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RTI International, TeleChem/ArrayIt, CuraGen, Health Discovery, University of California


GDB Back Online at North Carolina’s RTI International

RTI International, a nonprofit research institute in North Carolina, has relaunched the Genome Database (GDB), which stopped accepting submissions in January and has been offline for the past three months.

GDB, a curated human genome resource, was started at Johns Hopkins University in 1990, and moved to the Hospital for Sick Children in Toronto, Canada, in 1998 when the US Department of Energy discontinued funding for the project. A falling-out between GDB principal investigator Jamie Cuticchia and HSC administrators in late 2001 placed the future of the database in jeopardy [BioInform 11-19-01], but according to an RTI statement, RTI and HSC “have worked together to find a long-term home for the GDB.”

Cuticchia is currently director of genomics and bioinformatics at RTI, which will host the database as a free, public resource at RTI will also manage the GDB’s peer-reviewed curation process, which was coordinated by Johns Hopkins when the database was hosted at HSC. RTI said it is also planning to improve the GDB’s software and user interface. Cuticchia told BioInform’s sister publication, Genome Technology, that his goal is to take the resource “into the 21st century.”

TeleChem/ArrayIt Adds Computers to its Repertoire

Microarray provider TeleChem/ArrayIt is adding a new offering to its product line — computers.

Paul Haje, director of business development and marketing for TeleChem/ArrayIt, told BioInform at the recent Chips to Hits conference in Boston that the company just started marketing a computer it calls BioBlue to run third-party gene expression analysis software.

Haje said the company is taking advantage of its location in Silicon Valley to snap up low-priced components and build them into a customized system priced at $2,900. The company will provide annual chip upgrades for $750 per year. The system “performs like a $12,000 computer for one-quarter the price,” Haje said.

BioBlues are shipping now with Intel Pentium IV CPUs, hyperthreading for dual-processor workstation performance, and 2 GB of dual-channel DDR memory.

CuraGen, Academic Partners Release Drosophila Protein Interaction Map

CuraGen, with researchers at Johns Hopkins University, Wayne State University School of Medicine, and Yale University School of Medicine, has published a comprehensive protein interaction map for Drosophila melanogaster.

The results were posted online on ScienceExpress last week, and will appear in the Dec. 5 print edition of Science. The interactions have also been deposited with FlyBase, BIND, and DIP.

CuraGen built the map, which describes 4,679 proteins and 4,780 interactions, using yeast two-hybrid experiments to track more than 20,000 unique interactions involving approximately 7,000 genes. The researchers mathematically modeled interactions between apparently disconnected proteins to reveal both local and global connections among and within various protein complexes.

The company said it has been using the interaction map to select novel targets for drug development and identify biomarkers.

“As the discovery phases of our work have been completed for some time now, we wanted to make this information publicly available to enable other researchers to make use of this valuable information,” said Jonathan Rothberg, CuraGen CEO.

The company retains exclusive access to a similar set of human protein-protein interaction data.

Health Discovery Signs Collaboration with MD Anderson Cancer Center

Health Discovery (formerly Direct Wireless Communications) said it has signed an agreement with the University of Texas, MD Anderson Cancer Center to analyze a gene expression database to identify new biomarkers and pathways involved in leukemia.

Under the terms of the agreement, MD Anderson Cancer Center has granted Health Discovery a first option to commercialize any discovered biomarkers or pathways identified during the collaboration.

UCSC to Offer Bioinformatics Grad Degrees

The University of California has given formal approval to UC Santa Cruz to begin offering graduate degrees in bioinformatics, UCSC said last week.

UCSC’s Baskin School of Engineering, which has offered a BS degree in bioinformatics since 2001, will now has add programs leading to MS and PhD degrees.

There are currently 20 graduate students in computer science who will transfer into the new graduate program in bioinformatics, according to the university.

Filed under

The Scan

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Gene Co-Expression Database for Humans, Model Organisms Gets Update

GeneFriends has been updated to include gene and transcript co-expression networks based on RNA-seq data from 46,475 human and 34,322 mouse samples, a new paper in Nucleic Acids Research says.

New Study Investigates Genomics of Fanconi Anemia Repair Pathway in Cancer

A Rockefeller University team reports in Nature that FA repair deficiency leads to structural variants that can contribute to genomic instability.