The explosion of “omic” data has energized mathematical modeling and simulation of biological systems. Track 4 provides in-depth modeling approaches from in silico to in vivo with an emphasis on drug discovery, ADME predictions, and systems medicine.

TUESDAY, APRIL 20

2:00 - 6:00 pm Main Conference Registration

4:00 Event Chairperson’s Opening Remarks

Cindy Crowninshield, Conference Director, Cambridge Healthtech Institute

Presented by
4:05  Keynote Introduction: Ronald Ranauro, Chief Executive Officer, GenomeQuest, Inc.

4:15 PLENARY KEYNOTE: Drug Discovery Opportunities and Challenges -- VC, Biotech and Pharma Perspectives Christoph Westphal, M.D., Ph.D., CEO, Sitris Pharmaceuticals; Senior Vice President, Center of Excellence for External Drug Discovery, GlaxoSmithKline

 

5:00 - 7:00 pm Welcome Reception in the Exhibit Hall

***Drop off your business card at the CHI Sales Booth for a chance to win an Apple® - iPod nano®!  2 Winners will be announced at 6:45pm in the Exhibit Hall

 

Wednesday, April 21

7:30 am Registration and Morning Coffee

Sponsored by
 8:15 Event Chairperson’s Opening Remarks

Phillips Kuhl, Co-founder and President, Cambridge Healthtech Institute

Keynote Introduction: Jamie Wyatt, Vice President and General Manager Health and Life Sciences, Netezza

8:20 PLENARY KEYNOTE: Impact of HIT Stimulus on Novel Sources of Data for Research John Halamka, M.D., M.S., CIO, Harvard Medical School           9:00 Keynote Presentation & 2010 Benjamin Franklin Award  Alex Bateman, Ph.D., Senior Investigator, Pfam Database Project, Wellcome Trust Sanger Institute

 

Sponsored by
 9:30 Coffee Break, Poster and Exhibit Viewing

 ***Drop off your business card at the CHI Sales Booth for a chance to win 1 of 2 Prizes! (Nintendo® Wii™ System or Apple® - iPod touch®)

 

DATA MODELING:
ENABLING SYSTEMS MEDICINE

10:50 Track Chairperson’s Remarks
Mary Ann Brown, Executive Director of Conferences, Cambridge Healthtech Institute

11:00 Featured Speaker A Roadmap for Systems Medicine of Pulmonary Diseases Charles Auffray, Ph.D., Research Director, Functional Genomics and Systems Biology for Health, CNRS Institute of Biological Sciences Complex inflammatory diseases such as chronic obstructive pulmonary disease and asthma represent a major health burden worldwide. The primary causes and mechanisms of these diseases remain to a large extent unknown, preventing the development of more efficient diagnosis and treatment. An integrative systems biology research strategy is being developed to overcome these limitations. It relies on careful experimental design for the collection and integration of relevant data amenable to computational modeling and simulation, complying with the roadmap for systems medicine.

 

11:30 Systems Neuromedicine: Connecting the Periphery to the CNS

Timothy Mhyre, Ph.D., Assistant Professor, Neurology, Georgetown University

Many neurological disorders are systemic but such peripheral features often elude detection. We are exploiting a systems approach to define the peripheral characteristics of neurological disorders by analyzing blood. In the presentation our work on Alzheimer and Parkinson disease will be discussed to illustrate the approach. The scientific and clinical impact of the systems neuromedicine approach will be discussed.

12:00 pm Selected Poster Presentation: Hit Lists Are Just the Beginning
Dominique Gorse, Ph.D., Technical Manager, Advanced Informatics, University of Queensland

    Sponsored by
 12:30 Luncheon Presentation 

A Multi-Center Translational Research Informatics Platform Based on Cloud and Semantic Web Technologies for NCI EDRN Early Detection Cancer Research Program
Daniel Crichton, Informatics PI, NASA's Jet Propulsion Laboratories
James DeGreef, Vice President Market Strategy, GenoLogics Life Sciences Software
An end-to-end translational research informatics solution from discovery to validation to knowledge management, provisioned by NASA JPL and GenoLogics for NCI EDRN and Canary Foundation Lung Cancer Research Program, leveraging cloud computing and semantic web technologies.

