Jake Y. Chen, Ph.D.
Assistant Professor of Informatics and Computer Science
Indiana University School of Informatics
Purdue University Dept. of Computer & Information Science
Founding Director
Indiana Center for Systems Biology and Personalized Medicine
Advisory Committee Members of
IU School of Medicine Translational Genomics Core
IU Center for Environmental Health
Members of
IU Center for Computational Biology & Bioinformatics
IUPUI Center for Bio-computing
Office:
719 N. Indiana Ave
Phone: (317) 278-7604
E-mail: jakechen@iupui.edu
Disocery Informatics & Computing Lab:
http://bio.informatics.iupui.edu/
Lab Phone: (317) 274-7542
Primary Research Areas: Discovery Informatics, Systems and Network Biology, Scientific Data Management and Data Mining
An Brief Biography
Dr. Jake Chen is a scientist, educator, technologist, enthusiastic entrepreneur, and amateur investment analyst.
As a scientist, he conducts active research in the area of bioinformatics, scientific data management and data mining, functional genomics, proteomics, and systems and network biology. Since 2002, he has successfully obtained funding from institutional, foundation, federal, and international sources as principle investigator (PI) or co-PI, bringing in more than 10 grants and combined value of $7.2million to support research and education efforts in large interdisciplinary research teams. He has authored or co-authored more than 30 peer-reviewed articles in scientific journals, conference proceedings, or academic books. Each year, he serves on several international conference program committee in bioinformatics, chairs or co-chairs high-quality international conferences and workshops in his field, reviews research papers submitted to top journals in the field of bioinformatics, and gives many invited bioinformatics and database related seminars and lectures worldwide to disseminate scientific discovery methods and results. He is an IEEE senior member and chairs of several local, regional, and national professional organizations dedicated to bio-computing.
As an educator, he founded the "Discovery Informatics and Computing Laboratory" at Indiana University - Purdue University Indianapolis, IN in early 2004 with $30k startup fund, based on a novel concept of "Discovery Informatics" that dates back to his doctoral research at the University of Minnesota. Today, the laboratory has boasted the hosting of IU's largest Oracle-powered data warehouse, which consists of dozens of integrated biological databases available publicly, and high-performance computing infrastructure that links to IU Bloomington computing TeraGrid and Purdue's Bindley Bioscience Center at the Discovery Research Park. More than 10 Master/PhD Degree Students from campus-wide programs/departments in Bioinformatics, Computer Science, Biochemistry and Molecular Biology, and Statistics have been through training in the lab. The lab is open to students as "apprentices" to perform hands-on interdisciplinary but independent research projects in databases, data mining, systems biology, and translational biomedical computing. All of the research asssitants from the laboratory so far have been offered excellent internship positions and taken job opportunities in the IT, fiancial, biotech industries or Academic research institutes upon graduation. Many of them won prestigious awards at the school and university levels upon graduation. Many of his MS thesis student authored peer-reviewed research papers as either first or second authors. He teaches several graduate-level courses in "informatics" and enjoys converting the "non-believers" of computing/informatics to active participants of the emerging field.
As a technologist, he has materialized innovative ideas, managed teams, and led high-impact projects to create significant commercial values in emerging industrial markerts. In his PhD thesis work, he invented Similar_Join, a bio-specific database operator that ultimately led to the culmination of collaborative publication and wide-spread adoption of ODM_BLAST of the Oracle 10g database management system with the Oracle Corporation Life Sciences Group. While still a bioinformatics computer scientist at Affymetrix, Inc, Santa Clara, CA in 1998-2002, he developed the concept of "Complex Query Modeling", which he used to solve the challenging problem of bioinformatics GeneChip sequence selections prior to the completion of the human genome project. His innovation helped the company made successful multi-million launch in time for its flagship Human U95, Mouse U74, and Rat U34 commercial GeneChips products. During his tenure as head of computational proteomics at Myriad Proteomics, Inc., Salt Lake City, UT in 2002-2003, he led his department to spearhead data collection and data mining project for the $75million mapping and mining of the first human protein interactome of ~100,000 protein interactions obtained from systematic yeast 2-hybrid methods. His recent invention in systems and network biology informatics methods (US patent pending, pursued by IU) is expected to generate impacts in the discovery of novel drug targets as well as diagnostics biomarkers.
As an enthusiastic and "persistent" entrepreneur, he brings the Silicon Valley "can-do" attitude into several new high-tech business initiatives in Indiana. Drawing from his "garage-style" startup experience back in San Jose, California, he is active in regional entrepreneurial activities including: serving on the steering committee of Indiana Biomedical Entrepreneurs' Network (IBEN), founding MedeoLinx, LLC--a translational drug discovery and biomarker discovery services and technology company located in Indianapolis, IN, and co-founding Predictive Physiology and Medicine (PPM), Inc., a Bloomington, IN company focused on personalized medicine. He enjoys reading Jack Welch, Donald Trump, and Dilberts (yes, they are quite different!) for management and leadership inspirations. He believes that Ted Tuner's motto "Lead, Follow, or Get Out of the Way" is a sound principle to balance ego and teamwork in a result-driven environment.
His hobby used to be classical literature, modern arts, and photography. After witnessing the 2002 stock market meltdown, he found new passion in his "spare time" in investment strategy using statistical, mathmatical, data integration, and data mining techniques. His favorite reading is "A Mathematician Plays the Stock Market", although he disagrees with some of the pessimestic comments there.
