International Journal

2020 - present

• Seungjin Na and Eunok Paek* (2024) Demystifying PTM Identification Using MODplus: Best Practices and Pitfalls Protein Bioinformatics, 2386, 37-55. https://doi.org/10.1007/978-1-0716-4007-4_3
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• Seunghyuk Choi and Eunok Paek* (2024) pXg: Comprehensive Identification of Noncanonical MHC-I–Associated Peptides From De Novo Peptide Sequencing Using RNA-Seq Readst MOLECULAR & CELLULAR PROTEOMICS, 23(4), 1-13. (SCI Impact Factor: 7.0) https://doi.org/10.1016/j.mcpro.2024.100743
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• Jae-Won Lee, Jong-Hyun Won, Seonggwang Jeon, Yujin Choo, Yubin Yeon, Jin-Seon Oh, Minsoo Kim, SeonHwa Kim, InSuk Joung, Cheongjae Jang, Sung Jong Lee, Tae Hyun Kim, Kyong Hwan Jin, Giltae Song, Eun-Sol Kim, Jejoong Yoo, Eunok Paek, Yung-Kyun Noh*, Keehyoung Joo* (2023) DeepFold: enhancing protein structure prediction through optimized loss functions, improved template features, and re-optimized energy function Bioinformatics, 39(12), 1-11. (SCI Impact Factor: 6.931) https://doi.org/10.1093/bioinformatics/btad712
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• Seungjin Na, Yujin Choo, Tae Hyun Yoon and Eunok Paek* (2023) CyGate provides a robust solution for automatic gating of single cell cytometry data Analytical Chemistry, 95(46), 16918-16926. (SCI Impact Factor: 8.008) https://doi.org/10.1021/acs.analchem.3c03006
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• Juho Son, Seungjin Na* and Eunok Paek* (2023) DbyDeep: Exploration of MS-Detectable Peptides via Deep Learning Analytical Chemistry, 95(30), 11193-11200. (SCI Impact Factor: 8.008) https://doi.org/10.1021/acs.analchem.3c00460
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• 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 (2023) Proteogenomic landscape of human pancreatic ductal adenocarcinoma in an Asian population reveals tumor cell-enriched and immune-rich subtypes Nature Cancer, 4, 290-307. (SCI Impact Factor: 23.177) https://doi.org/10.1038/s43018-022-00479-7
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• Seungjin Na, Hyunjin Choi and Eunok Paek* (2022) Deephos: predicted spectral database search for TMT-labeled phosphopeptides and its false discovery rate estimation Bioinformatics, 38(11), 2980-2987. (SCI Impact Factor: 6.937) https://doi.org/10.1093/bioinformatics/btac280
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• Honglan Li, Seungjin Na, Kyu-Baek Hwang and Eunok Paek* (2022) TIDD: tool‑independent and data‑dependent machine learning for peptide identifcation BMC Bioinformatics, 23:109, 1-12. (SCI Impact Factor: 3.169) https://doi.org/10.1186/s12859-022-04640-y
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• In-Kang Song, Seungjin Na, Eunok Paek* and Kong-Joo Lee* (2020) Cataract-Associated New Mutants S175G/H181Q of βB2-Crystallin and P24S/S31G of γD-Crystallin Are involved in Protein Aggregation by Structural Changes International Journal of Molecular Sciences, 21(18), 6504, 1-18.(SCI Impact Factor: 4.556) https://doi.org/10.3390/ijms21186504
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• Seunghyuk Choi and Eunok Paek* (2020) MutCombinator: identification of mutated peptides allowing combinatorial mutations using nucleotide-based graph search Bioinformatics, 36, 203-209.(SCI Impact Factor: 4.531) https://doi.org/10.1093/bioinformatics/btaa504
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• 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* (2020) Integrated pharmaco-proteogenomics defines two subgroups in isocitrate dehydrogenase wild-type glioblastoma with prognostic and therapeutic opportunities Nature Communications, 11, 3288. (SCI Impact Factor: 11.878) https://doi.org/10.1038/s41467-020-17139-y
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• Seungjin Na and Eunok Paek* (2020) Computational methods in mass spectrometry-based structural proteomics for studying protein structure, dynamics, and interactions Computational and Structural Biotechnology Journal, 18. 1391-1402, (SCI Impact Factor: 6.018) https://doi.org/10.1016/j.csbj.2020.06.002
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• Seunghyuk Choi, Shinyeong Ju, Jinwon Lee, Seungjin Na, Cheolju Lee*, and Eunok Paek* (2020) Proteogenomic Approach to UTR Peptide Identification Journal of proteome research, 19(1), 212-220. (SCI Impact Factor: 3.78) https://doi.org/10.1021/acs.jproteome.9b00498
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  2015 - 19

