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Bioinformatics Briefs: Feb 24, 2002


I3C Incorporates; Membership Requirements under Discussion


At last week’s BioSilico 2002 conference in New York, Sia Zadeh of Sun Microsystems and Jeff Augen of IBM, founding members of the Interoperable Informatics Infrastructure Consortium, said that the group had recently incorporated as a non-profit organization.

Incorporation is a big step for the group, which had its beginnings over a year ago and demonstrated its first workable protocol at the BIO 2001 conference in June. Further actions have been in limbo, however, as prospective members awaited the I3C’s crystallization as a formal organization, complete with by-laws, membership requirements, and a dues structure.

While the specifics of membership are still under discussion, said Augen, hope are high that the pieces will fall into place quickly and “things will look very different a year from now.”


NSF Plants Seed for ‘Tree of Life’


The National Science Foundation has put aside $10 million in funding for 2002 for a phylogeny-based program called, “Assembling the Tree of Life.”

Designed to attract researchers from the fields of biology, computer science, geosciences, and social sciences, the multidisciplinary program will award between three and six five-year awards in 2002 at around $3 million each.

The NSF is seeking proposals for research that “will resolve phylogenetic relationships for large groups of organisms on the Tree of Life,” according to the program statement. The program will support projects in data acquisition, analysis, algorithm development, and dissemination in computational phylogenetics and phyloinformatics.

Additional information about the program is available at:


Accenture Teams with Tripos to Build ‘Scientific Workbench’


Consulting giant Accenture said it is joining forces with cheminformatics firm Tripos to build a comprehensive data integration and knowledge management platform based on Tripos’ MetaLayer middleware technology.

The alliance will result in what the companies have termed a “scientific workbench” for pharmaceutical and biotech companies to share data, knowledge, and decision-making ability across the global enterprise.

At a press conference announcing the alliance at the BIO CEO and Investors Conference last week in New York, Accenture partner Pradip Banerjee said that the company’s research shows that the large number of targets generated by genomic technologies have created a bottleneck in the lead generation and optimization stage of the drug discovery pipeline. The Accenture/Tripos platform will enable companies to increase the number of new molecular entities by 50 percent in order to meet 10-year growth projections, he said.


Gene Logic Licenses Oncology DataSuite to Morphochem


Gene Logic said last week that Morphochem of Munich, Germany, has subscribed to parts of its GeneExpress database.

Morphochem researchers will have access to the GeneExpress Oncology DataSuite as well as Gene Logic’s Reports, which offer a body-wide assessment of targeted genes.

Terms of the non-exclusive, multi-year agreement also call for Gene Logic to generate data from samples provided by Morphochem and then provide these additional data to Morphochem.

Financial terms of the agreement were not disclosed.


BioSeek Raises $8.4M in Series A Round


Burlingame, Calif.-based systems biology startup BioSeek said last week that it has raised $8.4 million in its first round of venture financing from Bay City Capital, Fremont Ventures, SImile Investors LLC, and Vanguard Ventures.

BioSeek was founded in 1999 by Rolf Ehrhardt and Ellen Berg, former senior scientists at Protein Design Laboratories, and Eugene Butcher, a professor in the department of pathology at Stanford University. The company has developed a systems biology/informatics platform to characterize and prioritize drugs and genes. Initial focus areas include inflammation, cardiovascular disease, and oncology.

“The successful completion of this initial financing is an important milestone for BioSeek,” said Ehrhardt in a statement. “Not only does it provide the resources for us to aggressively develop and exploit our platforms for functional genomics and drug discovery, it also represents a significant external validation of our technology by a very strong group of investors.”


AlgoNomics Wins 1M Government Award


Ghent, Belgium-based structural bioinformatics firm AlgoNomics said it has been awarded €1 million (US $875,000) by the Flemish Institute for Science and Technology for a two-year period.

AlgoNomics said the grant would help develop its structural bioinformatics platform, “including further improvements of its target validation and protein analysis technology,” as it applies to HIV research.

Founded in 1999, AlgoNomics raised €1.8 million in a second round of private financing last June, which brought its total capital at the time to over €3 million.


Beyond Genomics Inks Deal with DiaDexus


Waltham, Mass.-based Beyond Genomics said it has entered into an agreement with diaDexus. The companies will jointly apply Beyond Genomics’ systems biology technology to diaDexus’ cancer diagnostic and drug discovery research in order to identify new biomarkers and drug targets useful for the diagnosis and treatment of colon, breast, and ovarian cancer.

Under the terms of the agreement, diaDexus also made an equity investment of an undisclosed amount in Beyond Genomics. In addition to the equity investment and research funding for the program, diaDexus will provide milestone and royalty payments on products resulting from the research.

Under the partnership, Beyond Genomics will use its proteomic technologies as well as its “BioSystematics” suite of proprietary pattern recognition, clustering, and data-mining software and to analyze normal and cancerous samples.


[email protected] Joins Family of Distributed Bioinformatics Projects


A new screensaver-based distributed computing project from the Center for Molecular and Biomolecular Informatics in The Netherlands was recently described in the journal Bioinformatics [18(2):315-318]. The project, [email protected], runs the molecular modeling programs WHAT IF and YASARA (Yet Another Scientific Artificial Reality Application), developed at the University of Graz, Austria, and the CMBI, respectively.

The [email protected] screensaver is is freely available including source code and detailed instructions from

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The Scan

Genetic Tests Lead to Potential Prognostic Variants in Dutch Children With Dilated Cardiomyopathy

Researchers in Circulation: Genomic and Precision Medicine found that the presence of pathogenic or likely pathogenic variants was linked to increased risk of death and poorer outcomes in children with pediatric dilated cardiomyopathy.

Fragile X Syndrome Mutations Found With Comprehensive Testing Method

Researchers in Clinical Chemistry found fragile X syndrome expansions and other FMR1 mutations with ties to the intellectual disability condition using a long-range PCR and long-read sequencing approach.

Team Presents Strategy for Speedy Species Detection in Metagenomic Sequence Data

A computational approach presented in PLOS Computational Biology produced fewer false-positive species identifications in simulated and authentic metagenomic sequences.

Genetic Risk Factors for Hypertension Can Help Identify Those at Risk for Cardiovascular Disease

Genetically predicted high blood pressure risk is also associated with increased cardiovascular disease risk, a new JAMA Cardiology study says.