Enabled by New Sequencing Techs, JGI Projects 300 GB of Data for 2010 Community Sequencing Program

June 30, 2009

JGI expects to generate about a third of a terabase of sequence data for CSP 2010 projects, about half on 454's sequencing platform, the other half using Illumina's technology.

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In this issue of In Sequence

Video Spotlight

ScienceOnline2012

Genome Technology's Tracy Vence interviewed Sandra Porter, president of Digital World Biology, and Kristi Holmes, a bioinformaticist at the Becker Medical Library, Washington University School of Medicine at ScieneOnline2012.

February 02, 2012

Sponsored Video: Sage Science - Pippin DNA Size Selection

Sage Science is pleased to announce the introduction of the BluePippin DNA size selection system, a pulsed-field electrophoresis version of its popular Pippin Prep instrument.

January 31, 2012

Highlights from SC11 Part IV

In this video, we speak with Todd Smith, senior leader of research and applications of PerkinElmer, and researchers from Stockholm University on accelerating the GROMACS molecular dynamics software suite with GPUs and CPUs.

January 13, 2012

Mass Spec at NYU

We visited the NYU Protein Analysis Facility at the Skirball Institute of Biomolecular Medicine in New York City and discussed the facility's gear and its development with director, Thomas Neubert.

January 01, 2012
Young Investigator Profile

Uttiya Basu

Assistant Professor
Columbia University

Alterations & Adaptations

The Basu research group is looking at how activation induced cytidine deaminase (AID) predominately targets V genes and switch sequences, the mechanisms by which physiological targets of AID are repaired in a mutagenic fashion in B cells, how AID is prevented from acting as a pleiotropic cellular mutagen, and the physiological role of AID in non-B cells.
Blog

A Clearer Way

The career path for medical laboratory scientists needs to be better defined, Dark Daily says.

February 06, 2012

Cleaning up Messy Data with Google Refine

iPhlyo has a post demonstrating how to use Google Refine, a freely available web-based tool, to clean up messy data.

February 06, 2012

This Week in Clinical Chemistry

In Clinical Chemistry this week: fetal diagnostics, testing exhaled air, and more.

February 06, 2012

This Week in PLoS

In PLoS this week: rare base-pair variation in complex traits and diseases; diagnostic and prognostic markers for infective endocarditis; more.

February 06, 2012
Papers of Note

Chromosome-Scale Selective Sweeps and Genomic Diversity in C. elegans
Andersen, Gerke et al., Nature Genetics
Researchers at Princeton University and elsewhere discuss the effects of chromosome-scale selective sweeps on genomic diversity in Caenorhabditis elegans. Taking a high-throughput selective sequencing approach on a collection of 200 wild C. elegans strains, the team found that the nematode's "genome variation is dominated by a set of commonly shared haplotypes on four of its six chromosomes, each spanning many megabases." Further, the team reports on its population genetic modeling experiments, which showed that "this pattern was generated by chromosome-scale selective sweeps that have reduced variation worldwide; at least one of these sweeps probably occurred in the last few hundred years," it writes.

Dissecting the Regulatory Architecture of Gene Expression Quantitative Trait Loci
Gaffney, Veyrieras et al., Genome Biology
A team led by investigators at the University of Chicago this week report their use of a "Bayesian hierarchical model to estimate the enrichment of eQTLs [expression quantitative trait loci] in a wide variety of regulatory annotations" derived from 1,000 Genomes Project data. "We find that [approximately] 40 percent of eQTLs occur in open chromatin, and that they are particularly enriched in transcription factor binding sites, suggesting that many directly impact protein-DNA interactions," the authors write.
People on the Move

Life Technologies this week named Alan Sachs as head of global research and development and Ronnie Andrews as president of medical sciences.

Sachs was previously the vice president of exploratory and translational sciences for Merck Research Laboratories, where he spent 10 years in various leadership roles, Life Tech said. Prior to that Sachs served an associate professor of biochemistry and molecular biology at the University of California, Berkeley, and as a Whitehead fellow at the Whitehead Institute for Biomedical Research.

Andrews joins Life Tech from GE Molecular Diagnostics, where he served as a segment leader following GE's 2010 acquisition of Clarient, where Andrews was CEO. Andrews has also held executive positions with Abbott Diagnostics, Roche Diagnostics, and Immucor.

Stephen O'Brien has left the National Cancer Institute's Laboratory of Genomic Diversity after 25 years to help launch a genome bioinformatics program at St. Petersburg University in Russia. O'Brien received a $5 million grant from the Russian Ministry of Education and Science last year under a program that aims to lure big-name researchers to Russia. Over the coming three years, O'Brien will spend at least four months per year in Russia working at the center, which is scheduled to open in May.

Saladax Biomedical said today that President and CEO Edward Erickson has resigned due to personal and family reasons, and that he will be replaced by Kevin Harter on an interim basis. Erickson will remain a member of the company's board of directors. Harter is a co-founder and senior VP of the Life Sciences Greenhouse, and he has served as executive chairman at Saladax.
Upcoming Events

Conferences, Meetings & Deadlines

The World Cancer Immunotherapy Conference: Challenges & Opportunities in Clinical Development, Clinical Trial Design & Commercialization
Jan 25-26 / San Diego
Arrowhead Publishers

3rd Annual Health Outcomes and Pharmacoeconomics Research Conference
Jan 30-31 / Philadelphia
Marcus Evans

2012 Genitourinary Cancers Symposium
Feb 2-4 / San Francisco
ASCO

An Introduction to Genomics: Breast Cancer Diagnosis and Treatment
Feb 3 / Bethesda, Md.
NHGRI

SLAS 2012: 1st Annual Conference and Exhibition
Feb 4-8 / San Diego
SLAS

Abstract & Registration Deadlines

more

Science
Members of the International Stroke Genetics Consortium and the Wellcome Trust Case Control Consortium 2 did a GWAS involving thousands of individuals of European descent with or without a history of stroke and found a new genetic variant that contributes to a form of stroke called large vessel ischemic stroke. The variant was found in in the histone deacetylase 9 coding gene HDAC9 on chromosome 7.
Business
PerkinElmer reported fourth-quarter revenue growth of 15 percent, or 6 percent organically, compared to Q4 2010 and beat analysts' estimates on the top and bottom line. The firm is in the process of integrating Caliper Life Sciences and a few bioinformatics companies, and company officials said there would be a pause in M&A activity for the next several months - though diagnostics remains a "significant priority."
Funding
Canada launched a new program that will pump C$67.5 million (US$67.3 million) into projects that will use genomics-based research to advance personalized healthcare. The 2012 Large-Scale Applied Research Project Competition in Genomics and Personalized Health is funded with C$40 million from Genome Canada, C$22.5 million from the Canadian Institute of Health Research, and C$5 million from the Cancer Stem Cell Consortium.
Genome Technology Magazine
The National Center for Biotechnology Information's Teresa Przytycka and her team have developed a pathway-centric computational approach, which is based on eQTL analysis, graph theoretical techniques, and combinatorial algorithms, to identify causative genes for complex diseases. In a paper, her team applied the approach to glioblastoma multiforme, and they identified not only putative causal genes, but also potential nodes and pathways linking those genes.

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Enabled by New Sequencing Techs, JGI Projects 300 GB of Data for 2010 Community Sequencing Program

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In this issue of In Sequence

Video Spotlight

Young Investigator Profile

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Papers of Note

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Upcoming Events

Science

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