• Dr. Jake Y. Chen is the Chief Bioinformatics Officer at UAB Informatics Institute and a Professor of Genetics, Computer Science, and Biomedical Engineering. Previously, he was the founding director of Indiana Center for Systems Biology and Personalized Medicine. He has over 25 years of R&D experience in biological data mining and systems biology, with over 180 peer-reviewed publications. He is currently President-elect of the Midsouth Computational Biology and Bioinformatics Society. He is an elected fellow of the American College of Medical Informatics (ACMI) and the American Institute of Medical and Biological Engineering (AIMBE). He also serves on the editorial boards of BMC Bioinformatics, Journal of American Medical Informatics Association (JAMIA), and Frontiers in Artificial Intelligence and Big Data. In 2019, he was recognized by Deep Knowledge Analytics as one of the “Top 100 AI Leaders in Drug Discovery and Healthcare”.
  • Selected Publications

    Academic Article

    Year Title Altmetric
    2023 AdipoRon accelerates bone repair of calvarial defect in diet-induced obesity miceVaccine Reports.  9. 2023
    2023 How cancer hijacks the body's homeostasis through the neuroendocrine systemTrends in Neurosciences2023
    2022 WINNER: A network biology tool for biomolecular characterization and prioritizationFrontiers in Big Data.  5. 2022
    2022 Guest Editorial for Selected Papers from BIOKDD 2021IEEE/ACM Transactions on Computational Biology and Bioinformatics.  19:3068-3069. 2022
    2022 An in vivo model of glioblastoma radiation resistance identifies long noncoding RNAs and targetable kinasesJCI Insight.  7. 2022
    2022 DEMA: A distance-bounded energy-field minimization algorithm to model and layout biomolecular networks with quantitative featuresBioinformatics.  38:I359-I368. 2022
    2022 The Periodontal Pathogen Fusobacterium nucleatum Exacerbates Alzheimer’s Pathogenesis via Specific PathwaysFrontiers in Aging Neuroscience.  14. 2022
    2022 Single Nucleus Transcriptomics: Apical Resection in Newborn Pigs Extends the Time Window of Cardiomyocyte Proliferation and Myocardial RegenerationCirculation.  145:1744-1747. 2022
    2022 Identification and Characterization of a Novel Long Noncoding RNA that Regulates Osteogenesis in Diet-Induced Obesity MiceFrontiers in Cell and Developmental Biology.  10. 2022
    2022 PAGER Web APP: An Interactive, Online Gene Set and Network Interpretation Tool for Functional GenomicsFrontiers in Genetics.  13. 2022
    2022 A novel adiponectin receptor agonist (AdipoAI) ameliorates type 2 diabetes-associated periodontitis by enhancing autophagy in osteoclasts.Journal of Periodontal Research.  57:381-391. 2022
    2022 A nonredundant role for T cell-derived interleukin 22 in antibacterial defense of colonic cryptsImmunity.  55:494-511.e11. 2022
    2022 Editorial: Artificial Intelligence for Precision MedicineFrontiers in Artificial Intelligence.  4. 2022
    2022 A Crowdsourcing Approach to Develop Machine Learning Models to Quantify Radiographic Joint Damage in Rheumatoid ArthritisJAMA Network Open.  5. 2022
    2021 Metabolic alterations mediated by STAT3 promotes drug persistence in CMLLeukemia.  35:3371-3382. 2021
    2021 Vitamin D and lumisterol derivatives can act on liver X receptors (LXRs)Scientific Reports.  11. 2021
    2021 Editorial: AI-Enabled Data Science for COVID-19Frontiers in Big Data.  4. 2021
    2021 Corrigendum: Statistical Enrichment Analysis of Samples: A General-Purpose Tool to Annotate Metadata Neighborhoods of Biological Samples (Front. Big Data (2021), 4, (725276), 10.3389/fdata.2021.725276)Frontiers in Big Data.  4. 2021
    2021 Roles and Mechanisms of Irisin in Attenuating Pathological Features of OsteoarthritisFrontiers in Cell and Developmental Biology.  9. 2021
    2021 Statistical Enrichment Analysis of Samples: A General-Purpose Tool to Annotate Metadata Neighborhoods of Biological SamplesFrontiers in Big Data.  4. 2021
    2021 Polar Gini Curve: A Technique to Discover Gene Expression Spatial Patterns from Single-cell RNA-seq Data 2021
    2021 Guest Editorial for Selected Papers from BIOKDD 2019IEEE/ACM Transactions on Computational Biology and Bioinformatics.  18:809-810. 2021
