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Se-Ran Jun

TitleAssociate Professor
InstitutionUniversity of Arkansas for Medical Sciences
DepartmentBiomedical Informatics, College of Medicine
Address200 South Cedar
Mail Slot # 782
Little Rock AR 72202
Phone501-603-1766
ORCID ORCID Icon0000-0003-2681-3950 Additional info
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    Collapse Overview 

    Collapse Teaching 

    Collapse Research 
    Collapse research overview
    I am a data scientist and bioinformatician with mathematics background by training. I am working with non-omics and multiomics data (microbiome, genomics, metabolomics, lipidomics, DNA methylation, Proteomics, RNA-seq, single cell RNA-seq, and Tn-seq) integrated, using Machine Learning and Statistical Learning approaches. I am also working on Pathogen Surveillance using genomics and microbiome data. My research laboratory is focusing on real-time surveillance of antimicrobial resistant pathogens for immunocompromised patients, integrating omics data with EHR data.

    Collapse research activities and funding
    1946391     (JUN, SE-RAN)May 1, 2023 - Apr 30, 2025
    NSF - Pass Through: Arkansas Economic Development Commission
    Data Governance in Genomic Pathogen Surveillance
    Role: Principle Investigator
    2022-69015-36720     (HUANG, EN)Aug 1, 2022 - Jul 31, 2025
    USDA
    Assessment of antibiotic resistance in fresh vegetables from farm to fork
    Role: Co-Investigator
         (HUANG, EN)Jun 22, 2022 - Jun 21, 2023
    UAMS VCRI Pioneer Award
    Cefiderocol heteroresistance and resistance in carbapenem-resistant pathogens
    Role: Co-Investigator
    R21AI169138     (JUN, SE-RAN)May 10, 2022 - Apr 30, 2025
    NIH/Nat. Inst. of Allergy & Infectious Diseases
    Real-Time High Resolution Method for Genomic Surveillance of ESKAPE pathogens
    Role: Principal Investigator
    R01DK123246     (PARAJULI, NIRMALA)May 1, 2022 - Jan 31, 2026
    NIH/NIDDK
    Targeting heat shock protein 72 to improve renal function after transplantation
    Role: Co-Investigator
    P20GM109005     (BOERMA, MARJAN)Jan 1, 2022 - May 31, 2025
    NIH
    Center for Studies of Host Response to Cancer Therapy
    Role: Co-Investigator
         (JUN, SE-RAN)Jan 1, 2022 - Jun 30, 2023
    UAMS COM Barton
    The epigenomic stress-induced mechanisms in Daptomycin & Vancomycin-Resistant Enterococcus faecium
    Role: Principle Investigator
    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: Principle Investigator
    R03AI164158     (JUN, SE-RAN)Aug 18, 2021 - Jul 31, 2023
    NIH/Nat. Inst. of Allergy & Infectious Diseases - Pass Through: University of Arkansas at Fayetteville
    In vivo essential genome of Salmonella
    Role: Principal Investigator
         (JUN, SE-RAN)Aug 1, 2020 - Aug 31, 2021
    UAMS TRI Biomedical Informatics Pilot
    Using genomics to track carbapenem-resistant Enterobacteriaceae linking rural and urban health in Arkansas
    Role: Principle 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: Principle 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
         (JUN, SE-RAN)Jul 1, 2018 - Jun 30, 2019
    UAMS COM Barton Pilot
    Molecular Epidemiology of Vancomycin Resistant Enterococcus faecium in Cancer Patients
    Role: Principle 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: Other
         (JUN, SE-RAN)May 1, 2017 - Apr 30, 2018
    UAMS TRI Biomedical Informatics Pilot
    Genome-based mumps surveillance system using third generation sequencing technology
    Role: Principle Investigator

