbor Laboratory; and Mark Gerstein of Yale University.

June 2011

Two Program Manager positions for Genomic Sciences within BER's Biological Systems Science Division (BSSD) will be posted soon to the USAJobs website. The positions will be located at DOE headquarters in Germantown, MD. According to new federal rules, and unlike past hiring processes, these announcements will be posted for only 10 days. For the official announcements please regularly check the USAJobs website at https://www.usajobs.gov/.

April 2011

Abstracts available from the Genomic Science Contractor-Grantee Workshop held April 10-13, 2011. Joint meeting with USDA-DOE Plant Feedstock Genomics for Bioenergy.

JGI CSP letter of intent deadline has been extended to Monday, May 2. JGI CSP now accepting letters of intent for large-scale sequence based genomic science projects in alternative fuels, global carbon cycling and biogeochemistry. Submit at http://proposals.jgi-psf.org/.

Spring 2011 edition of the JGI newsletter The Primer is now available

DOE JGI offers several five-day workshops on Microbial Genomics and Metagenomics during 2010-2011. Next workshop September 26-30, 2011

March 2011

JGI’s Community Sequencing Program (CSP) is now accepting letters of intent for large-scale sequence based genomic science projects that address questions of relevance to DOE missions in alternative fuels, global carbon cycling and biogeochemistry. While applications will be accepted that address any aspect of these mission areas, up to50% of capacity for this call will be allocated for projects that address the following areas of special emphasis, and exploit the diversity of JGI capabilities. More information.

December 2010

2011 Genomic Science Meeting The Department of Energys Office of Biological and Environmental Research 2011 Genomic Science Annual Contractor-Grantee Workshop will be held jointly with the USDA-DOE Plant Feedstock Genomics for Bioenergy Awardee meeting. The meeting will take place from April 10th (evening reception) through April 13th (ending early afternoon) 2011, at the Hyatt Regency Crystal City at Reagan National Airport. Please note that the timing of the annual meeting was shifted to avoid snowfall. Attendance by invitation only.

2011 DOE JGI Meeting 6th Annual DOE Joint Genome Institute "Genomics of Energy & Environment" meeting March 22-24, 2011 in Walnut Creek, California. downloadable/printable color flyer For more information and/or to register go to: http://go.usa.gov/1FL

November 2010

Plant Feedstock Genomics for Bioenergy. DOE and USDA announce funding call. The U.S. Department of Energy's Office of Science, Office of Biological and Environmental Research (OBER), and the U.S. Department of Agriculture (USDA), National Institute of Food and Agriculture (NIFA), hereby announce their interest in receiving applications for genomicsbased research that will lead to the improved use of biomass and plant feedstocks for the production of fuels such as ethanol or renewable chemical feedstocks. Specifically, applications are sought for fundamental research on plants that will improve biomass characteristics, biomass yield, or sustainability. Systems biology approaches to identify genetic indicators enabling plants to be efficiently bred or manipulated, or research to predict phenotype from underlying genotype that could lead to improved feedstock characterization and sustainability are also encouraged. Potential applicants are required to submit a brief preapplication, referencing DE-FOA-0000417 for receipt by DOE by 4:30 p.m., Eastern Time, December 17, 2010.

October 2010

Carbon Cycling 2010 Awards Biological Systems Research on the Role of Microbial Communities in Carbon Cycling. Summary of projects awarded in summer 2010 under Funding Opportunity Announcement DE-PS02-09ER09-25 Download PDF

The Fall 2010 edition of the DOE Joint Genome Institute newsletter, The Primer, has arrived and can be downloaded here:http://go.usa.gov/aVu. Hard copies are available by request from MMLozano@lbl.gov.
Back issues of The Primer are available for download at this page: http://bit.ly/d0VkZt
Highlights include:

  • DOE JGI’s 2011 Community Sequencing Program Portfolio
  • Alga for Biodiesel Sequenced
  • Fungal Lessons on Breaking Biomass Better
  • Microbes That can Take the Heat
  • and more!

DOE JGI Workshops The DOE JGI offers several five-day workshops on Microbial Genomics and Metagenomics during 2010-2011. Each workshop presents the same agenda and content, and will include two days of intensive seminars and three days of hands-on tutorials, including tutorials for the following tools: IMG, IMG/M, IMG-ER, IMG-EDU, VISTA, GREENGENES and ARB . The goal is to provide you with training in microbial genomic and metagenomic analysis and demonstrate how the advancing science and technology of DOE JGI can enhance your research. Upcoming Workshops: October 18-22, 2010; Future workshops will be announced on JGI's website as they are scheduled.
Contact: Marsha Fenner
DOE Joint Genome Institute
2800 Mitchell Drive, B400
Walnut Creek, CA 94598
Phone: 925-296-5781
MWFenner@lbl.gov

September 2010

USDA and DOE Fund New Projects for Biomass Genomics Research Departments of Energy and Agriculture jointly selected 9 projects for awards totaling $9 million for biobased-fuel research. [Sept 2, 2010] List of Awardees

July 2010

Brochure: "Bioenergy Research Centers: An Overview of the Science," Revised July 2010 [faster-download PDF or higher-quality PDF]

The Summer 2010 edition of the DOE Joint Genome Institute newsletter, The Primer, has arrived and can be downloaded here: PDF

Highlights include:

  • A report from the recent, "The Sequencing, Finishing, Analysis in the Future" Meeting
  • The Volvox genome Science publication
  • Amazonian Stinkbird guts (research/researcher) profile
  • California Biomass Collaborative’s Seventh Annual Forum report
  • Genomics educational flash cards (in exchange for your science highlights!)
  • and more!
Hard copies are available by request from MLozano@lbl.gov

Back issues of The Primer are available for download at this page:http://www.jgi.doe.gov/News/primer/. Some older hard copies available as well.

May 2010

Funding Opportunity Announcement DE-FOA-0000368, "Genomic Science and Technology for Energy and the Environment"
The Office of Biological and Environmental Research (BER) hereby announces interest in receiving applications for research that supports the Genomics Science Program and addresses DOE's missions in energy and the environment in the following research areas:

  • a) Microbial Environmental Processes: To develop a systems-level understanding of the functional processes used by microbes and microbial consortia that link the internal metabolic processes of microbial species to their external biogeochemical activities;
  • b) Microbial and Plant Processes for Bioenergy: To develop new approaches that advance our understanding of the systems biology of plant and microbes in producing biofuels including the utilization of lignocellulosic biomass and microbial synthesis of advanced biofuel;
  • c) Characterizing Key Molecular Species, Events, and Multicellular Processes for Genomic Science: To develop innovative technology approaches to characterize biological processes and networks at the subcellular, cellular and multicellular levels.

Preapplications are REQUIRED and due June 28, 2010.
More details are available at this PDF and the full announcement is available on grants.gov.

New Dates! 2011 Genomic Science Meeting The Department of Energys Office of Biological and Environmental Research 2011 Genomic Science Annual Contractor-Grantee Workshop will be held jointly with the USDA-DOE Plant Feedstock Genomics for Bioenergy program meeting. The meeting will take place from April 10th (evening reception) through April 13th (ending early afternoon) 2011, at the Hyatt Regency Crystal City at Reagan National Airport. Please note that the timing of the annual meeting was shifted to avoid snowfall. Attendance by invitation only.

The DOE JGI Newsletter: The Spring 2010 edition is now available for download.. Hard copies can be requested from MMLozano@lbl.gov. Featured are highlights from the 5th Annual Genomics of Energy & Environment Meeting.  Videos of the talks. Save the date for next year's meeting:  March 21-25, 2011.