 

 

DATA GENERATION:
GOOD MODELS START WITH GOOD DATA

1:40 Chairperson’s Remarks

Paul McDonagh, Ph.D., VP, Discovery Biology, Gene Network Sciences

1:45 Advancing Predictive and Quantitative Personalized Medicine by Inferring Cause and Effect in Clinical and Molecular Data

Paul McDonagh, Ph.D., VP, Discovery Biology, Gene Network Sciences

With a simple blood test, newborn infants are tested for harmful metabolic conditions that aren’t apparent at birth. These simple and effective personalized medicine tests prevent future suffering. We show that they can also be used to illustrate logic that can be captured in mathematics and consistently applied to 10,000’s of variables, including genetics, gene expression and clinical outcomes collected from existing patients. The insights that come from this integrated data analysis include the ability to find new therapeutic targets, surrogate endpoints and patient stratification markers.

2:15 Data Integration not Isolation: The Role of Computational Systems Biology in the Discovery of Antibody Therapeutics

John M. Burke, Ph.D., Associate Director, Systems Biology, Boehringer Ingelheim Pharmaceuticals

Using this validated model, simulations predict that the effective half-life of higher binding affinity antibodies assumes the half-life of mechanistically irrelevant compartment and is insensitive to half-life extension, while the effective half-life of lower binding affinity antibodies are sensitive to half-life extension. This suggests that increasing affinities would make candidates less efficacious by reducing effective half-life, while half-life extension and affinity ‘de-maturation’ of low affinity therapeutics could potentially enhance efficacy. In an integrated fashion, Computational Systems Biology analysis offers suggestions to the project team to determine optimal binding affinities, doses, and optimal dosing strategies to maintain high efficacy, low cost of good and shorten timelines.

Presented by
2:45 Featured Presentation

The BIG Idea: Strategies to Achieve a Rapid-Learning Health System

(Joint Talk with Tracks 2, 3, 4, 6, and 7)

Ken Buetow, Ph.D., Associate Director, Bioinformatics and Information Technology, National Cancer Institute

Considerable momentum has been building in government, academe and the commercial sector towards implementation of a “rapid-learning health system”. In this approach to biomedicine, research and clinical care are seamlessly linked in a virtuous circle that enables the collection and analysis of information on clinical outcomes of large populations. This talk will outline the requisite components of such a system—including a mega-community called the BIG Health Consortium™ encompassing the various sectors of biomedicine and electronic interoperability that enables the liquidity of information—and will showcase this new model in action.

3:15 Refreshment Break, Poster and Exhibit Viewing

***Drop off your business card at the CHI Sales Booth for a chance to win 1 of 2 Prizes! (Nintendo® Wii™ System or Apple® - iPod touch®)   Winners will be announced at 3:30pm in the Exhibit Hall

DATA INTEGRATION:
MODELING DISPARATE “OMIC” SOURCES

3:45 Multi-Scale Cancer Modeling

Thomas S. Deisboeck, M.D., Associate Professor, Radiology, Massachusetts General Hospital, Harvard Medical School

This talk will focus on modeling cancer as a complex dynamic, multi-scaled biosystem where macroscopic behavior is determined by microscopic cell-cell and cell-microenvironment interactions that in turn are guided by dynamics on the sub-cellular level.

4:15 Controlling the Human Proteome: What Do We Know and What Can We Do?

Florian Nigsch, Ph.D., Postdoctoral Fellow, Lead Discovery Informatics, Novartis Institute for Biomedical Research

Our efforts to unite several chemical biology sources of compound activity information led to a repository that holds 20 million activity records of 3 million distinct compounds. This data was placed into a rich biological context through extensive target normalization and the use of GeneGo MetaBase to provide pathways, regulatory network, disease and other relevant information for drug discovery. An in-depth analysis reveals pharmacological hotspots and provides information on the global coverage of the human proteome, as well as new opportunities for drug discovery.

Sponsored by
4:45 Knowledge Management: Issues and Solutions from the Vendor’s Perspective

Yuri Nikolsky, Ph.D., CEO, GeneGo, Inc.

