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Briefs - Sept. 11, 2008

Optimata Wins Patent for Angiogenesis Modeling
Optimata received a U.S. Patent -“Treatment protocol generation for diseases related to angiogenesis” – which the company says “protects a system and methods for modeling diseases which relate to angiogenesis processes, and optimization methods to predict improved treatment regimens.”

There are a large number of antiangiogenic drugs in clinical trials (683 open interventional studies, according to NIH)). Optimata’s patent-protected technology, which comprises a computerized biosimulation system for optimizing drug therapies, is expected to benefit such studies. The patent protects technology that simulates the angiogenesis process and the way it is affected by diverse drugs.

“This patent reinforces Optimata's leadership position in the field of predictive oncology. By using Optimata’s Virtual Patient Engine drug developers will obtain early indications about the angiogenic effects of drugs in development,” said Zvia Agur, founder and CSO of Optimata, in a release. The company says the use of its Virtual Patient platform for personalizing several new antiangiogenic drugs, in particular Avastin, will be published in the journal Cancer Research in autumn.

Tripos to Acquire Pharsight for $57M
Informatics tools and services provider Tripos will acquire Pharsight, a PD/PK modeling tools and services specialist, for roughly $57 million in cash. Tripos has traditionally focused more on drug discovery and molecular modeling while Pharsight’s strength has been in development and clinical trials. 

Tripos is wholly owned by Vector Capital, a San Francisco-based private equity firm specializing in buyouts, spinouts and recapitalizations of established technology businesses. Under the terms of the agreement, Pharsight stockholders will receive $5.50 in cash for each outstanding share of common stock, a 29 percent premium over the average closing price of Pharsight's common stock over the thirty trading day period ending on September 8, 2008.

The blended company will certainly have a broader footprint, extending from discovery through Phase III work. It wasn’t immediately clear what the plans are for branding. Tripos is headquartered in St. Louis, MO. Pharsight Corp. is based in Mountain View, CA.

The Board of Directors of Pharsight has unanimously approved the agreement. The acquisition is subject to the approval of Pharsight's stockholders and other customary closing conditions. Certain directors, officers and stockholders of Pharsight, representing approximately 33 percent of Pharsight's outstanding common stock, have entered into voting agreements in support of the acquisition. The acquisition is expected to close in the fourth quarter of 2008.

Broad Institute Secures Future with $400 Million Endowment 
Billionaire philanthropist Eli Broad and his wife Edythe have announced a new $400 million endowment that secures the future of the Broad Institute. Read more.

Quantitative Protein Profiling Breakthrough?
Work from Lee Hood’s group at the Institute for Systems Biology (ISB) may lead to practical, quantitative protein profiling in serum. In a paper in Molecular and Cellular Proteomics, ISB researchers describe a label-free method for analyzing serum using surface plasmon resonance (SPR) imaging of antibody microarrays. 

Authors Christopher Lausted, Zhiyuan Hu, and Leroy Hood say they were able to detect levels of serum proteins known to be affected by a specific form of liver cancer, something that hadn’t been done before.

Here’s an excerpt: “We used the antibody microarray to compare the serum protein profiles from three liver cancer patients and three nonliver cancer patients. Hierarchical clustering of the serum protein levels clearly distinguished two distinct profiles. Thirty nine significant protein changes were detected (P<0.05), ten of which have been previously observed in serum. Alpha fetoprotein, a known liver cancer marker, was observed to increase. These results demonstrate the feasibility of this high-throughput approach for both absolute and relative protein expression profiling.”

Click to read the paper, Quantitative serum proteomics from surface plasmon resonance imaging.

ISMB/ECCB Seeks Special Session Proposals
The organizers of ISMB/ECCB 2009 have issued a call for Special Session proposals for the conference taking place in Stockholm, Sweden, June 29-July 2, 2009.  Proposals will be accepted at online submission site until October 8, 2008. These Special Sessions have the purpose of introducing the ISMB/ECCB community to relevant ‘hot’ topics that were not covered in previous meetings. Special Sessions were introduced at ISMB/ECCB 2007 in Vienna, repeated at ISMB 2008 in Toronto, and have become one of the most successful components of this meeting.

Pathway Studio V.6 Released
Ariadne released Pathway Studio V.6, featuring gene expression analysis tools, updated pathway collection, and an intuitive and attractive new look and feel. Pathway Studio organizes and visualizes knowledge from many data sources and facilitates different fields of research: RNAi, target or biomarker discovery, etc. Among other things, Ariadne says V. 6 makes it easy to build regulation networks from the most differentially expressed genes using its ResNet 6 database.

