Genome Research 2024.

Genome Research 2024

Identifying genes within pathways in unannotated genomes with PaGeSearch Sohyoung Won, Jaewoong Yu, and Heebal Kim [LINK]

Nature Biotechnology 2024.

Nature Biotechnology 2024

Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy Delphine Larivière, Linelle Abueg, Nadolina Brajuka, Cristóbal Gallardo-Alba, Bjorn Grüning, Byung June Ko, Alex Ostrovsky, Marc Palmada-Flores, Brandon D. Pickett, Keon Rabbani, Agostinho Antunes, Jennifer R. Balacco, Mark J. P. Chaisson, Haoyu Cheng, Joanna Collins, Melanie Couture, Alexandra Denisova, Olivier Fedrigo, Guido Roberto Gallo, Alice Maria Giani, Grenville MacDonald Gooder, Kathleen Horan, Nivesh Jain, Cassidy Johnson, Heebal Kim, Chul Lee, Tomas Marques-Bonet, Brian O’Toole, Arang Rhie, Simona Secomandi, Marcella Sozzoni, Tatiana Tilley, Marcela Uliano-Silva, Marius van den Beek, Robert W. Williams, Robert M. Waterhouse, Adam M. Phillippy, Erich D. Jarvis, Michael C. Schatz, Anton Nekrutenko and Giulio Formenti [LINK]

Scientific Data 2023.

Scientific Data 2023

Chromosome-level genome assembly of chub mackerel (Scomber japonicus) from the Indo-Pacific Ocean Young Ho Lee, Linelle Abueg, Jin-Koo Kim, Young Wook Kim, Olivier Fedrigo, Jennifer Balacco, Giulio Formenti, Kerstin Howe, Alan Tracey, Jonathan Wood, Françoise Thibaud-Nissen, Bo Hye Nam, Eun Soo No, Hye Ran Kim, Chul Lee, Erich D. Jarvis and Heebal Kim [LINK]

Molecular Biology and Evolution 2023.

Molecular Biology and Evolution 2023

Inference of admixture origins in indigenous African cattle Kwondo Kim, Donghee Kim, Olivier Hanotte, Charles Lee, Heebal Kim, Choongwon Jeong [LINK]

Scientific Data 2023.

Scientific Data 2023

The first high-quality genome assembly and annotation of Patiria pectinifera Jaehoon Jung, So Yun Jhang, Bongsang Kim, Bomin Koh, Chaeyoung Ban, Hyojung Seo, Taeseo Park, Won-Jae Chi, Soonok Kim, Heebal Kim & Jaewoong Yu [LINK]

Scientific Data 2023.

Scientific Data 2023

Chromosome-level genome assembly of Korean native cattle and pangenome graph of 14 Bos taurus assemblies Jisung Jang, Jaehoon Jung, Young Ho Lee, Sanghyun Lee, Myunggi Baik & Heebal Kim [LINK]

Nucleic Acids Research 2022.

Nucleic Acids Research 2022

HGTree v2.0: a comprehensive database update for horizontal gene transfer (HGT) events detected by the tree-reconciliation method Youngseok Choi, Sojin Ahn, Myeongkyu Park, SaetByeol Lee, Seoae Cho and Heebal Kim [LINK]

Genome Biology 2022.

Genome Biology 2022

False gene and chromosome losses in genome assemblies caused by GC content variation and repeats Juwan Kim, Chul Lee, Byung June Ko, DongAhn Yoo, Sohyoung Won, Adam Phillippy, Olivier Fedrigo, Guojie Zhang, Kerstin Howe, Jonathan Wood, Richard Durbin, Giulio Formenti, Samara Brown, Lindsey Cantin, Claudio V. Mello, Seoae Cho, Arang Rhie, Heebal Kim and Erich D. Jarvis. [LINK]

Genome Biology 2022.

Genome Biology 2022

Widespread false gene gains caused by duplication errors in genome assemblies. Byung June Ko, Chul Lee, Juwan Kim, Arang Rhie, DongAhn Yoo, Kerstin Howe, Jonathan Wood, Seoae Cho, Samara Brown, Giulio Formenti, Erich D. Jarvis, Heebal Kim [LINK]

Nature 2021.

