Juw Won Park, Ph.D.

Education: Jow Won Park, Ph.D.

B.S. in Computer Science, Korea University, Seoul, Korea, 1995
M.S. in Computer Science, University of Iowa, Iowa City, IA, 1999
Ph.D. in Computer Science, University of Iowa, Iowa City, IA, 2009
Postdoctoral Fellowship, Department of Internal Medicine, University of Iowa, IA, 2012
Postdoctoral Fellowship, Department of Microbiology, Immunology, & Molecular Genetics, UCLA, CA, 2015 

Curriculum Vitae

Current Positions:

Associate Professor of Medicine, University of Louisville School of Medicine
Director, Bioinformatics Core, Brown Cancer Center
Co-Director, Biostatistics & Informatics Facility Core, Center for Integrative Environmental Health Sciences
Member, Bioinformatics Training & Education Center, KY INBRE 

Contact Information: 

Clinical Translational Research Building, Room 211
505 S. Hancock St.
Louisville, KY 40202, USA
Phone 502-852-4030 Fax 502-852-7979
Email: juw.park@louisville.edu

Research Description: 

My research focuses on the intersection of bioinformatics and systems biology, with a particular emphasis on understanding the complex regulatory mechanisms governing alternative mRNA splicing in eukaryotic cells. I leverage high-throughput RNA sequencing (RNA-seq) and related genomic technologies to analyze massive datasets and develop innovative computational methods for elucidating the biological significance of alternative splicing. 

My expertise lies in the analysis and interpretation of high-throughput sequencing data, including RNA-seq, single-cell RNA-seq, CLIP-seq, 16S sequencing, PacBio HiFi sequencing, and Nanopore sequencing. Over the past decade, I have published numerous bioinformatics algorithms for tasks such as circular RNA detection, alternative splicing analysis, ERSP 1/2 regulated splicing, RNA-binding protein binding site prediction, and genomic variant identification. I have applied these computational approaches to a diverse range of biological systems, including human arsenic-induced cancer, mouse exosomes, human Zika virus, chicken and mouse cochlea, rat retina, and human regulatory T-cells. 

Representative Publications: 

