Posts Tagged ‘Genomics’

DOE JGI 2012 Community Sequencing Program Portfolio

November 4th, 2011

Trillions Served: Massive, Complex Projects Dominate DOE JGI 2012 Community Sequencing Program Portfolio.

‘The 2012 Community Sequencing Program (CSP) call invited researchers to submit proposals for projects that advance capabilities in fields such as plant-microbe interactions, microbes involved in carbon capture and greenhouse gas emission, and metagenomics—the characterization of complex collections of microbes from particular environmental niches. The total allocation for the coming year’s CSP portfolio will exceed 30 trillion bases (terabases or Tb), a 100-fold increase compared with just two years ago, when just a third of a terabase was allocated to more than 70 projects. This amounts to the equivalent of at least 10,000 human genomes in data …’ Read more

 

Photo:  The boreal forest, one of the ecosystem investigated by the CSP 2012 program. Denali Natl Park, Alaska  (© F Martin)

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Posted in Consortium activity, Genome sequencing, Interaction, Metagenomics, Mycology, Plant Biology, Symbiosis

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Botrytis/Sclerotinia Post-Genome Workshop 2011

March 25th, 2011

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Posted in conference, Consortium activity, Interaction, Mycology, Plant Biology, Symbiosis

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Genomics of Energy & Environment

February 15th, 2011

6jgiJust a reminder…that the deadline for poster/abstract submission for the 6th Annual DOE Joint Genome Institute Genomics of Energy & Environment meeting (http://go.usa.gov/g4N) is rapidly approaching: February 21.

The meeting brings together, in JGI’s hometown of Walnut Creek, California, an international network of researchers interest in: Synthetic Biology, Ecogenomics and Ecoresilience of the Gulf Oil Spill, Hardware and Software Trends in Genomics Supercomputing, Computational Approaches to Massive Short Read Metagenomic Data Sets, Genomics of Biofuel Crops, Behavioral Genetics of Pollinating Bees, Microbiome Analyses from Humans to Shipworms, Metatranscriptomics of Marine Microbial Communities, Successful Transposable Elements Secrets, and Great Prairie Soil Metagenomics.

Confirmed speakers: Peer Bork, (European Molecular Biology Laboratory), Ed Buckler, Cornell University, Dan Distel, Ocean Genome Legacy, Dusko Ehrlich, French National Institute for Agricultural Research (INRA), Terry Hazen, Lawrence Berkeley National Laboratory (LBNL), Scott Hodges, University of California, Santa Barbara, Tom Juenger, University of Texas at Austin, Rob Knight, University of Colorado, Ruth Ley, Cornell University, Mary Ann Moran, University of Georgia, Magnus Nordborg, Gregor Mendel Institute, Gene Robinson, University of Illinois at Urbana-Champaign, Christopher Scholin, Monterey Bay Aquarium Research Institute (MBARI), Stephan Schuster, Penn State University, Pam Silver, Harvard, Jim Tiedje, Michigan State University, Mike Thomashow, Michigan State University, Jerry Tuskan, Oak Ridge National Laboratory/DOE JGI and Katherine Yelick, National Energy Research Scientific Computing Center (NERSC).

Workshops include:

  • Integrated Microbial Genomes (IMG)/Metagenomes data analysis systems http://img.jgi.doe.gov/
  • Mycocosm fungal genomics portal provides data access, visualization, and analysis tools for comparative genomics of fungi http://genome.jgi-psf.org/ programs/fungi/index.jsf
  • Phytozome provides data access and visualization tools for comparative plant genomics http://www.phytozome.net/
  • RNA Technologies & Analysis: a comprehensive suite for transcriptome interrogation, including RNA-Seq for expression profiling, etc.

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Posted in Bioinformatics, conference, Consortium activity, Genome sequencing, Metagenomics, Mycology, Plant Biology, Workshops

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26th Fungal Genetics Conference 2011 at Asilomar

October 31st, 2010

26thFGCLogo640Time to register for the Fungal Genetics Conference 2011 at the Asilomar conference center. The registration site is now open and you have till December 14th, 2010 to register and submit your abstract. See you there.

