Jaeyoung Choi, Ph.D.

Associate Professor
Department of Oriental Medicine Biotechnology
College of Life Sciences
Kyung Hee Univesity

Office +82-31-201-2695
Email jaeyoung.choi [at] khu.ac.kr
Address 1732, Deogyeong-daero, Giheung-gu, Yongin-si, Gyeonggi-do 17104, Republic of Korea

Experience

Associate Professor

Department of Oriental Medicine Biotechnology
College of Life Sciences, Kyung Hee University, Yongin, Republic of Korea

March 2023 - Present

Senior Research Scientist

Smart Farm Research Center
Korea Institute of Science and Technology (KIST), Gangneung, Republic of Korea

April 2018 - February 2023

Bioinformatics Research Analyst

Bioinformatics & Scientific Computing / Microbial Symbiology Lab.
Noble Research Institute, Ardmore, OK, USA

October 2015 - February 2018

Postdoctoral Researcher

Department of Forest Sciences
University of Helsinki, Helsinki, Finland

September 2014 - August 2015

Postdoctoral Researcher

Center for Fungal Pathogenesis
Seoul National University, Seoul, Republic of Korea

March 2014 - August 2014

Education

Seoul National University

Ph.D. in Agricultural Biotechnology
Interdisciplinary Program in Agricultural Biotechnology
September 2007 - February 2014

Seoul National University

Bachelor of Science in Agriculture
Department of Applied Biology and Chemistry
March 2003 - February 2007

Skills

Programming Languages & Tools


Workflow
  • Genome assembly, gene prediction, and annotation
  • Comparative & evolutionary genomics
  • Molecular / Chemical ecology
  • Cross-omics analysis