More DOE JGI news:

5th annual Sequencing, Finishing and Analysis in the Future meeting will be held June 2-4, 2010 in Santa Fe, NM, and will feature keynote speakers Claire Fraser-Liggett, Director, Institute for Genome Sciences, Chad Nusbaum, Co-Director, Broad Institute Genome Sequencing and Analysis Program, and Folker Meyer, Associate Director, Institute for Genomics and Systems Biology, Argonne Natl. Lab. For more information

Animated JGI The DOE JGI collaborated with Emeryville, Calif.-based Ex’pression College for Digital Arts to create a short video on the DOE JGI’s role in developing sustainable clean energy. View it on YouTube.

Happy Anniversary IMG The Integrated Microbial Genomes (IMG) system (Nucleic Acids Research, 2010, Vol. 38) serves as a community resource for comparative analysis and annotation of all publicly available genomes from three domains of life in a uniquely integrated context.  On this occasion, IMG 3.1 has been released IMG/M, IMG ER and IMG/M ER have also been updated with the new IMG 3.1 reference genomes.

GenePRIMP Goes Live To assist in checking the quality of the microbial DNA sequences generated before they are submitted to the public archive GenBank, which is overseen by the National Center for Biotechnology Information, the JGI has been using a quality control tool known as the Gene Prediction IMprovement Pipeline or GenePRIMP, which is described in a paper was published online May 2 in Nature Methods. A video of first author Amrita Pati explaining how GenePRIMP works is available online

Lawrence Berkeley National Laboratory to host a free 2-day workshop introduces educational adaptations of iPlant discovery environments developed to support innovative curricula and exciting student research projects to prepare the scientists of the future.

April 2010

DOE JGI: 2009 Progress Report Now Available The U.S. Department of Energy Joint Genome Institute (DOE JGI) has just released its 2009 Progress Report, highlighting the achievements of the last year and touching on the initiatives ahead to advance the frontiers of DNA sequence-enabled science relevant to DOE's mission areas of bioenergy, carbon cycling and biogeochemistry. The 68-page color document can be downloaded from the JGI website (PDF). Free hard copies can be requested from MMLozano@lbl.gov

"Energy Genomics" Animation Debuts And for those who didn't already see it at the DOE JGI annual Energy & Environment User Meeting last week...we, in collaboration with recent graduates and staff at the Ex'pression College for Digital Arts, have developed a short animation, "Energy Genomic," to describe the role DOE JGI plays in advancing the Department of Energy mission by characterizing plants and microbes for next generation biofuels. The animation can be viewed here

March 2010

CSP 2011: Call for Proposals Letters of intent for the DOE Joint Genome Institute Community Sequencing Program (CSP) 2011 are due March 31, 2010. Sequencing projects will be chosen based on scientific merit--judged through independent peer review--and relevance to the DOE missions of bioenergy, global carbon cycling, and biogeochemistry.

Areas of emphasis are:

  • Large-scale resequencing of organisms with a reference sequence
  • Single cell genomes
  • Large-scale microbial isolate sequencing
  • Eukaryotic whole genome sequencing
  • Large-scale metagenome sequencing

Microbial Proposals for small-scale sequencing are accepted for review on a quarterly basis.

Deadline for the next microbial review is April 7, 2010. These will include projects for:

  • Bacterial and archaeal isolates
  • Bacterial resequencing

For more information about the CSP or to submit, see: http://proposals.jgi-psf.org

February 2010

JGI User Meeting March 24-26, 2010 in Walnut Creek, CA. Download Poster

Funding Opportunity Announcements Plant Feedstock Genomics for Bioenergy: A Joint Research Funding Opportunity Announcement USDA, DOE Details

Contribute to Defining Knowledgebase Requirements and Specifications A Wiki has been created to provide open access to an interactive resource for viewing, providing comments, and contributing to this community-driven effort to specify the requirements for the DOE Systems Biology Knowledgebase. Go to the Wiki and select “How to Participate” to join this effort. Wiki

Awardee Meeting Genomic Science Awardee meeting was held February 7-10, 2010. Abstracts available

January 2010

Awardee Meeting Genomic Science Awardee meeting will be held February 7-10, 2010. Attendance by invitation only. Poster and Speaker Abstracts now available.

December 2009

Funding Opportunity Announcement DE-FOA-0000223. Plant Feedstock Genomics for Bioenergy: A Joint Research Funding Opportunity Announcement USDA, DOE.The U.S. Department of Energy's Office of Science, Office of Biological and Environmental Research (OBER), and the U.S. Department of Agriculture (USDA), National Institute of Food and Agriculture (NIFA), hereby announce their interest in receiving applications for genomics-based research that will lead to the improved use of biomass and plant feedstocks for the production of fuels such as ethanol or renewable chemical feedstocks. Specifically, applications are sought for fundamental research on plants that will improve biomass characteristics, biomass yield, or sustainability. Systems biology approaches to identify genetic indicators enabling plants to be efficiently bred or manipulated, or research that yields fundamental knowledge of the structure, function and organization of plant genomes leading to improved feedstock characterization and sustainability are also encouraged. Preapplications required, deadline 4:30 p.m., Eastern Time, January 4, 2010. [More details at http://science.energy.gov/grants/pdf/DE-FOA-0000223.pdf]

Funding Opportunity Announcements Office of Science Annual Notices for Fiscal Year 2010 have been posted. These Announcements are published annually and will remain open until succeeded by another issuance by the Office of Science usually posted after the beginning of the Fiscal Year (October 1, 2010). Applications submitted under these Announcements, DE-FOA-0000178 and DE-FOA-0000179, may be awarded with funds and under the Terms and Conditions provided under the American Recovery and Reinvestment Act of 2009.

November 2009

Awardee Meeting Genomic Science Awardee meeting will be held February 7-10, 2010. Attendance by invitation only. Abstracts due December 11. Details available on website.

Contribute to Defining Knowledgebase Requirements and Specifications A Wiki has been created to provide open access to an interactive resource for viewing, providing comments, and contributing to this community-driven effort to specify the requirements for the DOE Systems Biology Knowledgebase. Go to the Wiki and select “How to Participate” to join this effort.

October 2009

The Fall 2009 edition of the DOE JGI newsletter, The Primer, has arrived.  Features include:
  • Gap Resolution software now available for academic use
  • New DOE JGI Fungal Program
  • Genomic Standards Consortium's 8th meeting notes
  • Marine microbial lifestyles
  • T. reesei redux
  • Upcoming 5th Annual Genomics of Energy & Environment meeting, March 24-26, 2010: http://www.jgi.doe.gov/meetings/usermeeting/
  • Follow us on TWITTER: doe_jgi
For those who would like access to an electronic file, it can be downloaded as a PDF and previous editions are available here. Hard copies can be requested from: MMLozano@lbl.gov

DOE JGI, Others, Propose a New set of Standards to build on Bermuda Standard. A group of researchers from several sequencing centers, including the DOE Joint Genome Institute (JGI), the Sanger Institute and the Human Microbiome Project (HMP) Jumpstart Consortium sequencing institutes, has proposed a new set of standards that expand upon the so-called Bermuda standard. In the October 9 issue of the journal Science, they propose four additional categories between draft and finished status that reflect varying levels of completeness. See press release. See Science.

