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Se-Ran Jun

TitleAssistant Professor
InstitutionUniversity of Arkansas for Medical Sciences
DepartmentBiomedical Informatics, College of Medicine
Address200 South Cedar
Mail Slot # 782
Little Rock AR 72202
ORCID ORCID Icon0000-0003-2681-3950 Additional info
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    Collapse Overview 
    Collapse overview
    My research interests are genomic and microbiome epidemiology at the intersection of next generation sequencing and systems biology for understanding pathogenesis of infectious disease and the role of human microbiome in health and disease. I have particular interests on genomic epidemiology of antimicrobial resistance and microbiome-targeted intervention for cancer infection and cancer therapy. Using Oxford Nanopore Technology, my research laboratory has focused on real-time genomic surveillance of antimicrobial resistance for infection control and antibiotic stewardship for immunocompromised cancer patients dealing with big data, EHR data, machine learning, visualization, and further multiomics integration.

    Collapse Teaching 

    Collapse Research 
    Collapse research overview
    Genomic Surveillance of Antimicrobial Resistance
    Microbiome Science
    MultiOmics Integration

    Collapse research activities and funding
    101446-01     (JUN, SE-RAN)Oct 1, 2021 - Jan 31, 2022
    Zoetis - Pass Through: University of Arkansas
    Comparative WGS analysis of the two commercial live Salmonella vaccine strains
    Role: Select

    1R03AI164158-01     (JUN, SE-RAN)Sep 1, 2021 - Aug 31, 2023
    NIAID - Pass Through: University of Arkansas
    In vivo essential genome of Salmonella
    Role: Principal Investigator

    PTC2020-05     (JUN, SE-RAN)Aug 1, 2020 - Aug 31, 2021
    UAMS Intramural Grant (CTSA)
    Using genomics to track carbapenem-resistant Enterobacteriaceae linking rural and urban health in Arkansas
    Role: Principal Investigator

    1946391     (PRIOR, FRED)Jul 1, 2020 - Jun 30, 2025
    National Science Foundation - Pass Through: Arkansas Economic Development Commission
    RII Track-1: Data analytics that are Robust and Trusted (DART): From Smart Curation to Socially Aware Decision Making
    Role: Co-Investigator

    U01A148308     (BOERMA, MARJAN)Feb 1, 2020 - Jan 31, 2025
    NIH/Nat. Inst. of Allergy & Infectious Diseases
    Development of a minimally invasive biomarker assay to detect delayed radiation injury
    Role: Co-Investigator

    U01AI148308     (BOERMA, MARJAN)Feb 1, 2020 - Jan 31, 2025
    Development of a minimally invasive biomarker assay to detect delayed radiation injury
    Role: Co-Investigator

    UG1HD090876-01     (ONARECKER, TIMOTHY)Dec 1, 2019 - Aug 31, 2020
    NIH, ISPCTN Pilot
    Rapid Genomic Sequencing of Pneumococcal Meningitis Isolates
    Role: Co-Investigator

    AWD00052801     (JUN, SE-RAN)Jul 1, 2018 - Jun 30, 2019
    UAMS COM Barton
    Molecular Epidemiology of Vancomycin Resistant Enterococcus faecium in Cancer Patients
    Role: Principal Investigator

    R01AG046171     (BHATTACHARYYA, SUDEEPA)Jun 1, 2018 - May 31, 2019
    NIH/Nat. Inst. on Aging - Pass Through: Duke University
    Metabolic Networks and Pathways in Alzheimer’s Disease - Parent
    Role: Co-Investigator

    PTC2017-02     (JUN, SE-RAN)May 1, 2017 - Apr 30, 2018
    UAMS TRI Pilot Grant
    Genome-based mumps surveillance system using third generation sequencing technology
    Role: Principal Investigator

