New Imaging Technology -- from Mayo Clinic
A new study shows that an imaging technology -- magnetic resonance elastography (MRE) -- developed by Mayo Clinic researchers can identify liver fibrosis with high accuracy and help eliminate the need for liver biopsies. MRE produces color-coded images known as elastograms that indicate how internal organs, muscles and tissues would feel to the touch. Red is the stiffest; purple, the softest. Other imaging techniques do not provide this information.
“Knowing the liver’s elasticity or stiffness is invaluable in diagnosing liver disease,” says Jayant Talwalkar, M.D., M.P.H., a Mayo Clinic hepatologist and co-investigator on the study. “A healthy liver is very soft, while a liver with early disease begins to stiffen. A liver with cirrhosis, advanced liver disease, can be rock hard.” The study, which included 113 patients, was scheduled for presentation Monday, at The Liver Meeting, an annual gathering of the American Association for the Study of Liver Disease, in San Francisco. Read full release.
HTP Imaging Speeds Analysis of Hormone Receptors
A new high-throughput microscopy technique enabled researchers at Baylor College of Medicine in Houston to analyze thousands of individual cells expressing androgen receptor, a finding that could herald new ways of evaluating the effect of drugs or other treatments on cells with normal or aberrant hormone receptors.
“As our ability to image cells using high-throughput microscopy got going faster and faster, we began to collect enormous amounts of functional data that was usually only accessible by separate (and slow) biochemical experiments. Our customized software approaches then allowed us to assemble the results into a more systems-level appreciation of the biology, linking together several functional characteristics of the androgen receptor,” said Dr. Michael Mancini in a report in the current issue of Public Library of Science One (PLoS One). He and collaborators reported a new, next-generation high-throughput image-based assay that helps determine the level and location of androgen receptor and its transcriptional activity on a cell-by-cell basis. Read full story.
Avalon Pharma Bought for $10M
Clinical Data and Avalon Pharmaceuticals announced a definitive merger agreement for Clinical Data to acquire Avalon in an all-stock transaction valued at approximately $10 million. The two say the combined company will have a significantly expanded oncology business with a pipeline of promising oncology biomarkers and compounds, and a biomarker discovery platform to identify additional therapeutic and diagnostic candidates.
“The acquisition of Avalon is aligned with our core strategy of identifying proprietary biomarkers that correlate with safety and efficacy in the development of targeted therapeutics and genetic tests used to diagnose disease and guide treatment decisions,” said Drew Fromkin, Clinical Data’s president and CEO. “Avalon’s comprehensive biomarker discovery platform, validated by partnerships with leading pharmaceutical companies, extensive library of biomarkers and compounds, and oncology expertise, add to our growing estate of proprietary oncology biomarkers and in-depth knowledge of biomarker and pharmacogenetic test development.”
The merger agreement was one of four separate definitive agreements signed by the companies, which included: a) a private placement, b) a secured term loan agreement, and c) an exclusive license to Avalon’s drug and biomarker discovery platform. Read full release.
“Waiting for Einstein: The dawn of a unified theory of biology may finally be upon us”
There’s a neat piece in The Scientist, with the title above, written by Steven Wiley, a Pacific Northwest National Laboratory Fellow and director of PNNL’s Biomolecular Systems Initiative. Enjoy!
Genedata Expands Bayer Schering Agreement
Genedata announced expansion of its 10-year informatics partnership with Bayer HealthCare to include all of Bayer Schering Pharma (BSP) drug discovery research sites. Separately, it announced a renewed agreement with FDA’s National Center for Toxicological Research (NCTR) for use of Genedata Expressionist biomarker discovery platform.
The collaboration with BSP includes the provision and tailoring of Genedata’s Expressionist and Phylosopher platforms to support research. In addition, Genedata will provide professional services to support integration and to provide interfaces to existing research logistics infrastructure, including laboratory technologies and related IT systems.
NCTR is using Genedata Expressionist, a modular computational platform for biomarker discovery that integrates transcriptomics, proteomics, and metabolomics data within a single enterprise software system. Weida Tong, director of the Center for Toxicoinformatics at FDA, said in a release, “We have successfully applied Genedata Expressionist in a number of FDA projects, including the Critical Path project and the Liver Toxicity Knowledge Base (LTKB) project. Expressionist is an excellent system for monitoring the quality of gene expression data.”
