• 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 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 Metabolic alterations mediated by STAT3 promotes drug persistence in CMLLeukemia2021
    2020 Guest Editorial for Selected Papers from BIOKDD 2018 and DMBIH 2018IEEE/ACM Transactions on Computational Biology and Bioinformatics.  17:1832-1834. 2020
    2020 Design and fabrication of integrated magnetic field sensing system with enhanced sensitivityJournal of Magnetism and Magnetic Materials.  511. 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 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 networks 2019
    2019 Coordinate regulation of cholesterol and bile acid metabolism by the clock modifier nobiletin in metabolically challenged old miceInternational Journal of Molecular Sciences.  20. 2019
    2019 BEERE: a web server for biomedical entity expansion, ranking and explorationsNucleic Acids Research.  47:W578-W586. 2019
    2019 Temporal Control of Appetite by AgRP ClocksCell Metabolism.  29:1022-1023. 2019
    2019 Central adiponectin induces trabecular bone mass partly through epigenetic downregulation of cannabinoid receptor CB1Journal of Cellular Physiology.  234:7062-7069. 2019
    2019 Room-temperature spin-to-charge conversion in sputtered bismuth selenide thin films via spin pumping from yttrium iron garnetApplied Physics Letters.  114. 2019
    2019 An Adiponectin Receptor Agonist Reduces Type 2 Diabetic PeriodontitisJournal of Dental Research.  98:313-321. 2019
    2019 Rosiglitazone reverses high fat diet-induced changes in BMAL1 function in muscle, fat, and liver tissue in miceInternational Journal of Obesity.  43:567-580. 2019
    2019 Tissue-specific BMAL1 cistromes reveal that rhythmic transcription is associated with rhythmic enhancer–enhancer interactionsGenes and Development.  33:294-309. 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 alopeciaJournal of Biological Research.  26. 2019
    2019 Emerging relevance of circadian rhythms in headaches and neuropathic pain 2019
    2019 Ghrelin receptor in agouti-related peptide neurones regulates metabolic adaptation to calorie restrictionJournal of Neuroendocrinology.  31. 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 A novel Lipidoid-MicroRNA formulation promotes calvarial bone regenerationBiomaterials.  177:88-97. 2018
    2018 Cluster headache is in part a disorder of the circadian systemJAMA Neurology.  75:783-784. 2018
    2018 Enhancement of tunneling magnetoresistance by inserting a diffusion barrier in L10-FePd perpendicular magnetic tunnel junctionsApplied Physics Letters.  112. 2018
    2018 Comprehensive characterization of alternative polyadenylation in human cancer 2018
    2018 MicroRNA-99a is a novel regulator of KDM6B-mediated osteogenic differentiation of BMSCsJournal of Cellular and Molecular Medicine.  22:2162-2176. 2018
    2018 The Genomic Landscape and Pharmacogenomic Interactions of Clock Genes in Cancer ChronotherapyCell Systems.  6:314-328.e2. 2018
    2018 Weak antilocalization and low-temperature characterization of sputtered polycrystalline bismuth selenideApplied Physics Letters.  112. 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 Mapping strain with magnetics 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 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 What’s next for chronobiology and drug discoveryExpert Opinion on Drug Discovery.  12:1181-1185. 2017
    2017 Myricetin improves endurance capacity and mitochondrial density by activating SIRT1 and PGC-1αScientific Reports.  7. 2017
    2017 Overexpression of MiR-335-5p Promotes Bone Formation and Regeneration in MiceJournal of Bone and Mineral Research.  32:2466-2475. 2017
    2017 Period2 3′-UTR and microRNA-24 regulate circadian rhythms by repressing PERIOD2 protein accumulation 2017
    2017 Guidelines for Genome-Scale Analysis of Biological RhythmsJournal of Biological Rhythms.  32:380-393. 2017
    2017 Multicenter epidemiological investigation of hospitalized elderly, young and middle-aged patients with severe burn 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 A filtration-based method of preparing high-quality nuclei from cross-linked skeletal muscle for chromatin immunoprecipitationJournal of Visualized Experiments.  2017. 2017