Research

Publications

2024
  • 53. Hong S-C, Hong CR, Kim M, Kang YJ, Jung YH, Park K-M, Choi J*, Chang P-S*. 2024. Process optimization for microfluidic preparation of liposomes using food-grade components. Food Chemistry, 451:139437.
  • 52. Truong TQ, Park YJ, Jeon J-S, Choi J, Koo SY, Choi YB, Huynh PK, Moon J, Kim SM. 2024. Myrosinase isogenes in wasabi (Wasabia japonica Matsum) and their putative roles in glucosinolate metabolism. BMC Plant Biology, 24:353.
2023
  • 51. Jeon BJ, Yoo N, Kim JD*, Choi J*. 2023. A peptide encoded by a highly conserved gene belonging to the genus Streptomyces shows antimicrobial activity against plant pathogens. Front. Plant Sci. 14:1250906.
  • 50. Lee S, Won HJ, Ban S, Park YJ, Kim SM, Kim HS, Choi J, Kim H-Y, Lee JH, Jung JH. 2023. Integrative analysis of metabolite and transcriptome reveals biosynthetic pathway and candidate genes for eupatilin and jaceosidin biosynthesis in Artemisia argyi. Frontiers in Plant Science, 14: 1186023.
  • 49. Park YJ, Kwon DW, Koo SY, Truong TQ, Hong SC, Choi J, Moon J, Kim SM. 2023. Identification of drought-responsive phenolic compounds and their biosynthetic regulation under drought stress in Ligularia fischeri. Frontiers in Plant Science, 14:1140509.
2022
  • 48. Kim D-E, Hong S-C, Yang Y, Choi J*, Park J-S*. 2022. Chemical and genomic analysis of a marine-derived Streptomyces sp. V17-9 producing amino acid derivatives and siderophores. Frontiers in Marine Science, 9:959690.
  • 47. Song H, Kim K-T, Park S-Y, Lee G-W, Choi J, Jeon J, Cheong K, Choi G, Hur J-S, Lee Y-H. 2022. A comparative genomic analysis of lichen-forming fungi reveals new insights into fungal lifestyles. Scientific Reports, 12:10724.
  • 46. Kang S, Kim K-T, Choi J, Kim H, Cheong K, Bandara AY, Lee Y-H. 2022. Genomics and informatics, conjoined tools vital for understanding and protecting plant health. Phytopathology, 112(5):981-995.
  • 45. Sodedji FAK, Ryu DH, Choi J, Agbahoungba S, Assogbadjo AE, N’Guetta S-PA, Jung JH, Nho CW, Kim H-Y. 2022. Genetic diversity and association analysis for carotenoid content among sprouts of cowpea (Vigna unguiculata Walp. L). International Journal of Molecular Sciences, 23(7):3696.
  • 44. Jeon J, Kim K-T, Choi J, Cheong K, Ko J, Choi G, Lee H, Lee G-W, Park S-Y, Kim S, Kim ST, Min CW, Kang S, Lee Y-H. 2022. Alternative splicing diversifies the transcriptome and proteome of the rice blast fungus during host infection. RNA Biology, 19(1):373-385.
2021
  • 43. Sodedji FAK, Agbahoungba S, Agoyi EE, Kafoutchoni MK, Choi J, Nguetta SA, Assogbadjo AE, Kim H-Y. 2021. Diversity, population structure, and linkage disequilibrium among cowpea accessions. The Plant Genome, 14:e20113.
  • 42. Park J-S, Kim D-E, Hong S-C, Kim S-Y, Kwon HC, Hyun C-G*, Choi J*. 2021. Genome analysis of Streptomyces nojiriensis JCM 3382 and distribution of gene clusters for three antibiotics and an azasugar across the genus Streptomyces. Microorganisms, 9(9):1802.
  • 41. Kwon DY, Vuong TT, Choi J, Lee TS, Um J-I, Koo SY, Hwang KT, Kim SM. 2021. Fucoxanthin biosynthesis has a positive correlation with the specific growth rate in the culture of microalga Phaeodactylum tricornutum. Journal of Applied Phycology, 33:1473-1485.
  • 40. Nam J, Alam ST, Kang K, Choi J, Seo M-H. 2021. Anti-staphylococcal activity of a cyclic lipopeptide, C15-bacillomycin D, produced by Bacillus velezensis NST6. Journal of Applied Microbiology, 131:93-104.