Adopt a GEBA Genome The DOE Joint Genome Institutes Education Program is providing opportunities for colleges and universities across the country to adopt bacterial genomes, such as those sequenced as part of the GEBA project, for analysis. This Adopt a GEBA Genome Education Program makes available a selection of recently sequenced genomes for use in undergraduate courses. The organisms ideally provide a unifying thread for concepts across the life sciences curriculum. For example, students can analyze the six open reading frames for a given fragment of DNA, compare the results of various gene calling algorithms, assign function by sequence homology, and use gene ortholog neighborhoods for comparative genomics and annotate biochemical pathways, while learning the underlying biological concepts in a variety of science courses. For more information, and to apply for the November 2, 2009 deadline, see: http://www.jgi.doe.gov/education/genomeannotation.html

August 2009

Funding Opportunity Announcement "Computational Biology and Bioinformatic Methods to Enable a Systems Biology Knowledgebase" (DE-FOA-0000143) BER hereby announces its interest in receiving applications for potential funding of computational biology and bioinformatic methods and analytics to enable the planned Systems Biology Knowledgebase. The goal of systems biology is to understand living systems, a simple microbe or a complex ecosystem, so well that we can develop predictive, computational models of the systems that "behave" the same way as the living system. Such predictive models would enable scientists to accurately predict an organism's or a more complex system's behavior. Preapplications required, deadline November 5, 2009. Formal applications must be received by January 29, 2010 [More details at http://science.energy.gov/grants/pdf/DE-FOA-0000143.pdf]

DOE JGI Releases Integrated Microbial Genomes (IMG) 2.9 IMG serves as a community resource for comparative analysis and annotation of all publicly available genomes from three domains of life in a uniquely integrated context. In addition to the content update (more than one million new genes) and User Interface extensions (all described in the "What's New" in IMG 2.9).  A notable new feature is the inclusion of protein expression data from a recent Arthrobacter chlorophenolicus study and tools for examining these data. [8/18/09]

Press Release: GLBRC Receives $8 Million in Recovery Act Funding. The Department of Energy (DOE) Great Lakes Bioenergy Research Center (GLBRC) has received $8.099 million in new funding from the U.S. Department of Energy through the American Recovery and Reinvestment Act to provide crucial support for plant cell wall imaging and sustainability research. CONTACT: Tim Donohue, 608-262-4663, tdonohue@bact.wisc.edu; John Ralph, 608-890-2429, jralph@wisc.edu; Phil Robertson, 269-671-2267, robertson@kbs.msu.edu [8/6/09] Press Release

July 2009

Microbial Genomics & Metagenomics workshop September 14-18, 2009. The U.S. Department of Energy Joint Genome Institute (DOE JGI) is offering a five-day workshop on Microbial Genomics and Metagenomics September 14-18, 2009 in Walnut Creek, California. The workshop will include two days of intensive seminars and three days of hands-on tutorials. Our goal is to provide you with training in microbial genomic and metagenomic analysis and demonstrate how the cutting-edge science and technology of DOE JGI can enhance your research. For more information, see: http://mgm.jgi.doe.gov/

USDA and DOE Jointly Fund 7 New Projects for Biomass Genomics Research. Departments of Energy and Agriculture jointly selected 7 projects for awards totaling $6.3 million for biobased-fuel research. See press release and list of awardees. [July 22, 2009]

Brochure: "Bioenergy Research Centers: An Overview of the Science," Revised July 2009 [faster-download PDF or higher-quality PDF]

Summer 2009 DOE JGI Newsletter The Primer Available Download the PDF; Back issues; Additional hard copies: MMLozano@lbl.gov. For IMG Expert Review (ER) and IMG/M ER users, the latest paper can be accessed here.

Funding Opportunity Announcement Biological Systems Research on the Role of Microbial Communities in Carbon Cycling (DE-PS02-09ER09-25) The Office of Biological and Environmental Research (BER) of the Office of Science (SC), U.S. Department of Energy (DOE), hereby announces its interest in receiving applications for research that supports the Genomics:GTL research program. In this Funding Opportunity Announcement (FOA), applications are solicited for: i.) Systems-level studies on regulatory and metabolic networks of microbes and microbial consortia involved in biogeochemical cycling of carbon, ii.) Development of metatranscriptomic, metaproteomic, and other genome-enabled approaches to understand how shifts in environmental variables impact microbially-mediated carbon cycling processes in terrestrial ecosystems, and iii.) Development of methods and techniques for imaging and analysis of microbially-mediated carbon cycling processes in terrestrial ecosystems. Closing date November 9, 2009. [More details at http://science.energy.gov/grants/pdf/DE-PS02-09ER09-25.pdf]

June 2009

DOE JGI Releases IMG/M 2.8. The Integrated Microbial Genomes system/with Microbiome Samples (IMG/M) 2.8 has now been released and includes reference genomes from IMG 2.8 (released in April 2009, see http://img.jgi.doe.gov) and 111 GEBA genomes (http://img.jgi.doe.gov/geba). New metagenome datasets include:

  • 1 Endophytic microbiome from rice;
  • 8 Yellowstone hot pool microbial communities;
  • 7 Marine planktonic communities from Hawaii Ocean Time-series;
  • 1 Bioreactor wastewater terephthalate-degrading community sample

Other new features are described here
Check out IMG/M 2.8

May 2009

DOE JGI Releases Expanded Phytozome.net. 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. [05/09] Details

Integrated Microbial Genomes Expert Review (IMG ER) Goes Primetime: Provides Expert-Driven QC for Microbial Genome Information. Scientists at the U.S. Department of Energy (DOE) Joint Genome Institute (JGI) and the Biological Data Management and Technology Center (BDMTC) at Lawrence Berkeley National Laboratory have launched the Expert Review (ER) version of the Integrated Microbial Genomes (IMG) system. IMG ER supports and enhances the review and revision of annotations for both publicly available genome datasets and those newly released from private institutions. Details and Press Release [5/18/09]

April 2009

DOE-USDA Biofuels Sustainability Workshop Report Available. Sustainability of Biofuels: Future Research Opportunities, a report from the October 2008 DOE-USDA workshop is now available. Details

February 2009

GTL Strategic Plan. The 2008 Genomics:GTL Strategic Plan is now available electronically. [02/09] Details

GTL Abstracts. Abstracts available from Genomics:GTL Awardee meeting, held Feb 8-11, 2009. Details

January 2009

DOE JGI Completes Sorghum Genome. Walnut Creek, CAScientists 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, 2009, edition of the journal Nature. See Release

DOE JGI Announces 2009 Users Meeting. March 25-27, 2009 in Walnut Creek, California. See Website for more details.

December 2008

Carbon Cycling and Biosequestration Report from the OBER hosted Carbon Cycling and Biosequestration Workshop, March 2008. This report outlines the workshop's findings and highlights key opportunities for research on biological aspects of the global carbon cycle. Further details and PDFs.

DOE JGI Issues Call for Genome Sequencing Proposals
The U.S. Department of Energy Joint Genome Institute (DOE JGI), through its Community Sequencing Program (CSP), is soliciting proposals related to the DOE missions of bioenergy, global carbon cycling and biogeochemical processes influencing contaminant transport. Targets include bacterial and archaeal isolates, large-scale eukaryotic or bacterial resequencing efforts that exploit next-generation sequencing technologies, eukaryotic reference genomes, and environmental microbial genomes (metagenomes). Letters of intent will be accepted beginning December 15, 2008 and are due January 30, 2009. For further details, see: http://www.jgi.doe.gov/CSP/user_guide/ and this PDF.

Soya genome sequenced Biofuel potential spurs U.S. consortium to map DNA of nutritious bean. December 10, 2008, Nature

November 2008

Awardee Meeting Genomics:GTL Awardee meeting will be held February 8-11, 2009. Attendance by invitation only. Abstracts due December 8.

USDA and DOE Funding Opportunity Announcement Departments of Energy and Agriculture have jointly issued a research funding opportunity. Preapplications due Dec. 9, 2008. See details.

October 2008

USDA and DOE Release National Biofuels Action Plan. [Oct. 7, 2008] See press release and download document (PDF 4.9 KB).

August 2008

DOE JGI Director Eddy Rubin Highlights the Genomics of Plant-Based Biofuels in Nature. [Aug. 13, 2008] See JGI press release and article.