  1. Hwang JY, Kook TL, Paulus SM, Park JW. Translation of Circular RNAs: Functions of Translated Products and Related Bioinformatics Approaches. Curr Bioinform. 2024;19(1):3–13. doi: 10.2174/1574893618666230505101059. PMCID: PMC10947221.
  2. Sundaram K, Teng Y, Mu J, Xu Q, Xu F, Sriwastva MK, Zhang L, Park JW, Zhang X, Yan J, Zhang SQ, Merchant ML, Chen SY, McClain CJ, Dryden GW, Zhang HG. Outer Membrane Vesicles Released from Garlic Exosome-like Nanoparticles (GaELNs) Train Gut Bacteria that Reverses Type 2 Diabetes via the Gut-Brain Axis. Small. 2024 May;20(20):e2308680. doi: 10.1002/smll.202308680. Epub 2024 Jan 15. PMID: 38225709; PMCID: PMC11102339.
  3. Sayed M, Park JW. miRinGO: Prediction of Biological Processes Indirectly Targeted by Human microRNAs. Noncoding RNA. 2023 Jan 22;9(1):11. doi: 10.3390/ncrna9010011. PMID: 36827544; PMCID: PMC9962180.
  4. Koo HY, Kim MA, Min H, Hwang JY, Prajapati-DiNubila M, Kim KS, Matzuk MM, Park JW, Doetzlhofer A, Kim UK, Bok J. Follistatin regulates the specification of the apical cochlea responsible for low-frequency hearing in mammals. Proc Natl Acad Sci. 2023 Jan 3;120(1):e2213099120.
  5. Teng Y, Mu J, Xu F, Zhang X, Sriwastva MK, Liu QM, Li X, Lei C, Sundaram K, Hu X, Zhang L, Park JW, Hwang JY, Rouchka EC, Zhang X, Yan J, Merchant ML, Zhang HG. Gut bacterial isoamylamine promotes age-related cognitive dysfunction by promoting microglial cell death. Cell Host Microbe. 2022 Jul 13;30(7):944-960.e8. doi: 10.1016/j.chom.2022.05.005. Epub 2022 Jun 1. PMID: 35654045; PMCID: PMC9283381.
  6. Ferragut Cardoso AP, Banerjee M, Al-Eryani L, Sayed M, Wilkey DW, Merchant ML, Park JW, States JC. Temporal Modulation of Differential Alternative Splicing in HaCaT Human Keratinocyte Cell Line Chronically Exposed to Arsenic for up to 28 Wk. Environ Health Perspect. 2022 Jan;130(1):17011. doi: 10.1289/EHP9676. Epub 2022 Jan 24. PMID: 35072517; PMCID: PMC8785870.
  7. Koo H, Hwang JY, Jung S, Park H, Bok J, Park JW. Position Specific Alternative Splicing and Gene Expression Profiles Along the Tonotopic Axis of Chick Cochlea. Front Mol Biosci. 2021 Sep 8;8:726976. doi: 10.3389/fmolb.2021.726976. PMID: 34568429; PMCID: PMC8456117.
  8. Kumar A, Sundaram K, Mu J, Dryden GW, Sriwastva MK, Lei C, Zhang L, Qiu X, Xu F, Yan J, Zhang X, Park JW, Merchant ML, Bohler HCL, Wang B, Zhang S, Qin C, Xu Z, Han X, McClain CJ, Teng Y, Zhang HG. High-fat diet-induced upregulation of exosomal phosphatidylcholine contributes to insulin resistance. Nat Commun. 2021 Jan 11;12(1):213. doi: 10.1038/s41467-020-20500-w. PMID: 33431899; PMCID: PMC7801461.
  9. Chaabane M, Andreeva K, Hwang JY, Kook TL, Park JW*, Cooper NGF*. seekCRIT: Detecting and characterizing differentially expressed circular RNAs using high-throughput sequencing data. PLoS Comput Biol. 2020 Oct 20;16(10):e1008338. doi: 10.1371/journal.pcbi.1008338. PMID: 33079938; PMCID: PMC7598922. *co-corresponding authors
  10. Hwang JY, Jung S, Kook TL, Rouchka EC, Bok J, Park JW. rMAPS2: an update of the RNA map analysis and plotting server for alternative splicing regulation. Nucleic Acids Res. 2020 Jul 2;48(W1):W300-W306. doi: 10.1093/nar/gkaa237. PMID: 32286627; PMCID: PMC7319468.
  11. Chaabane M, Williams RM, Stephens AT, Park JW. circDeep: deep learning approach for circular RNA classification from other long non-coding RNA. Bioinformatics. 2020 Jan 1;36(1):73-80. doi: 10.1093/bioinformatics/btz537. PMID: 31268128; PMCID: PMC6956777.
  12. Sundaram K, Miller DP, Kumar A, Teng Y, Sayed M, Mu J, Lei C, Sriwastva MK, Zhang L, Yan J, Merchant ML, He L, Fang Y, Zhang S, Zhang X, Park JW, Lamont RJ, Zhang HG. Plant-Derived Exosomal Nanoparticles Inhibit Pathogenicity of Porphyromonas gingivalis. iScience. 2019 Nov 22;21:308-327. doi: 10.1016/j.isci.2019.10.032. Epub 2019 Oct 21. Erratum in: iScience. 2020 Feb 21;23(2):100869. doi: 10.1016/j.isci.2020.100869. PMID: 31678913; PMCID: PMC6838522.
