 Se-Ran Jun
| Title | Associate Professor |
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| Institution | University of Arkansas for Medical Sciences |
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| Department | Biomedical Informatics, College of Medicine |
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| Address | 200 South Cedar
Mail Slot # 782
Little Rock AR 72202
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| Phone | 501-603-1766 |
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ORCID
.gif) | 0000-0003-2681-3950  |
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| vCard | Download vCard |
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 Overview Teaching Research 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.
R01AI175440-resubmission (HUANG, EN)Sep 1, 2024 - Aug 31, 2029 NIAID
Mechanisms of cefiderocol nonsusceptibility and resistance evolution in carbapenem resistant pathogens
Role: Co-Investigator |
| P30GM145393-03S1 (Smeltzer)May 1, 2024 - Apr 30, 2025 NIH/NIGMS
Center for Microbial Pathogenesis and Host inflammatory responses
Role: Co-Investigator |
| 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 |
| R01DK123246 (PARAJULI, NIRMALA)Jul 1, 2022 - Jun 30, 2026 NIDDK
Targeting heat shock protein 72 to improve renal function after transplantation
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 |
| R21AI169138 (JUN, SE-RAN)May 1, 2022 - Apr 30, 2025 NIAID
Real-time high-resolution method for genomic surveillance of ESKAPE pathogens
Role: Principal 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)Sep 1, 2021 - Aug 31, 2023 NIAID - pass through University of Arkansas
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 |
| OIA-1946391 (PRIOR, FRED)Jul 1, 2020 - Jun 30, 2025 NSF
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 |
| (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 |
| PTC2017-02 (JUN, SE-RAN)Apr 15, 2017 - Apr 30, 2018 UAMS Intramural Grant (CTSA)
Genome-based mumps surveillance system using third generation sequencing technology
Role: Principal Investigator |
Outreach Bibliographic
Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications.
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Sharma A, Jun SR, Bhattarai D, Panday S, Venugopal G, Panawan O, Washam C, Mackintosh S, Byrum S, Udaondo Z, Arthu JM, MacMillan-Crow LA, Parajuli N. Cold Storage Disrupts the Proteome and Phosphoproteome Landscape in Rat Kidney Transplants. Transplantion. 2024.
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Huang E, Thompson RN, Moon SH, Keck JM, Lowry MS, Melero J, Jun S-R, Rosenbaum ER, Dare RK. Treatment-emergent cefiderocol resistance in carbapenem-resistant Acinetobacter baumannii is associated with insertion sequence ISAba36 in the siderophore receptor pirA. Antimicrob Agents Chemother. 2024 Jul 09; 68(7):e0029024. PMID: 38809000.
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Kim D, Jun SR, D. Hwang. SoutheastCon 2024, Atlanta, GA, USA. doi: 10.1109/SoutheastCon52093.2024.10500051. Employing Machine Learning for the Prediction of Antimicrobial Resistance (AMR) Phenotypes. 2024; 1519-1524.
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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 May 01; 5(5):743-752. PMID: 38303110.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
This graph shows the total number of publications by year, by first, middle/unknown, or last author.
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| Year | Publications |
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| 1998 | 1 | | 2000 | 1 | | 2004 | 1 | | 2005 | 1 | | 2006 | 1 | | 2007 | 2 | | 2009 | 4 | | 2014 | 1 | | 2015 | 5 | | 2016 | 1 | | 2017 | 6 | | 2018 | 4 | | 2019 | 4 | | 2020 | 7 | | 2021 | 3 | | 2022 | 4 | | 2023 | 2 | | 2024 | 4 |
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