Positions

Overview

  • 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
    2021 Guest Editorial for Selected Papers from BIOKDD 2019.  IEEE/ACM Transactions on Computational Biology and Bioinformatics.  18:809-810. 2021
    2021 Scalable de Novo Genome Assembly Using a Pregel-Like Graph-Parallel System.  IEEE/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 exams.  BMC Medical Informatics and Decision Making.  21. 2021
    2021 PAGER-CoV: A comprehensive collection of pathways, annotated gene-lists and gene signatures for coronavirus disease studies.  Nucleic Acids Research.  49:D589-D599. 2021
    2021 Biological Network Mining.  Methods in Molecular Biology.  2328:139-151. 2021
    2021 Metabolic alterations mediated by STAT3 promotes drug persistence in CML.  Leukemia.  2021
    2020 Guest Editorial for Selected Papers from BIOKDD 2018 and DMBIH 2018.  IEEE/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 mice.  Journal 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 injury.  PLoS ONE.  15. 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 infection.  BMC Infectious Diseases.  19. 2019
    2019 WIPER: Weighted in-Path Edge Ranking for biomolecular association networks 2019
    2019 BEERE: a web server for biomedical entity expansion, ranking and explorations.  Nucleic Acids Research.  47:W578-W586. 2019
    2019 Gsslasso Cox: A Bayesian hierarchical model for predicting survival and detecting associated genes by incorporating pathway information.  BMC Bioinformatics.  20. 2019
    2019 A systematic simulation-based meta-analytical framework for prediction of physiological biomarkers in alopecia.  Journal of Biological Research.  26. 2019
    2018 Multiscale and Multimodal Analysis for Computational Biology.  IEEE/ACM Transactions on Computational Biology and Bioinformatics.  15:1951-1952. 2018
    2018 Super Gene Set Causal Relationship Discovery from Functional Genomics Data.  IEEE/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 toxins.  Frontiers in Microbiology.  9. 2018
    2018 Development and Therapeutic Potential of Small-Molecule Modulators of Circadian Systems 2018
    2018 PAGER 2.0: An update to the pathway, annotated-list and gene-signature electronic repository for Human Network Biology.  Nucleic Acids Research.  46:D668-D676. 2018
    2018 Regenerative potential of neonatal porcine hearts.  Circulation.  138:2809-2816. 2018
    2017 Repositioning drugs by targeting network modules: A Parkinson's disease case study.  BMC Bioinformatics.  18. 2017
    2017 Integrative Approaches to Understanding the Pathogenic Role of Genetic Variation in Rheumatic Diseases.  Rheumatic Disease Clinics of North America.  43:449-466. 2017
    2017 HAPPI-2: A Comprehensive and High-quality Map of Human Annotated and Predicted Protein Interactions.  BMC 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 mellitus.  Frontiers 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 application.  BMC Genomics.  17. 2016
    2016 Proteomic Characterization Reveals That MMP-3 Correlates With Bronchiolitis Obliterans Syndrome Following Allogeneic Hematopoietic Cell and Lung Transplantation.  American Journal of Transplantation.  16:2342-2351. 2016
    2015 A method for developing regulatory gene set networks to characterize complex biological systems.  BMC Genomics.  16. 2015
    2015 DMAP: A connectivity map database to enable identification of novel drug repositioning candidates.  BMC Bioinformatics.  16. 2015
    2015 MicroRNA expression profiling of human respiratory epithelium affected by invasive candida infection.  PLoS ONE.  10. 2015
    2015 Knowledge Discovery Using Big Data in Biomedical Systems.  IEEE/ACM Transactions on Computational Biology and Bioinformatics.  12:726-728. 2015
    2015 PAGER: Constructing PAGs and new PAG-PAG relationships for network biology.  Bioinformatics.  31:i250-i257. 2015
    2014 Pathway and network analysis in proteomics.  Journal of Theoretical Biology.  362:44-52. 2014
    2014 SLDR: A computational technique to identify novel genetic regulatory relationships.  BMC 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 approach.  Genomics.  104:24-35. 2014
    2014 Seed-weighted random walk ranking for cancer biomarker prioritisation: A case study in leukaemia.  International Journal of Data Mining and Bioinformatics.  9:135-148. 2014
    2013 Network medicine: Finding the links to personalized therapy.  Clinical 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 clocks.  Cellular and Molecular Life Sciences.  70:2985-2998. 2013
    2013 Predicting adverse drug reaction profiles by integrating protein interaction networks with drug structures.  Proteomics.  13:313-324. 2013
    2012 Genome-wide meta-analysis of genetic susceptible genes for Type 2 Diabetes.  BMC Systems Biology.  6. 2012
