Predictive Biomedicine -- Informatics tools and strategies driving decisions 

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We invite your comments and feedback for this edition of Predictive Biomedicine.
John Russell
Executive Editor

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Merck’s Eric Schadt Discusses Integrative Genomics 
ExonHit Bets on Sapio LIMS 
Merrimack’s SB Compound Enters Humans 
Cancer Biomarker Report
Short News & Analysis

Merck’s Eric Schadt on the Power of Integrative Genomics

By John Russell

Eric Schadt, the scientific executive director of genetics at Merck Research Laboratories and Merck's Rosetta Inpharmatics subsidiary, is a leading proponent of integrative genomics who is decisively proving his point by delivering novel targets to Merck – roughly one-third of Merck’s new targets in  diabetes and obesity.

Given the tough times technology advocates have encountered inside biopharma – largely because tech bets haven’t produced as expected – Schadt’s work is seen by many as the bow of an advancing icebreaker starting to shatter attitudes long frozen against predictive technologies. A mathematician by training, Schadt practices a brand of integrative genomics that builds predictive models of disease by integrating a wide variety of data (SNP, gene expression, etc.).

“I think there’s a growing belief that there’s such a massive amount of data being generated, dumped into the public domain, and the real question of the 21st century is, ‘Who are going to be the right kinds of groups to integrate that information in ways that best informs the biology at the earliest stages.’ I mean that is an information-based game, and who’s going to emerge as the information brokers, the Google of the biomedical and life sciences to tie that together?” he says. More...


Data Management
ExonHit Bets on Sapio LIMS

By John Russell

The laboratory information management system (LIMS) market has long had a reputation for being a messy place where giant and tiny vendors compete with internally developed software. Among the criticisms commonly lobbed at commercial vendors are: that their products inevitably require major customization; that customization is difficult and costly; and that once installed their products are inflexible and difficult to change. Yet these lingering ideas may no longer reflect reality.

What Heather Jordan found in her search for a LIMS for biotech ExonHit was a more nuanced marketplace that fulfilled and defied its stereotype. In the end, the director of operations for ExonHit Therapeutics was able to find a solid commercial offering – Exemplar from Sapio Sciences - whose key strengths were flexibility, ease of use, and fast deployment. Jordan’s experience is instructive and perhaps more representative of today LIMS offerings. More...


Systems Biology
Merrimack Compound Enters Humans

Merrimack Pharmaceuticals says it has advanced the first systems biology product to human clinical development. Merrimack announced the first patient has received an initial dose in a Phase 1 clinical study of its first oncology product, MM-121, a human monoclonal antibody and a first-in-class therapeutic designed to block signaling of the ErbB3 receptor. More...


Cancer Biomarkers Make Progress, Present Challenges

The rush to develop effective biomarkers has perhaps been greatest in cancer. In this interview, taken from Insight Pharma Reports’ recently published study, Cancer Biomarkers: Adoption Is Driving Growth, Roberto Hernán, head of business development for Dominion Pharmakine, reviews trends in cancer biomarker development. More...


Short News & Analysis

(Click To Read Full Briefs) 

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”...

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...

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...

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...

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...

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...

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...

ABI Announces Transcriptome Expression Kit 
Applied Biosystems announced development of a sequencing-based molecular tool for the genomic analysis of whole transcriptomes. This technology is expected to be available for limited release through an early access program in November 2008...

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... 

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...

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...

Click To Read Full Briefs 



Isilon Systems ~ Senior Marketing Communications Manager
Isilon Systems is the worldwide leader in clustered storage systems and software for digital content and unstructured data. We seek an experienced marketing communications professional/writer expert in creating and delivering effective and persuasive business communications. The ideal candidate can think at the strategic and conceptual level and act, simultaneously, as a highly-effective and productive individual contributor. The position is based in Seattle, WA. For additional information
 click here

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) - Manager, Software Engineering (Integrative Computational Sciences)
Join the Integrative Computational Sciences (ICS) department at Lilly Singapore Centre for Drug Discovery (LSCDD),as Manager Software Engineering.  Lead the development of 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. Masters in Computer Science/Engineering or related discipline, 10+ years post graduation experience , 2 years management experience needed. For a complete job description and requirements 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:

Memorial Sloan-Kettering Cancer Center - Linux Systems Administrator
MSKCC Bioinformatics Core in Manhattan seeks Linux Systems Administrator. Install, configure, update, monitor and troubleshoot HPC cluster, email and web servers. Bachelor's degree and 3 years experience with HPC, network security, Postfix, Apache, Tomcat, Grid Engine, Solaris. Email #015429. EOE/AA

Merck ~Sr. Computational Biologist 
Apply and develop computational biology/informatics techniques to support Oncology drug discovery; collaborate with scientists to develop in-depth understanding of deregulated signaling pathways, discover novel targets and treatment strategies, and identify associated candidate biomarkers.
Ph.D. in Computational Biology/Bioinformatics, solid statistics background and hands-on modeling and informatics techniques related to drug discovery experience required.  Click to Apply 

More Life Science Jobs ~ Add a Job Listing



ELNs: Advanced Laboratory Solutions-September 15 - 17 2008 • Crowne Plaza, Brussels, Belgium 

Discovery Knowledge & Informatics - September 15 - 17, 2008 • Crowne Plaza, Brussels, Belgium 

Multiplexed Genomics Tools: Targeting the Missing Links
Between Health and Disease
 - September 21-23, 2008 • Providence, RI

Next-Generation Sequencing Data Analysis -September 22-23, 2008 • Providence, RI

DIA 2nd Annual Clinical Forum: Data Driven Drug Development Decisions - October 20-23, 2008 | Ljubljana, Slovenia

The Fifteenth Annual Biopharmaceutical Applied Statistics Symposium - Nov 3-7,2008~ Savannah, GA

Barnett Educational Services, 2008 Schedule

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

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Tackling “Predictiveness”

Welcome to the inaugural issue of Bio-IT World’s Predictive Biomedicine newsletter which is the expanded, biweekly successor to Bio-IT World’s monthly Systems Biology newsletter.

