Systems Biology - Tools, Strategies, and Companies Driving Integrative Biology 


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Briefs from the Systems Biology Community

Genstruct, Sirtris Win Bio-IT World Best Practices Award
Genstruct and Sirtris Pharmaceuticals, a biopharmaceutical company focused on discovering and developing small-molecule drugs to treat diseases of aging, jointly won Bio-IT World magazine’s 2008 Best Practices Award in the Drug Discovery & Development category. The project was focused on discovering mechanisms of action (MOA) for Type 2 diabetes. The two companies collaborated to further characterize the molecular MOA of Sirt1 activating compounds.

In blinded analysis, Genstruct’s causal network modeling (CNM) approach concluded that the strongest hypothesis for the results seen in the Sirtris Type 2 diabetes study was caloric restriction (CR) – showing that Sirtris’ SIRT1 activators are mimicking the effects of CR. These results were confirmed by in vitro and in vivo experimentations. “Using our CNM platform, we were able to help develop a deep understanding of the SIRT1 pathway and allowed Sirtris to efficiently analyze a vast quantity of data. Sirtris has been a valued research partner for our firm,” said Keith Elliston, president and CEO at Genstruct. Read Release…

Pfizer Launches Systems Biology Consortium
Pfizer has launched a three-year, US$14-million systems-biology consortium to improve the understanding of diabetes and obesity. The consortium is called the Insulin Resistance Pathways Project (IRP Project). In the new Pfizer program, researchers at the University of California, Santa Barbara; the California Institute of Technology in Pasadena; the Massachusetts Institute of Technology in Cambridge, Mass.; the University of Massachusetts; and biotechnology company Entelos, based in Foster City, California, will examine the regulatory mechanisms involved in insulin signaling in fat cells.

“What is most exciting and unique about this effort is that we are combining distinct approaches to transform our picture of what happens inside the cell in response to insulin,” said Robert Garofalo, PhD, senior research fellow from Pfizer’s Cardiovascular, Metabolic and Endocrine Diseases therapeutic area and lead Pfizer scientist on the IRP. “Insulin actually initiates a three-dimensional network of interconnected responses. Our goal is to understand this network and how it changes in diseases like diabetes. Collaborating in this way will help us to identify better possibilities for new treatments.” Read More…

BioSeek to Collaborate with Lexicon
BioSeek announced a research collaboration with Lexicon Pharmaceuticals. BioSeek’s cell-based assay BioMAP Systems will be used to help further evaluate selected compounds associated with several of Lexicon’s drug discovery programs. BioMAP Systems are a series of human primary cell-based assay systems designed to replicate the cell and pathway interactions present in human disease biology. To date, BioSeek has developed systems for indications in vascular inflammation, cardiovascular and respiratory diseases, fibrosis and related conditions. Depending on their mechanism of action, compounds induce specific patterns of changes in these systems (BioMAP profiles) that can be compared to a large number of reference profiles in BioSeek’s database.
 Read More…

Entelos and Lilly Tackle Diabetes
Entelos has signed an agreement with Eli Lilly and Co. to conduct in silico research in the field of diabetes using the Entelos Metabolism PhysioLab platform. Financial terms were not disclosed. The Entelos Metabolism PhysioLab platform is an innovative and predictive computer model that simulates diabetic patients and is used to predict the effects of drugs, changes in diet and exercise, and other interventions. Entelos says the platform has already been used successfully with other pharmaceutical partners to select targets and compounds, find the best doses for patients, and support clinical trial design.
 Read More…

Genedata Expands Collaboration with U. Frieburg
A long
 collaboration between Genedata and the University of Freiburg as part of the Freiburg Initiative for Systems Biology (FRISYS) is growing deeper. Within the FRISYS framework, Genedata`s established Phylosopher research data management and analysis system has been applied to integrate public, experimental and in-licensed data, enabling systems biology for various model organisms like the moss Physcomitrella patens. Earlier in 2008, the International Moss Sequencing Consortium had reported the draft genome sequence of Physcomitrella patens, a moss with impressive survival qualities and important source to improve cultivated plants in biotech applications. “This outstanding FRISYS project builds a bridge from basic research to applied systems biology in industry for agro, biotech and biologics, or nutrition and cosmetics applications, to name just a few,” said Dr. Othmar Pfannes, CEO of Genedata. Separately, Genedata, announced the release of Expressionist version 5.0, its enterprise high-throughput biomarker discovery platform.