  • 39. Choi J*, Nam J, Seo M-H*. 2021. Complete genome sequence of Bacillus velezensis NST6 and comparison with the species belonging to operational group B. amyloliquefaciens. Genomics, 113(1):380-386.
2020
  • 38. Kim S, Kim C-Y, Park S-Y, Kim K-T, Jeon J, Chung H, Choi G, Kwon S, Choi J, Jeon J, Jeon JS, Khang CH, Kang S, Lee Y-H. 2020. Two nuclear effectors of the rice blast fungus modulate host immunity via transcriptional reprogramming. Nature Communications, 11:5845.
  • 37. Wu J†, Choi J†, Asiegbu FO, Lee Y-H. 2020. Comparative genomics platform and phylogenetic analysis of fungal laccases and multi-copper oxidases. Mycobiology, 48(5):373–382.
  • 36. Jin J-H, Lee K-T, Hong J, Lee D, Jang E-H, Kim J-Y, Lee Y, Lee S-H, So Y-S, Jung K-W, Lee D-G, Jeong E, Lee M, Jang Y-B, Choi Y, Lee MH, Kim J-S, Yu S-R, Choi J-T, La J-W, Choi H, Kim S-W, Seo KJ, Lee Y, Thak EJ, Choi J, Averette AF, Lee Y-H, Heitman J, Kang HA, Cheong E, Bahn Y-S. 2020. Genome-wide functional analysis of phosphatases in the pathogenic fungus Cryptococcus neoformans. Nature Communications, 11:4212.
2019
  • 35. Jung D-H, Kim H-J, Kim HS, Choi J, Kim JD, Park SH. 2019. Fusion of spectroscopy and cobalt electrochemistry data for estimating phosphate concentration in hydroponic solution. Sensors, 19:2596.
2018
  • 34. Choi J, Lee J-J, Jeon J. 2018. Genomic insights into the rice blast fungus through estimation of gene emergence time in phylogenetic context. Mycobiology, 46(4):361-369.
  • 33. So K-K, Ko Y-H, Chun J, Bal J, Jeon J, Kim J-M, Choi J, Lee Y-H, Huh JH, Kim D-H. 2018. Global DNA methylation in the chestnut blight fungus Cryphonectria parasitica and genome-wide changes in DNA methylation accompanied with sectorization. Frontiers in Plant Science, 9:103.
2016
  • 32. Lee K-T, So Y-S, Yang D-H, Jung K-W, Choi J, Lee D-G, Kwon H, Jang J, Wang LL, Cha S, Meyers GL, Jeong E, Jin J-H, Lee Y, Hong J, Bang S, Ji J-H, Park G, Byun H-J , Park SW, Park Y-M, Adedoyin G, Kim T, Averette AF, Choi J-S, Heitman J, Cheong E, Lee Y-H, Bahn Y-S. 2016. Systematic functional analysis of kinases in the fungal pathogen Cryptococcus neoformans. Nature Communications, 7:12766.
  • 31. Kim K-T, Jeon J, Choi J, Cheong K, Song H, Choi G, Kang S, Lee Y-H. 2016. Kingdom-wide analysis of fungal small secreted proteins (SSPs) reveals their potential role in host association. Frontiers in Plant Science, 7:186.
2015
  • 30. Mir AA, Park S-Y, Sadat MA, Kim S, Choi J, Jeon J, Lee Y-H. 2015. Systematic characterization of the peroxidase gene family provides new insights into fungal pathogenicity in Magnaporthe oryzae. Scientific Reports, 5:11831.
  • 29. Choi J, Kim K-T, Huh A, Kwon S, Hong C, Asiegbu FO, Jeon J, Lee Y-H. 2015. dbHiMo: a web-based epigenomics platform for histone-modifying enzymes. Database-The Journal of Biological Databases and Curation, Vol. 2015: article ID bav052.
  • 28. Jung K-W, Yang D-H, Maeng S, Lee K-T, So Y-S, Hong J, Choi J, Byun H-J, Kim H, Bang S, Song M-H, Lee J-W, Kim MS, Kim S-Y, Ji J-H, Park G, Kwon H, Cha S, Meyers GL, Wang LL, Jang J, Janbon G, Adedoyin G, Kim T, Averette AK, Heitman J, Cheong E, Lee Y-H, Lee Y-W, Bahn Y-S. 2015. Systematic functional profiling of transcription factor networks in Cryptococcus neoformans. Nature Communications, 6:6757.
  • 27. Kuo H-C, Détry N, Choi J, Lee Y-H. 2015. Potential roles of laccases on virulence of Heterobasidion annosum s.s. Microbial Pathogenesis, 81:16-21.
  • 26. Jeon J, Choi J, Lee G-W, Park S-Y, Huh A, Dean RA, Lee Y-H. 2015. Genome-wide profiling of DNA methylation provides insights into epigenetic regulation of fungal development in a plant pathogenic fungus, Magnaporthe oryzae. Scientific Reports, 5:8567.