Nature 2021

Towards complete and error-free genome assemblies of all vertebrate species Arang Rhie, Shane A. McCarthy, Olivier Fedrigo, Joana Damas, Giulio Formenti, Sergey Koren, Marcela Uliano-Silva, William Chow, Arkarachai Fungtammasan, Juwan Kim, Chul Lee, Byung June Ko, Mark Chaisson, Gregory L. Gedman, Lindsey J. Cantin, Francoise Thibaud-Nissen, Leanne Haggerty, Iliana Bista, Michelle Smith, Bettina Haase, Jacquelyn Mountcastle, Sylke Winkler, Sadye Paez, Jason Howard, Sonja C. Vernes, Tanya M. Lama, Frank Grutzner, Wesley C. Warren, Christopher N. Balakrishnan, Dave Burt, Julia M. George, Matthew T. Biegler, David Iorns, Andrew Digby, Daryl Eason, Bruce Robertson, Taylor Edwards, Mark Wilkinson, George Turner, Axel Meyer, Andreas F. Kautt, Paolo Franchini, H. William Detrich III, Hannes Svardal, Maximilian Wagner, Gavin J. P. Naylor, Martin Pippel, Milan Malinsky, Mark Mooney, Maria Simbirsky, Brett T. Hannigan, Trevor Pesout, Marlys Houck, Ann Misuraca, Sarah B. Kingan, Richard Hall, Zev Kronenberg, Ivan Sović, Christopher Dunn, Zemin Ning, Alex Hastie, Joyce Lee, Siddarth Selvaraj, Richard E. Green, Nicholas H. Putnam, Ivo Gut, Jay Ghurye, Erik Garrison, Ying Sims, Joanna Collins, Sarah Pelan, James Torrance, Alan Tracey, Jonathan Wood, Robel E. Dagnew, Dengfeng Guan, Sarah E. London, David F. Clayton, Claudio V. Mello, Samantha R. Friedrich, Peter V. Lovell, Ekaterina Osipova, Farooq O. Al-Ajli, Simona Secomandi, Heebal Kim, Constantina Theofanopoulou, Michael Hiller, Yang Zhou, Robert S. Harris, Kateryna D. Makova, Paul Medvedev, Jinna Hoffman, Patrick Masterson, Karen Clark, Fergal Martin, Kevin Howe, Paul Flicek, Brian P. Walenz, Woori Kwak, Hiram Clawson, Mark Diekhans, Luis Nassar, Benedict Paten, Robert H. S. Kraus, Andrew J. Crawford, M. Thomas P. Gilbert, Guojie Zhang, Byrappa Venkatesh, Robert W. Murphy, Klaus-Peter Koepfli, Beth Shapiro, Warren E. Johnson, Federica Di Palma, Tomas Marques-Bonet, Emma C. Teeling, Tandy Warnow, Jennifer Marshall Graves, Oliver A. Ryder, David Haussler, Stephen J. O’Brien, Jonas Korlach, Harris A. Lewin, Kerstin Howe, Eugene W. Myers, Richard Durbin, Adam M. Phillippy & Erich D. Jarvis [LINK]

Nature Genetics 2020.

Nature Genetics 2020

The mosaic genome of indigenous African cattle as a unique genetic resource for African pastoralism Kwondo Kim, Taehyung Kwon, Tadelle Dessie, DongAhn Yoo, Okeyo Ally Mwai, Jisung Jang, Samsun Sung, SaetByeol Lee, Bashir Salim, Jaehoon Jung, Heesu Jeong, Getinet Mekuriaw Tarekegn, Abdulfatai Tijjani, Dajeong Lim, Seoae Cho, Sung Jong Oh, Hak-Kyo Lee, Jaemin Kim, Choongwon Jeong, Stephen Kemp, Olivier Hanotte, and Heebal Kim. [LINK]

Scientific Reports 2019.

Scientific Reports 2019

Establishment and evaluation of prediction model for multiple disease classification based on gut microbial data Sohyun Bang, DongAhn Yoo, Soo-Jin Kim, So Yun Jhang, Seoae Cho, and Heebal Kim. [LINK]

Human genetics 2019.

Human genetics 2019

De novo emergence and potential function of human-specific tandem repeats in brain-related loci Kwondo Kim, Sohyun Bang, DongAhn Yoo, Heebal Kim, Shunsuke Suzuki. [LINK]

Scientific Reports 2018.

Scientific Reports 2018

Deciphering the evolutionary signatures of pinnipeds using novel genome sequences: The first genomes of Phoca largha, Callorhinus ursinus, and Eumetopias jubatus Jung Youn Park, Kwondo Kim, Hawsun Sohn, Hyunwoo Kim, Yong-Rock An, Jung-Ha Kang, Eun Mi Kim, Woori Kwak, Chul Lee, DongAhn Yoo, Jaehoon Jung, Samsun Sung, Joon Yoon, Heebal Kim. [LINK]

Nature Biotechnology 2018.

Nature Biotechnology 2018

Rhizosphere microbiome structure alters to enable wilt resistance in tomato. Min-Jung Kwak, Hyun Gi Kong, Kihyuck Choi, Soon-Kyeong Kwon, Ju Yeon Song, Jidam Lee, Pyeong An Lee, Soo Yeon Choi, Minseok Seo, Hyoung Ju Lee, Eun Joo Jung, Hyein Park, Nazish Roy, Heebal Kim, Myeong Min Lee, Edward M Rubin, Seon-Woo Lee, Jihyun F Kim. [LINK]