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Faculty Detail    
Name JAKE Y CHEN
Professor		  
Campus Address THT 137 Zip 1824
Phone  (205) 996-0738
E-mail  jakechen@uab.edu
Other websites Research Publications
Google Scholar Profile
UAB Faculty Profile
Lab Web Site
     

Education
Undergraduate  Peking University    1995  Molecular Biology and Biochemistry 
Graduate  University of Minnesota at Twin Cities    1998  MS in Computer Science and Engineering 
Graduate  University of Minnesota at Twin Cities    2001  PhD in Computer Science and Engineering (minor: Biochemistry and Molecular Biology) 


Faculty Appointment(s)
Appointment Type Department Division Rank
Primary    Professor
Secondary  Computer Science  Computer Science Professor
Secondary  Dept of Biomedical Engineering  Dept of Biomedical Engineering Professor
Center  Comprehensive Cancer Center  Comprehensive Cancer Center Professor
Center  Comprehensive Diabetes Center  Comprehensive Diabetes Center Professor
Center  Ctr for Clinical & Translational Sci  Ctr for Clinical & Translational Sci Professor
Center  Nephrology Research & Training Center  Nephrology Research & Training Center Professor
Center  UAB Immunology Institute  UAB Immunology Institute Professor

Graduate Biomedical Sciences Affiliations
Engineering 
Genetics, Genomics and Bioinformatics 
Immunology 

Biographical Sketch 
Dr. Jake Y. Chen is the Associate Director and Chief Bioinformatics Officer of the UAB Informatics Institute, a Professor of Genetics, Computer Science, and Biomedical Engineering, and Chief of the Informatics Section of the UAB Department of Genetics. Before joining UAB, Dr. Chen was the founding director of the Indiana Center for Systems Biology and Personalized Medicine at Indiana University and a tenured faculty member at Indiana University School of Informatics and Purdue University Computer Science Department. Dr. Chen has over 20 years of research and development experience in biological data mining, systems biology, and translational informatics in both Academia and the industry. He has over 150 peer-reviewed publications and presented worldwide on topics related to biocomputing, bioinformatics, and data sciences in life sciences. He was elected as the President-elect of the Midsouth Computational Biology and Bioinformatics Society (MCBIOS) in 2019. He also serves on the editorial boards of BMC Bioinformatics, Journal of American Medical Informatics Association (JAMIA), and Personalized Medicine. Dr. Chen’s contribution to the field of computational biology and bioinformatics was highly recognized. He was cited as one of “17 Informatics Experts Worth Listening To” by HealthTechTopia (2011), a grand-prize winner of the “Cancer Cell Drug Discovery Grand Challenge” by Innocentive.com (2012), three-time finalist as “Indiana’s Technology Educator of the Year” award by TechPoint (2012-14), and recently as one of the “Top 100 AI Leaders in Drug Discovery and Healthcare” by Deep Knowledge Analytics (2019).

Society Memberships
Organization Name Position Held Org Link
International Society for Computational Biology (ISCB)  Senior Member  www.iscb.org 
Institute of Electrical and Electronic Engineers (IEEE)  Senior Member  www.ieee.org 
Association of Computing Machinery (ACM)  Senior Member  www.acm.org 
American Medical Informatics Association (AMIA)  Member  www.amia.org 
American College of Medical Informatics (ACMI)  Fellow  https://www.amia.org/acmi-fellowship 
 



Research/Clinical Interest
Title
Bioinformatics, Data Mining, and Systems Biology for Precision Medicine Applications
Description
interested in developing bioinformatics algorithms and databases that help improve our understanding of biomedical big data--from genomes to diseases to drugs. Focus is on developing computational knowledge-based models that help predict disease prognosis and gain power in theurapeutic intervention and tailored treatment decision-making processes.

Selected Publications 
Publication PUBMEDID
Nucleic Acids Res. 2019 Jul 2;47(W1):W578-W586
BEERE: a web server for biomedical entity expansion, ranking and explorations.
by Yue Z, Willey CD, Hjelmeland AB, Chen JY. 		 31114876 
Nucleic Acids Res. 2018 Jan 4;46(D1):D668-D676.
PAGER 2.0: an update to the pathway, annotated-list and gene-signature electronic repository for Human Network Biology.
by Yue Z, Zheng Q, Neylon MT, Yoo M, Shin J, Zhao Z, Tan AC, Chen JY. 		 29126216 
Bioinformatics. 2015 Jun 15;31(12):i250-7.
PAGER: constructing PAGs and new PAG-PAG relationships for network biology.
by Yue Z, Kshirsagar MM, Nguyen T, Suphavilai C, Neylon MT, Zhu L, Ratliff T, Chen JY. 		 26072489  
Proteomics. 2013 Jan;13(2):313-24.
Predicting adverse drug reaction profiles by integrating protein interaction networks with drug structures.
by Huang LC, Wu X, Chen JY. 		 23184540  
BMC Syst Biol. 2012;6 Suppl 3:S16.
Genome-wide meta-analysis of genetic susceptible genes for Type 2 Diabetes.
by Hale PJ, López-Yunez AM, Chen JY. 		 23281828 
BMC Genomics. 2010 Nov 2;11 Suppl 2:S12.
Discovery of pathway biomarkers from coupled proteomics and systems biology methods.
Zhang F, Chen JY. 		 21047379  
BMC Genomics. 2009 Jul 7;10 Suppl 1:S16.
HAPPI: an online database of comprehensive human annotated and predicted protein interactions.
by Chen JY, Mamidipalli S, Huan T. 		 19594875 
PLoS Comput Biol. 2009 Jul;5(7):e1000450.
Building disease-specific drug-protein connectivity maps from molecular interaction networks and PubMed abstracts.
by Li J, Zhu X, Chen JY. 		 19649302  
Brief Bioinform. 2009 Mar;10(2):177-92.
Semantic web for integrated network analysis in biomedicine.
by Chen H, Ding L, Wu Z, Yu T, Dhanapalan L, Chen JY 		 19304873  
J Proteome Res. 2006 Nov;5(11):2985-95.
Disorder and sequence repeats in hub proteins and their implications for network evolution.
by Dosztányi Z, Chen J, Dunker AK, Simon I, Tompa P. 		 17081050  
Pac Symp Biocomput. 2006:367-78.
Mining Alzheimer disease relevant proteins from integrated protein interactome data.
by Chen JY, Shen C, Sivachenko AY. 		 17094253 
 

Keywords
Bioinformatics, data mining, data sciences, systems biology, biomarkers, drug discovery application, cancer genomics, personalized medicine