Publications
2025
Assessing Long-Term Stored Tissues for Multi-Omics Data Quality and Proteogenomics Suitability.
Kyu Jin Song🥇, Minsuh Kim, Yong Jin Heo, Kyung-Cho Cho, Jae-Won Oh, Dae Ho Kim, Chanwoong Hwa, Yeji Do, Seunghyuk Choi, Hee Sang Hwang, Kwoneel Kim, Kyunggon Kim, Seungjin Na, Eunok Paek, Joon-Yong An, Se Jin Jang, Min-Sik Kim✉️, Kwang Pyo Kim✉️.
Journal of Proteome Research, 2025.
Hypoxia increases methylated histones to prevent histone clipping and heterochromatin redistribution during Raf-induced senescence.
Soojeong Chang🥇, Ramhee Moon, Dowoon Nam, Sang-Won Lee, Insoo Yoon, Dong-Sung Lee, Seunghyuk Choi, Eunok Paek, Daehee Hwang, Junho K Hur, Youhyun Nam, Rakwoo Chang, Hyunsung Park✉️.
Nucleic Acids Research, 2025.
NovoRank: Refinement for De Novo Peptide Sequencing Based on Spectral Clustering and Deep Learning.
Jangho Seo🥇, Seunghyuk Choi✉️, Eunok Paek✉️.
Journal of Proteome Research, 2025.
2024
Proteogenomic analysis reveals non-small cell lung cancer subtypes predicting chromosome instability, and tumor microenvironment.
Kyu Jin Song🥇, Seunghyuk Choi🥇, Kwoneel Kim🥇, Hee Sang Hwang🥇, Eunhyong Chang, Ji Soo Park, Seok Bo Shim, Seunghwan Choi, Yong Jin Heo, Woo Ju An, Dae Yeol Yang, Kyung-Cho Cho, Wonjun Ji, Chang-Min Choi, Jae Cheol Lee, Hyeong-ryul Kim, Jiyoung Yoo, Hee-Sung Ahn, Gang-Hee Lee, Chanwoong Hwa, Seoyeon Kim, Kyunggon Kim, Min-Sik Kim, Eunok Paek, Seungjin Na✉️, Se Jin Jang✉️, Joon-Yong An✉️, Kwang Pyo Kim✉️.
Nature Communications, 2024.
pXg: Comprehensive Identification of Noncanonical MHC-I–Associated Peptides From De Novo Peptide Sequencing Using RNA-Seq Reads.
Seunghyuk Choi🥇, Eunok Paek✉️.
Molecular & Cellular Proteomics, 2024.
2023
Proteogenomic landscape of human pancreatic ductal adenocarcinoma in an Asian population reveals tumor cell-enriched and immune-rich subtypes.
Do Young Hyeon🥇, Dowoon Nam🥇, Youngmin Han🥇, Duk Ki Kim🥇, Gibeom Kim🥇, Daeun Kim🥇, Jingi Bae, Seunghoon Back, Dong-Gi Mun, Inamul Hasan Madar, Hangyeore Lee, Su-Jin Kim, Hokeun Kim, Sangyeop Hyun, Chang Rok Kim, Seon Ah Choi, Yong Ryoul Kim, Juhee Jeong, Suwan Jeon, Yeon Woong Choo, Kyung Bun Lee, Wooil Kwon, Seunghyuk Choi, Taewan Goo, Taesung Park, Young-Ah Suh, Hongbeom Kim, Ja-Lok Ku, Min-Sik Kim, Eunok Paek, Daechan Park✉️, Keehoon Jung✉️, Sung Hee Baek✉️, Jin-Young Jang✉️, Daehee Hwang✉️, Sang-Won Lee✉️.
Nature Cancer, 2023.
2020
MutCombinator: identification of mutated peptides allowing combinatorial mutations using nucleotide-based graph search.
Seunghyuk Choi🥇, Eunok Paek✉️.
Bioinformatics, 2020.
Integrated pharmaco-proteogenomics defines two subgroups in isocitrate dehydrogenase wild-type glioblastoma with prognostic and therapeutic opportunities.
Sejin Oh🥇, Jeonghun Yeom🥇, Hee Jin Cho🥇, Ju-Hwa Kim, Seon-Jin Yoon, Hakhyun Kim, Jason K Sa, Shinyeong Ju, Hwanho Lee, Myung Joon Oh, Wonyeop Lee, Yumi Kwon, Honglan Li, Seunghyuk Choi, Jang Hee Han, Jong Hee Chang, Eunsuk Choi, Jayeon Kim, Nam-Gu Her, Se Hoon Kim, Seok-Gu Kang, Eunok Paek✉️, Do-Hyun Nam✉️, Cheolju Lee✉️, Hyun Seok Kim✉️.
Nature Communications, 2020.
Proteogenomic approach to UTR peptide identification.
Seunghyuk Choi🥇, Shinyeong Ju🥇, Jinwon Lee🥇, Seungjin Na, Cheolju Lee✉️, Eunok Paek✉️.
Journal of Proteome Research, 2020.
2017
ACTG: novel peptide mapping onto gene models.
Seunghyuk Choi🥇, Hyunwoo Kim, Eunok Paek✉️.
Bioinformatics, 2017.