    2021 Scalable de Novo Genome Assembly Using a Pregel-Like Graph-Parallel SystemIEEE/ACM Transactions on Computational Biology and Bioinformatics.  18:731-744. 2021
    2021 Linking clinotypes to phenotypes and genotypes from laboratory test results in comprehensive physical examsBMC Medical Informatics and Decision Making.  21. 2021
    2021 PAGER-CoV: A comprehensive collection of pathways, annotated gene-lists and gene signatures for coronavirus disease studiesNucleic Acids Research.  49:D589-D599. 2021
    2021 Biological Network MiningMethods in Molecular Biology.  2328:139-151. 2021
    2020 Guest Editorial for Selected Papers from BIOKDD 2018 and DMBIH 2018IEEE/ACM Transactions on Computational Biology and Bioinformatics.  17:1832-1834. 2020
    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 miceJournal of Immunology.  205:346-358. 2020
    2020 Identifying the key regulators that promote cell-cycle activity in the hearts of early neonatal pigs after myocardial injuryPLoS One.  15. 2020
    2020 Polar Gini Curve: a Technique to Discover Single-cell Biomarker Using 2D Visual Information 2020
    2020 Erratum: Association of CMV genomic mutations with symptomatic infection and hearing loss in congenital CMV infection (BMC Infectious Diseases (2019) 19 (1046) DOI: 10.1186/s12879-019-4681-0)BMC Infectious Diseases.  20. 2020
    2019 Association of CMV genomic mutations with symptomatic infection and hearing loss in congenital CMV infectionBMC Infectious Diseases.  19. 2019
    2019 WIPER: Weighted in-Path Edge Ranking for biomolecular association networksQuantitative biology (Beijing, China).  7:313-326. 2019
    2019 BEERE: a web server for biomedical entity expansion, ranking and explorationsNucleic Acids Research.  47:W578-W586. 2019
    2019 Gsslasso Cox: A Bayesian hierarchical model for predicting survival and detecting associated genes by incorporating pathway informationBMC Bioinformatics.  20. 2019
    2019 A systematic simulation-based meta-analytical framework for prediction of physiological biomarkers in alopecia 2019
    2018 Multiscale and Multimodal Analysis for Computational BiologyIEEE/ACM Transactions on Computational Biology and Bioinformatics.  15:1951-1952. 2018
    2018 Super Gene Set Causal Relationship Discovery from Functional Genomics DataIEEE/ACM Transactions on Computational Biology and Bioinformatics.  15:1991-1998. 2018
    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 Development and Therapeutic Potential of Small-Molecule Modulators of Circadian SystemsAnnual Review of Pharmacology and Toxicology.  58:231-252. 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 Integrative Approaches to Understanding the Pathogenic Role of Genetic Variation in Rheumatic DiseasesRheumatic Disease Clinics of North America.  43:449-466. 2017
    2017 HAPPI-2: A Comprehensive and High-quality Map of Human Annotated and Predicted Protein InteractionsBMC Genomics.  18. 2017
    2017 Cellular signaling pathways in insulin resistance-systems biology analyses of microarray dataset reveals new drug target gene signatures of type 2 diabetes mellitusFrontiers in Physiology.  8. 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 MicroRNA expression signature for Satb2-induced osteogenic differentiation in bone marrow stromal cells 2014
    2014 Prioritizing drug targets in Clostridium botulinum with a computational systems biology approachGenomics.  104:24-35. 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 Transcriptome network analysis of potential candidate genes for heart failure 2013
    2013 Small molecule modifiers of circadian clocksCellular and Molecular Life Sciences.  70:2985-2998. 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 Towards a metadata model for mass-spectrometry based clinical proteomicsCurrent Bioinformatics.  7:246-254. 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 Biological knowledge discovery and data mining 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 Enhanced osseointegration of titanium implant through the local delivery of transcription factor SATB2Clinical materials.  32:8676-8683. 2011
    2011 HOMER: A human organ-specific molecular electronic repositoryBMC Bioinformatics.  12. 2011
