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National Library of Medicine, EPA, Gene Logic, STARLIMS, NextBio, Johnson & Johnson, CDC, DNAStar, NSF’s iPlant Initiative, US Army, GeneGo

NIH to Award $5M Per Year Through 2011 for Bioinformatics Research
The National Library of Medicine plans to grant up to $5 million dollars per year over the next three years to fund a number of research programs that can help advance biomedical informatics, according to a recent program announcement from the National Institutes of Health.
The NIH research project grant, which is a reissue of a 2005 funding program, will support between 12 and 15 programs for up to three years, NIH said.
Informatics issues the NLM is interested in pursuing include integrating information from various sources; new approaches for linking phenomic and genomic information; information retrieval techniques for databases and data mining techniques; modeling and simulation techniques; techniques for visualization and presentation of information; and information analysis and evaluation.
Application areas could include healthcare, public health, basic biological and behavioral research, complex modeling, and clinical translational research.
More information about this funding program can be found here.

EPA to Use Gene Logic's Bioinformatics Tools for ToxCast Program
The US Environmental Protection Agency’s National Center for Computational Toxicology has licensed access to Gene Logic’s bioinformatics platforms, the Ocimum Biosolutions subsidiary said this week.
Gene Logic said that the EPA will use its Genesis Enterprise System, GXR Connect software, and relevant portions of the ToxExpress System and BioExpress System for its work in the EPA's ToxCast program, which is exploring strategies and methods to screen a large number of chemicals for potential toxicity and risk to humans and the environment.
Robert Kavlock, director of the NCCT, said in a statement that the alliance with Gene Logic “will help us move forward with the incorporation of new technologies to improve predictive toxicology.”
The NCCT launched the ToxCast program early last year in an effort to help EPA researchers screen and prioritize large numbers of chemicals for potential risk to human health and the environment.

STARLIMS Signs Undisclosed Pharma for $2.1M LIMS Project
STARLIMS Technologies said this week that it has signed an agreement with “one of the world's leading pharmaceutical companies” for a LIMS development project worth $2.1 million.
The company said it will implement its STARLIMS v10 software in the company's R&D and quality assurance laboratories at eight sites in North America, Europe, and Asia.
Further terms of the agreement were not provided.

J&J To Use NextBio’s Life Sciences Search Engine
NextBio said this week that it has signed a licensing agreement with Johnson & Johnson for the use of its NextBio search engine and collaboration platform.
The company said that researchers at J&J’s Johnson & Johnson Pharmaceutical Research & Development, Tibotec Therapeutics, and Centocor business units will use the software.
Saeid Akhtari, NextBio's president and CEO, said in a statement that the agreement is a “milestone” for the company, which currently counts Stanford University, the University of California, Davis, the Scripps Research Institute, Celgene, and Genzyme among its customers.

CDC Signs Multi-Site Agreement for DNAStar’s Lasergene
The US Centers for Disease Control and Prevention has licensed DNAStar’s sequence analysis software for use at several of its facilities, DNAStar said this week.
The multi-site agreement is an extension of an existing licensing deal with the CDC and allows the CDC’s Coordinating Center for Infectious Disease to use the Lasergene software at its Atlanta base and at its campuses in Colorado, Alaska, and Puerto Rico.
Lasergene includes assembly, visualization, and analysis tools for traditional and next-generation sequencing data.
The CCID includes the National Center for Immunization and Respiratory Disease; the National Center for Zoonotic, Vector Borne and Enteric Disease; the National Center for HIV/AIDS, Viral Hepatitis, STD and TB Prevention; and the National Center for Preparedness, Control and Prevention of Infectious Diseases.
Financial terms of the agreement were not released.

NSF Awards $50M to Five Institutes Under ‘iPlant’ Computational Plant Biology Initiative
The National Science Foundation this week granted $50 million to five institutes to create a national cyberinfrastructure center for plant biology that will employ genomics and genetics sciences, along with various biological and computational sciences.   
The University of Arizona's BIO5 Institute will lead the so-called iPlant Collaborative, and will be joined by researchers at Cold Spring Harbor Laboratory, Arizona State University, the University of North Carolina at Wilmington, and Purdue University.
The program will “bring together researchers from every area within plant biology — molecular and cellular biologists, geneticists, genome scientists, as well as experts on ecosystems and biosystem diversity — by building infrastructure through which they can more readily interact and collaborate,” CSHL said in a statement.
NSF said in a statement that the initiative will rely on information generated through the National Plant Genome Initiative, "enabling more breadth and depth of research in every aspect of plant science."
The research will include interdisciplinary science, “for instance, plant genome experts working side-by-side with mathematicians and statisticians to interpret the results of innovative microarray scans of genomic mutations,” CSHL said.
“The idea is to develop an all-encompassing computer- and internet-based infrastructure that will transform the way plant science is done, and that will be accessible, at different levels, by scientists across the disciplines and across the planet,” Lincoln Stein, CSHL researcher and co-principal investigator of the collaborative, said in a statement.
Through its Dolan DNA Learning Center, CSHL also will work with other researchers to link plant research to education, and will create video and audio podcasts to publicize the iPlant initiative.
The five-year iPlant Collaborative is potentially renewable for a second five years and a total of $100 million, NSF said.

US Army Licenses GeneGo's MetaCore for Toxicity Research
The US Army has extended its license to use GeneGo’s software for biomarker research in its toxicity programs, the company said this week.
The Army’s Center for Environmental Health Research will use the company’s MetaCore software to identify biomarkers for exposure to toxic industrial chemicals and materials.
MetaCore is designed for researchers involved in target selection and validation and identification of biomarkers for diseases and toxicology.
Financial terms of the agreement were not released.

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The Scan

Single-Cell Sequencing Points to Embryo Mosaicism

Mosaicism may affect preimplantation genetic tests for aneuploidy, a single-cell sequencing-based analysis of almost three dozen embryos in PLOS Genetics finds.

Rett Syndrome Mouse Model Study Points to RNA Editing Possibilities

Investigators targeted MECP2 in mutant mouse models of Rett syndrome, showing in PNAS that they could restore its expression and dial down symptoms.

Investigators Find Shared, Distinct Genetic Contributors to Childhood Hodgkin Lymphoma

An association study in JAMA Network Open uncovers risk variants within and beyond the human leukocyte antigen locus.

Transcriptomic, Epigenetic Study Appears to Explain Anti-Viral Effects of TB Vaccine

Researchers report in Science Advances on an interferon signature and long-term shifts in monocyte cell DNA methylation in Bacille Calmette-Guérin-vaccinated infant samples.