Bristol-Myers Extends Ingenuity Agreement
Ingenuity Systems announced a multi-year agreement with Bristol-Myers Squibb, extending BMS’ use of Ingenuity Pathways Analysis (IPA) software application. The agreement provides enterprise-wide access to IPA for BMS scientists, including access to the newest IPA version, which supports Affymetrix GeneChip Exon Arrays and many new species, and includes recent enhancements such as the Path Designer publishing tool and capabilities for metabolomics, biomarker, and toxicology research. BMS has been an Ingenuity customer since 2004.

UTMB, GenoLogics to Develop Biomed Informatics Solution
GenoLogics and the Sealy Center for Molecular Medicine (SCMM) at the University of Texas Medical Branch at Galveston (UTMB) will collaborate on developing an integrated biomedical software solution. The Sealy Center for Molecular Medicine (SCMM) is an interdisciplinary research center and is part of the newly formed Institute for Translational Sciences. Its mission is to serve as a key interface between clinical and basic scientists addressing UTMB's strategic plan for personalized medicine.

SCMM is focused on understanding cell stress response pathways using high-throughput approaches. The biomarkers program is developing new tools to study and classify human diseases at a molecular level, allowing the prediction of individual susceptibility to disease. This research program in personalized medicine will allow the center to make better diagnostics for common medical diseases such as asthma, cancer, diabetes and degenerative diseases.

"We decided to collaborate to deploy a biomedical solution that will begin with user-friendly software to efficiently and effectively manage our biospecimens. Investing in a biomedical informatics solution that can also connect to our research data is going to assist the center with attracting future funding such as the Clinical and Translational Science Awards,” said Allan Brasier, director, SCMM, in a release.

ABI Announces Transcriptome Expression Kit
Applied Biosystems announced development of a sequencing-based molecular tool for the genomic analysis of whole transcriptomes. This technology, which provides detailed characterization of expressed protein-encoding genes, identifies many non-coding RNAs, and includes sample multiplexing capability, is expected to be available for limited release through an early access program that will begin in November 2008. This offering will expand the company’s RNA expression analysis solutions portfolio for use with its SOLiD System, the company’s ultra-high-throughput genomic analysis platform. The SOLiD Whole Transcriptome Expression Kit is expected to provide researchers greater insights into biological pathways and molecular mechanisms.

FDA Approves Aperio Image Analysis S/W
Aperio Technologies has received clearance from the U.S. Food and Drug Administration (FDA) to market the ER and PR image analysis applications available through its ScanScope slide scanning system. The FDA-cleared immunohistochemistry (IHC) image analysis applications are intended to be used as an aid to pathologists in detecting and quantifying ER (estrogen receptor) and PR (progesterone receptor) protein expressions from digital slide images created by Aperio’s slide scanning systems. The company reports more than 125% sales growth in 2007 and an installed base of more than 400 systems in 27 countries. 

Helicos Hires Three Execs
Helicos BioSciences reports hiring Stan Letovsky as VP for scientific informatics; he is one of three recent senior staff additions. Letovsky will oversee efforts to develop the computational and data analysis platform of the Helicos Genetic Analysis System, as well as build Helicos' scientific computing infrastructure and help drive the company's open source initiative. Letovsky has held informatics management roles with Codon Devices, Millennium Pharmaceuticals and Monsanto, as well as an associate professor post at the Johns Hopkins University School of Medicine.

Cellumen to Develop Tox Panel for Mitsubishi Tanabe
Cellumen announced an agreement with Mitsubishi Tanabe Pharma Corp. (MTPC) to develop panels of biomarkers that identify toxicity early in the drug development process. Cellumen is focused on decreasing the drug attrition rate due to toxicity. The company’s

CellCiphr CSB Toxicity Profiling Services can identify toxic compounds in late primary screening through early pre-clinical phases, before entering expensive pre-clinical testing. By integrating optimal cells, panels of functional biomarkers and classifier software, Cellumen creates a Safety Risk Index for compounds to help researchers predict potential rodent or human toxicity.

EUREKA! NIH Awards First Eureka Grants
The National Institutes of Health (NIH) has awarded $42.2 million to fund 38 exceptionally innovative research projects that could have an extraordinarily significant impact on many areas of science. The grants, the first made in a new program called EUREKA (for Exceptional, Unconventional Research Enabling Knowledge Acceleration), help investigators test novel, often unconventional hypotheses or tackle major methodological or technical challenges.

EUREKA researchers will receive direct costs of approximately $200,000 per year for up to four years, subject to the availability of appropriations. "EUREKA is an experiment in how to attract, identify, and support particularly creative approaches that, if successful, could move science forward dramatically," said Jeremy M. Berg, director of the National Institute of General Medical Sciences (NIGMS), which led the development of the EUREKA program. For a full list of EUREKA projects, see this page. Additional EUREKA awards may be made in fall, and NIH has re-announced the program for next year. More information.


This article first appeared in Bio-IT World’s Predictive Biomedicine newsletter. Click here for a free subscription.


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