김학민
Hak-Min kim
Education and training
2015-2019.8 Ph.D course, UNIST
2010-2012 M.S in Bioinformatics, Soongsil University
2003-2009 B.S in Bioinformatics, Sangmyung University
Professional Experiences
2009.02-2010.01 Researcher, Korean Bioinformation Center (KOBIC), KRIBB, Daejeon, Korea
2011.02-2014.07 Senior Researcher, Personal Genomics Institute, Genome Research Foundation, Suwon, Korea
2014.07-2015.08 Researcher, The Genomics Institute, Ulsan, Korea
2019.10-present Senior Researcher, Clinomics, Suwon, Korea
Work Experiences
- Bioinformatics: de novo genome assembly, comparative genomics, cancer genome analysis
List of Publications
29. (First author) Comparative analysis of 7 short-read sequencing platforms using the Korean Reference Genome: MGI and Illumina sequencing benchmark for whole-genome sequencing.
Hak-Min Kim, Sungwon Jeon, Oksung Chung, Je Hoon Jun, Hui-Su Kim, Asta Blazyte, Hwang-Yeol Lee, Youngseok Yu, Yun Sung Cho, Dan M Bolser, Jong Bhak. GigaScience (2021).
28. (co-author) The whale shark genome reveals how genomic and physiological properties scale with body size.
Jessica A. Weber, Seung Gu Park, Victor Luria, Sungwon Jeon, Hak-Min Kim, Yeonsu Jeon, Youngjune Bhak, Je Hun Jun, Sang Wha Kim, Won Hee Hong, Semin Lee, Yun Sung Cho, Amir Karger, John W. Cain, Andrea Manica, Soonok Kim, Jae-Hoon Kim, Jeremy S. Edwards, Jong Bhak, and George M. Church. PNAS (2020)
27. (co-author) Korean Genome Project: 1094 Korean personal genomes with clinical information
Sungwon Jeon, Youngjune Bhak, Yeonsong Choi, Yeonsu Jeon, Seunghoon Kim, Jaeyoung Jang, Jinho Jang, Asta Blazyte, Changjae Kim, Yeonkyung Kim, Jungae Shim, Nayeong Kim, Yeo Jin Kim, Seung Gu Park, Jungeun Kim, Yun Sung Cho, Yeshin Park, Hak-Min Kim, Byoung-Chul Kim, Neung-Hwa Park, Eun-Seok Shin, Byung Chul Kim, Dan Bolser, Andrea Manica, Jeremy S. Edwards, George Church, Semin Lee, and Jong Bhak. Science advances. 6:eaaz7835 (2020)
26. (co-author) Whole Genome Analysis of the Red-Crowned Crane Provides Insight into Avian Longevity.
Lee H, Kim J, Weber JA, Chung O, Cho YS, Jho S, Jun J, Kim HM, Lim J, Choi JP, Jeon S, Blazyte A, Edwards JS, Paek WK, Bhak J. Mol Cells. 10.14348/molcells.2019.0190. (2020)
25. (co-author) Depression and suicide risk prediction models using blood-derived multi-omics data
Youngjune Bhak, Hyoung-oh Jeong, Yun Sung Cho, Sungwon Jeon, Juok Cho, Jeong-An Gim, Yeonsu Jeon, Asta Blazyte, Seung Gu Park, Hak-Min Kim, Eun-Seok Shin, Jong-Woo Paik, Hae-Woo Lee, Wooyoung Kang, Aram Kim, Yumi Kim, Byung Chul Kim, Byung-Joo Ham, Jong Bhak & Semin Lee Translational Psychiatry volume 9, Article number: 262 (2019)
24. (co-author) Raptor genomes reveal evolutionary signatures of predatory and nocturnal lifestyles.
Yun Sung Cho, Je Hoon Jun, Jung A Kim, Hak-Min Kim, Oksung Chung, Seung-Gu Kang, Jin-Young Park, Hwa-Jung Kim, Sunghyun Kim, Hee-Jong Kim, Jin-ho Jang, Ki-Jeong Na, Jeongho Kim, Seung Gu Park, Hwang-Yeol Lee, Andrea Manica, David P. Mindell,11 Jérôme Fuchs, Jeremy S. Edwards, Jessica A. Weber, Christopher C. Witt, Joo-Hong Yeo, Soonok Kim, and Jong Bhak Genome Biology 20:181 (2019)
23. (co-first author) The genome of the giant Nomura's jellyfish sheds light on the early evolution of active predation.