Recently, “knowledge management” became one of the most popular buzz-words in the pharmaceutical and biotech industries. This term is associated with a paradigm shift in life science IT from data collection, integration and management (currently, a realm of IT professionals and computational scientists) to “data mining” and analysis to be done by end users – biologists, chemists and clinicians. The shift from “IT” to “knowledge management” requires unified representation of different types of data, significant simplification of data exchange and communication between different groups within drug discovery, and development of intuitive visualization and analytical tools for “functional” analysis – such as biological pathways and networks. Some of important issues to be discussed include:
- Knowledge organization – terms, vocabularies and ontologies. Currently, life sciences “knowledge space” is highly compartmentalized alongside the field of study. Each discipline operates in its own semantic environment, with terms not aligned or incompatible between the fields. This problem is particularly pronounced in novel “hybrid” fields such as translational medicine or “systems pharmacology”.
- Data organization and semantic consistency between databases. Every “knowledge base” in life sciences has its own philosophy and purpose, reflected in data structure, exchange and retrieval tools etc. In the absence of mandatory “common speech” standards, the databases are poorly compatible.
- Communication between different specialty groups within drug discovery. Different groups of end users apply different terminology and tools which need to be unified through synonyms and vocabularies.
- Standardization of terms, concepts and ontologies throughout the industry and pubic domain.
As one of the leading providers of tools and databases in pathway biology and functional data analysis, GeneGo is deeply involved in the transition to the “knowledge management” paradigm in life science IT. I will describe the challenges, possible solutions and the time frame the way we see it from a vendor’s perspective.

5:00 – 5:15 Sponsored Presentation (Opportunity Available)

5:15 – 6:15 2010 Best of Show Awards in the Exhibit Hall

6:15 Exhibit Hall Closes

Sponsored by
6:30 – 10:00 2010 Best Practices Awards Reception & Dinner

 

 

 

 

 

THURSDAY, APRIL 22

8:00 am Registration and Morning Coffee

Sponsored by
8:45 Event Chairperson’s Opening Remarks

Kevin Davies, Ph.D., Editor-in-Chief, Bio-IT World

Keynote Introduction:  Eric Blatte, Vice President of Sales, Commercial & Public Sector, Imprivata

8:50 PLENARY KEYNOTE: There is No Magic, There is Only Awesome: Scientific Computing with Amazon Web Services Deepak Singh, Ph.D., Business Development Manager, Amazon Web Services   Presentation delivered via a live, interactive videoconferencing platform.     9:30 KEYNOTE PANEL The Future of Personal Genomics A special plenary panel discussion featuring: James Heywood, Co-founder and Chairman, PatientsLikeMe Dan Vorhaus, J.D., M.A., Attorney, Robinson, Bradshaw & Hinson; Editor, Genomics Law Report Dietrich Stephan, Ph.D., President & CEO, Ignite Institute Kári Stefánsson, MD, Dr Med, Executive Chairman and President of Research, deCODE genetics Kevin Davies, Ph.D., Editor-in-Chief, Bio-IT World

 

10:30 Coffee Break, Poster Competition, Vendor Theater Presentations and Exhibit Viewing

***Drop off your business card at the CHI Sales Booth for a chance to win 1 of 2 Prizes! (Nintendo® Wii™ System or Apple® - iPod touch®)

DATA INTEGRATION:
MODELING DISPARATE “OMIC” SOURCES

10:55 Track Chairperson’s Remarks
Mary Ann Brown, Executive Director of Conferences, Cambridge Healthtech Institute

11:00 Integrative Genomics Approach Identifies Candidate Causal Gene Mediators of Sleep/Wake Phenotypes

Joshua Millstein, Ph.D., Biostatistics, Senior Scientist, Statistical Genetics, Sage Bionetworks

Despite the high prevalence of sleep disorders and overwhelming evidence linking sleep to a myriad of diverse diseases, including diabetes, cardiovascular disease, obesity, and depression, there has been slow progress identifying biomolecular determinants of sleep/wake patterns. We have broken new ground with a data-driven integrative genomics approach investigating the underlying genetics of sleep in mammals by measuring sleep phenotypes, genome-wide genotypes, and transcriptome-wide expression in three brain regions, frontal cortex, hypothalamus, and thalamus in over 300 mice.