    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions. Don't see publications published under other names? Login to add alternative names.
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    1. Moon SH, Udaondo Z, Abram KZ, Li X, Yang X, DiCaprio EL, Jun SR, Huang E. Isolation of AmpC- and extended spectrum ß-lactamase-producing Enterobacterales from fresh vegetables in the United States. Food Control. 2021; 108559,:ISSN 0956-7135.
    2. Moon SH, Udaondo Z, Abram KZ, Li X, Yang X, DiCaprio EL, Jun SR, Huang E. Isolation of AmpC- and extended spectrum ß-lactamase-producing Enterobacterales from fresh vegetables in the United States. Food Control. 2022 Feb; 132. PMID: 34629764.
      View in: PubMed
    3. Jun SR, Boerma M, Udaondo Z, Richardson S, Thrall KD, Miousse IR, Seng J, Pathak R, Hauer-Jensen M. Plasma Metabolomics in a Nonhuman Primate Model of Abdominal Radiation Exposure. Metabolites. 2021 Aug 13; 11(8). PMID: 34436481.
      View in: PubMed
    4. Moon SH, Udaondo Z, Li X, Yang X, Jun SR, Huang E. Isolation and characterisation of carbapenemase-producing and polymyxin B-resistant Enterobacter bugandensis from a vegetable. J Glob Antimicrob Resist. 2021 Sep; 26:264-265. PMID: 34329791.
      View in: PubMed
    5. Krishnan G, Udaondo Z, Jun SR, Kothari A. Open Forum Infectious Diseases. Outbreak of Vancomycin Resistant Enterococcus faecium (VREfm) in a Hematology Unit Identified Through Whole Genome Sequencing. 2020; 7:S472-S474.
    6. Bose C, Alves I, Singh P, Palade PT, Carvalho E, Børsheim E, Jun SR, Cheema A, Boerma M, Awasthi S, Singh SP. Sulforaphane prevents age-associated cardiac and muscular dysfunction through Nrf2 signaling. Aging Cell. 2020 11; 19(11):e13261. PMID: 33067900.
      View in: PubMed
    7. Jun SR, Cheema A, Bose C, Boerma M, Palade PT, Carvalho E, Awasthi S, Singh SP. Multi-Omic Analysis Reveals Different Effects of Sulforaphane on the Microbiome and Metabolome in Old Compared to Young Mice. Microorganisms. 2020 Sep 29; 8(10). PMID: 33003447.
      View in: PubMed
    8. Pornputtapong N, Acheampong DA, Patumcharoenpol P, Jenjaroenpun P, Wongsurawat T, Jun SR, Yongkiettrakul S, Chokesajjawatee N, Nookaew I. KITSUNE: A Tool for Identifying Empirically Optimal K-mer Length for Alignment-Free Phylogenomic Analysis. Front Bioeng Biotechnol. 2020; 8:556413. PMID: 33072720.
      View in: PubMed
    9. Adhikari B, Jun SR, Kwon YM, Kiess AS, Adhikari P. Effects of Housing Types on Cecal Microbiota of Two Different Strains of Laying Hens During the Late Production Phase. Front Vet Sci. 2020; 7:331. PMID: 32656252.
      View in: PubMed
    10. Udaondo Z, Jenjaroenpun P, Wongsurawat T, Meyers E, Anderson C, Lopez J, Mohan M, Tytarenko R, Walker B, Ussery D, Kothari A, Jun SR. Two Cases of Vancomycin-Resistant Enterococcus faecium Bacteremia With Development of Daptomycin-Resistant Phenotype and its Detection Using Oxford Nanopore Sequencing. Open Forum Infect Dis. 2020 Jun; 7(6):ofaa180. PMID: 32550237.
      View in: PubMed
    11. Jenjaroenpun P, Wongsurawat T, Udaondo Z, Anderson C, Lopez J, Mohan M, Tytarenko R, Walker B, Nookaew I, Ussery D, Kothari A, Jun SR. Complete Genome Sequences of Four Isolates of Vancomycin-Resistant Enterococcus faecium with the vanA Gene and Two Daptomycin Resistance Mutations, Obtained from Two Inpatients with Prolonged Bacteremia. Microbiol Resour Announc. 2020 Feb 06; 9(6). PMID: 32029568.
      View in: PubMed
    12. Wassenaar TM, Jun SR, Robeson M, Ussery DW. Comparative genomics of hepatitis A virus, hepatitis C virus, and hepatitis E virus provides insights into the evolutionary history of Hepatovirus species. Microbiologyopen. 2020 02; 9(2):e973. PMID: 31742930.
      View in: PubMed
    13. Alkam D, Jenjaroenpun P, Wongsurawat T, Udaondo Z, Patumcharoenpol P, Robeson M, Haselow D, Mason W, Nookaew I, Ussery D, Jun SR. Genomic characterization of mumps viruses from a large-scale mumps outbreak in Arkansas, 2016. Infect Genet Evol. 2019 11; 75:103965. PMID: 31319177.
