Jake Chen

Current

Founding Director at Indiana Center for Systems Biology and Personalized Medicine
Chief Informatics Office and co-Founder at Predictive Physiology and Medicine, Inc.
Founder and CEO at MedeoLinx, LLC

Assistant Professor of Informatics and Computer Science at Indiana University - Purdue University Indianapolis
Member at Indiana University Cancer Center

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2 more...

Past

Head of Computational Proteomics at Prolexys Pharmaceuticals, Inc. (Myriad Proteomics, Inc.)
Bioinformatics Computer Scientist at Affymetrix, Inc.

Education

University of Minnesota-Twin Cities
Peking University
Beijing No. 4 High School

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Recommended

9 people have recommended Jake

Connections

239 connections

Industry

Research

Websites

My Website

Jake Chen’s Summary

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. He is an assistant professor of Informatics (at Indiana University) and Computer Science (at Purdue) and the founding director of Indiana Center for Systems Biology and Personalized Medicine, located at Indiana University - Purdue University Indianapolis, IN. 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 $7.4million 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.

Jake Chen’s Specialties:

Research and Development in Bio-computing, Data Management, Data Mining, and Systems Network Biology. Silicon Valley business startup experience. High-tech research fund raising and business planning. Management of Informatics teams.

Jake Chen’s Experience

Founding Director

Indiana Center for Systems Biology and Personalized Medicine

(Educational Institution; 11-50 employees; Research industry)

January 2008 — Present (9 months)

* develop strategic directions and plans for center development
* develop focused research programs and members
* communicate with center members latest developmnet
* supervise research programs supported by the center
* develop intramural and extramural partnerships both within and beyond the Indiana community.
Chief Informatics Office and co-Founder

Predictive Physiology and Medicine, Inc.

(Privately Held; 1-10 employees; Biotechnology industry)

May 2006 — Present (2 years 5 months)

Planning of 500-TB level informatics build-up of a future personalized medicine company, in connection with solid scientific and business talents in central Indiana, USA.
Founder and CEO

MedeoLinx, LLC

(Privately Held; 1-10 employees; Biotechnology industry)

January 2006 — Present (2 years 9 months)

MedeoLinx is an informatics-driven biotech company dedicated to helping pharmaceutical, biotech, and diagnostic companies solve complex data management and knowledge discovery problems. The company is founded on the frontiers of university/industrial collaborative R&D in network bioinformatics, systems biology, virtual screening, and chemical screening.
Assistant Professor of Informatics and Computer Science

Indiana University - Purdue University Indianapolis

(Educational Institution; 5001-10,000 employees; Research industry)

January 2004 — Present (4 years 9 months)

* Founded the "Discovery Informatics and Computing Laboratory" at Indiana University - Purdue University Indianapolis, IN in early 2004 with $30k startup fund.
* The Lab is currently hosting IU's largest Oracle-powered bioinformatics data warehouse, which is the hub data resources that link 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 focuses on interdisciplinary research projects in databases, data mining, systems biology, and translational biomedical computing.
* Developed and teaches several graduate-level courses, including "Introduction to Informatics", "Database Systems", "Web Database Concepts", and "Discovery Informatics in Biomedical Sciences".
Member

Indiana University Cancer Center

(Research industry)

2004 — Present (4 years)
Head of Computational Proteomics

Prolexys Pharmaceuticals, Inc. (Myriad Proteomics, Inc.)

(Privately Held; 51-200 employees; Biotechnology industry)

May 2002 — December 2004 (2 years 8 months)

* Created and managed a bioinformatics department of 7 staffs (3 PhDs and 4 Masters) on an annual budget of ~1.5million dollars.
* In less than 2 years, led the group to create a terabyte-scale data processing and warehousing system to help company perform knowledge discovery of ~80,000 human protein interactions from 1.5 million yeast 2-hybrid search experiments.
* Led and executed successful collaborations with companies such as Oracle, Spotfire, PubGene and researchers at MIT Whitehead.
* Facilitated company's business model change based on group's bioinformatics discovery of dozens of promising drug candidates in colon cancer and neurodegenerative diseases.
Bioinformatics Computer Scientist

Affymetrix, Inc.

(Public Company; 1001-5000 employees; AFFX; Biotechnology industry)

June 1998 — May 2002 (4 years)

* First year as "senior informatics consultant" for the bioinformatics department.
* Led sequence selections for Affymetrix GeneChip products of human U95, mouse U74, and rat U34, which generated multi-million dollar monthly revenue for the company.
* Influenced corporate IT upgrade of Sun E6k to Sun E10k due to work in high-performance parallel computing.
* Conducted large-scale discovery informatics research in high-throughput EST clustering, complex data model design, datawarehouse design, SNP discovery, gene expression algorithm development, etc.

Jake Chen’s Education

University of Minnesota-Twin Cities

Ph.D., Computer Science, 1995 — 2001
Peking University

BS, Biochemistry and Molecular Biology, 1990 — 1995
Beijing No. 4 High School

diploma, 1987 — 1990

Additional Information

Jake Chen’s Websites:

My Website

Jake Chen’s Groups:

Institute of Electrical and Electronic Engineers (IEEE), Association of American Computing Machinery (ACM), International Society of Computational Biology (ISCB), Life Sciences Society (LSS), Indiana Biomedical Entrepreneur Network (IBEN)