    2012 Towards a metadata model for mass-spectrometry based clinical proteomics 2012
    2012 PAGED: A pathway and gene-set enrichment database to enable molecular phenotype discoveries.  BMC 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 stimulation.  BMC Systems Biology.  5. 2011
    2011 Predicting adverse side effects of drugs.  BMC Genomics.  12. 2011
    2011 Enhanced osseointegration of titanium implant through the local delivery of transcription factor SATB2.  Biomaterials.  32:8676-8683. 2011
    2011 HOMER: A human organ-specific molecular electronic repository.  BMC 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 iPSCs.  Biomaterials.  32:5065-5076. 2011
    2011 Effects of miR-335-5p in modulating osteogenic differentiation by specifically downregulating Wnt antagonist DKK1.  Journal of Bone and Mineral Research.  26:1953-1963. 2011
    2011 Roles of SATB2 in osteogenic differentiation and bone regeneration 2011
    2011 Data mining methods in Omics-based biomarker discovery..  Methods in Molecular Biology.  719:511-526. 2011
    2011 Adiponectin inhibits osteoclastogenesis and bone resorption via APPL1-mediated suppression of Akt1.  Journal 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 arthritis.  Journal of Rheumatology.  38:264-270. 2011
    2011 Application of induced pluripotent stem (iPS) cells in periodontal tissue regeneration.  Journal of Cellular Physiology.  226:150-157. 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 2,4DNT.  BMC 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 methods.  BMC Genomics.  11. 2010
    2010 PEPPI: A peptidomic database of human protein isoforms for proteomics experiments.  BMC 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 BIOKDD.  IEEE/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 networks 2010
    2010 A GMM-IG framework for selecting genes as expression panel biomarkers.  Artificial Intelligence in Medicine.  48:75-82. 2010
    2010 MG-132 Inhibits Carcinoid Growth and Alters the Neuroendocrine Phenotype.  Journal of Surgical Research.  158:15-19. 2010
    2009 Longitudinal spin transfer to Λ and Λ̄ hyperons in polarized proton-proton collisions at s=200GeV 2009
    2009 Osterix enhances BMSC-associated osseointegration of implants.  Journal of Dental Research.  88:1003-1007. 2009
    2009 HPD: An online integrated human pathway database enabling systems biology studies.  BMC 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 bMSCs.  Biomaterials.  30:4522-4532. 2009
    2009 Design of an online physician-mediated personal health record system.  Studies in Computational Intelligence.  224:265-279. 2009
    2009 HAPPI: An online database of comprehensive human annotated and predicted protein interactions.  BMC Genomics.  10. 2009
    2009 Building disease-specific drug-protein connectivity maps from molecular interaction networks and PubMed abstracts.  PLoS Computational Biology.  5. 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 cancer.  Proceedings 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 biomarkers.  Proteomics.  9:470-484. 2009
    2009 Finding fractal patterns in molecular interaction networks: A case study in Alzheimer's disease.  International Journal of Computational Biology and Drug Design.  2:340-352. 2009
    2009 Network topological reordering revealing systemic patterns in yeast protein interaction networks.  Proceedings 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 mining.  BMC Bioinformatics.  9. 2008
    2008 HIP2: an online database of human plasma proteins from healthy individuals..  BMC Medical Genomics.  1:12. 2008
    2008 Introduction.  Journal 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 technology.  International Journal of Bioinformatics Research and Applications.  3:286-302. 2007
    2007 DisProt: The database of disordered proteins.  Nucleic Acids Research.  35. 2007
    2007 International Journal of Bioinformatics Research and Applications: Editorial.  International 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 information.  Journal of Proteome Research.  6:2176-2185. 2007
    2006 Disorder and sequence repeats in hub proteins and their implications for network evolution.  Journal 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 vivo 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 mice 2005
    2005 Data mining in protein interactomics 2005
    2005 Silk implants for the healing of critical size bone defects.  BONE.  37:688-698. 2005
    Polar Gini Curve: a Technique to Discover Single-cell Biomarker Using 2D Visual Information

    Chapter

    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
  • 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
  • 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