Advances in Next-Gen Sequencing Speed Evolution of Bioinformatics Tools in 2009

December 18, 2009

A prime example of the progress made in bioinformatics over the last year was the publication this week in Nature of the panda genome, which the Beijing Genomics Institute in Shenzhen sequenced and assembled de novo using only the Illumina Genome Analyzer platform and the SOAPdenovo algorithm for assembly.

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In this issue of BioInform

Young Investigator Profile

Martin Beck

European Molecular Biology Laborator
Group Leader, Structural and Computational Biology Unit

Macromolecular Assemblies

Martin Beck's research group at EMBL combines biochemical approaches, proteomics and cryo-electron microscopy to study the structure and function of large macromolecular assemblies. The end goals of this work include developing integrated workflows for structure determination of large macromolecular assemblies such as the nuclear pore complex, elucidation of their function through real-time imaging, and ultimately revealing the steps of their assembly and disassembly process.
Blog

Considering a Cloud? Cost Isn't Everything...

Benchmark paper looks at the real cost of the CPU hour on the cloud.

March 19, 2010

Sequencers and Tanks

Nick Loman has updated his map of sequencers and begun a new estimate of sequencers being sold.

March 19, 2010

Cherry Picking Clauses

Andrew Yates wonders how genetic tests can help people make medical decisions if the tests are for research and educational purposes only.

March 19, 2010

Adding More SNPs to Breast Cancer Risk Models Doesn't Help

NCI researchers say breast cancer risk models don't perform better when researchers add common genetic variants linked to the disease.

March 19, 2010
Papers of Note

Sequencing and Analysis of the Hydra Genome
Chapman, Kirkness et al., Nature
An international research collaboration reports their sequencing and analysis of the Hydra magnipapillata genome, and compare it to the genomes of several other organisms. "The Hydra genome has been shaped by bursts of transposable element expansion, horizontal gene transfer, trans-splicing, and simplification of gene structure and gene content that parallel simplification of the Hydra life cycle," the authors write. They team suggests that comparisons of the Hydra genome to the reported sequences of other animals have helped them to elucidate the evolution of several of the organism's characteristics.

GWAS Identifies Risk Loci for Ulcerative Colitis
Abrecht, Wittig et al., Nature Genetics
Researchers present results from a genome-wide association study which identified risk loci at 7q22 and 22q13 for ulcerative colitis. Their analyses included 1,897,764 SNPs from 1,043 UC cases and 1,703 controls from Germany, and six replication panels from different regions in Europe.
People on the Move

Affymetrix has appointed Timothy Barabe to the chief financial officer post. He will run the firm's treasury and financial functions, investor relations, and its information technology departments. Barabe previously was senior VP and CFO at Human Genome Sciences, and he was CFO at Regent Medical. He also has worked in various roles at Novartis, including senior executive positions at CIBA Vision.

Barabe replaces John Batty, who was with Affymetrix for three years.

Wellcome Trust Sanger Institute Professor Leena Peltonen-Palotie died this week of cancer at her home in Finland, according to the Sanger Institute. Peltonen-Palotie was head of human genetics at Wellcome Trust, and she held appointments at the Broad Institute at MIT and Harvard and the Institute for Molecular Medicine Finland.
Upcoming Events

Conferences, Meetings & Deadlines

PTEN Pathways & Targets
Mar. 16-20 / Cold Spring Harbor, NY
CSHL

The Complex Life of mRNA: From Synthesis to Decay
Mar. 18-19 / Heidelberg, Germany
EMBL

Perspectives in Clinical Proteomics
Mar. 18-19 / Hinxton, UK
EMBL-EBI-Wellcome Trust

AUTM 2010 Annual Meeting
Mar. 18-20 / New Orleans, La.
Association of University Technology Managers

ABRF 2010
Mar. 20-23 / Sacramento, CA
Association of Biomolecular Resource Facilities

Abstract & Registration Deadlines

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Science
Adding data on 10 genetic variants to non-genetic risk models of breast cancer offers little improvement for predicting breast cancer risk, researchers from the National Cancer Institute and elsewhere concluded following a study of nearly 6,000 women with the disease.
Business
Osmetech has filed with the US Securities and Exchange Commission for an initial public offering of stock in the US under the name of its newly proposed parent, GenMark Diagnostics. The firm hopes to raise around $40 million and intends to relocate its headquarters to Pasadena, Calif.
Funding
The National Heart, Lung, and Blood Institute plans to pump $76 million over the next five years into a program aimed at combining cellular tools, molecular profiling, and genomics and integrating them into existing genotypic and clinical phenotypic data on naturally occurring human genetic variation.
Genome Technology Magazine
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Advances in Next-Gen Sequencing Speed Evolution of Bioinformatics Tools in 2009

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In this issue of BioInform

Young Investigator Profile

Blog

Papers of Note

People on the Move

Upcoming Events

Science

Business

Funding

Genome Technology Magazine

TechGuides Listings

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