Stanford Research Win ACM-Infosys Award
Stanford Researcher Daphne Koller was named the first-ever recipient of the ACM-Infosys Foundation Award in the Computing Sciences. The Association for Computing Machinery and the Indian technology giant Infosys created the $150,000 prize last year to recognize young researchers "whose contemporary innovations are having a dramatic impact on the computing field." Koller, who in 2004 was also named a MacArthur Fellow, will formally receive the ACM-Infosys award in June.

"Biology is a science in flux because it has gone from being purely experimental on small scales to becoming an information science on a large scale," Koller said. "But we are currently seeing only the tip of the iceberg in terms of the biological insights that we can extract from these data." Koller's favorite subjects are genes, proteins and metabolic pathways. Her methods are a fusion of logic and probabilistic (statistics-based) reasoning and machine learning that she has helped to pioneer. Read More...

SensiTrop II Assay Available
Pathway Diagnostics announced nationwide availability of its patented second generation molecular SensiTrop II assay, combining the sensitivity of molecular heteroduplex tracking assay (HTA) technology with the specificity of molecular sequencing for determining the co-receptor tropism status of HIV infected patients. Pathway performs the SensiTrop II assay in its CLIA-certified laboratory on samples received from national reference laboratories in the U.S. and Delphic Diagnostics in Europe. SensiTrop II is available nationwide through national reference laboratories and is also being used in CCR5 compound clinical trials. Separately, the company reported that Stanford University School of Medicine has initiated an investigational study of the Pathwork Tissue of Origin Test. The new test uses advanced genomics-based technology to help physicians determine a tumor’s origin in order to optimize cancer-specific treatment.

Schadt Publishes on Liver SNP Associations 
Chalk up another important paper for Eric Schadt of Rosetta Inpharmatics (Merck division). This one --
 Mapping the Genetic Architecture of Gene Expression in Human Liver – is in PLOS Biology. It’s the third recent paper on which Schadt was a lead author and in which systems biology approaches have produced significant results. Here’s an excerpt from the abstract: “…we profiled more than 39,000 transcripts and we genotyped 782,476 unique single nucleotide polymorphisms (SNPs) in more than 400 human liver samples to characterize the genetic architecture of gene expression in the human liver, a metabolically active tissue that is important in a number of common human diseases, including obesity, diabetes, and atherosclerosis. This genome-wide association study of gene expression resulted in the detection of more than 6,000 associations between SNP genotypes and liver gene expression traits, where many of the corresponding genes identified have already been implicated in a number of human diseases.”

NextBio Offer Free Version of Its Search
NextBio announced that a free version of its life science search engine has been made available to the general public. Using NextBio, any researcher or clinician can search the world's public life sciences data and literature - over 10,000 experiments, 16 million articles, and literally billions of data points. Moreover, users can import their own experimental data into the NextBio search engine, share it with the community, and collaborate with others as never before. Among those singing its praise is Leroy Hood, president of the Institute for Systems Biology: “The NextBio life science search engine presents a powerful and intuitive solution available for researchers and clinicians who wish to truly unlock the value of large-scale studies in the public domain." Videos explaining the NextBio life science search engine and how it works, as well as a demonstration of a search, are available for viewing here.

Agendia and Agilent to Collaborate
Agendia BV, a leader in the rapidly evolving field of molecular diagnostics, and Agilent Technologies announced terms under which they intend to collaborate to develop new in vitro diagnostic tests. The two companies also reported an agreement in which Agendia products will continue to be supplied on Agilent microarrays through December 31, 2011. Agilent has been manufacturing the components for the Agendia assay since its inception in 2003. The financial terms of the agreement were not disclosed.

Pfizer, Linguamatics Extend Collaboration
Linguamatics reported that Pfizer has extended its strategic collaboration with Linguamatics to use the I2E knowledge discovery platform for text mining across its R&D organization. Pfizer researchers and other decision-makers will use I2E to discover and extract key facts and relationships from internal and external literature sources to support decision-making. Financial details of the agreement were not disclosed. “Linguamatics I2E has been used to date for focused knowledge discovery from large document collections in a variety of R&D applications at Pfizer,” said David de Graaf, director systems biology, Pfizer. “We are now also applying its NLP-based querying to inform research decisions within the new Biotherapeutics and Bioinnovation Center.”