  • 25. Karlsson M, Durling MB, Choi J, Kosawang C, Lackner G, Tzelepis GD, Nygren K, Dubey MK, Kamou N, Levasseur A, Zapparata A, Wang J, Amby DB, Jensen B, Sarrocco S, Panteris E, Lagopodi AL, Pöggeler S, Vannacci G, Collinge DB, Hoffmeister D, Henrissat B, Lee Y-H, Jensen DF. 2015. Insights on the evolution of mycoparasitism from the genome of Clonostachys rosea. Genome Biology and Evolution, 7(2):465-480.
2014
  • 24. Sadat MA, Jeon J, Mir AA, Kim S, Choi J, Lee Y-H. 2014. Analysis of in planta expressed orphan genes in the rice blast fungus, Magnaporthe oryzae. The Plant Pathology Journal, 30(4):367-374.
  • 23. Wang Y†, Kwon SJ†, Wu J, Choi J, Lee Y-H, Agrawal GK, Tamogami S, Rakwal R, Park S-R, Kim B-G, Jung K-H, Kang KY, Kim SG, Kim ST. 2014. Transcriptome analysis of early responsive genes in rice during Magnaporthe oryzae infection. The Plant Pathology Journal, 30(4):343-354.
  • 22. Choi J, Kim K-T, Jeon J, Wu J, Song H, Asiegbu FO, Lee Y-H. 2014. funRNA: a fungi-centered genomics platform for genes encoding key components of RNAi. BMC Genomics, 15(S9):S14.
  • 21. Détry N†, Choi J†, Kuo H-C, Asiegbu FO, Lee Y-H. 2014. In silico sequence analysis reveals new characteristics of fungal NADPH oxidase genes. Mycobiology, 42(3):241-248.
  • 20. Sadat MA, Jeon J, Mir AA, Choi J, Choi J, Lee Y-H. 2014. Regulation of cellular diacylglycerol through lipid phosphate phosphatases is required for pathogenesis of the rice blast fungus, Magnaporthe oryzae. PLoS One, 9(6):e100726.
  • 19. Kuo H-C, Hui S, Choi J, Asiegbu FO, Valkonen JPT, Lee Y-H. 2014. Secret lifestyles of Neurospora crassa. Scientific Reports, 4:5135.
  • 18. Kim Y-M, Choi J, Lee G-W, Lee H, Lee Y-H, Choi D. 2014. dbCRY: a Web-based comparative and evolutionary genomics platform for blue-light receptors. Database-The Journal of Biological Databases and Curation, Vol. 2014: article ID bau037.
  • 17. Choi J†, Détry N†, Kim K-T, Asiegbu FO, Valkonen JPT, Lee Y-H. 2014. fPoxDB: fungal peroxidase database for comparative genomics. BMC Microbiology, 14:117.
  • 16. Kim S, Park M, Yeom S-I, Kim Y-M, Lee JM, Lee H-A, Seo E, Choi J, Cheong K, Kim K-T, Jung K, Lee G-W, Oh S-K, Bae C, Kim S-B, Lee H-Y, Kim S-Y, Kim M-S, Kang B-C, Jo YD, Yang H-B, Jeong H-J, Kang W-H, Kwon J-K, Shin C, Lim JY, Park JH, Huh JH, Kim J-S, Kim B-D, Cohen O, Paran I, Suh MC, Lee SB, Kim Y-K, Shin Y, Noh S-J, Park J, Seo YS, Kwon S-Y, Kim HA, Park JM, Kim H-J, Choi S-B, Bosland PW, Reeves G, Jo S-H, Lee B-W, Cho H-T, Choi H-S, Lee M-S, Yu Y, Choi YD, Park B-S, van Deynze A, Ashrafi H, Hill T, Kim WT, Pai H-S, Ahn HK, Yeam I, Giovannoni JJ, Rose JKC, Sørensen I, Lee S-J, Kim RW, Choi I-Y, Choi B-S, Lim J-S, Lee Y-H, Choi D. 2014. Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum species. Nature Genetics, 46(3):270-278.
2013
  • 15. Park B, Martin F, Geiser DM, Kim H-S, Mansfield MA, Nikolaeva E, Park S-Y, Coffey MD, Russo J, Kim SH, Balci Y, Abad G, Burgess T, Grünwald NJ, Cheong K, Choi J, Lee Y-H, Kang S. 2013. Phytophthora Database 2.0: update and future direction. Phytopathology, 103(12):1204-1208.
  • 14. Choi J, Kim K-T, Jeon J, Lee Y-H. 2013. Fungal Plant Cell Wall-degrading Enzyme Database: a platform for comparative and evolutionary genomics in fungi and Oomycetes. BMC Genomics, 14(S5):S7.