Atlantic Monthly Features JGI Termite Research. See article and accompanying video.

July 2008

USDA and DOE Fund 10 New Projects for Biomass Genomics Research. Departments of Energy and Agriculture jointly selected 10 projects for awards totaling $10 million for biobased-fuel research. [July 31, 2008] See Press Release and List of Awardees.

Interagency Opportunities in Metabolic Engineering. (NSF 08-588). This solicitation describes a collaborative effort among the Department of Agriculture, Department of Commerce, Department of Defense, Department of Energy, Environmental Protection Agency, National Aeronautics and Space Administration, National Institute of General Medical Sciences (National Institutes of Health), and the National Science Foundation. The intent of this interagency solicitation is to provide an opportunity for an interagency granting activity in the area of metabolic engineering (ME). The eight participating agencies or departments are providing research funding and agency in-kind support such as equipment, laboratory space, personnel time, and materials in support of this solicitation. Upon conclusion of the review process, meritorious proposals may be recommended for funding by a participating agency or department. Each participating agency will make its own awards and the subsequent grant administration procedures will be in accordance with the individual policies of the awarding agency or department. Full proposals are due October 22, 2008. Announcement.

JGI Announces 2009 Targets Pine Tree, Boat-Boring Bivalve Bugs, Duck Weed, Oil-Producing Microalgae, Stinkbird Gut, 40 Others Top DOE Joint Genome Institute 2009 Genome Sequencing Targets. Press Release.

May 2008

Position available: Director of the Life and Medical Sciences Division in U.S. Department of Energy (DOE)-Office of Science, Office of Biological and Environmental Research (BER). This Division manages the GenomicsGTL Program; Low Dose Radiation Research and Radiochemistry and Instrumentation programs; the DOE Bioenergy Research Centers; and scientific user facilities such as the DOE Joint Genome Institute.

The Life and Medical Sciences Division is seeking a motivated and highly qualified individual to be responsible for basic research impacting energy resources, production, conversion, efficiency, storage, and the mitigation of the adverse impacts of energy production and use.

The Office of Science is the single largest supporter of basic research in the physical sciences in the United States. We oversee and are the principal Federal funding organization of the nation's research programs in high-energy physics, nuclear physics, and fusion energy sciences. The Office of Science is also the Federal government's largest single provider of funds for the chemical and materials sciences. We manage fundamental research programs in basic energy science and support unique and vital parts of the United States research in climate changes, geophysics, genomics, life sciences, and science foundation.

April 2008

Data Sharing Policy Information and data sharing policy of the Genomics:GTL Program announced. PDF

March 2008

JGI Genomics of Energy & Environment Meeting DOE JGI meeting. March 26-28, 2008. Walnut Creek, CA Website

Pittcon Symposia Features BRCs The Analytical Instrumentation for Biofuels R&D Session at the March 1-7, Pittcon meeting in New Orleans will have presentations from each of the Bioenergy Research Centers.

February 2008

JGI Updates Microbial Metagenomics Data System The Joint Genome Institute of the U.S. Department of Energy has released an upgraded version of its metagenomics data management and analysis system that includes five new metagenome data sets taken from recent studies. Announcement

Abstracts from the Genomics:GTL Contractor-Grantee Workshop VI, Bethesda, Md., February 10-13, 2008

Brochure: "Bioenergy Research Centers: An Overview of the Science," February 9, 2008 Revised July 2009 [faster-download PDF; higher-quality PDF]

January 2008

Funding Opportunity: Biological Hydrogen Production. DE-PS02-08ER08-12, "Systems Biology, Model Organism Development, and Enzyme Discovery for Biological Hydrogen Production." Preapplications are required, due 2/22/2008. Applications are due 4/9/2008. The Office of Biological and Environmental Research (BER) of the Office of Science (SC), U.S. Department of Energy (DOE), hereby announces its interest in receiving applications for research that supports the Genomics: GTL research program (genomicscience.energy.gov). In this Solicitation, applications are solicited for: i.) systems-level research to improve understanding of microbial regulatory and metabolic networks related to hydrogen production, ii.) development of new model organisms for microbial hydrogen production, and iii.) targeted approaches for the identification and characterization of enzymes and biochemical pathways relevant to biological hydrogen production in genome and metagenome sequences. Announcement.

December 2007

Awardee Meeting Website Genomics:GTL Awardee meeting will be held February 10-13, 2008. Attendance by invitation only. [12/07]

October 2007

Funding Opportunity: Plant Feedstock Genomics for Bioenergy: A Joint Research Solicitation from USDA and DOE. DE-PS02-08ER08-03. Preapplications are required and due November 13, 2007; Application Due Date: January 23, 2008. DOE Office of Science, Office of Biological and Environmental Research (OBER), and USDA Cooperative State Research, Education, and Extension Service (CSREES) invite applications for genomics-based research that will lead to the improved use of biomass and plant feedstocks for the production of fuels such as ethanol or renewable chemical feedstocks. Specifically, applications are sought for fundamental research on plants that will improve biomass characteristics, biomass yield, or sustainability. Systems biology approaches to identify genetic indicators enabling plants to be efficiently bred or manipulated, or research that yields fundamental knowledge of the structure, function and organization of plant genomes leading to improved feedstock characterization and sustainability are also encouraged.

Funding Opportunity: International Cooperative Biodiversity Groups The National Institutes of Health, the National Science Foundation, the U.S. Department of Agriculture, and the U.S. Department of Energy invite applications for the establishment or continuation of "International Cooperative Biodiversity Groups" (ICBG) to address the interdependence of biodiversity exploration for potential applications in health, agriculture and energy, with investments in research capacity that support sustainable use of these resources, the knowledge to conserve them, and equitable partnership frameworks among research and development organizations in the U.S. and low and middle income countries. The Government is budgeting $3 – 4 million in FY 08 for the initial awards. Microbial organisms (inclusive of prokaryotes, virus, fungi, algae and protists) from terrestrial or marine sources as well as marine invertebrates are of greatest interest to the participating agencies in this competition. Announcement

DOE Provides $30 Million to Jump Start Bioenergy Research Centers. The U.S. Department of Energy (DOE) today announced it has invested nearly $30 million in end-of-fiscal-year (2007) funds to accelerate the start-up of its three new Bioenergy Research Centers, bringing total DOE Bioenergy Research Center investment to over $400 million. [10/1/07] Press Release

New GTL Awards for FY 2007 DOE announced the funding of 44 new projects. [10/1/07]. Details are available here.

September 2007

Awardee Meeting Dates Announced Genomics:GTL Awardee meeting will be held February 10-13, 2008. Attendance by invitation only. [9/07]

August 2007

Nature Collections Energy Supplement. Supported by the Department of Energy and Office of Science, this supplement outlines the promises and pitfalls of new energy technologies. Free access. [Aug. 2007] Supplement

Funding Opportunity: Development of Saccharifying Enzymes for Commercial Use. EERE is requesting applications for the development of hydrolytic enzymes or enzyme system preparations that can effectively saccharify pretreated lignocellulosics to produce fermentable sugars under process relevant conditions. Letter of Intent due Sept. 10, Applications due Oct. 15. [8/24/07]

June 2007

Energy Department Selects Three Bioenergy Research Centers for $375 Million in Federal Funding Secretary Samuel W. Bodman announced three new Bioenergy Research Centers intended to accelerate basic research in the development of cellulosic ethanol and other biofuels. [6/26/07] Press Release, more details

DOE Joint Genome Institute Announces 2008 Genome Sequencing Targets. June 8, 2007. Eucalyptus, foxtail millet, red algae, and novel microbial communities added to growing bioenergy and carbon cycling portfolio. Press Release

Energy and Agriculture Departments Provide $8.3 Million in Funding for Biofuels Research. June 7, 2007. U.S. Energy Secretary Samuel Bodman and Agriculture Secretary Mike Johanns today announced that the Department of Energy and the Department of Agriculture have jointly selected 11 projects for awards totaling $8.3 million for biobased fuels research that will accelerate the development of alternative fuel resources. Press Release

Plant Feedstock Genomics for Bioenergy Workshop at the 2008 Plant and Animal Genome Conference, January 15, 2008. Workshop announcement [http://www.intl-pag.org/16/16-bioenergy.html] on PAG web.