• Jihye Shin, Yumi Kwon, Seonjeong Lee, Seungjin Na, Eun Young Hong, Shinyeong Ju, Hyun-Gyo Jung, Prashant Kaushal, Sungho Shin, Ji Hyun Back, Seon Young Choi, Eun Hee Kim, Su Jin Lee, Yae Eun Park, Hee-Sung Ahn, Younghee Ahn, Mohammad Humayun Kabir, Seong-Jun Park, Won Suk Yang, Jeonghun Yeom, Oh Young Bang, Chul-Won Ha, Jin-Won Lee, Un-Beom Kang, Hye-Jung Kim, Kang-Sik Park, J. Eugene Lee, Ji Eun Lee, Jin Young Kim, Kwang Pyo Kim, Youngsoo Kim, Hisashi Hirano, Eugene C. Yi, Je-Yoel Cho, Eunok Paek, and Cheolju Lee* (2019) Common Repository of FBS Proteins (cRFP) To Be Added to a Search Database for Mass Spectrometric Analysis of Cell Secretome Journal of proteome research, 18(10), 3800-3806. (SCI Impact Factor: 3.78) https://doi.org/10.1021/acs.jproteome.9b00475
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• Seungin Na, Jihyung Kim and Eunok Peak* (2019) MODplus: Robust and Unrestrictive Identification of Post-Translational Modifications Using Mass Spectrometry Analytical Chemistry, 91, 11324-11333. (SCI Impact Factor: 6.35) https://doi.org/10.1021/acs.analchem.9b02445
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• Seungjin Na,  Jae-Jin Lee, JongWha J. Joo, Kong-Joo Lee & Eunok Paek* (2019) deMix: Decoding Deuterated Distributions from Heterogeneous Protein States via HDX-MS Scientific Reports, 9, 3176. (SCI Impact Factor: 4.122 ) https://doi.org/10.1038/s41598-019-39512-8
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• Dong-Gi Mun, Jinhyuk Bhin, Sangok Kim, Hyunwoo Kim, Jae Hun Jung, Yeonjoo Jung, Ye Eun Jang, Jong Moon Park, Hokeun Kim, Yeonhwa Jung, Hangyeore Lee, Jingi Bae, Seunghoon Back, Su-Jin Kim, Jieun Kim, Heejin Park, Honglan Li, Kyu-Baek Hwang, Young Soo Park, Jeong Hwan Yook, Byung Sik Kim, Sun Young Kwon, Seung Wan Ryu, Do Youn Park, Tae Yong Jeon, Dae Hwan Kim, Jae-Hyuck Lee, Sang-Uk Han, Kyu Sang Song, Dongmin Park, Jun Won Park, Henry Rodriguez, Jaesang Kim, Hookeun Lee, Kwang Pyo Kim, Eun Gyeong Yang*, Hark Kyun Kim*, Eunok Paek*, Sanghyuk Lee*, Sang-Won Lee*, and Daehee Hwang* (2019) Proteogenomic Characterization of Human Early-Onset Gastric Cancer Cancer Cell 35, 111-124. (SCI Impact Factor: 22.844) https://doi.org/10.1016/j.ccell.2018.12.003                                                                                                                                                                                                                                
• Hyunjin Jo  and Eunok Paek* (2018) Data-Dependent Scoring Parameter Optimization in MS-GF+ Using Spectrum Quality Filter Journal of Proteome Research 17, 3593-3598. (SCI Impact Factor: 4.173) https://doi.org/10.1021/acs.jproteome.8b00415
   
• Inamul HasanMadar , Wonyeop Lee, Xiaojing Wang, Seung-Ik Ko, Hokeun Kim, Dong-Gi Mun, Bing Zhang*, Eunok Paek* and Sang-Won Lee* (2018) Comprehensive and sensitive proteogenomics data analysis strategy based on complementary multi-stage database seach International Journal of Mass Spectrometry 427 11-19. (SCI Impact Factor: 1.702) https://doi.org/10.1016/j.ijms.2017.08.015
   
• Jeonghun Yeom , YunJin Choi, Shinyeong Ju, Cheolju Lee*, and Eunok Paek (2017) Comprehensive analysis of human protein N-termini enables assessment of various protein forms Scientific Reports, 7, 6599. (SCI Impact Factor: 4.259) https://doi.org/10.1038/s41598-017-06314-9
   