    2017 Suppression of ghrelin exacerbates HFCS-induced adiposity and insulin resistanceInternational Journal of Molecular Sciences.  18. 2017
    2017 Clock-enhancing small molecules and potential applications in chronic diseases and agingFrontiers in Neurology.  8. 2017
    2017 HAPPI-2: A Comprehensive and High-quality Map of Human Annotated and Predicted Protein InteractionsBMC Genomics.  18. 2017
    2017 Bone tissue regeneration - Application of mesenchymal stem cells and cellular and molecular mechanismsCurrent Stem Cell Research and Therapy.  12:357-364. 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 Exercise-induced irisin in bone and systemic irisin administration reveal new regulatory mechanisms of bone metabolismBone Research.  5. 2017
    2017 High performance MgO-barrier magnetic tunnel junctions for flexible and wearable spintronic applicationsScientific Reports.  7. 2017
    2017 Repositioning drugs by targeting network modules: a Parkinson's disease case study. 2017
    2017 Runx2/DICER/miRNA Pathway in Regulating OsteogenesisJournal of Cellular Physiology.  232:182-191. 2017
    2016 Multicenter epidemiological investigation of hospitalized children with severe burn 2016
    2016 Laser-initiated magnetization reversal and correlated morphological effects visualized with in situ Fresnel transmission electron microscopyPhysical Review B.  94. 2016
    2016 A method for identifying discriminative isoform-specific peptides for clinical proteomics applicationBMC Genomics.  17. 2016
    2016 Pacemaker-neuron-dependent disturbance of the molecular clockwork by a Drosophila CLOCK mutant homologous to the mouse Clock mutation 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
    2016 Time-Resolved Magneto-Optical Kerr Effect of Magnetic Thin Films for Ultrafast Thermal CharacterizationJournal of Physical Chemistry Letters.  7:2328-2332. 2016
    2016 Molecular targets for small-molecule modulators of Circadian clocksCurrent Drug Metabolism.  17:503-512. 2016
    2016 Epigenetic Modulation in Periodontitis: Interaction of Adiponectin and JMJD3-IRF4 Axis in MacrophagesJournal of Cellular Physiology.  231:1090-1096. 2016
    2016 The Small Molecule Nobiletin Targets the Molecular Oscillator to Enhance Circadian Rhythms and Protect against Metabolic SyndromeCell Metabolism.  23:610-621. 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 All-optical switching of magnetoresistive devices using telecom-band femtosecond laserApplied Physics Letters.  107. 2015
    2015 MicroRNA expression profiling of human respiratory epithelium affected by invasive candida infectionPLoS ONE.  10. 2015
    2015 Adenoviral vector-mediated overexpression of osteoprotegerin accelerates osteointegration of titanium implants in ovariectomized rats 2015
    2015 Epigenetically Modified Bone Marrow Stromal Cells in Silk Scaffolds Promote Craniofacial Bone Repair and Wound Healing 2015
    2015 Dual attenuation of proteasomal and autophagic BMAL1 degradation in Clock δ "19/+ mice contributes to improved glucose homeostasisScientific Reports.  5. 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
    2015 Ammonia-lowering activities and carbamoyl phosphate synthetase 1 (Cps1) induction mechanism of a natural flavonoid 2015
    2015 Transmissible microbial and metabolomic remodeling by soluble dietary fiber improves metabolic homeostasisScientific Reports.  5. 2015
    2015 Adiponectin regulates bone marrow mesenchymal stem cell niche through a unique signal transduction pathway: An approach for treating bone disease in diabetesSTEM CELLS.  33:240-252. 2015
    2015 Circadian gene expression predicts patient response to neoadjuvant chemoradiation therapy for rectal cancerInternational Journal of Clinical and Experimental Pathology.  8:10985-10994. 2015
    2015 Manipulating the circadian and sleep cycles to protect against metabolic diseaseFrontiers in Endocrinology.  6. 2015
    2015 Response to letter to the editor, BET inhibitor JQ1 blocks inflammation and bone destructionJournal of Dental Research.  94:230. 2015
    2014 Pathway and network analysis in proteomicsJournal of Theoretical Biology.  362:44-52. 2014