MathWorks is Lead Sponsor of iGEM
The International Genetically Engineered Machine (iGEM) 2008 student competition is held annually by the Massachusetts Institute of Technology (MIT). This year the competition brought together 84 undergraduate teams representing more than 1,000 students from 21 countries across Asia, Europe, Latin America, and the U.S. to design and assemble synthetic biological systems using advanced genetic components and technologies.
As a lead sponsor, The MathWorks is equipping teams with its software tools, including MATLAB and SimBiology, which provide advanced capabilities for modeling, simulating, analyzing, and visualizing complex biological networks. Additionally, The MathWorks is offering students in-person and online training sessions to help them become proficient with the tools. The teams also have been matched with experienced MathWorks staff, who serve as mentors and technical advisors. Read full release.
Harvard’s FAS Center for Systems Biology Seeks Applicants
The FAS Center for Systems Biology is an intensively collaborative, interdisciplinary center, where scientists from a wide variety of backgrounds study cellular pathways and networks, with the goal of finding general principles underlying the structure, behavior and evolution of cells and organisms. The Bauer Fellows are independent researchers who receive funding for a group of up to three people. Fellows are appointed for a three-year term, with the expectation that it will be extended to five years.
For more information about the Bauer Fellows program, visit this website. Applications are welcome at any time, but only those received by February 2, 2009, are guaranteed full consideration.
Pathworks Test Indicated Probable Tissue of Origin in 73 Percent of Tumors Tested
Pathwork Diagnostics will present three studies involving the gene expression-based Pathwork Tissue of Origin Test at the Association for Molecular Pathology (AMP) Annual Meeting. In a poster entitled “Gene Expression Microarray-Based Diagnostic Test May Identify Primary Tumor Site in Patients with Carcinoma of Unknown Primary (CUP),” Fabiola Medeiros, assistant professor of Laboratory Medicine and Pathology at the Mayo Clinic, found that the Pathwork Tissue of Origin Test indicated a probable origin of metastatic CUP in 73 percent of the tumors tested.
Since the test was validated and FDA-cleared using metastatic tumors for which the primary site was known, the purpose of this study was to examine the diagnostic performance of this test using CUP specimens. Analysis of the accuracy of these results is limited, since there is no reference diagnosis for comparison with CUP specimens where by definition the primary site is unknown. Read full release.
2009 Overton Prize Nominations Sought
The International Society for Computational Biology (ISCB) seeks nominations for the 2009 Overton Prize and the 2009 Accomplishment by a Senior Scientist Award. The Overton Prize is awarded to an early-career scientist, and the Accomplishment by a Senior Scientist Award is in recognition of highly significant, long-term career achievement. These are the most prestigious international awards designated exclusively to researchers in the field of computational biology/bioinformatics, and winners of both awards will deliver keynote talks at ISCB’s annual meeting, ISMB/ECCB 2009, in Stockholm, Sweden.
Nominations from all regions of the world are encouraged, and the selection of award winners will be made by an international panel of current and ISCB past board members, along with recent winners of each award. All nominations will be treated confidentially. Self nominations are not allowed.
IO Informatics Announces Scientific Advisory Board Change
Members of the new SAB include: Jack R. Collins, manager of scientific computing and program development for the Advanced Biomedical Computing Center (operated by SAIC-Frederick) for NCI; Johann Bauer, scientific information manager at the Max Plank Institute, Martinsried, Germany; Sangtae Kim, executive director, Morgridge Institute for Research, Madison Wisconsin; Robert L. Stevenson, founder and principal of the Abacus Group, which provides management assistance and business development for companies in separation sciences and analysis. Read full release.
Metabolon Wins Patent
Metabolon was awarded a patent for its proprietary metabolomics software, Visual PHIL. The software enables the analysis of a series of raw and complex data sets being generated from a variety of instruments into one comprehensive visual display that can indicate the presence of the selected metabolites across a group of samples.
The patent (US Patent 7’433’787), titled “A System, Method, and Computer Program Product Using a Database in a Computing System to Compile and Compare Metabolomic Data Obtained from a Plurality of Samples”, is the latest addition to Metabolon’s IP portfolio of more than 80 U.S. and international patents.
“In the past, studies were conducted through analysis of one sample at a time. This technology allows us to see a comprehensive study view—in a visual display—which enables us to more quickly, and with a higher degree of certainty, identify compounds and hone in on biomarkers,” said Michael Milburn, chief scientific officer at Metabolon.