  13. Alugubelly N, Mohammad AN, Edelmann MJ, Nanduri B, Sayed M, Park JW*, Carr RL*. Proteomic and transcriptional profiling of rat amygdala following social play. Behav Brain Res. 2019 Dec 30;376:112210. doi: 10.1016/j.bbr.2019.112210. Epub 2019 Sep 4. PMID: 31493430; PMCID: PMC6783381. *co-corresponding authors
  14. Harrison BJ, Park JW, Gomes C, Petruska JC, Sapio MR, Iadarola MJ, Chariker JH, Rouchka EC. Detection of Differentially Expressed Cleavage Site Intervals Within 3' Untranslated Regions Using CSI-UTR Reveals Regulated Interaction Motifs. Front Genet. 2019 Mar 12;10:182. doi: 10.3389/fgene.2019.00182. PMID: 30915105; PMCID: PMC6422928.
  15. Teng Y, Ren Y, Sayed M, Hu X, Lei C, Kumar A, Hutchins E, Mu J, Deng Z, Luo C, Sundaram K, Sriwastva MK, Zhang L, Hsieh M, Reiman R, Haribabu B, Yan J, Jala VR, Miller DM, Van Keuren-Jensen K, Merchant ML, McClain CJ, Park JW, Egilmez NK, Zhang HG. Plant-Derived Exosomal MicroRNAs Shape the Gut Microbiota. Cell Host Microbe. 2018 Nov 14;24(5):637-652.e8. doi: 10.1016/j.chom.2018.10.001. Epub 2018 Oct 25. PMID: 30449315; PMCID: PMC6746408 (featured on the journal cover)
  16. Lee J, Park N, Park JY, Kaplan BLF, Pruett SB, Park JW, Park YH, Seo KS. Induction of Immunosuppressive CD8+CD25+FOXP3+ Regulatory T Cells by Suboptimal Stimulation with Staphylococcal Enterotoxin C1. J Immunol. 2018 Jan 15;200(2):669-680. doi: 10.4049/jimmunol.1602109. Epub 2017 Dec 13. PMID: 29237775; PMCID: PMC5757107.
  17. Park JY, Moon BY, Park JW, Thornton JA, Park YH, Seo KS. Genetic engineering of a temperate phage-based delivery system for CRISPR/Cas9 antimicrobials against Staphylococcus aureus. Sci Rep. 2017 Mar 21;7:44929. doi: 10.1038/srep44929. PMID: 28322317; PMCID: PMC5359561.
  18. Park JW, Jung S, Rouchka EC, Tseng YT, Xing Y. rMAPS: RNA map analysis and plotting server for alternative exon regulation. Nucleic Acids Res. 2016 Jul 8;44(W1):W333-8. doi: 10.1093/nar/gkw410. Epub 2016 May 12. PMID: 27174931; PMCID: PMC4987942.
  19. Zhou R*, Park JW*, Chun RF, Lisse TS, Garcia AJ, Zavala K, Sea JL, Lu ZX, Xu J, Adams JS, Xing Y, Hewison M. Concerted effects of heterogeneous nuclear ribonucleoprotein C1/C2 to control vitamin D-directed gene transcription and RNA splicing in human bone cells. Nucleic Acids Res. 2017 Jan 25;45(2):606-618. doi: 10.1093/nar/gkw851. Epub 2016 Sep 26. PMID: 27672039; PMCID: PMC5314791. *These authors contributed equally
  20. Bebee TW, Sims-Lucas S, Park JW, Bushnell D, Cieply B, Xing Y, Bates CM, Carstens RP. Ablation of the epithelial-specific splicing factor Esrp1 results in ureteric branching defects and reduced nephron number. Dev Dyn. 2016 Oct;245(10):991-1000. doi: 10.1002/dvdy.24431. Epub 2016 Jul 28. PMID: 27404344; PMCID: PMC5096029.
  21. Lin L, Park JW, Ramachandran S, Zhang Y, Tseng YT, Shen S, Waldvogel HJ, Curtis MA, Faull RL, Troncoso JC, Pletnikova O, Ross CA, Davidson BL, Xing Y. Transcriptome sequencing reveals aberrant alternative splicing in Huntington's disease. Hum Mol Genet. 2016 Aug 15;25(16):3454-3466. doi: 10.1093/hmg/ddw187. Epub 2016 Jul 4. PMID: 27378699; PMCID: PMC5179942.
  22. Yang Y*, Park JW*, Bebee TW, Warzecha CC, Guo Y, Shang X, Xing Y, Carstens RP. Determination of a Comprehensive Alternative Splicing Regulatory Network and Combinatorial Regulation by Key Factors during the Epithelial-to-Mesenchymal Transition. Mol Cell Biol. 2016 May 16;36(11):1704-19. doi: 10.1128/MCB.00019-16. PMID: 27044866; PMCID: PMC4959312.  *These authors contributed equally
  23. Cieply B*, Park JW*, Nakauka-Ddamba A, Bebee TW, Guo Y, Shang X, Lengner CJ, Xing Y, Carstens RP. Multiphasic and Dynamic Changes in Alternative Splicing during Induction of Pluripotency Are Coordinated by Numerous RNA-Binding Proteins. Cell Rep. 2016 Apr 12;15(2):247-55. doi: 10.1016/j.celrep.2016.03.025. Epub 2016 Mar 31. PMID: 27050523; PMCID: PMC5718363. *These authors contributed equally
  24. Ji X*, Park JW*, Bahrami-Samani E, Lin L, Duncan-Lewis C, Pherribo G, Xing Y, Liebhaber SA. αCP binding to a cytosine-rich subset of polypyrimidine tracts drives a novel pathway of cassette exon splicing in the mammalian transcriptome. Nucleic Acids Res. 2016 Mar 18;44(5):2283-97. doi: 10.1093/nar/gkw088. Epub 2016 Feb 20. PMID: 26896798; PMCID: PMC4797308. *These authors contributed equally