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    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. Kim D, Jun SR, Hwang DS. . IEEE SoutheastCon. Employing Machine Learning for the Prediction of Antimicrobial Resistance (AMR) Phenotypes. 2024.
    2. Bhattarai D, Lee SO, Joshi N, Jun SR, Lo S, Jiang L, Gokden N, Parajuli N. Cold Storage Followed by Transplantation Induces Immunoproteasome in Rat Kidney Allografts: Inhibition of Immunoproteasome Does Not Improve Function. Kidney360. 2024 Feb 02; (0). PMID: 38303110.
      View in: PubMed
    3. Cooper G, Jun SR, Hwang DS, Kim DH. IEEE International Conference on Biomedical and Health Informatics (BHI). Prediction of antimicrobial resistance (AMR) phenotypes using machine learning. 2023.
    4. Udaondo Z, Abram K, Kothari A, Jun SR. Top-Down Genomic Surveillance Approach To Investigate the Genomic Epidemiology and Antibiotic Resistance Patterns of Enterococcus faecium Detected in Cancer Patients in Arkansas. Microbiol Spectr. 2023 06 15; 11(3):e0490122. PMID: 36995227.
      View in: PubMed
    5. Heo S, Shin MS, Lee MO, Kim SS, Kim SH, Randolph J, Jun SR, An MJ, Ounpraseuth S, Kim JS. Factors Related to Patients' Self-care and Self-care Confidence in Korean Patients With Heart Failure and Their Caregivers: A Cross-sectional, Correlational Study. J Cardiovasc Nurs. 2023; 38(2):140.
    6. Udaondo Z, Abram KZ, Kothari A, Jun SR. Insertion sequences and other mobile elements associated with antibiotic resistance genes in Enterococcus isolates from an inpatient with prolonged bacteraemia. Microb Genom. 2022 08; 8(8). PMID: 35921144.
      View in: PubMed
    7. Udaondo Z, Abram KZ, Gulley T, Garner K, Shray J, Whisnant M, Harris-Spotts A, Crawford M, Kothari A, Wongsurawat T, Moon SH, Huang E, Jun SR. Complete Genome Sequence of a Non-Carbapenemase-Producing Carbapenem-Resistant Providencia rettgeri Strain Isolated from a Clinical Urine Sample in Arkansas. Microbiol Resour Announc. 2022 Aug 18; 11(8):e0047422. PMID: 35894621.
      View in: PubMed
    8. Moon SH, Udaondo Z, Jun SR, Huang E. Cefiderocol heteroresistance in Klebsiella pneumoniae is linked to mutations in the siderophore receptor cirA and ?-lactamase activities. Int J Antimicrob Agents. 2022 09; 60(3):106635. PMID: 35820535.
      View in: PubMed
    9. Kim T, Roy SB, Moon S, Yoo S, Choi H, Parale VG, Kim Y, Lee J, Jun SC, Kang K, Chun SH, Kanamori K, Park HH. Highly Dispersed Pt Clusters on F-Doped Tin(IV) Oxide Aerogel Matrix: An Ultra-Robust Hybrid Catalyst for Enhanced Hydrogen Evolution. ACS Nano. 2022 Jan 25; 16(1):1625-1638. PMID: 36350111.
      View in: PubMed
    10. Abram KZ, Jun SR, Udaondo Z. Pseudomonas aeruginosa Pangenome: Core and Accessory Genes of a Highly Resourceful Opportunistic Pathogen. Adv Exp Med Biol. 2022; 1386:3-28. PMID: 36258067.
      View in: PubMed
    11. Moon SH, Udaondo Z, Abram KZ, Li X, Yang X, DiCaprio EL, Jun SR, Huang E. Isolation of AmpC- and extended spectrum ?-lactamase-producing Enterobacterales from fresh vegetables in the United States. Food Control. 2022 Feb; 132. PMID: 34629764.
      View in: PubMed
    12. 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
    13. 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 09; 26:264-265. PMID: 34329791.
      View in: PubMed
    14. 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.
      View Publication
    15. Bose C, Alves I, Singh P, Palade PT, Carvalho E, B?rsheim 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
    16. 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
    17. 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
    18. 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
    19. 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
    20. 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
    21. 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
    22. 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
    23. 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.
      View Publication
    24. 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
    25. 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
    26. 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
    27. 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
    28. Timm CM, Carter KR, Carrell AA, Jun SR, Jawdy SS, V?lez 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
    29. 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
    30. 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
    31. 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
    32. 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.
    33. 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.
      View Publication
    34. 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
    35. 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
    36. 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
    37. 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
    38. 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
    39. 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
    40. 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
    41. 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
    42. 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
    43. 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
    44. 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
    45. 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
    46. 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.
    47. 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.
    48. 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.
    49. 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
    50. 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.
    51. 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.
    52. 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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