• Honglan Li , Jonghun Park, Hyunwoo Kim, Kyu-Baek Hwang*, and Eunok Paek* (2017) A systematic comparison of false discovery rate-controlling strategies for proteogenomic search using spike-in experiments Journal of Proteome Research,16(6), 2231-2239. (SCI Impact Factor: 4.173) https://doi.org/10.1021/acs.jproteome.7b00033
   
• Seunghyuk Choi, Hyunwoo Kim , and Eunok Paek*. (2017) ACTG: novel peptide mapping onto gene models Bioinformatics ,33(8), 1218-1220. (SCI Impact Factor: 5.766) https://doi.org/10.1093/bioinformatics/btw787
   
• Honglan Li, Yoonsung Joh, Hyunwoo Kim, Eunok Paek, Sangwon Lee, and Kyubaek Hwang*. (2016) Evaluating the effect of database inflation in proteogenomics search on sensitive and reliable peptide identification BMC Genomics,17(13), 1471-2164.(SCI Impact Factor: 3.986) https://doi.org/10.1186/s12864-016-3327-5
   
• Hyunwoo Kim, Hosung Jo, Heejin Park*, and Eunok Paek. (2015) HiXCorr: A Portable High-speed XCorr Engine for High-resolution Tandem Mass Spectrometry Bioinformatics,31(24), 4026-4028.(SCI Impact Factor: 4.981) https://doi.org/10.1093/bioinformatics/btv490
   
• Hyunwoo Kim, Heejin Park*, and Eunok Paek*. (2015) NextSearch: A Search Engine for Mass Spectrometry Data against a Compact Nucleotide Exon Graph Journal of Proteome Research,14(7), 2784-2791.(SCI Impact Factor: 4.245) https://doi.org/10.1021/acs.jproteome.5b00047
   
• Seungjin Na, Eunok Paek, Jong-Soon Choi, Duwoon Kim, Seung Jae Lee*, and Joseph Kwon* (2015) Characterization of disulfide bonds by planned digestion and tandem mass spectrometry. Molecular BioSystems.,11(4), 1156-1164.(SCI Impact Factor: 3.183) https://doi.org/10.1039/c4mb00688g
   
• Seungjin Na and Eunok Paek* (2015) Software Eyes for Protein Post-translational Modifications. Mass Spectrometry Reviews, 34(2), 133-147.(SCI Impact Factor: 8.053) https://doi.org/10.1002/mas.21425
  
   

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  2010 - 14

• Heejin Park, Junwoo Bae, Hyunwoo Kim, Sangok Kim, Hokeun Kim, Dong-Gi Mun, Yoonsung Joh, Wonyeop Lee, Sehyun Chae, Sanghyuk Lee, HarkKyun Kim, Daehee Hwang, Sang-Won Lee and Eunok Paek*. (2014) A compact variant-rich customized sequence database and a fast and sensitive database search for efficient proteogenomic analyses PROTEOMICS., 14(23-24), 2742-2749.(SCI Impact Factor: 4.132) https://doi.org/10.1002/pmic.201400225
   
• Honglan Li, Kyu-Baek Hwang, Dong-Gi Mun, Hokeun Kim, Hangyeore Lee, Sang-Won Lee, and Eunok Paek*. (2014) Estimating Influence of Cofragmentation on Peptide Quantification and Identification in iTRAQ Experiments by Simulating Multiplexed Spectra. Journal of Proteome Research,13(7), 3488-97.(SCI. Impact Factor: 5.056) https://doi.org/10.1021/pr500060d
   
• Kyutae Kim, Seong-Jun Park, Seungjin Na, Jun Seok Kim, Hyungwon Choi, Yoon Ki Kim, Eunok Paek*, Cheolju Lee*. (2013) Reinvestigation of Aminoacyl-TRNA Synthetase Core Complex by Affinity Purification-Mass Spectrometry Reveals TARSL2 as a Potential Member of the Complex. PLOS One, 8(12), e81734. (SCIE. Impact Factor: 3.730) https://doi.org/10.1371/journal.pone.0081734
   