Organizers: Sharlene Weatherwax, U.S. Department of Energy (sharlene.weatherwax@science.doe.gov) and Chavonda Jacobs-Young, USDA/CSREES (cjacobs@csrees.usda.gov)

"Plant Feedstock Genomics for Bioenergy" workshop will provide an overview of genomics-based research that can lead to the improved use of biomass and plant feedstocks for the production of fuels such as ethanol or renewable chemical feedstocks. Presentations will focus on fundamental research opportunities on plants to improve biomass characteristics, biomass yield, or that will facilitate lignocellulosic degradation. Also, systems biology approaches to identify genetic indicators enabling plants to be efficiently bred or manipulated, or research that yields fundamental knowledge of the structure, function and organization of plant genomes leading to improved feedstock characterization and sustainability.

This will be the USDA-DOE Awardees meeting for 2008. The 2009 meeting will return to the Genomics:GTL Contractor-Grantee Workshop.

Future USDA-DOE Awardees Meetings. The 2008 Plant and Animal Genome Conference Workshop will be the USDA-DOE Awardees meeting for 2008. The 2009 meeting will return to the Genomics:GTL Contractor-Grantee Workshop.

March 2007

ASM Microbial Energy Conversion Report. ASM has released a new report on microbial energy conversion. This report is based on a colloquium, sponsored by the American Academy of Microbiology, convened March 10-12, 2006, in San Francisco, California. DOE BER contributed support for the report.

February 2007

Three Bioenergy Research Centers Planned (02/05/07)

  • Press Release Press Release: Department of Energy Requests $24.3 Billion for FY 2008 Budget

GTL Awardee Meeting 2007. Joint Genomics: GTL Awardee Workshop V and Metabolic Engineering 2007 and USDA-DOE Plant Feedstock Genomics for Bioenergy Awardee Workshop 2007, North Bethesda, MD, February 11 to February 14, 2007. Abstracts now available.

December 2006

Funding Opportunity: Ethical, Legal, and Societal Implications (ELSI) of Research on Alternative Bioenergy Technologies, Synthetic Genomics, or Nanotechnologies. Funding Opportunity Announcement DE-PS02-07ER07-16. The deadline for preapplications (which are required) is Thursday February 8, 2007. Formal applications are due on Thursday, April 19, 2007. The aims of this Notice are to support explorations of the potential societal implications arising from scientific research in areas of systems microbiology pertaining to the DOE mission of bioenergy, and, in addition, issues arising from synthetic genomics applied to bioenergy, and research on nanomaterials and nanotechnologies relevant to bioenergy. For more information, see the PDF.

JGI: Community Sequencing Program (CSP) Opportunity A letter of intent is due by January 12, 2007. Proposal deadline is March 2, 2007 For more information, see this website.

The Community Sequencing Program (CSP) was created to provide the scientific community at large with access to high-throughput sequencing at the Department of Energy's Joint Genome Institute (JGI) for projects of relevance to DOE missions. Sequencing projects will be chosen based on scientific merit--judged through independent peer review--and relevance to issues in global carbon cycling, alternative energy production, and bioremediation. Criteria for participation in this program, the review process, and interactions between JGI and participants are outlined on this web site. Through this program, the Department of Energy aims to advance sequence-based scientific research from a broad range of disciplines.

The CSP consists of two programs:

  • a small-genome program for shotgun sequencing of genomes smaller than 200 Mb and other sequencing projects with a total request of less than 1 Gb.
  • a large-genome program for shotgun sequencing of genomes larger than 200 Mb. Large-genome proposals must be supported by experimental evidence of the organism's genome size, polymorphism rate, and repeat content. In the absence of this information, applicants are encouraged to submit a small-genome proposal to obtain this information.

Proposals to the two programs will be reviewed separately, but the application and review processes are similar. For information about the site or program please write to csp2008@jgi.doe.gov.

November 2006

Keasling Named Scientist of the Year Discover magazine has named GTL researcher Jay Keasling, a chemical engineer with a joint appointment at Berkeley Lab and UC Berkeley, as its 2006 Scientist of the Year. Keasling was cited for "developing ways to program DNA as easily as people program computers." In an interview with writer Carl Zimmer, Keasling describes the synthetic biology techniques by which he engineered bacteria and yeast to produce a precursor to artemisinin, a super antimalarial drug. Similar techniques could be used to produce ethanol from plant cellulose, Keasling said. (Discover)

Program Announcement to DOE National Laboratories LAB 07-14. New Genomic Strategies and Technologies for Studying Complex Microbial Communities and Validating Genomic Annotations. Preproposal due January 18, 2007. See PDF

New Grant Opportunities. Program Notices DE-PS02-07ER07-12 - New Analytical and Imaging Technologies for Lignocellulosic Material Degradation, and for Multiplexed Screening for Plant Phenotypes and DE-PS02-07ER07-13 - Quantitative Microbial Biochemistry and Metabolic Engineering for Biological Hydrogen Production, have been posted today in Grants.gov.

  • DE-PS02-07ER07-12 has preapplication REQUIRED and due January 4, 2007 with the formals due March 6, 2007. [Notice PDF] Dr. Sharlene Weatherwax and Dr. John Houghton are the Program contacts.
  • DE-PS02-07ER07-13 has preapplication REQUIRED and due January 4, 2007 with the formals due March 8, 2007. [Notice PDF] Dr. Sharlene Weatherwax is the Program contact.

October 2006

DOE EERE Requests Applications to Develop Efficient Ethanol-Producing Organisms. The U.S. Department of Energy (DOE), Office of Energy Efficiency and Renewable Energy (EERE) has announced a Funding Opportunity Announcement (FOA) entitled “Development of Robust, Highly Efficient Fermentative Organisms for the Conversion of Lignocellulosic Biomass to Ethanol.” Funding Opportunity Number: DE-PS36-07GO97002 at Grants.gov. [10/25/2006]

President Bush Discusses Energy at Renewable Energy Conference. Remarks by the President on Energy. [10/12/06] Press release

Transcript of Remarks by Agriculture Secretary Mike Johanns [10/11/06]

"DOE Bioenergy Initiative," Presentation by Under Secretary for Science Dr. Raymond L. Orbach at the DOE/USDA Advancing Renewable Energy Conference, St. Louis, MO [10/12/06] PDF

Secretaries Bodman & Johanns Kick Off Renewable Energy Conference with $17.5 Million for Biofuels Research & Development Grants. U.S. Department of Agriculture (USDA) Secretary Mike Johanns and U.S. Department of Energy (DOE) Secretary Samuel Bodman today announced nearly $17.5 million for 17 biomass research, development and demonstration projects, to help break our nation's addiction to oil. [10/11/06] Press release

USDA-DOE Announce New Funding Opportunity for Biomass Genomics Research. The U.S. Departments of Energy and Agriculture (DOE and USDA) issued a solicitation for research proposals for new plant feedstock genomics research projects. Funding Opportunity Number: DE-PS02-07ER07-03. [10/10/06] more...

September 2006

First tree genome sequence published; consortium led by DOE Joint Genome Institute. Press release

DOE & USDA Advancing Renewable Energy Conference Oct. 10-12, 2006.