Linguamatics Text Mining Platform Chosen by TNO
Linguamatics , a provider of enterprise text mining, announced that TNO has deployed the I2E semantic knowledge-discovery platform to provide insights and intelligence within the food safety domain. Financial details of the agreement were not disclosed.
TIBCO Spotfire 2.2 Includes 3-D Visualization
TIBCO Spotfire version 2.2 was released, which includes new 3-D visualization. The company also introduced TIBCO Spotfire Network Analytics, a powerful new add-on product. The company says the new software allows business professionals to thoroughly explore relationships between different types of data, revealing hidden risks, fraud, threats and opportunities. In addition, TIBCO announced the TIBCO Spotfire Technology Network, a content-rich online resource for developers who are using the TIBCO Spotfire Software Development Kit to extend and adapt the market’s leading interactive visualization experience.
Optimata Publishes Angiogenesis Study
Optimata , developer of the Optimata Virtual Patient technology, reports publishing a paper – “Efficacy of Weekly Docetaxel and Bevacizumab in Mesenchymal Chondrosarcoma: a New Theranostic Method Combining Xenografted Biopsies with a Mathematical Model” - based on research carried out by company scientists. The paper appears in Cancer Research Journal 2008; edition 68: (21), on November 1, 2008.
The study involved personalizing treatment of a cancer patient by using unique technology combining in silico, in vitro and in vivo models. The proposed chemotherapy and angiogenesis inhibitor co-administration regimen resulted in temporary tumor stabilization, substantial recovery of blood counts, and six months of good quality of life for the patient treated. In the paper, the researchers expand the results to a general hypothesis that correlates between the patient’s angiogenesis state and the optimal inter-dosing interval of cytotoxic drugs.
“In this study the Optimata Virtual Patient shows almost 90 percent accuracy in predicting tumor growth inhibition of the patient’s biopsy Xenografts when treated by various cytotoxics and targeted angiogenic inhibitors. The success of the improved combination schedule recommended by the Virtual Patient indicates that angiogenesis biomarkers are going to be increasingly valuable in future personalized medicine,” said Zvia Agur, Optimata’s founder and CSO. Read full release.
University of Florida Renews Ariadne License
University of Florida renewed its site license for Ariadne's Pathway Studio, which it has used in medical and agricultural-related gene expression and proteomics studies. Pathway Studio streamlines hypothesis generation by creating visual interactive networks of biological relationships extracted from scientific literature and reference data sources. The license is available to all scientists at the University of Florida via ICBR Bioinformatics Core. “We work on many of non-model organisms and create microarrays for them using 454 and Agilent technologies”, said Li Liu, bioinformatics director at the ICBR Bioinformatics Core. “After mapping genes from these non-model organisms to model organisms, we use Pathway Studio to explore the gene networks.”
CombinatoRx Restructures
CombinatoRx reported financial results this week for the third quarter ended Sept. 30, 2008, and the company announced a strategic restructuring initiative, effective immediately, including a reduction of its Cambridge, MA, workforce by approximately 45 percent. As a result, the company expects to incur a restructuring charge of between $1.6 and $2.0 million, primarily in the fourth quarter of 2008. This restructuring is expected to allow the company to operate with current cash reserves into 2011.
"The decision to reduce our workforce was a very difficult one to make," commented Alexis Borisy, president and CEO of CombinatoRx. "We recognize the impact this restructuring will have on many of our outstanding employees who have made significant contributions to the company. However, we must take these difficult but necessary steps now to conserve capital, allowing us to marshal the capabilities and resources for our development opportunities moving forward." Read full release.
Plectix Nears Product Launch
Systems biology start-up Plectix BioSystems announced plans to launch Cellucidate, a new computational environment focused on cell signaling research. The Cellucidate collaborative workspace leverages an intuitive visual language for describing protein interactions coupled with advanced computational techniques to enable researchers to discover, model, and analyze signaling pathways and run virtual experiments.
“New empirical knowledge about protein interactions and transformations is emerging all the time,” commented Gordon Webster, vice president (biology) at Plectix. “By having this technology available in a web-based platform, we believe that researchers will be able to quickly and easily identify new knowledge, assess its impact on prior work and incorporate it.”
Genstruct Joins Biomarker Consortium
Genstruct reports becoming a member of The Biomarker Consortium, a public/private research partnership managed by the Foundation for the National Institutes on Health (FNIH), and founded by the National Institutes of Health (NIH), the Food and Drug Administration (FDA) and the Pharmaceutical Research and Manufacturers of America (PhRMA). Read full release.