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Gene Logic, Admet, Fujitsu


Gene Logic Lays off Database Developers in Rebalancing Act…

In a move to “rebalance” its workforce to better match its evolving strategic plan, Gene Logic last week said it has taken steps to eliminate certain positions and hire new positions.

The company said it eliminated approximately 50 positions, “principally in the areas of database development and production.”

New hires are planned over the coming quarters in the area of contract study services, marketing, and sales.

When Gene Logic acquired TherImmune for its contract services business earlier this year, its staff increased from 272 to around 500 employees.

…As it Embarks on Equine Database Deal

Earlier in the week, Gene Logic said that it had been contracted to build a custom equine gene expression database for Genetraks, an Australian biotech company developing diagnostic technologies for horses and other performance animals.

Financial details of the multiyear service agreement were not disclosed.

Gene Logic will build a database of genomic content from equine samples and related clinical information using custom microarrays provided by Genetraks.

Genetraks plans to use the database in developing diagnostics and performance monitoring technologies for thoroughbred racehorses. The company said that basing its technology on gene expression data, rather than bloodline and heritage trait data, will allow earlier disease diagnosis and monitoring of horses.

Report Forecasts 26 Percent Annual Growth for In Silico ADMET

A new market research report from Kalorama Information pegs the current market for in silico ADMET (absorption, distribution, metabolism, excretion, and toxicity) testing at $650 million worldwide, and predicts a 26 percent annual growth rate for the technology through 2007, when it will reach a total market value of $1.7 billion.

The report breaks down the in silico ADMET market into tools and services. Both segments are expected to grow at approximately the same rate, with tools currently comprising a $280 million market and services comprising a $370 million market. Kalorama expects these segments to grow to $700 million and $990 million, respectively, by 2007.

According to the report, growth for the in silico segment of the ADMET testing segment will outpace the growth of in vitro assays, in vivo approaches, and compound synthesis. The report estimates that in silico ADMET tools and services currently comprise around 24 percent of the total lead optimization market, but will make up 31 percent of the market by 2007.

Fujitsu Develops New Virtual Screening Technique

Fujitsu last week said that it has developed a new computational method of quantum chemical calculations that could reduce the number of animal experiments and other conventional techniques used in lead optimization.

The company will present details of the approach, called the Local Self-Consistent Field (Local SCF) method, at the 31st Symposium on Structure-Activity Relationships in Tokyo Nov. 18-19.

According to Fujitsu, Local SCF uses molecular orbital (MO) methods to calculate which small molecules will bind to a target, and which are based on quantum mechanics rather than the classical mechanics used in traditional computational docking programs.

MO calculations typically require a large amount of computational time, but according to Fujitsu, the new technique is able to overcome this limitation by speeding the process considerably.

Fujitsu said that in a collaboration with Tokai University, they were able to identify how inhibitors bind to HIV-1 protease “within a reasonable computation time” using the new method.

C. Briggsae Sequence Boosts Comparative Worm Genomics

The genome sequence of Caenorhabditis briggsae, the first cousin of the widely studied nematode C. elegans, appears in the Nov. 17 issue of PLoS Biology along with a comprehensive bioinformatics analysis that compares the two genomes.

Lincoln Stein of Cold Spring Harbor Laboratory and an international team of 36 researchers from 14 organizations used the two sequences to identify around 1,300 new C. elegans genes.

Both worms have around 19,500 protein-coding genes, but the C. briggsae genome has more repeated sequences, making its genome slightly larger at just over 100 million base pairs.

Stein and his colleagues used several ab initio gene prediction programs — including GeneFinder, Fgenesh, Twinscan, and the Ensembl annotation pipeline — to predict gene structures, and compared their output in order to find a representative prediction. To find protein-coding genes in C. briggsae, they developed an enhanced procedure that used the “concordance of predictions” between C. elegans and C. briggsae to predict the most likely gene model.

The paper is freely available at

Strand Taps United Bioinformatica For Canadian Distribution

Strand Genomics of Bangalore, India, said it has entered into a distributor agreement with Canadian bioinformatics distributor United Bioinformatica (UBI) for its Acuris gene and protein annotation software.

Acuris is an enterprise-wide software tool that gathers, parses, and presents gene-related public information and curated literature from public and private sources.

UBI will distribute the product in the Canadian market.

FlyBase Expects $20 Million in Continued NIH Funding

The FlyBase model organism database for Drosophila has been notified by the NIH that its request for around $20 million in continued funding has been approved, according to an announcement from Indiana University, Bloomington, which hosts the database.

IUB said it will receive around $3 million of the FlyBase funding, but added that the exact amount of the five-year grant “is not yet known because the budget for the US Department of Health and Human Services has not been approved by Congress and the president.”

CuraGen Fruit Fly Map Doubles BIND Database Content

Data from the protein interaction map for Drosophila melanogaster that CuraGen and its collaborators published in the Nov. 6 ScienceExpress has “in one day very nearly doubled the size of our BIND database,” according to Christopher Hogue, principal investigator of Blueprint North America, which manages the database.

In a statement announcing that BIND (Biomolecular Interaction Network Database) was the first resource to make the data publicly available, on Nov. 11, Hogue said that Blueprint has also produced a “query guide to aid researchers in making the most out of this enormous amount of data.”

The resource now contains 42,938 protein interactions.

Blueprint North America now employs 58 of a projected 74 staff to be hired over the next three years, including 21 of a planned total of 36 curators. Blueprint said it plans to hire and train 80 curators in both Blueprint Asia and Blueprint Europe for a global total of 106 data experts within the next three years.

Filed under

The Scan

International Team Proposes Checklist for Returning Genomic Research Results

Researchers in the European Journal of Human Genetics present a checklist to guide the return of genomic research results to study participants.

Study Presents New Insights Into How Cancer Cells Overcome Telomere Shortening

Researchers report in Nucleic Acids Research that ATRX-deficient cancer cells have increased activity of the alternative lengthening of telomeres pathway.

Researchers Link Telomere Length With Alzheimer's Disease

Within UK Biobank participants, longer leukocyte telomere length is associated with a reduced risk of dementia, according to a new study in PLOS One.

Nucleotide Base Detected on Near-Earth Asteroid

Among other intriguing compounds, researchers find the nucleotide uracil, a component of RNA sequences, in samples collected from the near-Earth asteroid Ryugu, as they report in Nature Communications.