August 2006

USDA and DOE Fund Genomics Projects For Bioenergy Fuels Research (DOE Press Release) Energy Secretary Samuel Bodman and Agriculture Secretary Mike Johanns today announced that the Department of Agriculture and the Department of Energy have jointly awarded nine grants totaling $5.7 million for biobased fuels research that will accelerate the development of alternative fuel resources. [8/9/06] more...

News Release: USDA and DOE Name Biomass Research and Development Technical Advisory Committee Members, August 9, 2006

DOE Issues Call for New Bioenergy Research Centers

July 2006

Biomass to Biofuels Plan Now Available. Breaking the Biological Barriers to Cellulosic Ethanol: A Joint Research Agenda is a research roadmap resulting from the December 2005 joint DOE SC-EERE Biomass to Biofuels Workshop.

DOE JGI Sequences, Releases Genome of Symbiotic Tree Fungus DNA sequence of Laccaria bicolor, a fungus that forms a beneficial symbiosis with trees and inhabits one of the most ecologically and commercially important microbial niches in North American and Eurasian forests, has been determined by the U.S. Department of Energy DOE Joint Genome Institute (DOE JGI). [7/24/06] Press Release

Genome Sequencing of Unculturable Bacteria. Conventional DNA sequencing of a microbial genome usually entails extracting sufficient DNA from a culture grown up from a single bacterium. Most microbes from natural environments, however, do not have established laboratory culture conditions, making it a challenge to obtain enough DNA for analysis. This situation holds for many strains of the most prevalent photosynthetic marine microbe, Prochlorococcus, which play major roles in carbon cycling and fixation. In the June 2006 issue of Nature Biotechnology, George Church led a GTL-funded team of MIT-Harvard Medical School scientists in developing a new strategy that allows high-fidelity amplification of DNA from a single cell. The breakthrough comes from using DNA-digesting enzymes to cut away undesirable branched DNA structures that tend to form during early rounds of DNA amplification, leaving only linear DNAs to be amplified tremendously for subsequent sequencing. This technique enabled researchers to obtain the genomic sequence from a single Prochlorococcus microbe, and opens a window to obtain genomic information from individual members in complex microbial communities. Reference: Kun Zhang et al, (2006) Sequencing genomes from single cells by polymerase cloning, Nat. Biotech 24 (6) 680-686.

Bug Juice: Harvesting Electricity from Microorganisms. Electricity-producing bacteria ("electricigens") such as Geobacter and Rhodoferax can effectively convert diverse organic matter to electricity. These organisms are able to transfer electrons directly to an electrode instead of using electron-shuttling intermediates. In an article appearing in the July 2006 issue of Nature Reviews Microbiology, GTL researcher Derek Lovley (University of Massachusetts, Amherst) describes the physiology and ecology of these organisms and discusses how to increase their power output for microbial fuel systems.

Energy-Rich Portfolio of New Genome Sequencing Targets for DOE JGI. Bioenergy crop plants switchgrass and cassava, other important agricultural commodities such as cotton, and microbes geared to break down plant material to render biofuels, round out the roster of more than 40 projects to be tackled by the U.S. Department of Energy Joint Genome Institute (DOE JGI) over the next year. More...

GTL Researchers at Pacific Northwest National Laboratory Discover Conductive Nanowires in Bacteria. Details published in the July 10 advance online Proceedings of the National Academy of Sciences. More...

June 2006

An Integrated Model of Microbial Stress Response. GTL researchers at Lawrence Berkeley National Laboratory discover key clues to microbial stress response and adaptation. Details appear in J. Bact. 188 (11) 4068-4078. [6/06] Details

May 2006

Image Gallery Updated: The Genomics:GTL image gallery has been updated.

April 2006

Call for Bioenergy Sequencing Targets. Recommendations are being sought for microbial sequencing targets in support of the bioenergy mission of the Office of Biological and Environmental Research (OBER). Nominations should be received by 4:30 p.m. (EDT), August 10, 2006, to be accepted for merit review.

March 2006

DOE Office of Science to Revise Plans for Genomics:GTL Facilities. The Department of Energys Office of Science announced today that it is revising its plans for the deployment of new research facilities to support its Genomics:GTL program. The decision to reshape plans for the new GTL research facilities comes in response to the Presidents recently announced Advanced Energy Initiative and a review of the GTL program by the National Research Council of the National Academies. The January 9, 2006, funding opportunity announcement has been canceled.

February 2006

Review of the Department of Energy’s Genomics: GTL Program, National Research Council of the National Academies (February 2006; PDF, 679 kb) NOTE: Final draft is posted at link above (May 2006).)

Abstracts for Joint Genomics: GTL Contractor-Grantee Workshop IV and Metabolic Engineering Working Group Interagency Conference on Metabolic Engineering. Abstracts for the joint workshop held February 12 - 15 are now posted. Abstracts were required from each DOE/BER funded project.

January 2006

Ari Patrinos, Associated Director of Science for Biological and Environmental Research of the Office of Science of the U.S. Department of Energy, is leaving DOE to become President of Synthetic Genomics, Inc., on February 8, 2006. For more information, see press release.

USDA and DOE to Coordinate Research of Plant and Microbial Genomics: Soybean DNA to be Decoded. The U.S. Departments of Agriculture and Energy announced January 16th they will share resources and coordinate the study of plant and microbial genomics, and the Department of Energy will tackle the sequencing of the soybean genome as the first project resulting from the agreement. For more information, see press release.

DOE Joint Genome Institute Announces First Annual Users Meeting. The meeting will be held March 29 - April 1, 2006 in Walnut Creek, CA. See announcement for more information.

[ CANCELED (03/28/06) ] Funding Opportunity Announced: January 9. Genomics:GTL Facility for the Production and Characterization of Proteins and Molecular Tags. This Funding Opportunity Announcement requests that the scientific community submit applications for the development of a scientific user facility for the Production and Characterization of Proteins and Molecular Tags that involves the design, construction (construction is used generically here and could include new construction, renovation of existing space, leasing space or other options proposed by the applicants), and research and development related to the design, configuration, and operation of the facility that will serve as a major scientific user facility for the scientific community including the Genomics: GTL program.

December 2005

Joint Genomics: GTL Contractor-Grantee Workshop IV and Metabolic Engineering Working Group Interagency Conference on Metabolic Engineering Feb 12-15, 2006. The next Genomes to Life (GTL) program workshop will be held February 12 - February 15 at the Bethesda North Marriott Hotel and Conference Center, located in North Bethesda, Md. Abstract submission due December 20, 2005. Abstracts are required from each DOE/BER funded project. Details on meeting logistics, including the workshop agenda, abstract submission, and hotel location and reservation information can be found on the workshop website at http://www.orau.gov/gtl2006/. [Contact: Sharlene Weatherwax at Sharlene.Weatherwax@science.doe.gov]

Chemical and Engineering News Article Features GTL Program. See "Genomics and Clean Energy: Developing Biotechnology Area is Attracting More Than Just Biologists" in the December 12, 2005 (83:50, pp. 39-41) issue.

GTL Researcher Jay Keasling featured in Time magazine, named one of the World Economic Forum's 2006 Tech Pioneers.

November 2005

GTL Researcher James Cate and Collaborators Provide New Insights into Ribosome Structure and Operation in the November 4, 2005, Issue of Science. In the November 4, 2005, issue of Science, GTL researcher James Cate (Lawrence Berkeley National Laboratory) and collaborators offer new insights into the operation of the ribosome, the molecular complex that manufactures proteins in the cell. The team determined two high-resolution ribosome crystal structures, resulting in the first detailed view of the interface between ribosome subunits as well as its center for producing proteins. The research is part of the GTL effort to develop strategies to label complexes to track their operation in cells. The National Institutes of Health partially supported this work.

