Stanford University and EMBL Platforms Aim to Give Users a Low-Pain Handle on Ontologies

March 20, 2009

By Vivien Marx

New web-based platforms presented at this week's American Medical Informatics Association Summit on Translational Bioinformatics could be a user-friendly way for scientists to use ontologies.

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In this issue of BioInform

Young Investigator Profile

Duncan Odom

Group Leader
Cancer Research UK
Cambridge Research Institute

Tissue Transcription

Duncan Odom is combining genome-wide transcription factor binding, gene expression perturbation using genetic manipulations, comparative genomics, and physiological approaches to help elucidate how tissue are defined. So far, his work has revealed the core circuitry of human hepatocytes and pancreatic islets, as well as the connections that exist between miRNA programs and transcription factor binding events.
Blog

Thinking Big About Something Small

One blogger says that when it comes to bacteria, researchers have to think outside the box.

September 03, 2010

3 … 2 … 1 … Blast Off!

NIH teams up with NASA for biomedical research in space.

September 03, 2010

Finding the Number

Washington University researchers detail a way to determine copy number through pyrosequencing.

September 03, 2010

A Brainy Map

Allan Jones and Caroline Overly discuss the Allen Human Brain Atlas.

September 03, 2010
Papers of Note

Method to Detect CNV via Mated Short Reads
Medvedev, Fiume et al., Genome Research
Researchers at the University of Toronto describe a method to detect copy-number variation via mated short reads, wherein "matepairs mapping discordantly to the reference serve to indicate the presence of variation." CNVer — the team's algorithm — combines this information and allows researchers to "mitigate the sequencing biases that cause uneven local coverage and accurately predict CNVs." The team used CNVer on a recently described genome of a Yoruban individual and detected 4,879 CNVs. "CNVer can reconstruct the absolute copy counts of segments of the donor genome and evaluate the feasibility of using CNVer with low coverage datasets," the authors add.

Draft Sequence of the Domestic Apple Genome
Velasco, Zharkikh et al., Nature Genetics
An international research team reports a draft sequence of the domestic apple genome. "We show that a relatively recent (>50 million years ago) genome-wide duplication has resulted in the transition from nine ancestral chromosomes to 17 chromosomes in the Pyreae," the authors write. The team suggests that in apple, MADS-box genes — involved in flower and fruit development — include 15 members. The apple genome also contains other expanded gene families, including those "involved in Rosaceae-specific metabolism, such as transport and assimilation of sorbitol."
People on the Move

Emergent Biosolutions has appointed former National Cancer Institute Director John Niederhuber to serve on its board of directors.

Niederhuber was director at NCI from 2005 to 2010, and he recently joined Inova Health System as executive VP and CEO of the Inova Institute for Translational Research and Personalized Medicine. He also still works as an adjunct investigator at NCI’s Center for Cancer Research.

Judd Jessup has been named CEO of CombiMatrix, the firm said this week. Judd will take over the company's top position from interim CEO Mark McGowan, effective Aug. 23. Upon stepping down, McGowan will continue his duties as chairman of the firm's board of directors.

Jessup most recently was CEO of US Labs, a cancer diagnostic and genetic testing services lab. He also previously served as president of the Health Plans Division for FHP International, as well as the president of publicly traded HMO TakeCare.

The National Institutes of Health this week said that it has appointed James Anderson to be director of the NIH Division of Program Coordination, Planning, and Strategic Initiatives.
Upcoming Events

Conferences, Meetings & Deadlines

Structure and Function of Neural Circuits
Sep. 5-8 / Heidelberg, Germany
EMBO/EMBL Symposium

Computational Aspects of Protein Structure Determination and Analysis: From Data to Structure to Function
Sep. 6-10 / Hinxton, UK
EMBO Practical Course

Human Genetics and Genomics
Sep. 6-10 / Suzhou, China
Cold Spring Harbor Asia Conferences

4th CPTC Annual Meeting: Establishing the Standards in Clinical Proteomics
Sep. 8-9 / Bethesda, MD
NCI

Quantitative and Systems Pharmacology Workshop II
Sep. 9-10 / Bethesda, MD
NIGMS

Abstract & Registration Deadlines

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Science
An international research team used a combination of Sanger and Roche 454 GS FLX Titanium sequencing to sequence a draft of the domesticated apple genome — a feat that's expected to lead to a better understanding of the biology of apples and related plants as well as improved apple varieties.
Business
GenomeWeb Daily News talked with industry analysts about the recent IPO filings for Complete genomics and Pacific Biosciences. While the recent activity suggests that the IPO market may be opening up to the sequencing space, whether or not it will extend to the broader 'omics market is debatable.
Funding
The University of Michigan has reeled in a $7.5 million grant from the National Institutes of Health to study the genetic factors involved in Clostridium difficile infections in humans. The university is one of four Cooperative Research Centers nationwide that will form the NIH-sponsored Enterics Research Investigational Network.
Genome Technology Magazine
Many researchers are switching over to RNA-seq from microarrays for their transcriptomic studies. But RNA-seq is still a young technique and researchers are struggling to handle all the data it generates.

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Stanford University and EMBL Platforms Aim to Give Users a Low-Pain Handle on Ontologies

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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

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