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Bioinformatics Briefs: Dec 5, 2008

Two UK Institutes to Use InforSense Software for Alzheimer’s Disease Project
InforSense said this week that two UK research institutes will use its translational research software tools in Alzheimer's disease studies.
Informaticians, researchers, and clinicians at the National Institute for Health Research Biomedical Research Centre for Mental Health at the South London and Maudsley National Health Service Foundation Trust and the Institute of Psychiatry at King's College London will be able to access patient and omics data through a common data analysis platform.
"This will result in improved data sharing and removal of access bottlenecks, speeding up the speed and accuracy of novel biomarker identification," Simon Lovestone, professor of Old Age Psychiatry at King's College London and director of the Biomedical Research Centre for Mental Health, said in a statement.
The InforSense Translational Research solution includes the analytic modules ClinicalSense, GenSense, and BioSense. It will be used to integrate and analyze patient, genotyping, transcriptomics, proteomics, and MRI data to support the identification of biomarkers. Researchers will also be able to access and analyze data using the VisualSense interactive web portal, which generates interactive reports and visualizes data. 

GNS Creates Spin-off Focused on Quantitative Finance and E-Commerce
Gene Network Sciences said last week that it has launched a spin-off company called Fina Technologies, which will use its proprietary Reverse Engineering, Forward Simulation, or REFS, software platform for e-commerce and quantitative financing.
REFS was developed to rapidly process raw clinical and genomics data to identify drug targets, biomarkers, and drug and disease mechanisms for disease categories such as cancer, diabetes, and inflammation.
GNS said it launched Fina to “monetize” its REFS technology in the e-commerce and financial trading markets, while remaining focused on its original drug development mission.
Fina Technologies has obtained from GNS an exclusive license to “certain non-biological applications” of the technology, such as quantitative finance, e-commerce, insurance, and fraud detection.
"Fina will use REFS to create quantitative trading algorithms and deliver business solutions for a new class of data intensive problems," said Josh Holden, CEO of Fina.
"After spending 13 years trading on Wall Street, this is the first tool I've seen that automates the discovery of complex and evolving relationships from massive amounts of data, leading to more reliable and more profitable trading strategies," Holden said.
Fina Technologies has raised an undisclosed amount of funding in a round led by Reed Elsevier Ventures, and through its board of directors which includes Colin Hill, co-founder and president and CEO of GNS; Bill Trenchard, founder of online calendaring company Jump Networks, which was sold to Microsoft for $50 million in 1999. Other Fina board members include Kevin Brown, Partner at Reed Elsevier Ventures, and Robert Maroney, investment manager at Connecticut Investments.

University of Alabama at Birmingham Using Genedata Software for Biomarker Discovery
Genedata said this week that the Comprehensive Cancer Center Proteomics Facility of the University of Alabama at Birmingham is using its Expressionist system to identify protein biomarkers for human diseases using animal models.
No financial details were disclosed. 
According to the company, UAB will use Expressionist for analyzing data related to pancreatic cancer, prostate cancer, and cystic fibrosis.
The researchers will use Refiner MS and Analyst modules for pre-processing and statistical analyses on LC-MS spectra. 
The UAB researchers have created matched peak lists across samples and then performed uni- and multivariate statistical analyses to identify peaks differentiating normal and disease states. Statistical analysis led the researchers to identify the peptides found in the differentiating peaks. According to the company, by doing the peak processing and analyses up front and using raw MS data, researchers were able to identify biomarker peptides that they would have otherwise missed had they only captured secondary MS traces running instruments in a more typical data-dependent mode.
“Using Expressionist in a systems biology approach advanced our research in two fundamental ways,” James Mobley, director of the Comprehensive Cancer Center Proteomics Facility, said in a statement. “First, because of the reproducibility inherent in the system, we were able to identify key biomarkers with a relatively small cohort. Second, the reproducibility of this approach also increased the confidence in our resulting protein biomarker hits and enabled us to identify key associated pathways that were otherwise difficult to discern.”