October 2005

Energy Department Awards $92 Million for Genomics Research.Press Release (Oct. 3, 2005).

Genomics:GTL Roadmap Now Available. The Genomics:GTL Roadmap, a systems microbiology plan for DOE missions, is now available in PDF form.

June 2005

GTL Researcher Derek Lovley Describes New Discovery in 23 June Issue of Nature (435: 1098-1101). An Electrifying Discovery. In the June 23 issue of Nature (435: 1098-1101), GTL researcher Derek Lovley of the University of Massachusetts, Amherst, described the discovery of electron-conducting "nanowires" on the outer cell surface of the metal-reducing microorganism Geobacter. These projections (called pili) appear to be conduits by which the microbe transfers electrons onto iron oxides during the process of dissimilatory iron reduction. Normally, the pili that extend from bacteria play a role in attachment or motility. But Geobacter uses pili to gain energy by transferring electrons onto the iron oxide surface, a process that has been harnessed for remediation of contaminated groundwater. Discovery of this fundamental mechanism of microbial metal reduction could lead to better models for subsurface bioremediation processes. The authors say this finding also suggests that we might be able to mass-produce protein nanowires based on Geobacter biology.

Time Magazine Features Venter, DOE Genomics Research (06/20/05)

May 2005

Protein Study Finds Clues to Microbes' Survival Techniques. In the first comprehensive study of gene expression in a microbial community from an "extreme" natural environment, scientists from Lawrence Livermore and Oak Ridge national laboratories, the University of California, Berkeley, and Xavier University in New Orleans have identified more than 2,000 proteins produced by five key species in the community. The findings appeared May 5 on the Science Express Website, an advance online publication of the journal Science.

April 2005

JGI Study Reveals New Technique for Fingerprinting Environmental Samples.Groundbreaking research led by the JGI demonstrates for the first time that the signatures of genes in terrestrial and aquatic samples can accurately diagnose the health of sampled environments. The study, published in the April 22nd issue of Science, predicts that large-scale genome sequencing will accelerate advances in environmental sciences akin to the contributions DNA sequencing has made to the biomedical sciences. [More...]

GTL Featured in Recent Issues of The Scientist and The Economist. GTL was the subject of a Vision column by Dr. Ari Patrinos [DOE Office of Biological and Environmental Research (BER)] in the March 14, 2005, issue of The Scientist. The column presents a case for being "bullish" on the promise of biotechnology to deliver solutions to principal DOE energy and environmental security missions. The use of bacteria to precipitate uranium out of groundwater, the potential for a synthetic genome to provide organisms with selected characteristics that address DOE needs, and the use of the DNA sequence of the Populus tree to create opportunities for enhancing biomass potential were cited as examples of biotechnologys promise for DOE needs. Additionally, in 2005 in The World, a companion publication to The Economist, BER is cited as leading the way to use microbes for generating energy and cleaning up pollution. Development of a synthetic bacterium from "off-the-shelf" parts in the laboratories of J. Craig Venter and George Church offers the promise of synthetic biology to form the basis of important and possibly revolutionary technology.

JGI Microbial Genome Database Tool Reported in Science. The March 18, 2005, issue of Science reports on the new Integrated Microbial Genomes (IMG) site at the DOE Joint Genome Institute (JGI) (p. 1701, “Microbial Get Together.”) This new DOE clearinghouse (http://img.jgi.doe.gov/cgi-bin/pub/main.cgi) helps researchers analyze the deluge of DNA data on microorganisms. The IMG site currently stores nearly 300 draft or completed genome sequences from archaea, bacteria, and other microbes, along with tools for sifting through the data. Visitors can get acquainted with all 2526 protein-coding genes carried by the marine cyanobacterium Synechococcus, for example. Besides accessing basic information about the gene, its protein, and its function, visitors can summon diagrams illustrating which biochemical pathways are influenced by the gene. Browsing tools make it easy to pinpoint similar genes in different organisms and compare them side by side.

March 2005

Call for DNA Sequencing Targets. Recommendations are being sought for microbial sequencing targets in support of the science missions of the Office of Biological and Environmental Research. Federal Register notice available here. Nominations should be received by 4:30 p.m. (EDT), July 14, 2005, to be accepted for merit review.

GTL in The Scientist. "Vision: Biotechnology reenergized," an article by Ari Patrinos discussing how the goals and promise of the Genomes to Life program have energy and environmental applications, was featured in the March 14, 2005, issue of The Scientist. Free registration is required.

February 2005

Third GTL Contractor-Grantee Workshop Held. The third Genomics:GTL program workshop was held February 6-9. Abstracts available here.

January 2005

DOE Establishes Institutes for the Advancement of Computational Biology Research & Education. In the fall of 2004, DOE established three institutes for the advancement of computational biology research and education. The institutes will support the advancement of computational biology research as an intellectual pursuit and will provide innovative approaches to educating biologists as computational scientists. The institutes will focus on advancing computational biology research and education as counterbalancing and complementary activities to experimental biology. [More about the institutes...] (January 27, 2005)

D. ethenogenes. TIGR scientists decipher genome of Dehalococcoides ethenogenes, a microbe that can be used to clean up groundwater contaminants. Science 307: 105-108. Press Release. (January 7, 2005)

December 2004

Call for DNA Sequencing Proposals. Joint Genome Institute (JGI) Community Sequencing Program (CSP) is calling for proposals to two programs. Letter of intent due January 28, 2005. Applications due February 25, 2005. [more...]

GTL-Related Call for Proposals. A solicitation to DOE National Laboratories on Poplar Genome-Based Research for Carbon Sequestration in Terrestrial Ecosystems. See Announcement LAB 05-10. Preproposals due by January 18, 2005, and formal proposals by March 8, 2005.

November 2004

GTL Contrator-Grantee Workshop.The third Genomes to Life (GTL) program workshop will be held February 6 (no-host evening reception) through February 9 (ending at noon) at the Wardman Park hotel in Washington, D.C. Abstract submission due December 10, 2004. Abstracts are required from each DOE/BER funded project. Details on meeting logistics, including the workshop agenda, abstract submission, and hotel location and reservations, can be found on the workshop website at http://www.orau.gov/gtl2005/. [Contact: Timothy Boyle at 301/903-0353 or timothy.boyle@science.doe.gov]

October 2004

Resesarcher Wins Innovators' Award. GTL researcher Colin Hill wins MIT’s Technology Review “World’s 100 Top Young Innovators” award. [More... ]

September 2004

Funding Solicitation. OBER and OASCR are requesting proposals from large, well-integrated, multidisciplinary research teams in support of the Genomics:GTL program. See Notice DE-FG01-04ER04-32 and Announcement LAB 04-32. Preapplications due by October 25, 2004. Formal applications due by January 18, 2005. See Funding for more...

Diatom Genome Revealed, Key to Global Carbon Cycling: The draft genome sequence for the 34-Mb genome of the saltwater diatom Thallassiosira pseudonana appears in the October 1, 2004, issue of Science. [More...]

News Brief. Radiation-resistant bug's survival tied to high levels of manganese in a Science Express paper published on October 30, 2004. More...

Consortium Releases First Tree DNA Sequence.An international consortium including DOE, Genome Canada, and a Swedish team has released the first complete DNA sequence of a tree, Populus trichocarpa. 9/21/04 [Details...]

July 2004

News Brief. GTL researcher Derek Lovley (University of Massachusetts) was highlighted in a syndicated Knight-Ridder newspaper article for his Geobacter work. 7/26/04 [More...]

May 2004

Feedback. The public is invited to provide comments and suggestions on this Genomics:GTL program by completing this form.

