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March 19, 2009 | ISCB Honors Webb Miller and Trey Ideker for Bioinformatics
The International Society for Computational Biology named Webb Miller of Pennsylvania State University as the winner of its Accomplishment by a Senior Scientist Award for 2009, and Trey Ideker of UC San Diego as winner of the 2009 Overton Prize for early- to mid-career scientists.

Miller began his career at Penn State in the late 1960’s as a computer scientist. By the time he entered the emerging field of bioinformatics in 1987 he was already a full professor there. Initially, his research revolved around developing algorithms for aligning pairs of DNA or protein sequences; he worked on the algorithms that were used in the BLAST program for searching databases for similar sequences, which is still one of the most widely used bioinformatics tools worldwide.

Ideker also started his career as an engineer and computer scientist. A burgeoning interest in molecular biology led him to join a graduate program in molecular biology run by Leroy Hood, founder of the Institute of Systems Biology in Seattle, Washington. There, he began to model and analyse networks of molecular interactions using genome-scale measurements, an emerging field in which he became a pioneer. He was still a Ph.D. student when, in 2001, he published a classic paper demonstrating how biological networks are mapped and tested using a systems biology approach that has attracted well over 800 citations to date. More information.

Genomatix Wins Patent for Cross Species Reg. Network Identification
Genomatix Software was issued a European patent (No. EP 1 800 232 B1) for the “Identification and assignment of functionally corresponding regulatory sequences for orthologous loci in eukaryotic genomes.” The Patent relates to a sophisticated method for identification of networks of functionally related regulatory DNA sequences in different eukaryotic species. The patent describes a method using a defined transcriptional start side from a well annotated genome (like human) as an anchor to identify corresponding regulatory regions in the orthologuous areas of less defined species.

Dr. Andreas Klingenhoff, Genomatix´ Head of Genomics and Annotation and the inventor of the approach says: “We developed the method over several years, running many projects aimed to identify the evolutionary conserved regulatory elements shared between different eucaryots. It was essential in understanding regulatory networks, mechanisms and pathways, including disease mechanisms in humans. With increasing insight into the extreme complexity of the transcriptome, the method becomes more and more valuable. We continuously work on further improvements and apply it to an increasing number of species, especially in light with our efforts in next generation sequencing data analysis.” Read release.

BGM Signs CRADA with National Heart, Lung and Blood Institute and B.U.
Under the agreement, the three parties will jointly conduct a series of biomarker discovery studies for heart disease and early detection of metabolic syndrome -- a combination of certain risk factors, including abdominal obesity, hypertension, and insulin resistance -- which are believed to increase the risk of developing cardiovascular disease and diabetes. BGM will analyze biosamples obtained during years of collection by Framingham Heart Study researchers. The collaborative research aims to identify those at high risk of heart attack and stroke, two of the world's leading killers. Read release.

Harvard Researchers Create First Synthetic Ribosome
Harvard researchers have successfully constructed an essential cellular component responsible for synthesizing proteins—a discovery that marks a major stride towards creating artificial life, according to the lead investigator behind the project. The first man-made ribosome was announced to an assembly of Harvard alumni Saturday afternoon in a symposium titled “The Future of Life,” by George M. Church, the lead investigator of the project and a professor of genetics at Harvard Medical School.

“[The ribosome is] the catalytic core of the cell,” said Michael C. Jewett, a research fellow who worked with Church. “The advantage of building them [in a lab] is that you can manipulate the system directly. It’s like opening the hood of a car and having direct access to the machination.” Although their work is “a milestone...towards artificial life,” according to Jewett, both he and Church emphasized that they have not yet created any synthetic life, nor is that their main goal. Instead, the research team’s aim is to “make useful products,” said Church. Read Crimson report.

Synthetic Gene Circuit Allows Precise Dosing of Gene Expression
M.D. Anderson researchers have crafted a gene circuit that permits precise tuning of a gene’s expression in a cell, an advance that should allow for more accurate analysis of the gene’s role in normal and abnormal cellular function. This gene “dosing effect” is achieved by installing a negative feedback loop in the synthetic gene circuit, a concept similar to signal distortion control in electronics, a team led by scientists at M. D. Anderson Cancer Center reports this week in the Online Early Edition of the Proceedings of the National Academy of Sciences.

