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Monitoring Merrimack Pharmaceutical's Marathon Run 
Quackenbush on Integrating Clinical and Genomics Data 
Pfizer: Ted Slater's Semantic Technologies 
Novartis Savors Early Modeling Successe
Short News & Analysis

Systems Biology Q&A
Monitoring Merrimack's Marathon Run

By John Russell

Merrimack Pharmaceuticals is frequently seen as a poster child for the systems biology approach to drug discovery. Founded in 2000, it has made few missteps. Last spring, Cambridge, Mass-based Merrimack had the good fortune to raise $65 million in a series F financing round before the economy soured. In July, the company's first compound developed using its systems biology approach, MM121 (oncology), entered Phase One.

Merrimack hit a minor speed bump near the end of 2008 when its most advanced compound, MM093 (rheumatoid arthritis), did not meet its Phase Two primary end-point and work on the program was suspended. But MM093 is an in-licensed compound, and not the product of its distinctive "network biology" approach which pairs experiments with heavy use of in silico modeling to derive detailed mechanistic understanding of pathways, targets, and compounds. Currently the company's focus is on biologics.

Clearer evidence for or against Merrimack's brand of systems biology is expected late this year when data from MM121's Phase One is released. The broad idea, of course, is that these systems approaches will reduce pipeline attrition and perhaps be more naturally suited for developing targeted therapies and companion diagnostics.

Last month, Merrimack elevated Ulrik Nielsen (above), a company founder, to SVP and Chief Science Officer, and Predictive Biomedicine editor John Russell took the opportunity to talk with Nielsen and Kathleen Petrozzelli, senior manager, corporate communications, about Merrimack's progress and course adjustments. One recent change: Merrimack is seeking a partner to help it bring MM121 to market, a departure from its past go-it-alone strategy. More...


Integrating Clinical and Genomics Data
By Alissa Poh

How does a physicist wind up at the vanguard of translational medicine, bridging genomics, bioinformatics, and IT in an effort to shed light on cancer biology? That's among the chief responsibilities of John Quackenbush, professor of  biostatistics and computational biology at the Dana-Farber Cancer Institute (DFCI) in Boston. An affable personality with slightly greying, shoulder-length hair, Quackenbush is a theoretical physicist by training. He rose to prominence during an eight-year stint at The Institute for Genomic Research (TIGR), founded by Craig Venter, developing and sharing a range of software tools and databases for microarray analysis. More...


Pfizer: Ted Slater's Semantic Technologies
By Kevin Davies and Phillips Kuhl

The theoretical benefits of the semantic web for life sciences have been debated for a few years now, but practical examples within pharma remain scarce. Pfizer's Ted Slater is an interesting exception. Slater heads a small group of four informatics scientists in St. Louis called the Indications and Pathways Center of Emphasis (IPCoE), which supports Pfizer research efforts in identifying and validating inflammation targets. More...


Top Story Last Issue
Novartis Savors Early Modeling Success

By John Russell

Modeling and Simulation (M&S) has a complex history in the life sciences. Big pharma and small biotechs alike have struggled with finding the right recipe. Like a good wine, having the right general ingredients--management buy-in, modeling talent, sufficient resources, suitable problems--is necessary but not enough for success. A certain amount of vintner's experiment and bottle aging has to occur and more than a few companies have gulped some awful tasting stuff along the way.

Pretty clearly there won't be a single best recipe, but Novartis has been demonstrating it has found one that works and works quite well. A bit more than three years ago, Donald Stanski, M.D. (above), during his recruitment process convinced Novartis that Modeling and Simulation would never reach its potential embedded in the biostatistics department. It needed to be its own department; organized in close alignment with Novartis' drug development therapeutic franchises; enjoy the right reporting structure; and have enough resources and time to prove itself. More...


Short News & Analysis

(Click Here for Full Briefs)

Teva to Use Compugen Nephrotoxicity Biomarkers
Teva Pharmaceutical Industries has exercised its option to use a novel combination of biomarkers discovered by Compugen..

Sapio Sciences Debuts Exemplar LIMS 3.0
The company says significant enhancements include: introduction of automatic form\list view combinations..
Ariadne Launches ChemEffect
The new knowledge base contains in excess of 425,000 biological facts and relationships linked to more than 17,000 small..