It's clear that drug developers and healthcare providers want to move beyond their heavy dependence on trial-and-error methods which are costly and often don’t produce the best care. To some extent, the launch of the Systems Biology newsletter two and half years ago was Bio-IT World’s first step in promoting the idea that predictive technologies were needed and in fact being developed. Today, these technologies – while far from reaching their full potential – are decidedly more plentiful and proven. 

This first issue provides a glimpse of how Predictive Biomedicine will tackle its mission. The lead story is an in-depth Q&A with Eric Schadt of Merck Research Laboratory and Merck's Rosetta Inpharmatics subsidiary. Schadt is pioneering the use of integrative genomics to build predictive models of disease and health. About a third of Merck’s targets in Type 1 diabetes and obesity programs have come from Schadt’s group’s work. He says more targets (and in more disease areas) are coming soon.

These leading-edge technologies, however, don’t exist in a vacuum. Predictive Biomedicine will also cover the critical supporting cast of informatics and IT infrastructure without which the modern lab and modern researcher could not function. For example, in a second article, Heather Jordan, director of operations for alternative splicing specialist ExonHit, describes the process she followed in assessing LIMS options before settling on a Sapio Sciences LIMS.

As a subscriber to Systems Biology you will automatically receive Predictive Biomedicine, and we hope you find its content useful and interesting; however you may also easily opt out when you receive the first (or any) issue. Simply scroll down to the bottom of the newsletter and follow the “unsubscribe” link.

Write to me – – with your suggestions for coverage topics or leads to important stories, or thoughts on how we can improve the newsletter. Predictive Biomedicine also welcomes guest commentaries and letters and short papers, so send your ideas for those as well. We’re especially interested in hearing of projects in which the informatics or computational tools drove key decisions. 

To recap, Predictive Biomedicine will cover the development and use of informatics, IT infrastructure, and computational tools to manage, present, and interpret experimental data as well as those used in modeling and bio-simulation. Companies and thought-leaders; products and technologies; relevant research programs and their results will be covered. From data management challenges to systems biology initiatives, Predictive Biomedicine will report on industry’s efforts to reduce dependence on trial and error and to adopt more data-driven predictive methods to drive drug discovery and development and even healthcare delivery.


“Storage for Science – Methods for Managing Large and Rapidly Growing Data Stores in Life Science Research Environments” sponsored by Isilon
Large and rapidly growing stores of file-based and other data are a hallmark of life science research and bioinformatics. Determining how best to manage those data stores has become a significant challenge for Researchers and IT Pros alike.  This paper is intended to:  Provide guidance on the many storage  requirements common to Life Science research;  Explain the evolution of modern storage architectures; Summarize the major data storage architectures currently in use.  Additionally, it will present the Isilon IQ clustered storage product as a strong and flexible solution to those needs. Download now      

Will Healthcare IT Trends Standardize?
A new wave of activities are driving transformation within the healthcare market. One solution is found in a guide to PDF Healthcare Best Practices. This “Best Practices Guide” describes Portable Document Format (PDF) attributes and use to facilitate the capture, exchange, preservation and protection of healthcare information. This webinar will focus on trends in today’s healthcare market, the challenges in overcoming these issues, and finally how to use best practices to improve patient care, enhance productivity and eliminate paperwork. It’s hosted by Adobe and moderated by Digital Healthcare & Productivity Executive Editor, John Russell. Click here... 

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 Expo
Video Highlights

Personalized Genetics: Advancements and Driving Change
Linda Avey, co-founder of 23andMe, delivers her keynote at the 2008 Bio-IT World Conference & Expo in Boston, April 30, 2008.
View the webcast.

The Future of Personal Genomics
A distinguished panel of personal genomics experts discuss the future of personal genomics at the 2008 Bio-IT World Conference & Expo in Boston, April 30, 2008.  They include Dietrich Stephan (co-founder, Navigenics); George Church (Harvard Medical School); Jeff Drazen (editor-in-chief, New England Journal Medicine); Fred Ledley (Bentley College); John Halamka (CIO, Harvard Medical School); and Linda Avey (23andMe). Bio-IT World Editor-in-Chief Kevin Davies moderates the discussion.
View the webcast.


View the Systems Biology newsletter archives here.

Cambridge Healthtech InstitutePublished by Cambridge Healthtech Media Group, division of CHI, Copyright © 2008; 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. 
For reprints and/or copyright permission, please contact The YGS Group, 1808 Colonial Village Lane, Lancaster, PA 17601.  Phone: 717-399-1900, ext. 125. Email: