Compendia to Use $1.3M NIH Grant to Develop Informatics Pipeline for miRNA Data

September 03, 2010

The company will develop bioinformatics pipelines that will process, normalize, and analyze miRNA data from the public domain and make it available to cancer researchers in its database of cancer gene expression data.

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In this issue of BioInform

Video Spotlight

Sponsored Video: Ambry Genetics - "Fully Automated"

RainDance's ThunderStorm System is a fully-automated and walkaway high-throughput targeted sequencing solution that enables researchers to process 96 samples per day run on a proven platform that generates higher-quality data faster than ever before.

February 07, 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

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 ScienceOnline2012.

February 02, 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
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 Growth Spurt

A recent Battelle report discusses the genetics and genomics clinical laboratory testing sector.

February 07, 2012

This Week in Modern Pathology

In Modern Pathology this week: patterns of promoter CpG island methylation in breast cancer subtypes, the mTOR pathway in leiomyosarcomas and pleomorphic sarcomas, and more.

February 07, 2012

Amazon Cuts Cloud Storage Prices

Amazon Web Services is cutting prices on their cloud computing storage offering, S3.

February 07, 2012

Double Down

A researcher recently pleaded guilty to accepting funding from two sources for the the same project.

February 07, 2012
Papers of Note

Human Genetic Variation Alters Anthrax Toxin Sensitivity
Martchenko, Candille et al., PNAS
Researchers at Stanford University School of Medicine show that genetic variation affecting capillary morphogenesis gene 2, or CMG2, dramatically alters toxin sensitivity in humans. In its analysis, the team reports on "a CMG2 single-nucleotide polymorphism occurring frequently in African and European populations [that they found] independently altered toxin uptake." The group goes on to suggest "testing of genomically characterized human cell populations may offer a broadly useful strategy for elucidating effects of genetic variation on infectious disease susceptibility."

Genomic Epidemiology of the 2011 Escherichia coli O104:H4 Outbreaks
Grad, Lipsitch et al., PNAS
An international team led by investigators at Brigham and Women's Hospital in Boston reports on the genomic epidemiology of the 2011 Escherichia coli O104:H4 outbreaks in Europe, saying that the "striking difference in diversity between the German and French outbreak samples" it observed "is consistent with several hypotheses, including a bottleneck that purged diversity in the German isolates, variation in mutation rates in the two E. coli outbreak populations, or uneven distribution of diversity in the seed populations that led to each outbreak."
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.
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Feb 19-23 / San Francisco
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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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Compendia to Use $1.3M NIH Grant to Develop Informatics Pipeline for miRNA Data

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