    2011 Erratum: Tumor necrosis factor-α- and interleukin-1-induced cellular responses: Coupling proteomic and genomic information (Journal of Proteome Research (2007) 6 (2176-2185) DOI: 10.1021/pr060665l)Journal of Proteome Research.  10:4886. 2011
    2011 Critical-size calvarial bone defects healing in a mouse model with silk scaffolds and SATB2-modified iPSCsClinical materials.  32:5065-5076. 2011
    2011 Effects of miR-335-5p in modulating osteogenic differentiation by specifically downregulating Wnt antagonist DKK1Journal of Bone and Mineral Research.  26:1953-1963. 2011
    2011 Roles of SATB2 in osteogenic differentiation and bone regeneration 2011
    2011 Adiponectin inhibits osteoclastogenesis and bone resorption via APPL1-mediated suppression of Akt1Journal of Biological Chemistry.  286:12542-12553. 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
    2011 Application of induced pluripotent stem (iPS) cells in periodontal tissue regenerationJournal of Cellular Physiology.  226:150-157. 2011
    2011 Data Mining Methods in Omics-Based Biomarker DiscoveryMethods in Molecular Biology.  719:511-526. 2011
    2011 New threats to health data privacy.BMC Bioinformatics.  12 Suppl 12. 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 diseaseCardiovascular Therapeutics.  28:350-355. 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 Data mining in bioinformatics: Selected papers from BIOKDDIEEE/ACM Transactions on Computational Biology and Bioinformatics.  7:195-196. 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 GeneTerrain: Visual exploration of differential gene expression profiles organized in native biomolecular interaction networksInformation Visualization.  9:1-12. 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 Osterix enhances BMSC-associated osseointegration of implants 2009
    2009 HPD: An online integrated human pathway database enabling systems biology studiesBMC Bioinformatics.  10. 2009
    2009 HPD: an online integrated human pathway database enabling systems biology studies.BMC Bioinformatics.  10 Suppl 11:S5. 2009
    2009 Mandibular repair in rats with premineralized silk scaffolds and BMP-2-modified bMSCsClinical materials.  30:4522-4532. 2009
    2009 Design of an online physician-mediated personal health record systemStudies in Computational Intelligence.  224:265-279. 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.AMIA Joint Summits on Translational Science proceedings AMIA Summit on Translational Science.  2009:1-5. 2009
    2009 Building disease-specific drug-protein connectivity maps from molecular interaction networks and PubMed abstractsPLoS Computational Biology.  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 cancerConference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference.  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 networksConference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference.  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
    2008 IntroductionJournal of Bioinformatics and Computational Biology.  6. 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 DisProt: The database of disordered proteinsNucleic Acids Research.  35. 2007
    2007 International Journal of Bioinformatics Research and Applications: EditorialInternational Journal of Bioinformatics Research and Applications.  3:261-267. 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 Disorder and sequence repeats in hub proteins and their implications for network evolutionJournal of Proteome Research.  5:2985-2995. 2006
    2006 A statistical framework to discover true associations from multiprotein complex pull-down proteomics data sets 2006
    2006 Porous silk fibroin 3-D scaffolds for delivery of bone morphogenetic protein-2 in vitro and in vivoJournal of Biomedical Materials Research Part A.  78:324-334. 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 Tissue- and bone cell-specific expression of bone sialoprotein is directed by a 9.0 kb promoter in transgenic miceMatrix Biology.  24:341-352. 2005
    2005 Data mining in protein interactomicsIEEE Pulse.  24:95-102. 2005
    2005 Silk implants for the healing of critical size bone defectsBone.  37:688-698. 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