11:30 Developing Combinatorial Biomarker Panels for End-Stage Organ Failures

Raymond Ng, CIO, PROOF Centre; Professor of Computer Science, University of British Columbia

The PROOF Centre is a Canadian National Centre of Excellence, with a mandate to develop biomarker panels for clinical use. In this talk, we will give an overview of our projects for heart, kidney and lung failures. We describe a general combinatorial approach which involves transciptomics, proteomics and metabolomics data. If time permits, we will highlight the importance of data cleansing in biomarker discovery.

12:00 pm Informatics Best Practices for Pre-GLP Safety Assessment: Results of Pharma R&D Expert Interviews and Industry Survey

Ernest D. Bush, Ph.D., VP & Research Director, Cambridge Healthtech Associates (CHA)

In order to better understand current strategies and define best or optimal practices in pre-GLP safety assessment, CHA recently conducted a project to explore standard and emerging procedures in safety assessment before the initiation of expensive and resource consuming in vivo GLP toxicology studies. Of particular interest were the use and/or non-use of informatics tools to help predict safety outcomes very early in the drug discovery process. This presentation will focus on the results from interviews of industry experts and the complementary findings from a broad survey of current practitioners in the field; with special focus on what informatics approaches have demonstrated value added insights to pre-GLP safety evaluation.

12:30 Luncheon in the Exhibit Hall

***Drop off your business card at the CHI Sales Booth for a chance to win 1 of 2 Prizes! (Nintendo® Wii™ System or Apple® - iPod touch®) Winners will be announced at 1:45pm in the Exhibit Hall

2:00 Exhibit Hall Closes

 

DATA VALIDATION: FROM BENCHTOP
TO CLINICAL OUTCOMES

1:55 Track Chairperson’s Remarks
Stephen Edwards, Ph.D., Systems Biologist, National Health and Environmental Effects Research Laboratory (NHEERL), U.S. Environmental Protection Agency

2:00 Systems Biology & Mode of Action Based Risk Assessment

Stephen Edwards, Ph.D., Systems Biologist, National Health and Environmental Effects Research Laboratory (NHEERL), U.S. Environmental Protection Agency

The application of systems biology for risk assessment of environmental chemicals is a natural extension of its use in pharmaceutical research. The basis for this is the concept of a key event network that builds on existing mode of action frameworks for risk assessment. The application of molecular networks derived from gene expression data for prediction of susceptible subpopulations of asthmatics and for characterization of disruption of the hypothalamic-pituitary-gonadal axis in fish will be presented.

2:30 Using Computational Neuropharmacology to Support Research & Development in CNS Disorders

Hugo Geerts, Ph.D., COO, Computational Neuropharmacology, In Silico Biosciences

Computational Neuropharmacology is a mathematical and mechanistic CNS disease model, based upon the physiology of brain targets, the interaction of drugs with these targets and the introduction of human pathology from imaging, genotypic and postmortem data. This platform for schizophrenia and cognitive disorders is retrospectively validated by correlating the model outcomes with actual clinical effects of antipsychotics on well-defined clinical scales. This technology is a powerful tool to support a variety of decision processes in preclinical and clinical CNS R&D.

3:00 Design of Surrogate Safety Biomarkers Using Pre-Clinical Poly Pharmacology and in vivo Data by a Novel Multi-Dimensional Data Mining Technology (KEM)

Mohammad Afshar, M.D., Ph.D., CEO, Management, Ariana Pharmaceuticals

Development of surrogate Safety Markers is a key driver to increasing success in clinical trials. The contrast between the small number of patients versus the large number of parameters observed pushes existing statistical methods to their limits. Logic based data mining techniques such as KEM has been shown to be effective in early identification of robust safety signatures. Examples will be shown.

3:30 Safety Informatics: Enhancing Quality of Integrated Risk Assessment

Dmitri Mikhailov, Ph.D., Center for Proteomic Chemistry, Novartis Institutes for Biomedical Research, Inc.

Novartis has established informatics approaches to enable integrated safety assessment in discovery phase. These include decision support applications for prospective risk evaluation based on broad in vitro safety pharmacology panel. In addition, we have developed and applied predictive chemogenomics methods to generate off-target mechanistic hypotheses for compounds that have shown toxicity in preclinical and clinical studies and to suggest possible follow up studies. The talk will include several case studies.

4:00 Conference Adjourns

Apple® - iPod touch®,  Nano®, Nintendo® Wii™, are  not sponsors or participants in this program.