Bacteria Found in Hanford Waste. Scientists studying the soil beneath a leaking Hanford nuclear waste storage tank have discovered more than 100 species of bacteria living in a toxic, radioactive environment that most would have thought inhospitable to all forms of life. (Seattle Post-Intelligencer, 5/26/04)

JGI Decodes Wood and Toxic Waste-Degrading Fungus Genome. The Joint Genome Institute (JGI) announced the publication of a high-quality draft genome sequence of the white rot fungus, Phanerochaete chrysosporium. These are the only known microbes capable of efficiently degrading the recalcitrant aromatic plant polymer lignin, one of the most abundant natural materials on earth. They also have demonstrated the ability to remediate explosive contaminants, pesticides, and toxic waste with similar chemical structures to lignin. The sequence findings were published in the June 2004 issue of Nature Biotechnology.

April 2004

DNA Sequence Completed for Corrosive Bacterium Desulfovibrio vulgaris. A team of scientists led by The Institute for Genomic Research has sequenced the genome of Desulfovibrio vulgaris, a bacterium that damages oil and natural gas pipelines and causes staggering economic losses at industrial sites worldwide. In their analysis, scientists also found a network of proteins that have the potential to remediate pollutants such as uranium and chromium, commonly found at DOE contaminated sites.The study, funded by DOE, was reported in the May 2004 issue of Nature Biotechnology. [More...]

Sequencing Targets.Recommendations are sought for sequencing targets in support of the science missions of the Office of Biological and Environmental Research (BER). Candidates due by July 1, 2004.

March 2004

Researchers Discover 1.2 Million New Genes in Sargasso Sea Microbes. Department of Energy-funded researchers at the Institute for Biological Energy Alternatives (IBEA) have sequenced microbes in the Sargasso Sea and have discovered at least 1,800 new species and more than 1.2 million new genes. The results will be published in the journal Science. IBEA researchers’ discoveries include 782 new rhodopsin-like photoreceptor genes (only a few dozen have been characterized in microorganisms to date). March 4, 2004

February 2004

JGI Microbial Sequencing Priorities for FY 2004. Progress updated monthly.

JGI Launches Community Sequencing Program (CSP). “The primary goal of the CSP is to provide a world-class sequencing resource for the expanding the diversity of disciplines—geology, oceanography, and ecology, among others—that can benefit from the application of genomics,” says JGI Director Eddy Rubin. Press Release

Contractor-Grantee Abstracts. Genomics:GTL Contractor-Grantee Workshop II, Washington, D.C., February 29-March 4, 2004, meeting abstracts are now available in PDF.

First Genomes Revealed from Environmental Microbial Communities. Researchers from the Department of Energy Joint Genome Institute and the University of California, Berkeley, report the first genomic characterization of a microbial community. The results announced February 1st online in the journal Nature reveal how the genetic identities of microorganisms thriving in toxic conditions, "extremophiles," were recovered from a natural biofilm growing at an Environmental Protection Agency Superfund site. Four of the five microbes have to this point defied laboratory culture and have been studied only in their natural habitat, in this instance runoff from an abandoned mine, or acid mine drainage.

Jillian Banfield and her colleagues from U.C. Berkeley, who have been studying this site for the past 8 years, retrieved the sample from the depths of one of the nation's worst Superfund sites in Iron Mountain, California, near the northern town of Redding. [2-2-04]
JGI Press Release
Nature 04 March 2004 428: 37-49

January 2004

Funding Solicitation. OBER is requesting proposals from the DOE national labs in support of the Microbial Genome Program. See Announcement 04-07. Preapplications due by January 29, 2004. Formal applications due by April 15, 2004. See Funding for more...

Funding Solicitation. OBER is requesting applications in support of the Microbial Genome Program. See Notice 04-07 at http://science.energy.gov/grants/pdf/DE-FG01-04ER04-07.pdf. Preapplications due by January 29, 2004. Formal applications due by April 15, 2004. See Funding for more...

Genomatica Awarded Prestigious Frost & Sullivan Technology Leadership Award for SimPheny™.
Frost & Sullivan, a leading international marketing consulting company, has named Genomatica, Inc., a leader in silico systems biology companies, as recipient of the 2003 Technical Insights Award for Technology Leadership. January 07, 2004 [More...]

December 2003

Online Article. "Complete Genome Sequence of the Metabolically Versatile Photosynthetic Bacterium Rhodopseudomonas palustris," Nature Biotechnology, December 14, 2003, Frank W Larimer, et al . See also Website Rhodopseudomonas palustris Complete Genome Sequence and Annotation

News Brief. "Energy Department-Funded Scientists Decode DNA of Bacterium that Cleans Up Uranium Contamination and Generates Electricity," December 11, 2003 (Press Release and Science Article)

Computing Report. Report on Three Genomes to Life Workshops: Data Infrastructure, Modeling and Simulation, and Protein Structure Prediction, Gaithersburg, Maryland; July 22–24, 2003 (PDF file, 410 kb)

November 2003

News Brief. "Researchers Funded by the DOE "Genomes to Life" Program Achieve Important Advance in Developing Biological Strategies to Produce Hydrogen, Sequester Carbon Dioxide and Clean Up the Environment." See November 13, 2003, press release. See also remarks by Secretary of Energy Spencer Abraham.

October 2003

PNNL Awarded Proteomics Grant. The National Institutes of Health has awarded Pacific Northwest National Laboratory a large grant to study proteomics. See the October 7, 2003 press release.

Funding Solicitations. FY 2004 DOE SBIR/STTR Program Solicitations are now available and will close on January 6, 2004 (http://sbir.er.doe.gov/sbir). More information on Funding.

September 2003

Funding Awards. 2003 SBIR Phase II Awards Announced. Next solicitation will be issued on October 7, 2003 (http://sbir.er.doe.gov/sbir). More information on Funding.

August 2003

News Brief. Natural and Accelerated Bioremediation Research (NABIR) Highlighted in the San Francisco Chronicle, August 6, 2003

News Brief. Genomes of Tiny Microbes Yield Clues to Global Climate Change, August 13, 2003

Facility Workshop. GTL and Beyond: Data Standards Workshop. September 10-11, 2003, San Francisco, California

July 2003

News Brief. New Phase II SBIR Awards Support Genomes to Life Research, July 30, 2003

News Brief. PNNL's Richard Smith Wins 7th R&D 100 Award for FT-MS Proteome Express Project, July 30, 2003

May 2003

Facility Workshop. Characterization and Imaging of Molecular Machines Facility Workshop, June 17-18, 2003. Atlanta Airport Hilton, Atlanta, Georgia

News Brief. DOE Joint Genome Institute and Oregon State University Sequence Key Soil Microorganism in Carbon and Nitrogen Cycles

News Brief. Two DOE SC BER Genome Scientists Win Major Microbiology Awards

Facility Workshop. Protein Production & Characterization Facility Workshop, Argonne National Laboratory, May 29-30, 2003

Announcement. Recommendations for Sequencing Targets Sought. Deadline June 26, 2003

April 2003

Press Release. Energy Department Awards $9 Million for Energy Related Genomic Research. April 23, 2003

DOE Jobs. Microbial Geneticist; Office of Science, Office of Biological and Environmental Research, Life Sciences Division. Closes 6/06/2003.

Special Articles. "Realizing the Potential of the Genome Revolution: The Genomes to Life Program," Marvin E. Frazier, Gary M. Johnson, David G. Thomassen, Carl E. Oliver, and Aristides Patrinos, Science 300, 290 (2003)

February 2003

New Publications. Genomes to Life Contractor - Grantee Workshop I Abstracts, Arlington, Virginia, February 9-12, 2003

Call for Applications. See Funding for current call for research applications.

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