• Dr. Chen conducts research in “translational bioinformatics”—the science of collecting, representing, storing, retrieving and processing data and knowledge for the improvement of human health. His research interest focus on systems biology, data mining, advanced visual analytics for therapeutic discovery and clinical decision-making applications. He has published more than 130 peer-reviewed scientific papers and edited two bioinformatics books, “Biological Database Modeling” and “Biological Data Mining”. He has organized many conferences, among which the BIOKDD workshop at the Annual ACM Knowledge Discovery and Data Mining Conference have been running consecutively for nearly two decades. He is a frequent grant review panelist for NIH, NSF, and DOD in bioinformatics. He was named a finalist as “Indiana’s Technology Educator of the Year” for his contribution to informatics research, education, and entrepreneurship in the state of Indiana.
  • Selected Publications

    Academic Article

    Year Title Altmetric
    2020 Decoding SARS-CoV-2 hijacking of host mitochondria in COVID-19 pathogenesis. 2020
    2020 IL-23 Promotes a Coordinated B Cell Germinal Center Program for Class-Switch Recombination to IgG2b in BXD2 Mice.Journal of Immunology.  205:346-358. 2020
    2019 Association of CMV genomic mutations with symptomatic infection and hearing loss in congenital CMV infectionBMC Infectious Diseases.  19. 2019
    2019 A systematic simulation-based meta-analytical framework for prediction of physiological biomarkers in alopecia.Journal of Biological Research.  26:2. 2019
    2019 BEERE: a web server for biomedical entity expansion, ranking and explorationsNucleic Acids Research.  47:W578-W586. 2019
    2018 Simulation study of cDNA dataset to investigate possible association of differentially expressed genes of human THP1-monocytic cells in cancer progression affected by bacterial shiga toxinsFrontiers in Microbiology.  9. 2018
    2018 PAGER 2.0: An update to the pathway, annotated-list and gene-signature electronic repository for Human Network BiologyNucleic Acids Research.  46:D668-D676. 2018
    2018 Regenerative potential of neonatal porcine heartsCirculation.  138:2809-2816. 2018
    2017 Repositioning drugs by targeting network modules: A Parkinson's disease case studyBMC Bioinformatics.  18. 2017
    2017 HAPPI-2: A Comprehensive and High-quality Map of Human Annotated and Predicted Protein InteractionsBMC Genomics.  18. 2017
    2017 Repositioning drugs by targeting network modules: a Parkinson's disease case study. 2017
    2016 A method for identifying discriminative isoform-specific peptides for clinical proteomics applicationBMC Genomics.  17. 2016
    2016 Proteomic Characterization Reveals That MMP-3 Correlates With Bronchiolitis Obliterans Syndrome Following Allogeneic Hematopoietic Cell and Lung TransplantationAmerican Journal of Transplantation.  16:2342-2351. 2016
    2015 A method for developing regulatory gene set networks to characterize complex biological systemsBMC Genomics.  16. 2015
    2015 DMAP: A connectivity map database to enable identification of novel drug repositioning candidatesBMC Bioinformatics.  16. 2015
    2015 MicroRNA expression profiling of human respiratory epithelium affected by invasive candida infectionPLoS ONE.  10. 2015
    2015 Knowledge Discovery Using Big Data in Biomedical SystemsIEEE/ACM Transactions on Computational Biology and Bioinformatics.  12:726-728. 2015
    2015 PAGER: Constructing PAGs and new PAG-PAG relationships for network biologyBioinformatics.  31:i250-i257. 2015
    2014 Pathway and network analysis in proteomicsJournal of Theoretical Biology.  362:44-52. 2014
    2014 SLDR: A computational technique to identify novel genetic regulatory relationshipsBMC Bioinformatics.  15. 2014
    2014 Seed-weighted random walk ranking for cancer biomarker prioritisation: A case study in leukaemiaInternational Journal of Data Mining and Bioinformatics.  9:135-148. 2014
    2013 Network medicine: Finding the links to personalized therapyClinical Pharmacology and Therapeutics.  94:613-616. 2013
    2013 Predicting adverse drug reaction profiles by integrating protein interaction networks with drug structuresProteomics.  13:313-324. 2013
    2012 Genome-wide meta-analysis of genetic susceptible genes for Type 2 DiabetesBMC Systems Biology.  6. 2012
    2012 PAGED: A pathway and gene-set enrichment database to enable molecular phenotype discoveriesBMC Bioinformatics.  13. 2012
    2012 Network Expansion and Pathway Enrichment Analysis towards Biologically Significant Findings from Microarrays.Journal of Integrative Bioinformatics.  9:113-125. 2012
