Ki-Tae Kim

Fungal Genomicist | Bioinformatician | Pathologist

Career Summary

Not sturdy pathogens survive, but pathogens that adapt to the changing environment are sturdy. Like pathogens, I am an adaptive and studious genome scientist | bioinformatician | pathologist with 8+ years of experience in fungal genome analysis. But not like pathogens, I consult wet-lab scientists with in silico problems such as NGS, omics, and programming (R & Python) in a symbiotic way. Through comparative genomics and evolutionary analyses, I am trying to reveal the secrets of fungal biology and the mysterious mechanisms of pathogenesis. However, not limited to fungi but also interested and involved in the genome analysis of plants, animals, and other microorganisms. I am looking forward to putting my expert knowledge of genome research to good use.


Join KakaoTalk Open Chat Group for Bionformaticans running by me for fast discussion (in Korean).

Work Experience

Postdoctoral Researcher

Plant Immunity Research Center
2020.3 - 2020.11

Analyzing core- and pan-genomes and constructing protein-protein interaction networks of the blast fungus. Also, developing a fungal genome web-portal service. Coming soon...

Achievements:

Ph.D.

Fungal Plant Pathology Lab (Fungal Bioinformatics Lab)
2012.9 - 2020.2

Constructed protein effector prediction pipeline and analyzed ~200 fungal species with various lifestyles. Fungal effectors are molecules that are secreted by a fungus to a host to modulate host physiology and metabolism in favor of fungus. This revealed the correlation between the repertoire of fungal effectors and host association of fungi. Performed phylogenomic analysis of blast fungus Magnaporthe oryzae infecting different Poaceae hosts and explained how effector genes were evolutionarily diversified by different hosts. Involved in database construction, annotation tool development, and NGS (genome & transcriptome) analyses.

Achievements:

Publications

2021

Homeobox transcription factors are required for fungal development and the suppression of host defense mechanisms in the Colletotrichum scovillei-pepper pathosystem
Teng Fu, Joon-Hee Han, Jong-Hwan Shin, Hyeunjeong Song, Jaeho Ko, Yong-Hwan Lee, Ki-Tae Kim†, Kyoung Su Kim†
mBio 12: e01620-21

2021

Comparative genome analyses of four rice-infecting Rhizoctonia solani isolates reveal extensive enrichment of homogalacturonan modification genes
Da-Young Lee, Jongbum Jeon, Ki-Tae Kim, Kyeongchae Cheong, Hyeunjeong Song, Gobong Choi, Jaeho Ko, Stephen O. Opiyo, James C. Correll, Shimin Zuo, Sheshu Madhav, Guo-Liang Wang, Yong-Hwan Lee
BMC Genomics 22: 242

2020

Two nuclear effectors of the rice blast fungus modulate host immunity via transcriptional reprogramming
Seongbeom Kim, Chi-Yeol Kim, Sook-Young Park, Ki-Tae Kim, Jongbum Jeon, Hyunjung Chung, Gobong Choi, Seomun Kwon, Jaeyoung Choi, Junhyun Jeon, Jong-Seong Jeon, Chang Hyun Khang, Seogchan Kang, Yong-Hwan Lee
Nature Communications 11: 1-11

2020

TGFam-Finder: a novel solution for target-gene family annotation in plants
Seungill Kim, Kyeongchae Cheong, Jieun Park, Myung-Shin Kim, Jihyun Kim, Min-Ki Seo, Geun Young Chae, Min Jeong Jang, Hyunggon Mang, Sun-Ho Kwon, Yong-Min Kim, Namjin Koo, Cheol Woo Min, Kwang-Soo Kim, Nuri Oh, Ki-Tae Kim, Jongbum Jeon, Hyunbin Kim, Yoon-Young Lee, Kee Hoon Sohn, Honour C McCann, Sang-Kyu Ye, Sun Tae Kim, Kyung-Soon Park, Yong-Hwan Lee, Doil Choi
New Phytologist 227: 1568-1581

2020

Transcriptome profiling of the rice blast fungus Magnaporthe oryzae and its host Oryza sativa during infection
Ki-Tae Kim*, Jongbum Jeon*, Gir-Won Lee*, Sook-Young Park, Seongbeom Kim, Seomun Kwon, Aram Huh, Hyunjung Chung, Da-Young Lee, Chi-Yeol Kim, Yong-Hwan Lee
Molecular Plant-Microbe Interactions 33: 141-144

2019

Evolution of the genes encoding effector candidates within multiple pathotypes of Magnaporthe oryzae
Ki-Tae Kim, Jaeho Ko, Hyeunjeong Song, Gobong Choi, Hyunbin Kim, Jongbum Jeon, Kyeongchae Cheong, Seogchan Kang, Yong-Hwan Lee
Frontiers in Microbiology 10: 2575

2019

A novel approach to investigate hypoxic microenvironment during rice colonization by Magnaporthe oryzae
Hyunjung Chung, Seongbeom Kim, Ki-Tae Kim, Bae-Geun Hwang, Hye-Jeong Kim, Sang-Joon Lee, Yong-Hwan Lee
Environmental microbiology 21: 1151-1169