Burnham Institute for Medical Research Licenses GeneGo Software 
GeneGo said this week that the Burnham Institute for Medical Research has become a certified GeneGo Center of Excellence.
GeneGo said that Burnham researchers will have institution-wide access to its MetaCore data analysis suite, training, and advanced support.
The Burnham Institute performs research in many areas including cancer, stem cells, and neurobiology. It has research locations in La Jolla and Santa Barbara, Calif., and Orlando, Fla. 
MetaCore will provide a central data repository, management and collaboration platform integrated with a manually curated knowledge base and tools for analyses of these studies.
"Burnham is in our backyard and we are very pleased to welcome them as a new GeneGo customer and Center of Excellence," said Julie Bryant, GeneGo's VP of business development. "Stem cells, chemical biology, and disease specific pathway analysis platforms are among our research priorities and we are looking forward to a long term productive partnership."

Biomatters Partners with U of Queensland on Metagenomic Sequencing Software
The University of Queensland will work with the New Zealand software company Biomatters to develop metagenomic sequencing data analysis software, Biomatters said this week.
Biomatters said it will work with the university on research funded by the Australian Research Council to further develop the company’s Geneious software.
The multi-year partnership will aim to “further develop special tools within Geneious that will give biologists the power to use next-generation sequence data for significantly furthering biomedical, agricultural, and environmental research,” Biomatters CEO Candace Toner said in a statement.
The company said the collaboration will develop algorithms for bacterial metagenomics, and the university will use sequencing hardware from Applied Biosystems and Illumina.
“The lack of adequate visualization tools for biological research is a major impediment to progress for researchers interested in analyzing the vast data output from the new sequencing technologies now available,” University of Queensland Professor David Edwards said.

Definiens, Bioscan to Co-Market Imaging Instruments, Software
Definiens and Bioscan have signed an agreement to co-market Bioscan’s instruments for noninvasive in vivo animal imaging with Definiens’ image analysis software, the companies said.
Bioscan, based in Morristown, NJ, and Definiens, based in Munich, Germany, said they have agreed to “conduct cooperative marketing activities and host joint workshops and events” that will offer customers integrated training and implementation programs.
The firms said they will “continue to explore further opportunities for cooperation,” which could include the co-development of user interfaces to incorporate Definiens’ software into Bioscan’s hardware.
Existing Bioscan customers will also receive “introductory offers” for Definiens applications, the partners said.
Bioscan offers the NanoSPECT/CT and NanoPET/CT in vivo animal imaging systems, which analyze molecular function at the nanoliter scale.
Definiens’ Cognition Network Technology software is used for analyzing image data from a range of platforms, including cell and tissue-based assays and in vivo imaging systems.

Symyx Technologies To Lay Off 15 Percent of Staff in Restructuring
Symyx said this week that it is restructuring its business operations to “drive performance, improve operating efficiency, and increase positive cash flow in 2009.”
As part of the restructuring, Symyx is laying off around 15 percent of its workforce, primarily concentrated within Symyx's Tools and Research operations and in the company's general and administrative areas.
According to SEC filings, the company had 585 employees as of April 17.
Symyx Tools and Symyx Research will be merged to create Symyx High Productivity Research. Richard Boehner, president of Symyx Research, will serve as president of HPR. 
Sales forces within Symyx Software and Symyx HPR will be set up in 2009 to “improve market focus and sales execution.”
The company said the restructuring should help reduce 2009 expenses by an estimated $15 million compared to fiscal 2008, excluding restructuring charges.
Symyx expects to substantially complete the restructuring by Dec. 31, 2008.

Filed under

The Scan

Expanded Genetic Testing Uncovers Hereditary Cancer Risk in Significant Subset of Cancer Patients

In Genome Medicine, researchers found pathogenic or likely pathogenic hereditary cancer risk variants in close to 17 percent of the 17,523 patients profiled with expanded germline genetic testing.

Mitochondrial Replacement Therapy Embryos Appear Largely Normal in Single-Cell 'Omics Analyses

Embryos produced with spindle transfer-based mitochondrial replacement had delayed demethylation, but typical aneuploidy and transcriptome features in a PLOS Biology study.

Cancer Patients Report Quality of Life Benefits for Immune Checkpoint Inhibitors

Immune checkpoint inhibitor immunotherapy was linked in JAMA Network Open to enhanced quality of life compared to other treatment types in cancer patients.

Researchers Compare WGS, Exome Sequencing-Based Mendelian Disease Diagnosis

Investigators find a diagnostic edge for whole-genome sequencing, while highlighting the cost advantages and improving diagnostic rate of exome sequencing in EJHG.