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Biobase to Build In Silico Drug Development Toolbox


Biobase has been tapped to lead a €3 million ($4 million) European Union research project that aims to develop a “toolbox” that will integrate bioinformatics and cheminformatics software with experimental ’omics platforms such as transcriptomics, proteomics, and metabolomics.

The three-year project, called Net2Drug, was awarded under the EU’s 6th Framework Program. In addition to Biobase, participants include Spain’s Progenika Biopharma, the University of Helsinki, the Fraunhofer Institute of Toxicology and Experimental Medicine, the University of Göttingen Medical School, Russia’s Institute of Systems Biology, the Institute of Biomedical Chemistry at the Russian Academy of Medical Sciences, the Karolinska Institute, and the Italian National Research Council’s Institute of Biomedical Technologies.

Edgar Wingender, president and CSO of Biobase, says that the collaborative effort grew out of a “network that we’ve built up for many, many years of scientific collaboration.”

The first step of the effort will be integrating the experimental and computational platforms of the various participants, Wingender says. Then, as a proof of principle, the collaborators will apply the combined suite of tools to breast cancer. In terms of the analytical workflow, he says that the researchers will first run a battery of transcriptomics, proteomics, and metabolomics experiments on normal cells and cancer cells in order to identify the molecular underpinnings of different tumor types.

Then the data will be analyzed in the context of biological pathways in order to identify potential “master nodes” in the regulatory network that controls expression of the genes of interest. Next, cheminformatics tools will come into play in order to identify small molecules that might be able to control the activity of these key nodes.

“At the end, if everything runs optimally, then we can not only come up with the hypothesis for a crucial drug target, but even with a potential lead structure that would be a good starting point to develop a drug,” he says.
Bernadette Toner

Short Reads

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According to Labvantage, an unnamed pharmaceutical giant has licensed its Sapphire Biobanking Solution to support its biorepository operations. The new software will replace an existing system based on Excel spreadsheets and internally developed solutions.

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The University of Washington has hired OpenHelix to provide training for its SeattleSNPs tool and Genome Variation server. SeattleSNPs is used to identify and genotype the associations between SNPs, genes, and pathways that may be related to human inflammatory responses.

Boehringer Ingelheim expanded its license agreement for GeneGo’s MetaCore data-mining software suite. Under the expanded agreement, Boehringer will use the software in its toxicogenomics programs.

Sigma-Aldrich uploaded more than 1,100 bioactive small molecules to the National Institutes of Health’s PubChem database, the company announced.


US Patent 7,197,400. System and computer software products for comparative gene expression analysis. Inventors: Wei-min Liu and Xiaojun Di. Assignee: Affeymetrix. Issued: March 30, 2007.

This patent claims methods and computer software products for the analysis of gene expression data. In one version of the invention, methods and software use independent normalization factors to provide comparative gene expression analysis.

US Patent 7,186,513. Methods for monitoring multiple gene expression. Inventors: Randy Berka, Michael Rey, Jeffrey Shuster, Sakari Kauppinen, Ib Grothh Clausen, and Peter Bjarke Olsen. Assignee: Novozymes. Issued: March 6, 2007.

According to the abstract, this patent covers methods for monitoring the “differential expression of a plurality of genes in a first filamentous fungal cell relative to expression of the same genes in one or more second filamentous fungal cells using microarrays containing filamentous fungal expressed sequenced tags.” This invention also includes a computer readable media and substrates containing tags for monitoring the expression of those genes.

Data Point

$40 million

The amount of investment capital Hewlett-Packard expects its new Institute for Biomedical Informatics to receive during the next five years.

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