  25. Lin L*, Jiang P*, Park JW*, Wang J, Lu ZX, Lam MP, Ping P, Xing Y. The contribution of Alu exons to the human proteome. Genome Biol. 2016 Jan 28;17:15. doi: 10.1186/s13059-016-0876-5. PMID: 26821878; PMCID: PMC4731929. *These authors contributed equally
  26. Ruscetti M, Dadashian EL, Guo W, Quach B, Mulholland DJ, Park JW, Tran LM, Kobayashi N, Bianchi-Frias D, Xing Y, Nelson PS, Wu H. HDAC inhibition impedes epithelial-mesenchymal plasticity and suppresses metastatic, castration-resistant prostate cancer. Oncogene. 2016 Jul 21;35(29):3781-95. doi: 10.1038/onc.2015.444. Epub 2015 Dec 7. PMID: 26640144; PMCID: PMC4896852.
  27. Stein S, Lu ZX, Bahrami-Samani E, Park JW, Xing Y. Discover hidden splicing variations by mapping personal transcriptomes to personal genomes. Nucleic Acids Res. 2015 Dec 15;43(22):10612-22. doi: 10.1093/nar/gkv1099. Epub 2015 Nov 17. PMID: 26578562; PMCID: PMC4678817.
  28. Bebee TW*, Park JW*, Sheridan KI, Warzecha CC, Cieply BW, Rohacek AM, Xing Y, Carstens RP. The splicing regulators Esrp1 and Esrp2 direct an epithelial splicing program essential for mammalian development. Elife. 2015 Sep 15;4:e08954. doi: 10.7554/eLife.08954. PMID: 26371508; PMCID: PMC4566030. *These authors contributed equally. Selected and recommended by “Faculty of 1000” (http://f1000.com/prime/725787938)
  29. Lu ZX*, Huang Q*, Park JW*, Shen S, Lin L, Tokheim CJ, Henry MD, Xing Y. Transcriptome-wide landscape of pre-mRNA alternative splicing associated with metastatic colonization. Mol Cancer Res. 2015 Feb;13(2):305-18. doi: 10.1158/1541-7786.MCR-14-0366. Epub 2014 Oct 1. PMID: 25274489; PMCID: PMC4336826. *These authors contributed equally.This paper was highlighted by the journal
  30. Shen S*, Park JW*, Lu ZX, Lin L, Henry MD, Wu YN, Zhou Q, Xing Y. rMATS: robust and flexible detection of differential alternative splicing from replicate RNA-Seq data. Proc Natl Acad Sci U S A. 2014 Dec 23;111(51):E5593-601. doi: 10.1073/pnas.1419161111. Epub 2014 Dec 5. PMID: 25480548; PMCID: PMC4280593. *These authors contributed equally
  31. Guo R, Zheng L, Park JW, Lv R, Chen H, Jiao F, Xu W, Mu S, Wen H, Qiu J, Wang Z, Yang P, Wu F, Hui J, Fu X, Shi X, Shi YG, Xing Y, Lan F, Shi Y. BS69/ZMYND11 reads and connects histone H3.3 lysine 36 trimethylation-decorated chromatin to regulated pre-mRNA processing. Mol Cell. 2014 Oct 23;56(2):298-310. doi: 10.1016/j.molcel.2014.08.022. Epub 2014 Sep 25. PMID: 25263594; PMCID: PMC4363072.
  32. Tokheim C, Park JW, Xing Y. PrimerSeq: Design and visualization of RT-PCR primers for alternative splicing using RNA-seq data. Genomics Proteomics Bioinformatics. 2014 Apr;12(2):105-9. doi: 10.1016/j.gpb.2014.04.001. Epub 2014 Apr 18. PMID: 24747190; PMCID: PMC4411361.
  33. Park JW, Tokheim C, Shen S, Xing Y. Identifying differential alternative splicing events from RNA sequencing data using RNASeq-MATS. Methods Mol Biol. 2013;1038:171-9. doi: 10.1007/978-1-62703-514-9_10. PMID: 23872975.
  34. Zhao K, Lu ZX, Park JW, Zhou Q, Xing Y. GLiMMPS: robust statistical model for regulatory variation of alternative splicing using RNA-seq data. Genome Biol. 2013 Jul 22;14(7):R74. doi: 10.1186/gb-2013-14-7-r74. PMID: 23876401; PMCID: PMC4054007.
  35. Dittmar KA*, Jiang P*, Park JW*, Amirikian K, Wan J, Shen S, Xing Y, Carstens RP. Genome-wide determination of a broad ESRP-regulated posttranscriptional network by high-throughput sequencing. Mol Cell Biol. 2012 Apr;32(8):1468-82. doi: 10.1128/MCB.06536-11. Epub 2012 Feb 21. PMID: 22354987; PMCID: PMC3318588. *These authors contributed equally
  36. Shen S, Park JW, Huang J, Dittmar KA, Lu ZX, Zhou Q, Carstens RP, Xing Y. MATS: a Bayesian framework for flexible detection of differential alternative splicing from RNA-Seq data. Nucleic Acids Res. 2012 Apr;40(8):e61. doi: 10.1093/nar/gkr1291. Epub 2012 Jan 20. PMID: 22266656; PMCID: PMC3333886. 

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