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Faculty Detail    
Campus Address THT 137 Zip 1824
Phone  (205) 996-0738
Other websites Research Publications
Google Scholar Profile
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Lab Web Site

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  Genetics   Genetics Chair Office 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  General Clinical Research Center  Ctr for Clinical & Translational Sci Professor

Graduate Biomedical Sciences Affiliations
Genetics, Genomics and Bioinformatics 

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 (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
American College of Medical Informatics (ACMI)  Fellow 
American Medical Informatics Association (AMIA)  Member 
Association of Computing Machinery (ACM)  Senior Member 
Institute of Electrical and Electronic Engineers (IEEE)  Senior Member 
International Society for Computational Biology (ISCB)  Senior Member 

Research/Clinical Interest
Bioinformatics, Data Mining, and Systems Biology for Precision Medicine Applications
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. 
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. 
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. 
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. 
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. 
BMC Genomics. 2010 Nov 2;11 Suppl 2:S12.
Discovery of pathway biomarkers from coupled proteomics and systems biology methods.
Zhang F, Chen JY. 
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. 
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. 
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 
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. 
Pac Symp Biocomput. 2006:367-78.
Mining Alzheimer disease relevant proteins from integrated protein interactome data.
by Chen JY, Shen C, Sivachenko AY. 

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