2019

A high-quality draft genome sequence of Colletotrichum gloeosporioides sensu stricto SMCG1#C, a causal agent of anthracnose on Cunninghamia lanceolata in China
Ki-Tae Kim*, Lin Huang*, Ji-Yun Yang, Hyeunjeong Song, Gobong Choi, Jongbum Jeon, Kyeongchae Cheong, Jaeho Ko, Haibin Xu, Yong-Hwan Lee
Molecular Plant-Microbe Interactions 32: 139-141

2018

SUMOylation is required for fungal development and pathogenicity in the rice blast fungus Magnaporthe oryzae
You-Jin Lim, Ki-Tae Kim, Yong-Hwan Lee
Molecular Plant Pathology 19: 2134-2148

2018

Global gene expression profiling for fruit organs and pathogen infections in the pepper, Capsicum annuum L.
Myung-Shin Kim, Seungill Kim, Jongbum Jeon, Ki-Tae Kim, Hyun-Ah Lee, Hye-Young Lee, Jieun Park, Eunyoung Seo, Saet-Byul Kim, Seon-In Yeom, Yong-Hwan Lee, Doil Choi
Scientific Data 5: 180103

2017

New reference genome sequences of hot pepper reveal the massive evolution of plant disease-resistance genes by retroduplication
Seungill Kim, Jieun Park, Seon-In Yeom, Yong-Min Kim, Eunyoung Seo, Ki-Tae Kim, Myung-Shin Kim, Je Min Lee, Kyeongchae Cheong, Ho-Sub Shin, Saet-Byul Kim, Koeun Han, Jundae Lee, Minkyu Park, Hyun-Ah Lee, Hye-Young Lee, Youngsill Lee, Soohyun Oh, Joo Hyun Lee, Eunhye Choi, Eunbi Choi, So Eui Lee, Jongbum Jeon, Hyunbin Kim, Gobong Choi, Hyeunjeong Song, JunKi Lee, Sang-Choon Lee, Jin-Kyung Kwon, Hea-Young Lee, Namjin Koo, Yunji Hong, Ryan W Kim, Won-Hee Kang, Jin Hoe Huh, Byoung-Cheorl Kang, Tae-Jin Yang, Yong-Hwan Lee, Jeffrey L Bennetzen, Doil Choi
Genome Biology 1: 1-11

2017

Comparative analysis of genome sequences of the conifer tree pathogen, Heterobasidion annosum s.s.
Jaeyoung Choi, Gir-Won Lee, Ki-Tae Kim, Jongbum Jeon, Nicolas Detry, Hsiao-Che Kuo, Hui Sun, Fred O Asiegbu, Yong-Hwan Lee
Genomics Data 14: 106-113

2017

Gapless genome assembly of Colletotrichum higginsianum reveals chromosome structure and association of transposable elements with secondary metabolite gene clusters
Jean-Felix Dallery, Nicolas Lapalu, Antonios Zampounis, Sandrine Pigne, Isabelle Luyten, Joelle Amselem, Alexander HJ Wittenberg, Shiguo Zhou, Marisa V de Queiroz, Guillaume P Robin, Annie Auger, Matthieu Hainaut, Bernard Henrissat, Ki-Tae Kim, Yong-Hwan Lee, Olivier Lespinet, David C Schwartz, Michael R Thon, Richard J O'Connell
BMC Genomics 1: 1-22

2017

Genome sequence of an endophytic fungus, Fusarium solani JS-169, which has antifungal activity
Jung A Kim, Jongbum Jeon, Sook-Young Park, Ki-Tae Kim, Gobong Choi, Hyun-jung Lee, Yangsun Kim, Hee-sun Yang, Joo-Hong Yeo, Yong-Hwan Lee, Soonok Kim
Genome Announcements 5: e01071-17

2017

Draft genome sequence of Aspergillus persii NIBRFGC000004109, which has antibacterial activity against plant-pathogenic bacteria
Jung A Kim, Jongbum Jeon, Sook-Young Park, Ki-Tae Kim, Gobong Choi, Hoa Thi Nguyen, Sun Jeong Jeon, Hyang Burm Lee, Chang-Hwan Bae, Hee-sun Yang, Joo-Hong Yeo, Jin-Cheol Kim, Yong-Hwan Lee, Soonok Kim
Genome Announcements 5: e00932-17

2017

Draft genome sequence of the fungus associated with oak wilt mortality in South Korea, Raffaelea quercus-mongolicae KACC44405
Jongbum Jeon, Ki-Tae Kim, Hyeunjeong Song, Gir-Won Lee, Kyeongchae Cheong, Hyunbin Kim, Gobong Choi, Yong-Hwan Lee, Jane E Stewart, Ned B Klopfenstein, Mee-Sook Kim
Genome Announcements 5: e00797-17

2017

Draft genome sequence of an endophytic fungus, Gaeumannomyces sp. strain JS-464, isolated from a reed plant, Phragmites communis
Jung A Kim, Jongbum Jeon, Ki-Tae Kim, Gobong Choi, Sook-Young Park, Hyun-Jung Lee, Sang-Hee Shim, Yong-Hwan Lee, Soonok Kim
Genome Announcements 5: e00734-17

