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Cornell University, OrphaMed, IDBS, Cambridge Crystallographic Data Center, University of Cambridge, Ingenuity Systems, FDA, Laboratoires Fournier, Temis, SLIM Search, Elan Pharmaceuticals, Ariadne Genomics, Genedata

Evolutionary Comparison Finds New Human Genes
Researchers from Cornell University have used supercomputers to discover some 300 previously unidentified human genes, and found extensions of several hundred genes already known.
Their discovery, which has already appeared in an online version of Genome Research and will appear in its December issue shows there still could be many more genes that have been missed using current biological methods. These methods are very effective at finding genes that are widely expressed but may miss those that are expressed only in certain tissues or at early stages of embryonic development, Siepel said in a statement.
The researchers started with alignments of up to several thousand bases and used large-scale computer clusters, including an 850-node cluster at the Cornell Center for Advanced Computing.
The entire project, from building and testing the mathematical models to running final laboratory tests, took about three years, according to Adam Siepel, assistant professor of biological statistics and computational biology at Cornell, and a co-author of the study.
The work was supported by the National Cancer Institute, a National Science Foundation Early Career Development Grant and a University of California graduate research fellowship.

OrphaMed Adopts IDBS’ Data-Management System
Spanish start-up biotechnology company OrphaMed has licensed IDBS’ ActivityBase suite and E-WorkBook to manage its complete drug-discovery workflow, the companysaid this week.
Initially looking for new drug indications against certain blood cancers, OrphaMed sought a comprehensive data-management solution that could store its research data. For its project, OrphaMed will integrate the ActivityBase XE and E-WorkBook.

Advances Touted in Prediction of Crystal Structures
A 4th blind computational test of crystal structure prediction an exercise conducted by an international group of 15 research groups organized by the Cambridge Crystallographic Data Center and the University of Cambridge has resulted in a breakthrough in predicting crystal structures of small organic molecules.
The ability to make reliable crystal structure predictions could help drug makers because pharmaceutical molecules are prone to crystallize in more than one crystal structure, or polymorph, depending on the conditions under which the molecule is crystallized.
The results of previous blind tests, in 1999, 2001 and 2004, demonstrated that the crystal structures of small organic molecules can occasionally be predicted under favorable conditions, but the rates of success were low and no one method was consistently successful over the range of types of molecules studied.

Ingenuity Systems and FDA Pen $6M PGx Biomarker Collaboration
Ingenuity Systems stands to pocket $6 million as part of a Cooperative Research and Development Agreement with the US Food and Drug Administration to expand the software company’s content and software solutions. Ingenuity said this week.
The alliance could also help the FDA to research and review regulatory filings of biomarker, pharmacogenomic, and toxicogenomic data.
The collaboration relates to the FDA's need to identify biomarkers to monitor drugs for early signs of toxicity, which could help the agency to identify individuals at high risk for serious drug-related side effects..
Ingenuity Systems, a member of the Biomarkers Consortium, recently launched its IPABiomarker solution within IPA, which is designed for diagnostic, drug response, and toxicity biomarker discovery in diseases such as autism, Alzheimer’s disease, diabetes, schizophrenia, Crohn’s disease, and more than a dozen kinds of cancer.

Temis Text Analytics to Support Laboratoires Fournier's Drug Discovery
Laboratoires Fournier, a French affiliate of French drug maker Solvay Pharmaceuticals, has chosen Temis’ Text Analytics software to accelerate its drug-discovery process, the company said this week.
Solvay Pharmaceuticals develops drugs in several areas, such as women’s health and gastroenterology, while Laboratoires Fournier's Exploratory Biology Unit works toward discovering substances that could indicate a biological state and biomarkers.

SLIM Search’s New Academic Pricing Program Cuts 87 Percent Off
SLIM Search has unveiled its academic pricing program, which shaves 87 percent off the commercial cost of the SLIM Search solution, which will now cost $199 for a single academic annual license.
SLIM Search is designed to improve the efficiency of indexing a subject into memory, and scanning for web hits, the company said (see related story on Accelrys’ academic pricing program, here).

Elan Pharma Licenses Ariadne Software
Elan Pharmaceuticals has licensed Ariadne Genomics’ Pathway Studio software to support its therapeutics research for neurological and autoimmune diseases, Ariadne said this week.
The Pathway Studio includes the ResNet database of functional relationships, which is used to interpret microarray data and to study signaling networks, and MedScan, which extracts pathway-related information from research literature.
Financial terms of the agreement were not released.

FDA Will Use Genedata’s Expressionist Software in VGDS Program
The US Food and Drug Administration’s National Center for Toxicological Research will use Genedata’s biomarker-discovery software, the company said this week.
The NCTR’s Center for Toxicoinformatics will use the Expressionist software to support the “vast quantities and varied sources of microarray data” reviewed as part of its voluntary genomics data submission program.
The software is used to research biomarkers involving transcriptomics, proteomics, and metabolomics data, Genedata said.

Filed under

The Scan

Study Points to Tuberculosis Protection by Gaucher Disease Mutation

A mutation linked to Gaucher disease in the Ashkenazi Jewish population appears to boost Mycobacterium tuberculosis resistance in a zebrafish model of the lysosomal storage condition, a new PNAS study finds.

SpliceVault Portal Provides Look at RNA Splicing Changes Linked to Genetic Variants

The portal, described in Nature Genetics, houses variant-related messenger RNA splicing insights drawn from RNA sequencing data in nearly 335,700 samples — a set known as the 300K-RNA resource.

Automated Sequencing Pipeline Appears to Allow Rapid SARS-CoV-2 Lineage Detection in Nevada Study

Researchers in the Journal of Molecular Diagnostics describe and assess a Clear Labs Dx automated workflow, sequencing, and bioinformatic analysis method for quickly identifying SARS-CoV-2 lineages.

UK Team Presents Genetic, Epigenetic Sequencing Method

Using enzymatic DNA preparation steps, researchers in Nature Biotechnology develop a strategy for sequencing DNA, along with 5-methylcytosine and 5-hydroxymethylcytosine, on existing sequencers.