EECS500 Fall 2011 Department Seminar

Jake Chen
Modeling Drug Efficacy and Side Effects using Systems Pharmacology
Indiana University-Purdue University Indianapolis
White Bldg., Room 411
11:30am - 12:30pm
April 26, 2012

Future growth of predictive and personalized medicine relies on integrative development of “robust biomarkers” and “silver-bullet drugs”. While plenty of bioinformatics research studies has focused on identifying biomarkers from genomics, functional genomics, proteomics, and metabolomics data sets, few has asked the fundamental question “What if the drugs being individualized are inadequate to begin with?” To improve success rate of drug discovery, new computational modeling techniques to study both “on-target” and “off-target” effects are needed.

In this talk, I will explore the opportunities and challenges in applying systems biology techniques to modern Omics-era drug discovery. For systems pharmacology, I refer to the development of techniques that utilize network models and dynamic models of genes, drug perturbens, and diseases to the management and improvement of drug efficacy and side effect profiles. Using cancers primarily as examples, I will describe how we 1) develop computational connectivity map to gain high-quality data 2) apply high-coverage high-precision connectivity map data to the study of drug efficacy 3) evaluation of drugs’ therapeutic and side effect profiles from network models. I will share research opportunities and challenges for computational scientists interested in applying “translational bioinformatics” techniques to future pharmacological studies.


Dr. Jake Chen is an associate professor of bioinformatics and computer science at Indiana University - Purdue University Indianapolis (IUPUI), and the founding director of Indiana Center for Systems Biology and Personalized Medicine. He has published more than 100 research papers in bioinformatics, bio-computing, and systems biology, and currently serves on the editorial boards of several international journals including BMC Systems Biology, Personalized Medicine, and Network Biology. He also had substantial biotech industry research experience, which included designing HU-95 Human GeneChip microarrays at Affymetrix in the Silicon Valley and mapping the first draft human protein interactome at Myriad Proteomics, Inc.  He holds a BS degree in Biochemistry and Molecular Biology from Peking University, China, and both MS and PhD degrees in Computer Science and Engineering from the University of Minnesota, Twin Cities.

His efforts in translating informatics discoveries to practical impacts have been recognized nationally. His Indiana startup company Medeolinx has been named a statewide “MIRA Award Finalist” for three years since 2010. In 2011, he was selected by the National Academy to serve on an Institute of Medicine committee that advises FDA on food and drug regulation matters in developing countries. In the same year, he was honored as one of the “17 Informatics Experts Worth Listening To” by HealthTechTopia. In March 2012, he received a “Grand Challenge Award” in cancer systems biology drug discovery by competing against more than 1,000 worldwide research teams at Innocentive.com for the top prize.