    2014 Transcriptional program of Kpna2/Importin-α2 regulates cellular differentiation-coupled circadian clock development in mammalian cells 2014
    2014 SLDR: A computational technique to identify novel genetic regulatory relationshipsBMC Bioinformatics.  15. 2014
    2014 Central adiponectin administration reveals new regulatory mechanisms of bone metabolism in mice 2014
    2014 Adiponectin ameliorates experimental periodontitis in diet-induced obesity micePLoS ONE.  9. 2014
    2014 MicroRNA expression signature for Satb2-induced osteogenic differentiation in bone marrow stromal cells 2014
    2014 BET inhibitor JQ1 blocks inflammation and bone destructionJournal of Dental Research.  93:657-662. 2014
    2014 China's balancing actScience.  346:1194. 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 Transcription factor and bone marrow stromal cells in osseointegration of dental implants 2013
    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 Association of CD14-260 polymorphisms, red-complex periodontopathogens and gingival crevicular fluid cytokine levels with cyclosporine A-induced gingival overgrowth in renal transplant patientsJournal of Periodontal Research.  48:203-212. 2013
    2013 Competing E3 ubiquitin ligases govern circadian periodicity by degradation of CRY in nucleus and cytoplasmCell.  152:1091-1105. 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 proteomics 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 Sustained release of adiponectin improves osteogenesis around hydroxyapatite implants by suppressing osteoclast activity in ovariectomized rabbitsActa Biomaterialia.  8:734-743. 2012
    2012 Identification of diverse modulators of central and peripheral circadian clocks by high-throughput chemical screening 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 The use of injectable sonication-induced silk hydrogel for VEGF 165 and BMP-2 delivery for elevation of the maxillary sinus floorBiomaterials.  32:9415-9424. 2011
    2011 Enhanced osseointegration of titanium implant through the local delivery of transcription factor SATB2Biomaterials.  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 iPSCsBiomaterials.  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 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 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 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 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 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 networks 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 Longitudinal spin transfer to Λ and Λ̄ hyperons in polarized proton-proton collisions at s=200GeV 2009
    2009 Osterix enhances BMSC-associated osseointegration of implantsJournal of Dental Research.  88:1003-1007. 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 Apatite-coated silk fibroin scaffolds to healing mandibular border defects in caninesBONE.  45:517-527. 2009
    2009 Mandibular repair in rats with premineralized silk scaffolds and BMP-2-modified bMSCsBiomaterials.  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 Applications of transgenics in studies of bone sialoproteinJournal of Cellular Physiology.  220:30-34. 2009
    2009 Building disease-specific drug-protein connectivity maps from molecular interaction networks and PubMed abstractsPLoS 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 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
    2009 Targeted overexpression of BSP in osteoclasts promotes bone metastasis of breast cancer cellsJournal of Cellular Physiology.  218:135-145. 2009
    2008 Corrigendum to "Silk implants for the healing of critical size bone defects" [Bone 37 (2005) 688-698] (DOI:10.1016/j.bone.2005.06.010)BONE.  43:1122. 2008
    2008 Overexpression of bone sialoprotein leads to an uncoupling of bone formation and bone resorption in miceJournal of Bone and Mineral Research.  23:1775-1788. 2008
    2008 Haploinsufficiency of Runx2 results in bone formation decrease and different BSP expression pattern changes in two transgenic mouse modelsJournal of Cellular Physiology.  217:40-47. 2008
    2008 ProteoLens: A visual analytic tool for multi-scale database-driven biological network data miningBMC Bioinformatics.  9. 2008
