National Institutes of Health Library to Use Computable Genomix' GeneIndexer

December 01, 2009

Computable Genomix of Memphis, Tenn., said this week that the National Institutes of Health Library has bought a subscription to its online genomics research tool GeneIndexer.

No financial information was released.

The NIH Library purchased the GeneIndexer subscription as part of its "revamping of services focused on being an information commons," the company said.

As company executives explained to BioInform in October, GeneIndexer applies a technique called latent semantic indexing to extract gene associations from Medline abstracts. It applies a vector-space model to text-mining that represents documents with weighted index terms in a multidimensional space. LSI calculates the similarity between documents by capturing the spatial relationships between these terms [http://www.genomeweb.com/informatics/computable-genomix-wants-make-laten... ">BioInform, October 30, 2009].

Computable Genomix was founded in 2007 by computer scientist Michael Berry at the University of Tennessee and Ramin Homayouni, a biologist at the University of Memphis.

In this issue of BioInform

Young Investigator Profile

Christopher Maher

University of Michigan Medical School
Research Investigator

Gene Fusions and Transcriptome Sequencing

Christopher Maher is focused on elucidating gene fusions, which he first became acquainted with during his potdoctoral work at the Michigan Center for Translational Pathology. Maher hopes to continue discovering novel gene fusions as well as draw new findings out of already-known gene fusions. Last year, he published a paper in Nature in January of 2009 entitled "Transcriptome sequencing to detect gene fusions in cancer," which he says provides a validation for the approach of using next-gen sequencing to find gene fusions in cancer. This was followed up by a PNAS paper in July which demonstrated the gene fusion concept using paired-end transcriptome sequencing.
Blog

New Choice for NSF

MIT's Subra Suresh may be the next director of the National Science Foundation.

March 16, 2010

Running Around the CDC

The New York Times profiles Thomas Frieden, the director of the CDC.

March 16, 2010

Large Medco-Mayo Clinic Study Could Drive Genetic Testing for Warfarin Dosing

The large prospective study found that hospitalization rates for heart patients taking the blood thinner fell by nearly one-third "when genetic information was available to doctors prescribing the drug."

March 16, 2010

But Does It Come with a Corkscrew and Tweezers?

Researchers at HHMI are unveiling a new software package for analyzing complex biological images in 3D.

March 16, 2010
Papers of Note

Regulation and Function of miR-218 in Gastric Cancer Metastasis
Tie, Pan et al., PLoS Genetics
Researchers describe a negative feedback system between Robo1, a Slit receptor, and miR-218, wherein “decreased miR-218 levels eliminate Robo1 repression, which activates the Slit-Robo1 pathway through the interaction between Robo1 and Slit2, thus triggering tumor metastasis.” The authors suggest that the restoration of miR-218 supresses Robo1 espression and inhibits tumor cell invasion.

Method to Label and Isolate N-terminal Peptides from Human Plasma
Wildes and Wells, PNAS
A pair of researchers report their method to “dramatically reduce the complexity” of human serum samples by eliminating internal peptides. The authors write that, with their method, it's possible to identify substrates from specific proteases with the exogenous addition of the protease along with N-terminal isolation and quantitative mass spectrometry.
People on the Move

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.

Three leaders from the Human Genome Project — David Botstein, Francis Collins, and Eric Lander — have been named co-winners of the 2010 Albany Medical Center Prize in Medicine and Biomedical Research, which carries with it a purse of $500,000.

Adrian Dillon will resign from his job as executive VP of finance and administration and CFO of Agilent Technologies to become chief financial and administrative officer at Skype. He will be replaced at the beginning of April by Didier Hirsch, who currently is VP of corporate controllership and taxes and who will serve as acting CFO.
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

more

Science
Researchers from the Institute for Systems Biology and elsewhere used Complete Genomics' sequencing service to identify mutations behind a Mendelian condition called Miller syndrome and an inherited lung disorder called ciliary dyskinesia in a family of four.
Business
Bruker will acquire certain mass spectrometry and chromatography product lines from Varian, clearing the way for Agilent to complete its $1.5 billion acquisition of Varian. The divestitures were part of conditions set by EU authorities for approval of the merger.
Funding
HHS expects that in 2010 NIH will spend another roughly $5.2 billion overall in stimulus funds that were left over from ARRA's first year. NIH still has more than $1.6 billion to spend in stimulus funds for lab construction and renovation, buildings and facilities, and shared instruments.
Genome Technology Magazine
Check out this month's humor page here:

Search

National Institutes of Health Library to Use Computable Genomix' GeneIndexer

Related Stories

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

Poll