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Bioinformatics Briefs: Jan 23, 2009


Wellcome Trust Centre Using GenoLogics' Data Management Tools

The UK's Wellcome Trust will use GenoLogics' lab and data management solution in its next-generation sequencing and disease research programs, the company said.

The Wellcome Trust Centre for Human Genetics will use the company's Geneus platform in its studies seeking the genetic basis of multi-factorial diseases such as diabetes, heart disease, multiple sclerosis, hypertension, and psychiatric disorders.

WTCHG chose the software "because of its flexibility to automate data capture from a wide range of genomics instruments and applications, while allowing us to more efficiently track samples and QC results across numerous projects," WTCHG Head of Genomics Ioannis Ragoussis said in a statement.

Ragoussis also said that the "primary consideration" in using the Geneus platform was its capability to "fully integrate our next-generation sequencing instruments from Illumina and Roche, and automatically pipeline data for downstream analysis."

The Genomics Group also provides services for other University of Oxford groups in areas of interest such as microarray, high-throughput quantitative gene expression, high-throughput genotyping, and other specialties.

Protelica Wins $500K NSF Bioinformatics Grant

The National Science Foundation has given Protelica a $500,000 grant to continue developing its DNA mutagenesis technologies in a bioinformatics-based project aimed at developing protein therapies, the company said.

Protelica will use the two-year, Phase II Small Business Innovation Research funding to develop "a bioinformatics-based understanding of nature’s evolutionary rules, [that] utilizes Protelica's proprietary DNA mutagenesis technologies to develop small, specific and potent protein blockers," the company said.

This grant is part of a project that began two years ago called "Bioinformatics knowledge-based, universal library design for a non-immunoglobulin, protein-scaffold," according to the Hayward, Calif.-based company.

Pacific Northwest National Laboratory Becomes a GeneGo Center of Excellence

GeneGo said this week that the Department of Energy's Pacific Northwest National Laboratory has become a certified GeneGo Center of Excellence, which gives PNNL researchers institution-wide access to GeneGo's MetaCore data analysis suite, training and advanced support.

According to the company, MetaCore will be used throughout many research programs both as a central data repository, management, and collaboration platform for omics data analysis and as an integrative pathway analysis suite.

NCRR Gives USC $22.2M for National Bioinformatics Center

The University of Southern California has landed a $22.2 million grant from the National Institutes of Health to become a central coordinating point for a national bioinformatics and biomedical data collection and integration project, according to NIH's Biomedical Informatics Research Network.

The National Center for Research Resources funding, which will span five years, will support the establishment of the Biomedical Informatics Research Network Coordinating Center at USC, which the university said will make it "a central clearing house" for information from the BIRN.

BIRN, was launched in 2001, to foster large-scale collaborations in biomedical science by using new information technologies, and it aims to implement and distribute shared resources that will be usable to all biomedical researchers involved in disease diagnosis and treatment studies.

The need for a center for biomedical data springs from the "overwhelming quantity of data that geneticists and others produce," which can keep medical researchers from connecting with new discoveries and therapies.

The center will be led by USC Professor Carl Kesselman at the Viterbi School of Engineering Epstein Department of Industrial and Systems Engineering and the USC Information Sciences Institute. "Without a sophisticated bioinformatics capability — which only top engineers can provide — we cannot hope to translate the basic science into drugs and treatments that will improve the quality of life," Kesselman said in a statement.

He also said that the BIRNCC program "can accelerate the rate of discoveries for many areas of biomedical research."

The BIRN program has data centers at universities across the country that are involved in data collection, storage and management, quality assurance and analysis, and data sharing, integration, and discovery.

Utrecht University Using GeneBio's Proteomics Software

Geneva Bioinformatics said this week that Utrecht University will use its proteomics software in its high-throughput data analysis development program.

Utrecht will use the Phenyx software at its Biomolecular Mass Spectrometry and Proteomics group with the Lys-N workflow, which is a proteomics analysis tool that is focused on post-translational modifications and de novo sequencing.

Phenyx is used to identify, quantify, and characterize proteins and peptides from mass spectrometry data.

Financial terms of the agreement were not released.

Filed under

The Scan

Genome Sequences Reveal Range Mutations in Induced Pluripotent Stem Cells

Researchers in Nature Genetics detect somatic mutation variation across iPSCs generated from blood or skin fibroblast cell sources, along with selection for BCOR gene mutations.

Researchers Reprogram Plant Roots With Synthetic Genetic Circuit Strategy

Root gene expression was altered with the help of genetic circuits built around a series of synthetic transcriptional regulators in the Nicotiana benthamiana plant in a Science paper.

Infectious Disease Tracking Study Compares Genome Sequencing Approaches

Researchers in BMC Genomics see advantages for capture-based Illumina sequencing and amplicon-based sequencing on the Nanopore instrument, depending on the situation or samples available.

LINE-1 Linked to Premature Aging Conditions

Researchers report in Science Translational Medicine that the accumulation of LINE-1 RNA contributes to premature aging conditions and that symptoms can be improved by targeting them.