Hak-Min Kim, Jessica A. Weber, Nayoung Lee, Seung Gu Park, Yun Sung Cho, Youngjune Bhak, Nayun Lee, Yeonsu Jeon, Sungwon Jeon, Victor Luria, Amir Karger, Marc W. Kirschner, Ye Jin Jo, Seonock Woo, Kyoungsoon Shin, Oksung Chung, Jae-Chun Ryu, Hyung-Soon Yim, Jung-Hyun Lee, Jeremy S. Edwards, Andrea Manica, Jong Bhak, and Seungshic Yum BMC Biology 17:28 (2019).
22. (co-author) The draft genome of an octocoral, Dendronephthya gigantea
Yeonsu Jeon, Seung Gu Park, Nayun Lee, Jessica A Weber, Hui-Su Kim, Sung-Jin Hwang, Seonock Woo, Hak-min Kim, Youngjune Bhak, Sungwon Jeon, Nayoung Lee, Yejin Jo, Asta Blazyte, Taewoo Ryu, Yun Sung Cho, Hyunho Kim, Jung-Hyun Lee, Hyung-Soon Yim, Jong Bhak, and Seungshic Yum Genome Biol Evol. pii:evz043 (2019).
21. (co-author) The Galleria mellonella Hologenome Supports Microbiota-Independent Metabolism of Long-Chain Hydrocarbon Beeswax
Hyun Gi Kong, Hyun Ho Kim, Joon-hui Chung, JeHoon Jun, Soohyun Lee, Hak-Min Kim, Sungwon Jeon, Seung Gu Park, Jong Bhak, Choong-Min Ryu Cell Rep. 26:2451-2464 (2019).
20. (co-author) KoVariome: Korean National Standard Reference Variome database of whole genomes with comprehensive SNV, indel, CNV, and SV analyses
Jungeun Kim, Jessica A. Weber, Sungwoong Jho, Jinho Jang, JeHoon Jun, Yun Sung Cho, Hak-Min Kim, Hyunho Kim, Yumi Kim, OkSung Chung, Chang Geun Kim, HyeJin Lee, Byung Chul Kim, Kyudong Han, InSong Koh, Kyun Shik Chae, Semin Lee, Jeremy S. Edwards, and Jong Bhak Sci Rep. 8:5677 (2018).
19. (co-author) Myotis rufoniger genome sequence and analyses: M. rufoniger’s genomic feature and the decreasing effective population size of Myotis bats
Youngjune Bhak, Yeonsu Jeon, Sungwon Jeon, Oksung Chung, Sungwoong Jho, JeHoon Jun, Hak-Min Kim, Yongsoo Cho, Changhan Yoon, Seungwoo Lee, Jung-Hoon Kang, Jong-Deock Lim, Junghwa An, Yun Sung Cho, Doug-Young Ryu, and Jong Bhak PLoS One 12:e0180418 (2017).
18. (co-author) Genome-wide data from two early Neolithic East Asian individuals dating to 7700 years ago
Veronika Siska, Eppie Ruth Jones, Sungwon Jeon, Youngjune Bhak, Hak-Min Kim, Yun Sung Cho, Hyunho Kim, Kyusang Lee, Elizaveta Veselovskaya, Tatiana Balueva, Marcos Gallego-Llorente, Michael Hofreiter, Daniel G. Bradley, Anders Eriksson, Ron Pinhasi, Jong Bhak, and Andrea Manica Sci Adv. 3:e1601877 (2017).
17. -(co-author) Genomes of coral dinoflagellate symbionts highlight evolutionary adaptations conducive to a symbiotic lifestyle.
Aranda M, Li Y, Liew YJ, Baumgarten S, Simakov O, Wilson MC, Piel J, Ashoor H, Bougouffa S, Bajic VB, Ryu T, Ravasi T, Bayer T, Micklem G, Kim H, Bhak J, LaJeunesse TC, Voolstra CR Sci. rep. 6:39734 (2016)
16. (co-author) An ethnically relevant consensus Korean reference genome is a step towards personal reference genomes.
Yun Sung Cho, Hyunho Kim, Hak-Min Kim, Sungwoong Jho, JeHoon Jun, Yong Joo Lee, Kyun Shik Chae, Chang Geun Kim, Sangsoo Kim, Anders Eriksson, Jeremy S. Edwards, Semin Lee, Byung Chul Kim, Andrea Manica, Tae-Kwang Oh, George M. Church, and Jong Bhak Nat commun. 7:13637 (2016).
15. (co-first author) Comparison of carnivore, omnivore, and herbivore mammalian genomes with a new leopard assembly.