      View in: PubMed
    14. Jenkins S, Vang K, Gies A, Griffin R, Jun SR, Nookaew I, Dings R. AACR Annual Meeting. Sample storage conditions alter microbiome profiles - its potential relevance for cancer patients undergoing fecal microbial transplants. 2019; 79(13 Suupl):2823.
    15. Udaondo Z, Wongsurawat T, Jenjaroenpun P, Anderson C, Lopez J, Mohan M, Tytarenko R, Walker B, Nookaew I, Ussery D, Kothari A, Jun SR. Draft Genome Sequences of 48 Vancomycin-Resistant Enterococcus faecium Strains Isolated from Inpatients with Bacteremia and Urinary Tract Infection. Microbiol Resour Announc. 2019 Apr 11; 8(15). PMID: 30975810.
      View in: PubMed
    16. Jenkins SV, Vang KB, Gies A, Griffin RJ, Jun SR, Nookaew I, Dings RPM. Sample storage conditions induce post-collection biases in microbiome profiles. BMC Microbiol. 2018 12 27; 18(1):227. PMID: 30591021.
      View in: PubMed
    17. Wongsurawat T, Athipanyasilp N, Jenjaroenpun P, Jun SR, Kaewnapan B, Wassenaar TM, Leelahakorn N, Angkasekwinai N, Kantakamalakul W, Ussery DW, Sutthent R, Nookaew I, Horthongkham N. Case of Microcephaly after Congenital Infection with Asian Lineage Zika Virus, Thailand. Emerg Infect Dis. 2018 09; 24(9). PMID: 29985788.
      View in: PubMed
    18. Cabal A, Jun SR, Jenjaroenpun P, Wanchai V, Nookaew I, Wongsurawat T, Burgess MJ, Kothari A, Wassenaar TM, Ussery DW. Genome-Based Comparison of Clostridioides difficile: Average Amino Acid Identity Analysis of Core Genomes. Microb Ecol. 2018 Oct; 76(3):801-813. PMID: 29445826.
      View in: PubMed
    19. Timm CM, Carter KR, Carrell AA, Jun SR, Jawdy SS, Vélez JM, Gunter LE, Yang Z, Nookaew I, Engle NL, Lu TS, Schadt CW, Tschaplinski TJ, Doktycz MJ, Tuskan GA, Pelletier DA, Weston DJ. Abiotic Stresses Shift Belowground Populus-Associated Bacteria Toward a Core Stress Microbiome. mSystems. 2018 Jan-Feb; 3(1). PMID: 29404422.
      View in: PubMed
    20. Jun SR, Wassenaar TM, Wanchai V, Patumcharoenpol P, Nookaew I, Ussery DW. Suggested mechanisms for Zika virus causing microcephaly: what do the genomes tell us? BMC Bioinformatics. 2017 12 28; 18(Suppl 14):471. PMID: 29297281.
      View in: PubMed
    21. Alkam D, Wongsurawat T, Jenjaroenpun P, Connor S, Hobbs C, Wassenaar TM, Jun SR, Nookaew I, Ussery D. Three Complete Genome Sequences of Genotype G Mumps Virus from the 2016 Outbreak in Arkansas, USA. Genome Announc. 2017 Aug 10; 5(32). PMID: 28798162.
      View in: PubMed
    22. Jun SR, Nookaew I, Hauser L, Gorin A. Assessment of genome annotation using gene function similarity within the gene neighborhood. BMC Bioinformatics. 2017 Jul 19; 18(1):345. PMID: 28724412.
      View in: PubMed
    23. Linda J. Larson-Prior, Gohar Azhar, David G. Davila, Se-Ran Jun, Aaron S. Kemp, Intawat Nookaew, Jeanne Y. Wei, Trudy M. Wassenaar. Neurobiology of Sleep and Microbiomics in Aging. OBM Neurobiology. 2017; 1(2):doi:10.21926/obm.neurobiol.170.
    24. Trudy M. Wassenaar, Se-Ran Jun, Visanu Wanchai, Preecha Patumcharoenpol, Intawat Nookaew, Katrina Schlum, Michael R. Leuze, David W. Ussery. Insights from comparative genomics of the Genus Salmonella. Current Topics in Salmonella and Salmonellosis. 2017.
    25. Zhang Q, Jun SR, Leuze M, Ussery D, Nookaew I. Viral Phylogenomics Using an Alignment-Free Method: A Three-Step Approach to Determine Optimal Length of k-mer. Sci Rep. 2017 01 19; 7:40712. PMID: 28102365.
      View in: PubMed
    26. Leekitcharoenphon P, Hendriksen RS, Le Hello S, Weill FX, Baggesen DL, Jun SR, Ussery DW, Lund O, Crook DW, Wilson DJ, Aarestrup FM. Global Genomic Epidemiology of Salmonella enterica Serovar Typhimurium DT104. Appl Environ Microbiol. 2016 Apr; 82(8):2516-26. PMID: 26944846.
      View in: PubMed