2016

Kingdom-wide analysis of fungal small secreted proteins (SSPs) reveals their potential role in host association
Ki-Tae Kim, Jongbum Jeon, Jaeyoung Choi, Kyeongchae Cheong, Hyeunjeong Song, Gobong Choi, Seogchan Kang, Yong-Hwan Lee
Frontiers in Plant Science 7: 186

2015

Integrative structural annotation of de novo RNA-Seq provides an accurate reference gene set of the enormous genome of the onion (Allium cepa L.)
Seungill Kim, Myung-Shin Kim, Yong-Min Kim, Seon-In Yeom, Kyeongchae Cheong, Ki-Tae Kim, Jongbum Jeon, Sunggil Kim, Do-Sun Kim, Seong-Han Sohn, Yong-Hwan Lee, Doil Choi
DNA Research 22: 19-27

2015

dbHiMo: a web-based epigenomics platform for histone-modifying enzymes
Jaeyoung Choi, Ki-Tae Kim, Aram Huh, Seomun Kwon, Changyoung Hong, Fred O Asiegbu, Junhyun Jeon, Yong-Hwan Lee
Database 2015: bav052

2014

funRNA: a fungi-centered genomics platform for genes encoding key components of RNAi
Jaeyoung Choi, Ki-Tae Kim, Jongbum Jeon, Jiayao Wu, Hyeunjeong Song, Fred O Asiegbu, Yong-Hwan Lee
BMC Genomics 15: S14

2014

fPoxDB: fungal peroxidase database for comparative genomics
Jaeyoung Choi, Nicolas Detry, Ki-Tae Kim, Fred O Asiegbu, Jari PT Valkonen, Yong-Hwan Lee
BMC Microbiology 14: 117

2014

Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum species
Seungill Kim, Minkyu Park, Seon-In Yeom, Yong-Min Kim, Je Min Lee, Hyun-Ah Lee, Eunyoung Seo, Jaeyoung Choi, Kyeongchae Cheong, Ki-Tae Kim, Kyongyong Jung, Gir-Won Lee, Sang-Keun Oh, Chungyun Bae, Saet-Byul Kim, Hye-Young Lee, Shin-Young Kim, Myung-Shin Kim, Byoung-Cheorl Kang, Yeong Deuk Jo, Hee-Bum Yang, Hee-Jin Jeong, Won-Hee Kang, Jin-Kyung Kwon, Chanseok Shin, Jae Yun Lim, June Hyun Park, Jin Hoe Huh, June-Sik Kim, Byung-Dong Kim, Oded Cohen, Ilan Paran, Mi Chung Suh, Saet Buyl Lee, Yeon-Ki Kim, Younhee Shin, Seung-Jae Noh, Junhyung Park, Young Sam Seo, Suk-Yoon Kwon, Hyun A Kim, Jeong Mee Park, Hyun-Jin Kim, Sang-Bong Choi, Paul W Bosland, Gregory Reeves, Sung-Hwan Jo, Bong-Woo Lee, Hyung-Taeg Cho, Hee-Seung Choi, Min-Soo Lee, Yeisoo Yu, Yang Do Choi, Beom-Seok Park, Allen Van Deynze, Hamid Ashrafi, Theresa Hill, Woo Taek Kim, Hyun-Sook Pai, Hee Kyung Ahn, Inhwa Yeam, James J Giovannoni, Jocelyn KC Rose, Iben Sorensen, Sang-Jik Lee, Ryan W Kim, Ik-Young Choi, Beom-Soon Choi, Jong-Sung Lim, Yong-Hwan Lee, Doil Choi
Nature Genetics 46: 270-278

2013

Fungal plant cell wall-degrading enzyme database: a platform for comparative and evolutionary genomics in fungi and Oomycetes
Jaeyoung Choi, Ki-Tae Kim, Jongbum Jeon, Yong-Hwan Lee
BMC Genomics 14: S7

Skills

Sequence analysis

  • Sequencing
  • Assembly
  • Annotation
  • Evolution
  • Genomics

Expression analysis

  • Gene expression
  • Protein expression
  • Cellular regulation

Cellular analysis

  • Cellular image
  • Protein localization
  • Nuclear organization

Structural bioinformatics

  • Protein structure

Systems biology

  • Interaction network

Others

  • Lieterature analysis
  • Single cell data analysis
  • Microbiome analysis
  • Ontologies and data integration
  • Databases

Education

  • PhD Agricultural Biotechnology
    Seoul Natioanl University
    Korea
    2012 - 2020
  • BSc Biological Sciences
    The University of Auckland
    New Zealand
    2007 - 2010

Language

  • Korean (Native)
  • English (Professional)

  • Phython (Expert)
  • R (Expert)
  • Perl (Intermediate)
  • SQL (Intermediate)
  • HTML/CSS (Intermediate)

Interests

  • Microbiome
  • Single cell RNA-seq
  • Phylogenomics