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Posted in conference, Consortium activity, Mycology, Workshops

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PYFF4

February 23rd, 2010

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PYFF4-logo2Research on the physiology of yeasts and filamentous fungi is booming and scientific interest in these ‘lower’ eukaryotes continues to grow. Key drivers include their relevance for industrial biotechnology, food and pharmaceutical industries and their role as highly accessible eukaryotic models for systems biology.

Three previous, highly successful editions of the Physiology of Yeasts and Filamentous Fungi (PYFF) conferences in Hindsgavl (2001), Anglet (2004) and Helsinki (2007) have brought together researchers active at the frontline of research on yeasts and filamentous fungi. Since the Helsinki meeting, the field has seen further spectacular developments, including the sequencing and analysis of important yeast and filamentous fungal genomes, the introduction of single-cell approaches in fungal research and breakthrough results in metabolic engineering. PYFF4 will celebrate these scientific developments and, once again, provide a platform for exchange of concepts between the yeast and fungal research communities.

PYFF4 will be organized in a dynamic environment: the harbour City of Rotterdam, the Netherlands. The conference venue, the Rotterdam World Trade Center, is located in the city centre, with excellent accessibility (plane, train) and many hotels in the immediate vicinity. The social event, an evening boat tour through the harbour area with an onboard dinner, will provide ample opportunity to take in more than fungal physiology.

The conference will be held from Tuesday June 1 (evening reception) – Friday June 4, 2010.
The scientific programme covers 3 full days.

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Posted in conference, Genome sequencing, Mycology

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Waking the Dead

February 14th, 2010

InukIt’s not a plant genome …  It’s not a fungal genome … But this paper is so exciting. For the first time, the nuclear genome of an extinct human being — a Palaeo-Eskimo – has been reconstructed and this spectacular findings are published in the February 10th, 2010 issue of Nature.

Morten Rasmussen and Eske Willerslev, from the Centre of Excellence in GeoGenetics, The Natural History Museum at the University of Copenhagen, Denmark, led the international team of scientists responsible for the sequencing of a male individual, Inuk*, who lived in Greenland 4,000 years ago and belonged to the first culture to settle in the New World Arctic, the Saqqaq. Genomic DNA was extracted from permafrost-preserved hair, found in Qeqertasussuk, an archaeological site in southwest Greenland. The sequencing was performed by using Illumina GAII and yielded a total of 3.5 billion reads, from a total of 242 lanes.

The genome-wide SNP analysis suggested that Inuk was genetically adapted to cold temperatures (according to its p53 gene sequence) and has a tendency to baldness, dry earwax, brown eyes, dark skin, the blood type A+, and shovel-shaped front teeth .

Analysis of 350,000 SNPs revealed that populations closest to the Saqqaq are the contemporary Koryaks and Chukchis inhabiting Chukotka and northern Kamchatka of the Siberian far east. This provides evidence for a migration from Siberia into the New World some 5,500 years ago, independent of that giving rise to the modern Native Americans and Inuit. Inuk’s ancestors separated from their Chukchis relatives and almost immediately crossed the Bering land bridge connecting Siberia and the New World.

Rasmussenn et al. (2010) Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature 463, 757-762.

* “Inuk” means “man” or “human” in Greenlandic.

Image: Nuka Godfredsen/Nature. Artist’s impression of Inuk.

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Posted in Genome paper, Genome sequencing

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August 28th, 2009

hongosThe Xth International Fungal Biology Conference will be held in Ensenada, Baja California, Mexico on December 6 – 10, 2009. The International Fungal Biology Conferences are a prestigious series of conferences held at 3-4 year intervals at different locations around the world.

Several talks and symposia will be dedicated to genomics and postgenomics of fungi.

Please visit the website for details on the scientific programme, registration, hotel accommodations, transportation etc.

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Posted in Workshops

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