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Gene Logic Says Genomics Biz Poised for Growth


Following several acquisitions that added two new business units to its core genomics operations over the last few years, Gene Logic has kept relatively quiet about the database and software products that have historically generated the bulk of its revenues, but company officials stressed recently that the genomics business is not only alive and well, but poised for growth over the course of 2006.

Gene Logic’s genomics business reported its fourth consecutive profitable quarter, posting a 27 percent increase in revenues to $17.5 million from $13.8 million in the fourth quarter of 2004 and an operating profit of $4.7 million compared to a loss of $459,000 in the prior-year period.

The strong performance of the genomics group offset declining revenues in the company’s nonclinical services group and flat performance in its drug repositioning business for both the quarter and the full year.

CEO Mark Gessler says that “2005 was a big step forward for Gene Logic,” with an “outstanding year” for the genomics business, which was “profitable for the first time.”

Earlier this year, the company released an updated version of its BioExpress database and version 3.0 of its Genesis Enterprise System software. Loralyn Mears, vice president of marketing and partner alliances in the genomics group, says the upgrades are the result of a “significant investment” in the company’s core genomics business during 2005.

This year, she says, the company is placing a similar focus on its toxicogenomics business, and product upgrades in that half of the genomics segment are slated for release later in 2006.

The latest upgrades join Ascenta 2.0, a Web-based platform that the company released last October that offers access to a subset of its gene expression data. Mears says all three product updates are in line with Gene Logic’s strategy to become “the outsourcing partner of choice to this industry.”

— Bernadette Toner


US Patent 7,003,403. Quantifying gene relatedness via nonlinear prediction of gene. Inventors: Edward Dougherty, Seungchan Kim, Michael Bittner, and Yidong Chen. Assignees: US Department of Health and Human Services, The Texas A & M University System. Issued: February 21, 2006.

This patent covers constructing nonlinear models to predict gene expression as a way to quantify relatedness between genes. “Effectiveness of the model is evaluated to provide a measurement of the relatedness of genes associated with the model. Various types of models, including full-logic or neural networks, can be constructed,” according to the abstract.

US Patent 6,996,477. Computational subtraction method. Inventor: Matthew Meyerson. Assignee: Dana-Farber Cancer Institute. Issued: February 7, 2006.

This invention “provides a method and system for performing computational subtraction to detect microbes within a host organism,” according to the abstract. In one use, “the system is used to identify sequences belonging to these pathogens which can then be used in methods of diagnosis and treatment.”



Annual funding Microsoft will provide to the Microsoft Institute for High-Performance Computing, which will be part of the Computational Biology Service Unit at Cornell University’s Theory Center. The funding will be renewable each year indefinitely.


Accelrys reported signing multi-year pharma deals worth $29 million for licenses to its software and informatics tools. The company also announced that it received a noncompliance notice from Nasdaq for not filing its quarterly report on time.

Gene Network Sciences opened a new office in Cambridge, Mass., and has moved its Ithaca, NY, headquarters to the Cornell Business and Technology Park. The new office houses eight employees and will serve as the lead site for GNS’s oncology modeling and business development activities.

The National Center for the Multiscale Analysis of Genomic and Cellular Networks at Columbia University is leading an effort to help computational biologists evaluate the performance and accuracy of the community’s algorithms. The initiative was part of the proposal that won the center a five-year, $18.5 million grant through the NIH National Center for Biomedical Computing progam.

IBM and the Scripps Research Institute teamed up with “Project Check-mate.” This program aims to anticipate, manage, and contain infectious disease outbreaks like avian flu. The joint research team, based at Scripps’ Florida research facility, will use IBM’s Blue Gene supercomputer.

GeneGo and Genedata have integrated their computational systems to create a data-analysis workflow to support target identification and validation along with biomarker and diagnostic applications.

The Scan

For Better Odds

Bloomberg reports that a child has been born following polygenic risk score screening as an embryo.

Booster Decision Expected

The New York Times reports the US Food and Drug Administration is expected to authorize a booster dose of the Pfizer-BioNTech SARS-CoV-2 vaccine this week for individuals over 65 or at high risk.

Snipping HIV Out

The Philadelphia Inquirer reports Temple University researchers are to test a gene-editing approach for treating HIV.

PLOS Papers on Cancer Risk Scores, Typhoid Fever in Colombia, Streptococcus Protection

In PLOS this week: application of cancer polygenic risk scores across ancestries, genetic diversity of typhoid fever-causing Salmonella, and more.