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Genedata, Roche, CLC Bio, IDBS, UCB, Spotfire, Definiens, Cenix, UVP, Nonlinear Dynamics, GeneGo, Transinsight

Roche R&D Group To Use Genedata’s Refiner MS Module
Genedata said this week that Roche Molecular Medicine Laboratories in Basel, Switzerland, will integrate its Expressionist Refiner MS module within its proteomics analysis pipeline.
Refiner MS automatically assesses and pre-processes mass spectrometry-based proteomics and metabolomics data.
Genedata CEO Othmar Pfannes told BioInform that the agreement builds on a collaboration that the companies began several years ago to validate the throughput of Refiner MS.
He said that the software is designed to handle MS data from clinical studies involving several thousand patients, and that Roche is one of several customers that validated the software in smaller studies involving 30 to 40 patients.
Pfannes said that pre-processing of MS data is particularly important for large-scale proteomics and metabolomics studies because the mis-identification of just a single peak “could lead to a lot of wrong comparisons.”
He said that a number of Genedata’s customers are moving toward using mass spec in large-scale clinical studies, and noted that “It looks like this is going to be a major success for us over the next six months or so.”

CLC Bio Partners with South Africa’s Inqaba on TB Sequencing Study
CLC Bio said this week that it is partnering with Inqaba Biotechnical Industries, a genomic services firm based in Pretoria, South Africa, to sequence, assemble, and analyze data from multiple strains of Mycobacterium tuberculosis.
Inqaba will use 454 Life Sciences’ Genome Sequencer FLX to sequence drug-resistant strains of M. tuberculosis and CLC Bio will analyze the data with a new platform it is developing called CLC Genomics Workbench, which is aimed at next-generation sequencing and whole-genome assembly.
Oliver Preisig, executive director at Inqaba, said that the company plans to identify specific markers that it will include in a PCR diagnostic.
The sequencing project is funded by BioPAD, a biotechnology investment trust funded by the Department of Science and Technology of South Africa. Other partners in the project include the Chris Hani Baragwanath business unit of South Africa’s National Health Laboratory Services and the Respiratory and Meningeal Pathogens Research Unit at the University of Witwatersrand.
CLC Bio said it will release CLC Genomics Workbench in May.

UCB Using IDBS BioBook for DMPK, Pharmacology Studies
IDBS said this week that UCB has licensed its BioBook electronic lab notebook for drug metabolism, pharmacokinetics, and pharmacology projects.
Hector Sanchez, senior director of R&D informatics at UCB, said that the company was already using IDBS’ ActivityBase to store its screening data.
“However, for DMPK and pharmacology we required a solution that would capture both structured and unstructured data, which is why we selected BioBook for these disciplines,” he said. 
Financial terms of the agreement were not provided.

Cenix Licenses Spotfire’s DXP, Definiens Cellenger for RNAi Research
Spotfire, a division of Tibco Software, said this week that Cenix BioScience has licensed the Spotfire DXP 2.0 analysis platform to support its RNA interference research services offering.
Separately, Definiens said that it has expanded an existing licensing agreement with Cenix for its Cellenger image analysis software.
Cenix is using both packages to help it predict the cellular functions of genes and the future therapeutic potential of drug candidates.
Maria Mirotsou, group leader at Cenix, said in a statement that the Spotfire DXP software allows the firm to offer “faster and more accurate results because our scientists have the ability to mine these complex datasets much faster and in more depth, ask and answer questions on demand, pull information from multiple data sources, and integrate new information as it becomes available.”
Cenix will use Cellenger to develop and implement high-content microscopy assays for RNAi studies in cultured human and rodent cells.
Financial terms of the agreements were not provided.

UVP to Market Nonlinear’s SameSpots Software with Imaging System
UVP will market Nonlinear Dynamics’ 2D gel analysis software alongside its own imaging system through its worldwide sales and distribution force, Nonlinear said this week.
Under the agreement, UVP will promote Nonlinear’s SameSpots analysis software in tandem with its BioSpectrum 800 imaging system, which Nonlinear said is cheaper than “slower 2D laser scanner systems.”
UVP CEO Leighton Smith called the combined offerings “a fast yet affordable option” for proteomics researchers.

Netherlands Toxicogenomics Center To Use GeneGo Software for Predictive Tox Project
GeneGo said this week that it will collaborate with the Netherlands Toxicogenomics Center on a five-year, €25 million ($37 million) project to develop predictive screens for chemical risk assessment.
The NTC will use GeneGo's MetaCore and MetaDrug data analysis platform to analyze chemical, metabolomic, proteomic, and gene expression data generated by the project members, and to identify biological functions and pathways contributing to the adverse effects of xenobiotic exposure.
GeneGo said it will also work with the NTC’s bioinformatics group to use its Functional Descriptor technology to predict adverse effects in animals from short-term in vivo experiments, or from in vitro experiments.

Unilever Taps Transinsight To Customize GoPubMed
Tansinsight said this week that it has signed an agreement with Unilever to develop a customized version of the open source GoPubMed search engine that incorporates semantic text-mining technology.
The agreement builds on an existing collaboration between the firms to develop a corporate semantic search platform.
Wendy Filsell, a senior informaticist in the Unilever Information Group, said in a statement that Unilever has been using GoPubMed for two years so far, and that it “fits the needs of most users searching biomedical literature from the Medline database.” However, she noted, the company believes that the resource “can lead to a lot more insight and time saving if users get the chance to customize the underlying knowledge base so that the system can be used to search the Internet as well as our in-house data.”
Transinsight said that its search technology is able to “intelligently match” large amounts of textual material to classification networks like the Gene Ontology, MeSH, or customer-tailored ontologies.
Both Unilever and Transinsight plan to add some capabilities developed under the collaboration to the free version of GoPubMed.

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The Scan

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.

Study Reveals Potential Sex-Specific Role for Noncoding RNA in Depression

A long, noncoding RNA called FEDORA appears to be a sex-specific regulator of major depressive disorder, affecting more women, researchers report in Science Advances.

New mRNA Vaccines Offer Hope for Fighting Malaria

A George Washington University-led team has developed mRNA vaccines for malaria that appear to provide protection in mice, as they report in NPJ Vaccines.

Unique Germline Variants Found Among Black Prostate Cancer Patients

Through an exome sequencing study appearing in JCO Precision Oncology, researchers have found unique pathogenic or likely pathogenic variants within a cohort of Black prostate cancer patients.