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Bioinformatics Briefs: Jan 28, 2002




Celera Genomics reported second-quarter 2002 revenues of $35 million last week, up from $20.3 million for the same quarter in fiscal 2001. The company attributed the bulk of the revenue increase to new subscription agreements with commercial and academic customers. Celera said it now has a total of 19 commercial customers and 180 academic and institutional subscribers to the Celera Discovery System.


Collaborations and Deals


InforMax and TissueInformatics have entered a three-year toxicology collaboration to integrate quantitative tissue data with genomic data.

TissueInformatics, based in Pittsburgh, has developed tools for collecting and analyzing tissue data. Under the terms of the agreement, the companies will merge quantitative histomorphometric data derived from digital tissue images with gene expression and protein function data to understand the molecular toxicological effects of pharmaceutically relevant compounds. InforMax of Bethesda, Md., will also collaborate with TissueInformatics on the development and validation of software tools to integrate and analyze tissue and genomic data. The companies plan to jointly market these tools and will establish a services partnership in investigative toxicology.

“Toxicology was chosen as the first application area in part because it is an extremely attractive market for products and services,” said Steve Lincoln, executive VP and CSO at InforMax. According to the Pharmaceutical Research and Manufacturers of America’s 2001 annual survey, toxicology and safety testing made up approximately $1.4 billion, or 4.5 percent, of all pharmaceutical R&D spending in 2001.

Additionally, TissueInformatics will acquire a license to InforMax’s GenoMax enterprise solution and Xpression NTI desktop software while InforMax will gain access to TissueInformatics’ analysis tools.

InforMax also invested $1.5 million in a $12.5 million stock financing round for TissueInformatics that closed last week. This investment gives InforMax approximately five percent of TissueInformatics’ stock, observation rights on the company’s board of directors, and participation on its scientific advisory board.


IBM and MatrixOne said last week that they intend to target the life science industry with so-called “collaborative product commerce solutions” developed under a strategic alliance.

MatrixOne, of Westford, Mass., is teaming up with IBM to develop its eMatrix collaboration platform on IBM hardware, software, and middleware.




The North Carolina Supercomputing Center has been named the official US mirror site for the ExPASy (Expert Protein Analysis System) proteomics server of the Swiss Institute of Bioinformatics.

NCSC is a division of the nonprofit corporation MCNC, which provides electronic and information technologies to support education and industry in North Carolina. MCNC is operating the mirror site ( on a dedicated Sun server on behalf of the North Carolina Genomics and Bioinformatics Consortium, which was established in December 2000 by the NC Biotechnology Center to stimulate genomics, bioinformatics, and proteomics efforts in the state.

“By establishing a mirror site in North Carolina, our researchers and educators will enjoy improved access to ExPASy’s resources because of the outstanding networking services provided by the North Carolina Research and Education Network to higher-education’s faculty and students. We will also serve higher education throughout the US using NCREN’s high-speed Internet2 connection,” said Thom Dunning, vice president for high-performance computing and communications at MCNC.

NCSC joins current ExPASy mirror sites in Switzerland, Australia, Canada, China, Korea, and Taiwan.




Lion Biosciences’ SRS will serve as the backbone for a web portal that Derwent Information has commissioned for its Geneseq and Geneseq Fastalert patent information databases, the companies said last week.

Lion, of Heidelberg, Germany, will build a customized sequence-based portal for Derwent’s databases, which contain annotated genetic sequences from worldwide patents.

“This initiative is aimed to address the needs of the research bioinformaticians and biotechnologists engaged in sequence-based drug discovery research and development within the pharmaceutical and biotechnology industries. It will have particular relevance for small to medium sized organizations who do not have the resources to develop powerful bioinformatic information systems internally,” said Shirley Bailey-Wood, director of chemistry and life sciences at London-based Derwent.

Lion has also built portals based on SRS for Celera Genomics and Affymetrix.


The Wisconsin Alumni Research Foundation was awarded US Patent 6,340,567, “Genomics via optical mapping with ordered restriction maps,” last week.

David Schwartz, Bhubaneswar Mishra, and Thomas Anantharaman are named as inventors on the patent, which describes a method of producing restriction maps based on data created from the images of individual DNA clones digested by restriction enzymes. The method relies on detailed modeling, a statistical algorithm, an interactive algorithm based on dynamic programming, and a heuristic method to find the most likely restriction map based on the experimental data.


US Patent 6,341,256, “Consensus configurational bias Monte Carlo method and system for pharmacophore structure determination,” was awarded to Michael Deem, Jonathan Rothberg, and Gregory Went of CuraGen last week.

The patent covers a combination of computational modeling and simulation, experimental distance constraints, and molecular biology to determine a consensus pharmacophore structure shared by compounds that bind selectively to a target molecule.

A computer-implemented modeling and simulation method described in the patent determines a consensus structure for the pharmacophore and a structure for the remainder of the molecule from diversity library members that bind to the protein target of interest. “Where prior structure determination methods focused on the structure of the target molecule or of the target, the method of this invention is uniquely adapted to focus instead on the structures of molecules that bind to the target,” according to the patent.




The Virginia Bioinformatics Institute and the Johns Hopkins University Bloomberg School of Public Health have entered a $10 million bioinformatics research collaboration to target human infectious diseases.

Each university will invest a minimum of $1 million per year for five years to better understand tuberculosis, AIDS, malaria, measles, and other illnesses. VBI and JHU will also pursue outside funding for this effort.

The universities intend to discern how infectious pathogens spread, how pathogen genomes change over time because of various environmental factors, and how humans respond to pathogens on the molecular, cellular, and organismal level.

“With this partnership, we will be able to compare gene regulation across different organisms and evaluate human immune responses to numerous pathogens simultaneously,” said Bruno Sobral, director of the VBI, in a statement. The VBI will compile this data into an integrated pathogen database, he added.

VBI will also develop bioinformatics tools to compare multiple human responses to different pathogens.

The project will begin in February. During its first phase, the universities will study how disease parasites resuscitate from dormancy, model cellular responses to viruses, collect data from malaria outbreak sites, and develop gene chips to assess virulence factors of pathogens. The second phase will involve computational analysis to understand mechanisms of disease resistance and the development of new tools for prevention, diagnosis, and cure.

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The Scan

Genome Sequences Reveal Range Mutations in Induced Pluripotent Stem Cells

Researchers in Nature Genetics detect somatic mutation variation across iPSCs generated from blood or skin fibroblast cell sources, along with selection for BCOR gene mutations.

Researchers Reprogram Plant Roots With Synthetic Genetic Circuit Strategy

Root gene expression was altered with the help of genetic circuits built around a series of synthetic transcriptional regulators in the Nicotiana benthamiana plant in a Science paper.

Infectious Disease Tracking Study Compares Genome Sequencing Approaches

Researchers in BMC Genomics see advantages for capture-based Illumina sequencing and amplicon-based sequencing on the Nanopore instrument, depending on the situation or samples available.

LINE-1 Linked to Premature Aging Conditions

Researchers report in Science Translational Medicine that the accumulation of LINE-1 RNA contributes to premature aging conditions and that symptoms can be improved by targeting them.