    2012 C²Maps: a network pharmacology database with comprehensive disease-gene-drug connectivity relationships.BMC Genomics.  13 Suppl 6:S17. 2012
    2012 Network expansion and pathway enrichment analysis towards biologically significant findings from microarrays.Journal of Integrative Bioinformatics.  9:213. 2012
    2012 Reordering based integrative expression profiling for microarray classification.BMC Bioinformatics.  13 Suppl 2. 2012
    2011 An integrated proteomics analysis of bone tissues in response to mechanical stimulationBMC Systems Biology.  5. 2011
    2011 Predicting adverse side effects of drugsBMC Genomics.  12. 2011
    2011 HOMER: A human organ-specific molecular electronic repositoryBMC Bioinformatics.  12. 2011
    2011 Data mining methods in Omics-based biomarker discovery.Methods in Molecular Biology.  719:511-526. 2011
    2011 Disease phenotypes and gender association of FCRL3 single-nucleotide polymorphism -169T/C in Taiwanese patients with systemic lupus erythematosus and rheumatoid arthritisJournal of Rheumatology.  38:264-270. 2011
    2010 A new approach to construct pathway connected networks and its application in dose responsive gene expression profiles of rat liver regulated by 2,4DNTBMC Genomics.  11. 2010
    2010 Impact of sildenafil therapy on pulmonary arterial hypertension in adults with congenital heart disease 2010
    2010 Discovery of pathway biomarkers from coupled proteomics and systems biology methodsBMC Genomics.  11. 2010
    2010 PEPPI: A peptidomic database of human protein isoforms for proteomics experimentsBMC Bioinformatics.  11. 2010
    2010 PEPPI: a peptidomic database of human protein isoforms for proteomics experiments.BMC Bioinformatics.  11 Suppl 6:S7. 2010
    2010 [The use of kidney-shaped pressure bandage to prevent postoperative salivary fistula].Shanghai kou qiang yi xue = Shanghai journal of stomatology.  19:144-146. 2010
    2010 A GMM-IG framework for selecting genes as expression panel biomarkersArtificial Intelligence in Medicine.  48:75-82. 2010
    2010 MG-132 Inhibits Carcinoid Growth and Alters the Neuroendocrine PhenotypeJournal of Surgical Research.  158:15-19. 2010
    2009 HPD: an online integrated human pathway database enabling systems biology studies.BMC Bioinformatics.  10 Suppl 11:S5. 2009
    2009 HAPPI: An online database of comprehensive human annotated and predicted protein interactionsBMC Genomics.  10. 2009
    2009 Pattern discovery in breast cancer specific protein interaction network.Summit on translational bioinformatics.  2009:1-5. 2009
    2009 Connecting protein interaction data, mutations, and disease using bioinformatics.Methods in Molecular Biology.  541:449-461. 2009
    2009 Disease gene-fishing in molecular interaction networks: A case study in colorectal cancerProceedings of the 31st Annual International Conference of the IEEE Engineering in Medicine and Biology Society: Engineering the Future of Biomedicine, EMBC 2009.  6416-6419. 2009
    2009 Dissecting the human plasma proteome and inflammatory response biomarkersProteomics.  9:470-484. 2009
    2009 Finding fractal patterns in molecular interaction networks: A case study in Alzheimer's diseaseInternational Journal of Computational Biology and Drug Design.  2:340-352. 2009
    2009 Network topological reordering revealing systemic patterns in yeast protein interaction networksProceedings of the 31st Annual International Conference of the IEEE Engineering in Medicine and Biology Society: Engineering the Future of Biomedicine, EMBC 2009.  6954-6957. 2009
    2008 ProteoLens: A visual analytic tool for multi-scale database-driven biological network data miningBMC Bioinformatics.  9. 2008
    2008 HIP2: an online database of human plasma proteins from healthy individuals.BMC Medical Genomics.  1:12. 2008
    2007 A systems biology approach to the study of cisplatin drug resistance in ovarian cancers.Journal of Bioinformatics and Computational Biology.  5:383-405. 2007
    2007 A case study of integrating protein interaction data using semantic web technologyInternational Journal of Bioinformatics Research and Applications.  3:286-302. 2007
    2007 Tumor necrosis factor-α- and interleukin-1-induced cellular responses: Coupling proteomic and genomic informationJournal of Proteome Research.  6:2176-2185. 2007
    2006 A statistical framework to discover true associations from multiprotein complex pull-down proteomics data sets 2006
    2006 A systems biology case study of ovarian cancer drug resistance.Computational systems bioinformatics / Life Sciences Society. Computational Systems Bioinformatics Conference.  389-398. 2006
    2005 Data mining in protein interactomics 2005