    27. Jun SR, Wassenaar TM, Nookaew I, Hauser L, Wanchai V, Land M, Timm CM, Lu TY, Schadt CW, Doktycz MJ, Pelletier DA, Ussery DW. Diversity of Pseudomonas Genomes, Including Populus-Associated Isolates, as Revealed by Comparative Genome Analysis. Appl Environ Microbiol. 2016 01 01; 82(1):375-83. PMID: 26519390.
      View in: PubMed
    28. Timm CM, Campbell AG, Utturkar SM, Jun SR, Parales RE, Tan WA, Robeson MS, Lu TY, Jawdy S, Brown SD, Ussery DW, Schadt CW, Tuskan GA, Doktycz MJ, Weston DJ, Pelletier DA. Metabolic functions of Pseudomonas fluorescens strains from Populus deltoides depend on rhizosphere or endosphere isolation compartment. Front Microbiol. 2015; 6:1118. PMID: 26528266.
      View in: PubMed
    29. Jun SR, Robeson MS, Hauser LJ, Schadt CW, Gorin AA. PanFP: pangenome-based functional profiles for microbial communities. BMC Res Notes. 2015 Sep 26; 8:479. PMID: 26409790.
      View in: PubMed
    30. Jun SR, Leuze MR, Nookaew I, Uberbacher EC, Land M, Zhang Q, Wanchai V, Chai J, Nielsen M, Trolle T, Lund O, Buzard GS, Pedersen TD, Wassenaar TM, Ussery DW. Ebolavirus comparative genomics. FEMS Microbiol Rev. 2015 Sep; 39(5):764-78. PMID: 26175035.
      View in: PubMed
    31. Land M, Hauser L, Jun SR, Nookaew I, Leuze MR, Ahn TH, Karpinets T, Lund O, Kora G, Wassenaar T, Poudel S, Ussery DW. Insights from 20 years of bacterial genome sequencing. Funct Integr Genomics. 2015 Mar; 15(2):141-61. PMID: 25722247.
      View in: PubMed
    32. Land ML, Hyatt D, Jun SR, Kora GH, Hauser LJ, Lukjancenko O, Ussery DW. Quality scores for 32,000 genomes. Stand Genomic Sci. 2014; 9:20. PMID: 25780509.
      View in: PubMed
    33. Jun SR, Sims GE, Wu GA, Kim SH. Whole-proteome phylogeny of prokaryotes by feature frequency profiles: An alignment-free method with optimal feature resolution. Proc Natl Acad Sci U S A. 2010 Jan 05; 107(1):133-8. PMID: 20018669.
      View in: PubMed
    34. Sims GE, Jun SR, Wu GA, Kim SH. Whole-genome phylogeny of mammals: evolutionary information in genic and nongenic regions. Proc Natl Acad Sci U S A. 2009 Oct 06; 106(40):17077-82. PMID: 19805074.
      View in: PubMed
    35. Wu GA, Jun SR, Sims GE, Kim SH. Whole-proteome phylogeny of large dsDNA virus families by an alignment-free method. Proc Natl Acad Sci U S A. 2009 Aug 04; 106(31):12826-31. PMID: 19553209.
      View in: PubMed
    36. Sims GE, Jun SR, Wu GA, Kim SH. Alignment-free genome comparison with feature frequency profiles (FFP) and optimal resolutions. Proc Natl Acad Sci U S A. 2009 Feb 24; 106(8):2677-82. PMID: 19188606.
      View in: PubMed
    37. Kim SH, Hou J, Jun SR, Sims GE, Choi IG. Structure, function, and evolution mapping of the protein structure universe. Federation of American Societies for Experimental Biology. 2007; 21(6):A1003-A1003.
    38. Se-Ran Jun, Sungkwon Kang, YoungHoon Kwon. A direct solver for the legendre tau approximation for the two-dimensional poisson problem . Journal of Applied Mathematics & Computing. 2007; 23(1-2):25-42.
    39. Kim SH, Hou J, Jun SR, Choi IG. A global view of the protein structure universe and evolution of protein structure families. Federation of American Societies for Experimental Biology. 2006; 20(4):A530-A530.
    40. Hou J, Jun SR, Zhang C, Kim SH. Global mapping of the protein structure space and application in structure-based inference of protein function. Proc Natl Acad Sci U S A. 2005 Mar 08; 102(10):3651-6. PMID: 15705717.
      View in: PubMed
    41. Se-Ran Jun, Sung-Kwon Kang, and YongHoon Kwon. A spectral approximation scheme for the Stokes equations. Mathematical and Computer Modelling. 2004; 40:535-552.
    42. Se-Ran Jun, Sung-Kwon Kang, and YongHoon Kwon. Legendre Tau method for the 2-D Stokes problem. Journal of the Korean Society for Industrial and Applied Mathematics. 2000; 4:111-133.
    43. Se-Ran Jun, Sung-Kwon Kang, and YongHoon Kwon. A variational spectral method for the two-dimensional Stokes problem. Computers and Mathematics with Applications. 1998; 35(4):1-17.
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