“To understand what a gene does, you need to change its expression and observe the results. Present methods do not allow close control of gene expression,” said senior author Gábor Balázsi, Ph.D., assistant professor in M. D. Anderson’s Department of Systems Biology. Knocking out genes is an all-or-nothing approach, and suppressing them with small interfering RNA has undesired effects. Transfecting cells with a gene expression vector overexpresses the gene, but still in an uncontrolled way, Balázsi noted. The synthetic gene expression system the researchers developed in a yeast model would allow more detailed investigation of a gene’s effects. Read release.

Genedata Completes Tox DB for Consortium Project
Genedata announced the successful completion of the InnoMed PredTox Non-Clinical Safety Project organized around a series of animal studies using compounds terminated in drug development due to nephro- and hepatotoxicity. The project showed that biomarkers could be identified based on a novel systems toxicology approach that integrates the analysis of different omics data and conventional experimental data. The project workflows and research processes were supported by a computional infrastructure developed and provided by Genedata.
 
Over the course of the three-year consortium project aimed at improving the assessment of drug safety before new drugs enter the clinical research phase, Genedata has developed software for omics and conventional experimental data integration, processing and analysis. The resulting project-specific database, ‘PredTox DB’, represents one of the most comprehensive collections of molecular profiling (omics) across various technologies and conventional endpoint data on any selection of compounds. Multiplex-assay technologies employed included microarrays for mRNAs, LC-MS and NMR for metabolites as well as 2D-PAGE and 2D-DIGE for proteins, complemented by conventional clinical chemistry, histopathology and in life observations. Read release.

Hamner, Entelos to Co-Development DILI PhysioLab Platform
The Hamner Institutes for Health Sciences and Entelos announced a partnership to create a computer model of liver function in virtual patients that will improve understanding of how pharmaceutical drugs and chemical agents can sometimes damage the liver. Drug induced liver injury(DILI) is the most frequent cause of acute liver failure and is a major reason why drugs are abandoned in development or fail to gain regulatory approval. Recent withdrawals and restrictions on use of marketed drugs, due to incidence of DILI, highlight the limitation of existing approaches to determine a drugs safety risk profile. Two FDA scientists will join the scientific advisory board for the project. This partnership will combine Entelos’ clinically validated PhysioLab biosimulation platform technology with The Hamner’s expertise in liver injury and systems biology. Read release.

GeneGo Licenses DrugMatrix Data
GeneGo will use Entelos’ DrugMatrix gene expression data to further develop GeneGo’s Functional Descriptor predictive toxicology models. “Access to a comprehensive, pharmacologically-diverse and fully annotated compendium of gene expression data is critical to developing high-performance predictive models,” said Richard Brennan, Director of Toxicology at GeneGo. “This is one of the key goals of our MetaTox partnership. DrugMatrix is the largest toxicogenomic database available, and will allow us apply the lessons we have learned from our participation in the Microarray Quality Control Consortium to expand our collection of biological pathway-based classifiers with toxicity models for wide variety of adverse drug effects in key target tissues.” Read release.

PeptideAtlas is Now Searchable by Google
Members of the Ruedi Aebersold Lab at the Institute for Systems Biology have made their PeptideAtlas database searchable via Google. Scientists worldwide will now find it easier to access information about proteins detectable by mass spectrometry. Abhishek Pratap, a former intern and lab assistant at the Institute for Systems Biology (ISB) who now serves as a bioinformatics software engineer at the Institute for Genome Sciences, School of Medicine, University of Maryland, facilitated Google search of the PeptideAtlas by creating an indexed XML site and static pages for each peptide.

"Researchers around the world already use Google on a regular basis, so we thought, 'why make them take the extra step of going to the PeptideAtlas search page?'”, said Pratap. "Now they can just conduct a Google search for a specific peptide sequence and get directly to the information they want.” More information.

Rosetta Debuts Copy Number Variation Management
Rosetta Biosoftware announced availability of copy number variation (CNV) data management and analysis capabilities in the latest release of the Syllego™ system. Syllego version 3.5 also offers scientists the ability to co-analyze gene expression (GE), CNV and genotyping data through enhanced statistical and visualization features and a data exchange gateway to the Rosetta Resolver® system. Read release.

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This article first appeared in Bio-IT World’s Predictive Biomedicine newsletter. Click here for a free subscription.
http://www.bio-itworld.com/BioIT/NewsletterSubscribe.aspx

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