Soonok Kim, Yun Sung Cho, Hak-Min Kim, Oksung Chung, Hyunho Kim, Sungwoong Jho, Hong Seomun, Jeongho Kim, Woo Young Bang, Changmu Kim, Junghwa An, Chang Hwan Bae, Youngjune Bhak, Sungwon Jeon, Hyejun Yoon, Yumi Kim, JeHoon Jun, HyeJin Lee, Suan Cho, Olga Uphyrkina, Aleksey Kostyria, John Goodrich, Dale Miquelle, Melody Roelke, John Lewis, Andrey Yurchenko, Anton Bankevich, Juok Cho, Semin Lee, Jeremy S. Edwards, Jessica A. Weber, Jo Cook, Sangsoo Kim, Hang Lee, Andrea Manica, Ilbeum Lee, Stephen J. O’Brien, Jong Bhak and Joo-Hong Yeo Genome Biol. 17:211 (2016).
14. (co-author) The first whole genome and transcriptome of the Cinereous vulture reveals adaptation in the gastric and immune defense systems and possible convergent evolution between the Old and New World vultures.
Oksung Chung, Seondeok Jin, Yun Sung Cho, Jeongheui Lim, Hyunho Kim, Sungwoong Jho, Hak-Min Kim, JeHoon Jun, HyeJin Lee, Alvin Chon, Junsu Ko, Jeremy Edwards, Jessica A. Weber, Kyudong Han, Stephen J. O’Brien, Andrea Manica, Jong Bhak and Woon Kee Paek. Genome Biol. 16:215 (2015).
13. (co-author) Whole genome sequencing of an ethnic Pathan (Pakhtun) from the north-west of Pakistan.
Muhammad Ilyas, Jong-Soo Kim, Jesse Cooper, Young-Ah Shin, Hak-Min Kim, Yun Sung Cho, Seungwoo Hwang, Hyunho Kim, Jaewoo Moon, Oksung Chung, JeHoon Jun, Achal Rastogi, Sanghoon Song, Junsu Ko, Andrea Manica, Ziaur Rahman, Tayyab Husnain and Jong Bhak. BMC Genomics. 16:172 (2015).
12. (co-author) Whole genome sequence and analysis of the Marwari horse breed and its genetic origin.
JeHoon Jun, Yun Sung Cho, Haejin Hu, Hak-Min Kim, Sungwoong Jho, Priyvrat Gadhvi, Kyung Mi Park, Jeongheui Lim, Woon Kee Paek, Kyudong Han, Andrea Manica, Jeremy S Edwards, Jong Bhak. BMC Genomics. 15(Suppl 9), S4 (2014).
11. (co-author) Homozygous deletions at 3p22, 5p14, 6q15, and 9p21 result in aberrant expression of tumor suppressor genes in gastric cancer.
Lee B, Yoon K, Lee S, Kang JM, Kim J, Shim SH, Kim HM, Song S, Naka K, Kim AK, Yang HK, Kim SJ. Genes Chromosomes Cancer. 54, 142-155 (2015)
10. (co author) Whole-genome analysis of a patient with early-stage small-cell lung cancer.
Han JY, Lee YS, Kim BC, Lee GK, Lee S, Kim EH, Kim HM, Bhak J. Pharmacogenomics J. 14, 503-508 (2014)
9. (co-author) Variation block-based genomics method for crop plants.
Yul Ho Kim, Hyang Mi Park, Tae-Young Hwang, Seuk Ki Lee, Man Soo Choi, Sungwoong Jho, Seungwoo Hwang, Hak-Min Kim, Dongwoo Lee, Byoung-Chul Kim, Chang Pyo Hong, Yun Sung Cho, Hyunmin Kim, Kwang Ho Jeong, Min Jung Seo, Hong Tai Yun, Sun Lim Kim, Young-Up Kwon, Wook Han Kim, Hye Kyung Chun, Sang Jong Lim, Young-Ah Shin, Ik-Young Choi, Young Sun Kim, Ho-Sung Yoon, Suk-Ha Lee, Sunghoon Lee. BMC Genomics. 15, 477 (2014).
8. (co-author) Genomic profile analysis of diffuse-type gastric cancers.
Yeon-Su Lee, Yun Sung Cho, Geon Kook Lee, Sunghoon Lee, Young-Woo Kim, Sungwoong Jho, Hak-Min Kim, Seung-Hyun Hong, Jung-Ah Hwang, Sook-young Kim, Dongwan Hong, Il Ju Choi, Byung Chul Kim, Byoung-Chul Kim, Chul Hong Kim, Hansol Choi, Youngju Kim, Kyung Wook Kim, Gu Kong, Hyung Lae Kim, Jong Bhak, Seung Hoon Lee, Jin Soo Lee. Genome Biol. 15, R55 (2014).
7. (co-author) Minke whale genome and aquatic adaptation in cetaceans.