    2008 Expression of Osterix in mechanical stress-induced osteogenic differentiation of periodontal ligament cells in vitroEuropean Journal of Oral Sciences.  116:199-206. 2008
    2008 Evidence for an overlapping role of CLOCK and NPAS2 transcription factors in liver circadian oscillatorsMolecular and Cellular Biology.  28:3070-3075. 2008
    2008 HIP2: an online database of human plasma proteins from healthy individuals.BMC Medical Genomics.  1:12. 2008
    2008 Systemically transplanted bone marrow stromal cells contributing to bone tissue regenerationJournal of Cellular Physiology.  215:204-209. 2008
    2008 IntroductionJournal of Bioinformatics and Computational Biology.  6. 2008
    2008 Phenotypic analysis of Dlx5 overexpression in post-natal boneJournal of Dental Research.  87:45-50. 2008
    2007 A conserved DNA damage response pathway responsible for coupling the cell division cycle to the circadian and metabolic cyclesCell Cycle.  6:2906-2912. 2007
    2007 Osterix overexpression in mesenchymal stem cells stimulates healing of critical-sized defects in murine calvarial bone 2007
    2007 Restriction of DNA replication to the reductive phase of the metabolic cycle protects genome integrityScience.  316:1916-1919. 2007
    2007 Cbfa1/Runx2-deficiency delays bone wound healing and locally delivered Cbfa1/Runx2 promotes bone repair in animal modelsWound Repair and Regeneration.  15:404-412. 2007
    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 Effects of platelet concentrate on palatal wound healing after connective tissue graft harvestingJournal of Periodontology.  78:601-610. 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 vivo 2006
    2006 Osterix enhances proliferation and osteogenic potential of bone marrow stromal cellsBiochemical and Biophysical Research Communications.  341:1257-1265. 2006
    2006 Cloning of hamster osteopontin and expression distribution in normal tissues and experimentally induced oral squamous-cell carcinomaArchives of Oral Biology.  51:236-245. 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 An in vivo model to study osteogenic gene regulation: Targeting an avian retroviral receptor (TV A) to bone with the bone sialoprotein (BSP) promoterJournal of Bone and Mineral Research.  20:1403-1413. 2005
    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
    2004 Bone sialoprotein promotes bone metastasis of a non-bone-seeking clone of human breast cancer cells 2004
    2004 Autoregulation of bone sialoprotein gene in pre-osteoblastic and non-osteoblastic cellsBiochemical and Biophysical Research Communications.  316:461-467. 2004
    Polar Gini Curve: a Technique to Discover Single-cell Biomarker Using 2D Visual Information


    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
    2013 Transplanted bone marrow stromal cells and bone tissue regeneration.  22-43. 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

  • Role of Bone Marrow Tregs in Maintaining Stromal Cell Function  awarded by National Heart, Lung, and Blood Institute/NIH/DHHS 2020 - 2024
  • 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
  • Sub-regional Expression of IncRNAs and their Transcriptomic Targets Regulating Key Molecular Pathways in GBM  awarded by SWEDISH HEALTH SERVICES 2020 - 2023
  • B Cell Intrinsic Interferon-beta Regulates Autoreactive B Cell Development  awarded by National Institute of Allergy and Infectious Diseases/NIH/DHHS 2018 - 2023
  • Molecular Mechanisms of Multiple Sclerosis Disease Severity in African Americans  awarded by NATIONAL INSTITUTE ON MINORITY HEALTH AND HEALTH DISPARITIES/NIH/DHHS 2020 - 2022
  • Genetic Prediction for Treatment Resistance in Kawasaki Disease  awarded by SEATTLE CHILDREN'S RESEARCH INSTITUTE 2018 - 2021
  • Metabolic Checkpoints in Anti-CTLA-4 and Anti-PD-1 Immunotherapies  awarded by V FOUNDATION FOR CANCER RESEARCH 2018 - 2021
  • 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
  • Network Biology Modeling to Enhance Bioinformatic Characterization of Heart Regeneration  awarded by University of Maryland 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
  • 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