    Year Title Altmetric
    2014 Computational biomarker discovery.  355-386. 2014
    2013 Ethics and privacy considerations for systems biology applications in predictive and personalized medicine.  1378-1404. 2013
    2010 Techniques for Prioritization of Candidate Disease Genes.  307-324. 2010
    2009 Molecular Interaction Networks: Topological and Functional Characterizations.  145-174. 2009

    Investigator On

  • Center for Clinical and Translational Science (3 Linked Awards UL1, KL2, TL1)  awarded by National Center for Advancing Translational Sciences/NIH/DHHS 2019 - 2024
  • Biological Comparisons Among Three Derivative Models of Glioma Patient Cancers Under Microenvironmental Stress  awarded by National Cancer Institute/NIH/DHHS 2018 - 2023
  • Characterization of the Lupus Nephritis microRNAome  awarded by National Institute of Arthritis & Musculoskeletal & Skin Diseases/NIH/DHHS 2018 - 2023
  • B Cell Intrinsic Interferon-beta Regulates Autoreactive B Cell Development  awarded by National Institute of Allergy and Infectious Diseases/NIH/DHHS 2018 - 2023
  • Targeting Metabolic Checkpoints in the Tumor Microenvironment to Boost Efficacy of Anti-CTLA-4  awarded by National Cancer Institute/NIH/DHHS 2019 - 2021
  • Private Grant  awarded by BRISTOL-MYERS SQUIBB COMPANY 2019 - 2021
  • Genetic Prediction for Treatment Resistance in Kawasaki Disease  awarded by SEATTLE CHILDREN'S RESEARCH INSTITUTE 2018 - 2020
  • Metabolic Checkpoints in Anti-CTLA-4 and Anti-PD-1 Immunotherapies  awarded by V FOUNDATION FOR CANCER RESEARCH 2018 - 2020
  • Molecular, Functional and Structural Analyses of Anti-PAD Antibodies in Rheumatoid Arthritis  awarded by National Institute of Allergy and Infectious Diseases/NIH/DHHS 2019 - 2020
  • A National Center for Digital Health Informatics Innovation  awarded by Oregon Health & Science University 2019 - 2020
  • Network Biology Modeling to Enhance Bioinformatic Characterization of Heart Regeneration  awarded by University of Maryland 2020
  • Single Nucleus RNA Sequencing in Pig Heart Development and Regeneration  awarded by University of Maryland 2020
  • B-Cell Control Point Dysregulation in African Americans with SLE  awarded by LUPUS RESEARCH ALLIANCE 2018 - 2020
  • Biomedical Data Translator Technical Feasibility Assessment of Reasoning Tool: University of Alabama at Birmingham  awarded by National Center for Advancing Translational Sciences/NIH/DHHS 2017 - 2019
  • Comprehensive Cancer Center Core Support Grant  awarded by National Cancer Institute/NIH/DHHS 2016 - 2017
  • Education And Training

  • Doctor of Philosophy in Computer and Information Sciences, University of Minnesota-Twin Cities 2001
  • Full Name

  • Jake Chen