Scripps Joins GeneGo-Led Cardiac Consortium
GeneGo reported that The Scripps Translational Science Institute has joined the MetaMiner Cardiac Consortium. The goal of the consortium is to build the first systems biology and pathway analysis platform for cardiovascular diseases in the world. Consortium members will vote on deliverables that will include disease-specific pathway maps and networks built by experts in the field. GeneGo will also develop relevant ontologies for cardiovascular diseases and drugs. The MetaMiner environment will also serve as a repository for OMICs and other experimental data. Read the full release.



Memorial Sloan-Kettering Cancer Center - Bioinformatics Engineer
MSKCC Bioinformatics Core in Manhattan seeks Bioinformatics Engineer. Design and develop bioinformatics
processing and analysis pipelines for traditional and next-gen sequence data. Consult with, train, and analyze data for researchers. Master's degree and 5 years experience in Bioinformatics software development, sequence assembly, SQL, Perl, Python. Email or #015415. EOE/AA

Memorial Sloan-Kettering Cancer Center - Linux Systems Administrator -
MSKCC Bioinformatics Core in Manhattan seeks Linux Systems Administrator. Install, configure and update OS, databases, software. Monitor and troubleshoot HPC cluster, email and web servers. Master's degree and 5 years experience with HPC, network security, Postfix, Apache, Tomcat, Grid Engine. Email or #015429. EOE/AA

Paradigm-Sales/Business Development – IT Solutions and Services
Paradigm ( is a global IT services and solutions provider. Paradigm has over 1000 employees and is the recipient INC. 500 and D&T Fast 50 consistently.  Paradigm is looking for SALES / BUSINESS DEVELOPMENT PEOPLE.  Experience: 2-3 years Direct sales experience in Software Solutions or Services including Application development or support and preferably selling to Pharmaceutical, CROs or Health care industries. Location:Columbia, MD,Contact:  Erin Lowman,, 410-872-1008 x 100

Lilly Singapore Center for Drug Discovery (LSCDD) - Associate Director of Informatics,
Lead and mentor a strong team for the Bioinformatics group at the Integrative Computational Sciences (ICS) department at LSCDD towards the development of novel algorithms, data analysis methods and software tools for drug discovery. Work closely with the Software Engineering group at ICS, and collaborate with the Discovery IT organization in Europe and USA. For additional information, or to apply visit:

Lilly Singapore Center for Drug Discovery (LSCDD)- Senior Bioinformatics Scientist,
Contribute to the development of novel algorithms, data analysis methods and software tools for drug discovery as part of the Integrative Computational Sciences (ICS) department at LSCDD.  Work closely with informatics and software engineering peers at ICS, and collaborate with the Discovery IT organization in Europe and USA. The successful candidate will offer hands-on insight and expertise in tailored therapeutic informatics and statistical analyses at the post-genomic era. For additional information, or to apply visit:

Lilly Singapore Center for Drug Discovery(LSCDD) -Senior Software Engineer,
Join a strong team of software engineers in our Integrative Computational Sciences (ICS) at LSCDD. Collaborate with, and help develop integrated applications to process and visualize data from cutting-edge technologies used by scientists at Lilly Research Labs (LRL) and the Drug Discovery Research (DDR) teams. The Software Engineering team provides computational tools and tailored software solutions that enable the global effort of Tailored Therapeutics; ‘The Right Drug, at The Right Dose for The Right Patient at The Right Time'. For additional information, or to apply visit:

More Life Science Jobs ~ Add a Job Listing



MIT PROFESSIONAL INSTITUTE - 2008 Short Courses - Cambridge,MA

TEPR 2008 -- May 17-21, 2008 Ft. Lauderdale,FL 

EMC World 2008, May 19-22, 2008, Las Vegas,NV 

BIO International Convention - June 17 – 20, 2008, San Diego Convention Center, San Diego, CA

5th Annual Meeting on the NCI’s cancer Biomedical Informatics Grid—CaBIG—initiative (Annual Meeting)S -June 23-25, 2008, Washington,DC

2nd Label-Free Protein Array- Latest Advances in Analysis of Macromolecular Interactions,July 3-4th 2008 -Paris- France

GOT Summit: Getting Optimized Tools for Diagnostics - May 19-21, 2008, Boston,MA

To have your event featured here, contact Lynn Cloonan for more information.