    Research Overview

  • Bioinformatics, systems biology, network biology, artificial intelligence in medicine
  • Investigator On

  • A National Center for Digital Health Informatics Innovation  awarded by Oregon Health & Science University
  • B Cell Intrinsic Interferon-beta Regulates Autoreactive B Cell Development  awarded by National Institute of Allergy and Infectious Diseases/NIH/DHHS
  • B-Cell Control Point Dysregulation in African Americans with SLE  awarded by LUPUS RESEARCH ALLIANCE
  • Biological Comparisons Among Three Derivative Models of Glioma Patient Cancers Under Microenvironmental Stress  awarded by National Cancer Institute/NIH/DHHS
  • Biomedical Data Translator Technical Feasibility Assessment of Reasoning Tool: University of Alabama at Birmingham  awarded by National Center for Advancing Translational Sciences/NIH/DHHS
  • Center for Clinical and Translational Science (3 Linked Awards UL1, KL2, TL1)  awarded by National Center for Advancing Translational Sciences/NIH/DHHS
  • Characterization of the Lupus Nephritis microRNAome  awarded by National Institute of Arthritis & Musculoskeletal & Skin Diseases/NIH/DHHS
  • Comprehensive Cancer Center Core Support Grant  awarded by National Cancer Institute/NIH/DHHS
  • Credentialing Next-generation Human Glioma Models for Precision Therapeutics  awarded by National Cancer Institute/NIH/DHHS
  • Genetic Prediction for Treatment Resistance in Kawasaki Disease  awarded by SEATTLE CHILDREN'S RESEARCH INSTITUTE
  • Genetic Prediction for Treatment Resistance in Kawasaki Disease  awarded by SEATTLE CHILDREN'S RESEARCH INSTITUTE
  • Identifying Secreted Protein Networks Affecting Human Pancreatic Islet Function In Type 2 Diabetes Using Public Omic Databases  awarded by National Institute of Diabetes and Digestive and Kidney Diseases/NIH/DHHS
  • Metabolic Checkpoints in Anti-CTLA-4 and Anti-PD-1 Immunotherapies  awarded by V FOUNDATION FOR CANCER RESEARCH
  • Modeling Dynamic Immune Cell Modulation in a 3-D Tissue Engineered Platform to Enhance Patient-specific Immunotherapy for Lung Cancer  awarded by National Cancer Institute/NIH/DHHS
  • Molecular Mechanisms of Multiple Sclerosis Disease Severity in African Americans  awarded by NATIONAL INSTITUTE ON MINORITY HEALTH AND HEALTH DISPARITIES/NIH/DHHS
  • Molecular, Functional and Structural Analyses of Anti-PAD Antibodies in Rheumatoid Arthritis  awarded by National Institute of Allergy and Infectious Diseases/NIH/DHHS
  • Network Biology Modeling to Enhance Bioinformatic Characterization of Heart Regeneration  awarded by University of Maryland
  • Private Grant  awarded by BRISTOL-MYERS SQUIBB COMPANY
  • Role of Bone Marrow Tregs in Maintaining Stromal Cell Function  awarded by National Heart, Lung, and Blood Institute/NIH/DHHS
  • Single Nucleus RNA Sequencing in Pig Heart Development and Regeneration  awarded by University of Maryland
  • Sub-regional Expression of IncRNAs and their Transcriptomic Targets Regulating Key Molecular Pathways in GBM  awarded by SWEDISH HEALTH SERVICES
  • Targeting Metabolic Checkpoints in the Tumor Microenvironment to Boost Efficacy of Anti-CTLA-4  awarded by National Cancer Institute/NIH/DHHS
  • Education And Training

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

  • Jake Chen