Hyung-Soon Yim, Yun Sung Cho, Xuanmin Guang, Sung Gyun Kang, Jae-Yeon Jeong, Sun-Shin Cha, Hyun-Myung Oh, Jae-Hak Lee, Eun Chan Yang, Kae Kyoung Kwon, Yun Jae Kim, Tae Wan Kim, Wonduck Kim, Jeong Ho Jeon, Sang-Jin Kim, Dong Han Choi, Sungwoong Jho, Hak-Min Kim, Junsu Ko, Hyunmin Kim, Young-Ah Shin, Hyun-Ju Jung, Yuan Zheng, Zhuo Wang, Yan Chen, Ming Chen, Awei Jiang, Erli Li, Shu Zhang, Haolong Hou, Tae Hyung Kim, Lili Yu, Sha Liu, Kung Ahn, Jesse Cooper, Sin-Gi Park, Chang Pyo Hong, Wook Jin, Heui-Soo Kim, Chankyu Park, Kyooyeol Lee, Sung Chun, Phillip A Morin, Stephen J O’Brien, Hang Lee, Jumpei Kimura, Dae Yeon Moon, Andrea Manica, Jeremy Edwards, Byung Chul Kim, Sangsoo Kim, Jun Wang, Jong Bhak, Hyun Sook Lee, Jung-Hyun Lee. Nat. Genet. 46, 88-92 (2014).
6. (co-first author) Whole genome comparison of donor and cloned dogs.
Hak-Min Kim, Yun Sung Cho, Hyunmin Kim, Sungwoong Jho, Bongjun Son, Joung Yoon Choi, Sangsoo Kim, Byeong Chun Lee, Jong Bhak, Goo Jang. Sci. Rep. 3, 2998 (2013).
5. (co-author) The tiger genome and comparative analysis with lion and snow leopard genomes.
Cho YS, Hu L, Hou H, Lee H, Xu J, Kwon S, Oh S, Kim HM, Jho S, Kim S, Shin YA, Kim BC, Kim H, Kim CU, Luo SJ, Johnson WE, Koepfli KP, Schmidt-Küntzel A, Turner JA, Marker L, Harper C, Miller SM, Jacobs W, Bertola LD, Kim TH, Lee S, Zhou Q, Jung HJ, Xu X, Gadhvi P, Xu P, Xiong Y, Luo Y, Pan S, Gou C, Chu X, Zhang J, Liu S, He J, Chen Y, Yang L, Yang Y, He J, Liu S, Wang J, Kim CH, Kwak H, Kim JS, Hwang S, Ko J, Kim CB, Kim S, Bayarlkhagva D, Paek WK, Kim SJ, O'Brien SJ, Wang J, Bhak J. Nat. Commun. 4, 2433 (2013).
4. (co-author) Comprehensive genome- and transcriptome-wide analyses of mutations associated with microsatellite instability in Korean gastric cancers.
Yoon K, Lee S, Han TS, Moon SY, Yun SM, Kong SH, Jho S, Choe J, Yu J, Lee HJ, Park JH, Kim HM, Lee SY, Park J, Kim WH, Bhak J, Yang HK, Kim SJ. Genome Res. 23, 1109-1117 (2013)
3. (co-author) Peeling back the evolutionary layers of molecular mechanisms responsive to exercise-stress in the skeletal muscle of the racing horse.
Kim H, Lee T, Park W, Lee JW, Kim J, Lee BY, Ahn H, Moon S, Cho S, Do KT, Kim HS, Lee HK, Lee CK, Kong HS, Yang YM, Park J, Kim HM, Kim BC, Hwang S, Bhak J, Burt D, Park KD, Cho BW, Kim H. DNA Res. 20, 287-298 (2013)
2. (co-author) Whole transcriptome analyses of six thoroughbred horses before and after exercise using RNA-Seq.
Park KD, Park J, Ko J, Kim BC, Kim HS, Ahn K, Do KT, Choi H, Kim HM, Song S, Lee S, Jho S, Kong HS, Yang YM, Jhun BH, Kim C, Kim TH, Hwang S, Bhak J, Lee HK, Cho BW. BMC Genomics. 13, 473 (2012)
1. (co-author) COMUS: Clinician-Oriented locus-specific MUtation detection and deposition System.
Jho S, Kim BC, Ghang H, Kim JH, Park D, Kim HM, Jung SY, Yoo KY, Kim HJ, Lee S, Bhak J. BMC Genomics. 10(Suppl 3), S35 (2009)
Patents
- (발명자) 공통서열을 포함한 참조표준 게놈지도 구축 장치 및 방법(1019302530000, 대한민국 특허청 등록), 2018
- (발명자) 백색 털 형질에 대한 신규 단일염기변이 마커 (101480207, 대한민국 특허청 등록), 2014
- (발명자) 저산소증 적응 형질에 대한 신규 단일염기변이 마커 (101480208, 대한민국 특허청 등록), 2014