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Why the Time Is Right for a System Biology Breakthrough

Late last month, Bio-IT World held its 2008 Best Practices Awards dinner, and one of the featured speakers was Colin Hill, co-founder and CEO, of systems biology pioneer Gene Network Sciences. Take a moment to hear Hill’s brief (~ten minutes) but forceful argument that the industry’s high hopes for technology-driven drug discovery weren’t misplaced, just a few years premature. Recent results such as those from Merck’s Rosetta division, he says, are clear proof that important discoveries are being made now by these platforms and soon such approaches will dominate the drug development process.  Click for video. 

This Bio•IT World Briefing On “Next-Generation Sequencing,”underwritten by GenomeQuest, Inc.,

presents a selection of feature stories, interviews,commentaries, conference reports, and editorials on the emergence, opportunities, and challenges posed by high-throughput sequencing. Covered in this collection: the launch of new platforms from Applied Biosystems and Helicos; new applications of nextgen sequencing; the rise of personal genomics; and informatics solutions to vexing problem of managing the vast volumes of next-gen data. Download now 

SGI's Meeting Today’s Computational Needs for Science

The quest to better understand disease mechanisms and find new treatments is driven by new laboratory technologies and ever-more sophisticated modeling and simulation efforts. As such, life sciences R&D investigations increasingly are relying on more powerful computing resources. The challenge is how to accommodate the broad mix of applications.
Addressing this issue, this paper produced by the Bio-IT World Custom Publishing Group discusses a new SGI Hybrid Computing Environment approach. It optimally uses shared memory systems, multi-processor clusters, and FPGAs to accelerate computational workflows. Download This Free Paper 

SGI's Supercharging Proteomics Discovery

The deeper study of proteins and their interactions can reveal scientific information once considered nearly untouchable to scientists and researchers. Today, unprecedented advancements in computing power are enabling the creation of mounds of proteomic based data along with the accompanying bottlenecks data can create.  Rather than just “simplify the experiment” to fit the computational resources an alternative is now available with the SGI Proteomics Appliance. This complimentary white paper, produced by the Bio-IT World Custom Publishing Group, looks at ways to use the Proteomic Appliance to handle the most intensive proteomics computing tasks facing science today. Download This Free Paper

To have your white paper featured here, contact Lynn Cloonan for more information.


NEW! Life Science Webcasts from Bio-IT World and Cambridge Healthtech Media Group

Life Science Webcasts

Bio-IT World proudly introduces Life Science Webcasts -- a series of informal conversations with leading researchers and executives in the bio-IT and biopharma arena.

This week, Dr. Samuel Levy, (senior scientist, Human Genomic Medicine, J. Craig Venter Institute) discusses 'Sequencing of the first diploid human genome-that of Craig Venter' with Bio-IT World's Kevin Davies.

View the Webcast Now


GNS: Building a "SNPs-to-Outcomes" Engine
April 16, 2008

Genstruct Adapts for Today's Challenges
March 19, 2008

Inside Strand Life Sciences
Feb. 14, 2008

India Is Connexios' Competitive Advantage
Jan. 16, 2008
Bio-IT World SB Links

Pathway Pioneers

Marvelous Models of Biological Systems

Pharsight Lands CRADA to Assist FDA with Modeling Initiative

Harvard Researchers Discuss Systems Biology

FDA Mulls Drug/Disease Model Library

Welcome MIRIAM: Researchers Propose Modeling Standard

Cambridge Healthtech InstitutePublished by Cambridge Healthtech Media Group, division of CHI, Copyright © 2008; All rights reserved. Systems Biology may not be reproduced, electronically or in print, by any means, mechanical or electronic, in whole or in part, without written permission of Cambridge Healthtech Media Group, 250 First Ave., Suite 300, Needham, MA, 02494. 
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