M. D. Anderson Launches Grad Program in Cancer Metastasis
A one-of-a-kind graduate program that focuses on the most lethal aspect of cancer will open this fall..

HHMI Gives 50 Early Career Awards
Fifty of the nation's best early career science faculty will have more time and resources to focus on their boldest..

Novo Nordisk Licenses Linguamatics Tool
Novo Nordisk, a leader in diabetes care, entered a multi-year agreement to use the I2E semantic knowledge..

Hood Paper Pries into Prion Disease
Working with brain transcriptomes from mice they report finding a "core of 333 differential expressed genes [which] appear to..

Genedata to Collaborate with TcLand
As part of the deal, the Genedata Phylosopher and Expressionist biomarker discovery platforms will be..

SharePoint Integrated with Pipeline Pilot
Accelrys says it now supports Microsoft Office SharePoint Server 2007 as a publication platform..

Open-Source Sys-Bio Tools Support Deep Data Analysis
University of Michigan researchers have outlined how open-source computational tools for systems biology research can better..

(Click Here for Full Briefs)


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Insight Pharma Reports

Direct-To-Consumer Genetic Testing: Business Prospects in the United States 
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Direct-To-Consumer Genetic Testing: Business Prospects in the United StatesGenetic testing has come a long way since the development of the first genetic test in 1963. According to NIH, almost 1,500 genetic tests are now in use. This report focuses on health-related decision making applications of DTC genetic tests and examines various components of this emerging business environment. Read more.



Bio-IT World Conference & ExpoApril 27-29, 2009  

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BIO IT Coalition's 8th annual Conference - April 22, 2009 

Combining Technology and PK/PD Expertise to Optimize Drug Development: A New Era for Collaborative Environments in Translational Medicine- Wednesday, April 22nd

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Electronic Submissions
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The Statistical Center for HIV/AIDS Research and Prevention (SCHARP) statisticians and internal IT staff created an Integrated Data Management System for Clinical Research working closely with open-source LabKey Server systems. The system enables collaborators to more rapidly: Analyze / Validate / Share datasets from labs and clinics around the world, as they are collected.  Learn more about this system, and how it can be rapidly deployed. Download this complimentary whitepaper and case study. 

Applications of LIMS for Enhanced Productivity in Translational Discovery Research
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Translational research can improve the effectiveness of drug research and target discovery pursuits. However, managing the massive amounts of data has posed enormous challenges for –omics and biorepository labs. This white paper discusses the latest developments in translational research and describes how an adaptive data infrastructure and a flexible Lab Information Management Solution (LIMS) framework can be pivotal for successful Translational Research. Download now

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

Life Science Webcasts
Modeling Caloric Restriction
Using their causal network modeling (CNM) platform, Renee Kenney and her team at Genstruct helped Sirtris Pharmaceuticals model how two of their SIRT1 compounds worked and show that one compound in particular is much more potent at mimicking caloric restriction than resveratrol, an active ingredient in red wine.
 View the webcast.

Paul Bleicher, Looking Back at Phase Forward
After founding Phase Forward more than a decade ago and serving as Chairman until late last year, Paul Bleicher has had a prime perch from which to observe and drive change in the e-clinical industry. In this exclusive Life Sciences TV Webcast to mark his decision to step down as Chairman last last year, Bleicher looks back with Bio-IT World Editor Kevin Davies on a decade of achievement and hints at his next venture in the health care arena.
 View the webcast.

Exploring Next-Generation Sequencing
Bio-IT World Editor-in-Chief Kevin Davies interviews BGI's Laurie Goodman on the sequencing of the first Asian genome.
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View the Predictive Biomedicine newsletter archives here.

Cambridge Healthtech InstitutePublished by Cambridge Healthtech Media Group, division of CHI, Copyright © 2009; All rights reserved. Predictive Biomedicine 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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Translational research can improve the effectiveness of drug research and target discovery pursuits. However, managing the massive amounts of data has posed enormous challenges for –omics and biorepository labs. This white paper discusses the latest developments in translational research and describes how an adaptive data infrastructure and a flexible Lab Information Management Solution (LIMS) framework can be pivotal for successful Translational Research. Download now