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January 8, 2009 | FDA Drugs Approved in 2008
The Wall Street Journal reports FDA approved more new drugs – 24 - in 2008 than in any of the prior three years, “a consolation of sorts to an industry struggling with greater scrutiny, thousands of layoffs and thinning drug pipelines.” That compares to 18 in 2007, 22 in 2006 and 20 in 2005. The agency also approved dozens of other applications for new formulations or new uses of existing drugs. Read full article.

Major Step Forward in Assessing Protein Interactomes
In a series of four papers published in this month's issue of the journal Nature Methods, investigators in Dana-Farber's Center for Cancer Systems Biology (CCSB) start to answer protein interactome questions – e.g. how reliable is the data produced by different techniques; what portion of the interactome of different organisms has been mapped so far; and why do existing experimental techniques fail to detect certain interactions - by examining the accuracy and thoroughness of current interactome maps and the techniques by which they are compiled.

The studies — in a special issue of the journal on the interactome — provide a set of ground rules for future research and demonstrate the power of such research when backed by well-proven experimental techniques. The Dana-Farber team found that each technique captures only 20-30 percent of all the interactions within cells. That led them to determine that the human interactome contains about 130,000 interactions, a small minority of which have been mapped so far CCSB's director, Marc Vidal, PhD, is the senior author of the papers. More.

First Catalog of Tissue-Specific Disease Gene Expression
Researchers used high performance computing to derive the first catalog of tissue-specific gene expression changes, according to a recent report - A large-scale analysis of tissue-specific pathology and gene expression of human disease genes and complexes – published online in PNAS.

Authors say they conducted “…a systematic analysis of the link between tissue-specific gene expression and pathological manifestations in many human diseases and cancers. Diseases were systematically mapped to tissues they affect from disease-relevant literature in PubMed to create a disease–tissue covariation matrix of high-confidence associations of >1,000 diseases to 73 tissues. By retrieving >2,000 known disease genes, and generating 1,500 disease-associated protein complexes, we analyzed the differential expression of a gene or complex involved in a particular disease in the tissues affected by the disease, compared with nonaffected tissues.“

Supercomputers were used to "model biological processes in tissues across the human organism, based on the knowledge from millions of already published articles," explained co-author Niclas Tue Hansen, of the Center for Biological Sequence Analysis, Technical University of Denmark. "In this way, we were able to create an extensive map of the interactions of molecules in many diseases -- a sort of molecular manual -- without carrying out experiments in patients." Read the report.

Ariadne Plug-in for Illumina Genome Studio
Ariadne now provides advanced integration and interpretation capabilities for data generated by Illumina’s iScan and BeadArray Reader platforms. “Ariadne is the first to offer a plug-in with our newly launched GenomeStudio Software program. By providing a graphical representation of Illumina’s microarray data, Pathway Studio offers researchers a unique way to complete advanced downstream analysis,” said Omoshile Clement, Ph.D., Senior Product Manager of Software Informatics at Illumina.  “Illumina and its software partners continue to improve tools that aid in the interpretation of data across multiple applications.” Read release.

Genedata Strengthens HCS Offering 
This week Genedata announced the release of High Content Analyzer, the latest addition to its Genedata Screener enterprise solution for high content screening data analysis. The new module features streamlined processing, systematic quality control and optimized management of HCS data. It can flexibly capture and load assay data from any plate-based HCS instrument or image analysis software and can interface with in-house instrumentation and existing IT infrastructure. Read release.
 
Ingenuity Debuts IPA 7
Pathway tool providers Ingenuity Systems this week released IPA 7 with contextual data analysis. Contextual data analysis is comprised of a series of powerful biological filters and other tools that make it easier to quickly understand experimental results and fine-tune scientific hypotheses in relation to a particular experimental context or model. More on IPA 7.

Now for Something Different
Blind trust in modeling can be problematic, as described in a piece in the New York Times last week, Risk Mismanagement. Writer Joe Nocera describes and decries the financial industry’s use of the so-called VaR (value risk) model and its failure to anticipate the market swoon. It’s a good cautionary tale for those in other industries wishing to ensure modeling is used correctly. Read the NYT article.

GeneGo, Bayer, Renew Agreement
Bayer Schering renewed its MetaCore licenses for another three years. Bayer Schering Pharma has programs for cancer, cardiovascular diseases and gynecological therapies and GeneGo has good coverage of these diseases and others. GeneGo is also in the process of building disease specific platforms in cancer and the cardiovascular area that include blueprint pathway maps for the disease, processes and mechanisms as well as offering public domain experimental data and disease ontologies. Read report.

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This article first appeared in Bio-IT World’s Predictive Biomedicine newsletter. Click here for a free subscription.

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