  • 13. Park S-Y, Choi J, Lim S-E, Lee G-W, Park J, Kim Y, Kong S, Kim SR, Rho H-S, Jeon J, Chi M-H, Kim S, Khang CH, Kang S, Lee Y-H. 2013. Global expression profiling of transcription factor genes provides new insights into pathogenicity and stress responses in the rice blast fungus. PLoS Pathogens, 9:e1003350.
  • 12. Kim Y, Park S-Y, Kim D, Choi J, Lee Y-H, Lee J, Choi W. 2013. Genome-scale analysis of ABC transporter genes and characterization of the ABCC type transporter genes in Magnaporthe oryzae. Genomics, 101:354-361.
  • 11. Jeon J, Choi J, Lee G-W, Dean RA, Lee Y-H. 2013. Experimental evolution reveals genome-wide spectrum and dynamics of mutations in the rice blast fungus, Magnaporthe oryzae. PLoS One, 8:e65416.
  • 10. Choi J, Cheong K, Jung K, Jeon J, Lee G-W, Kang S, Kim S, Lee Y-W, Lee Y-H. 2013. CFGP 2.0: a versatile web-based platform for supporting comparative and evolutionary genomics of fungi and Oomycetes. Nucleic Acids Research, 41:D714-D719.
2012
  • 9. Moktali V, Park J, Fedorova-Abrams ND, Park B, Lee Y-H, Choi J, Kang S. 2012. Systematic and searchable classification of cytochrome P450 proteins encoded by fungal and oomycete genomes. BMC Genomics, 13:525.
  • 8. O’Connell RJ, Thon MR, Hacquard S, Amyotte SG, Kleemann J, Torres MF, Damm U, Buiate EA, Epstein L, Alkan N, Altmüller J, Alvarado-Balderrama L, Bauser CL, Becker C, Birren BW, Chen Z, Choi J, Crouch JA, Duvick JP, Farman ML, Gan P, Heiman D, Henrissat B, Howard RJ, Kabbage M, Koch C, Kracher B, Kubo Y, Law AD, Lebrun M-H, Lee Y-H, Miyara I, Moore N, Neumann U, Nordström K, Panaccione DG, Panstruga R, Place M, Proctor RH, Prusky D, Rech G, Reinhardt R, Rollins JA, Rounsley S, Schardl CL, Schwartz DC, Shenoy N, Shirasu K, Sikhakolli UR, Stüber K, Sukno SA, Sweigard JA, Takano Y, Takahara H, Trail F, van der Does HC, Voll LM, Will I, Young S, Zeng Q, Zhang J, Zhou S, Dickman MB, Schulze-Lefert P, van Themaat EVL, Ma L-J, Vaillancourt LJ. 2012. Lifestyle transitions in plant pathogenic Colletotrichum fungi deciphered by genome and transcriptome analyses. Nature Genetics, 44(9):1060-1067.
2011
  • 7. Park B, Park J, Cheong K, Choi J, Jung K, Kim D, Lee Y-H, Ward TJ, O’Donnell K, Geiser DM, Kang S. 2011. Cyber infrastructure for Fusarium: three integrated platforms supporting strain identification, phylogenetics, comparative genomics and knowledge sharing. Nucleic Acids Research, 39:D640-D646.
2010
  • 6. Choi J, Park J, Kim D, Jung K, Kang S, Lee Y-H. 2010. Fungal Secretome Database: integrated platform for annotation of fungal secretomes. BMC Genomics, 11:105.
2009
  • 5. Lee W, Park J, Choi J, Jung K, Park B, Kim D, Lee J, Ahn K, Song W, Kang S, Lee Y-H, Lee S. 2009. IMGD: an integrated platform supporting comparative genomics and phylogenetics of insect mitochondrial genomes. BMC Genomics, 10:184.
2008
  • 4. Jung K, Park J, Choi J, Park B, Kim S, Ahn K, Choi J, Choi D, Kang S, Lee Y-H. 2008. SNUGB: a versatile genome browser supporting comparative and functional fungal genomics. BMC Genomics, 9:586.
  • 3. Park J, Lee S, Choi J, Ahn K, Park B, Kang S, Lee Y-H. 2008. Fungal cytochrome P450 database. BMC Genomics, 9:402.
  • 2. Park J, Park J, Jang S, Kim S, Kong S, Choi J, Ahn K, Kim J, Lee S, Kim S, Park B, Jung K, Kim S, Kang S, Lee Y-H. 2008. FTFD: an informatics pipeline supporting phylogenomic analysis of fungal transcription factors. Bioinformatics, 24(7):1024-1025.
  • 1. Park J, Park B, Jung K, Jang S, Yu K, Choi J, Kong S, Park J, Kim S, Kim H, Kim S, Kim JF, Blair JE, Lee K, Kang S, Lee Y-H. 2008. CFGP: a web-based, comparative fungal genomics platform. Nucleic Acids Research, 36:D562-D571.