Jim Watson’s Genome in an E-Mail? UC Irvine Team Develops Method to Compress Genomic Data

January 30, 2009

By Vivien Marx

The team’s compression techniques enabled them to reduce Jim Watson's genome from around 3 gigabytes to 4 megabytes, which they said made the new data "small enough to be sent as an e-mail attachment."

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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.
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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.
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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.
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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.
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Jim Watson’s Genome in an E-Mail? UC Irvine Team Develops Method to Compress Genomic Data

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