• Jin Wook Kim, Sunho Lee, Kunsoo Park*, Seungjin Na, Eunok Paek*, Hyung Seo Park, Heejin Park, Kong-Joo Lee, Jaeho Jeong, and Hwa-Young Kim. (2012) Monoisotopic mass determination algorithm for selenocysteine-containing polypeptides from mass spectrometric data based on theoretical modeling of isotopic peak intensity ratios. Journal of Proteome Research, 11(9), 4488-4498. (SCI. Impact Factor: 5.113) https://doi.org/10.1021/pr300232y
   
• Seungjin Na, Nuno Bandeira, and Eunok Paek*. (2012) Fast multi-blind modification search through tandem mass spectrometry. Molecular and Cellular Proteomics, 11(4), M111.010199-1~13. (SCI. Impact Factor: 8.354) https://doi.org/10.1074/mcp.M111.010199
   
• Revati Wani, Jiang Qian, Leimiao Yin, Erika Bechtold, S. Bruce King, Leslie B. Poole, Eunok Paek, Allen W. Tsang, and Cristina M. Furdui*. (2011) Isoform-specific regulation of Akt by PDGF-induced reactive oxygen species. Proc. Natl. Acad. Sci. USA, 108(26), 10550-10555. (SCI. Impact Factor: 9.771) https://doi.org/10.1073/pnas.1011665108
   
• Jaeho Jeong, Yongsik Jung, Seungjin Na, Jihye Jeong, Eunsun Lee, Mi-Sun Kim, Sun Choi, Dong-Hae Shin, Eunok Paek, Hee-Yoon Lee*, and Kong-Joo Lee*. (2011) Novel oxidative modifications in redox-active cysteine residues. Molecular and Cellular Proteomics, 10(3), M110.000513. (SCI. Impact Factor: 8.791) https://doi.org/10.1074/mcp.m110.000513
   
• Joo Young Yoon, Jeonghun Yeom, Heebum Lee, Kyutae Kim, Seungjin Na, Kunsoo Park*, Eunok Paek*, and Cheolju Lee*. (2011) High-throughput peptide quantification using mTRAQ reagent triplex. BMC Bioinformatics, 12(Suppl 1), S46. (SCI. Impact Factor: 3.43) https://doi.org/10.1186/1471-2105-12-S1-S46
   
• Katleen Denoncin, Didier Vertommen, Eunok Paek, and Jean-François Collet*. (2010) The protein-disulfide isomerase DsbC cooperates with SurA and DsbA in the assembly of the essential ß-barrel protein LptD. Journal of Biological Chemistry, 285, 29425-29433. (SCI. Impact Factor: 5.328) https://doi.org/10.1074/jbc.M110.119321
   
• Joo Young Yoon, Kyung Young Lim, Sunho Lee, Kunsoo Park*, Eunok Paek*, Un-Beom Kang, Jeonghun Yeom, and Cheolju Lee. (2010) Improved quantitative analysis of mass spectrometry using quadratic equations. Journal of Proteome Research, 9(5), 2775-2785. (SCI. Impact Factor: 5.684) https://doi.org/10.1021/pr100183t
   
• Jong Wha J. Joo, Seungjin Na, Je-Hyun Baek, Cheolju Lee, and Eunok Paek*. (2010) Target-Decoy with Mass Binning: a simple and effective validation method for shotgun proteomics using high resolution mass spectrometry. Journal of Proteome Research, 9(2), 1150-1156. (SCI. Impact Factor: 5.684) https://doi.org/10.1021/pr9006377
   
• Seonhwa Choi, Jaeho Jeong, Seungjin Na, Hyo Sun Lee, Hwa-Young Kim, Kong-Joo Lee*, and Eunok Paek*. (2010) New algorithm for the identification of intact disulfide linkages based on fragmentation characteristics in tandem mass spectra. Journal of Proteome Research, 9(1), 626-635. (SCI. Impact Factor: 5.684) https://doi.org/10.1021/pr900771r
  
   

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  2004 - 09
   

• Seungjin Na and Eunok Paek*. (2009) Prediction of novel modifications by unrestrictive search of tandem mass spectra. Journal of Proteome Research, 8(10), 4418-4427. (SCI. Impact Factor: 5.684) https://doi.org/10.1021/pr9001146
   
• Seungjin Na, Jaeho Jeong, Heejin Park, Kong-Joo Lee, and Eunok Paek*. (2008) Unrestrictive identification of multiple post-translational modifications from tandem mass spectrometry using an error-tolerant algorithm based on an extended sequence tag approach. Molecular and Cellular Proteomics, 7(12), 2452-2463. (SCI. Impact Factor: 9.425) https://doi.org/10.1074/mcp.M800101-MCP200
   
• Kunsoo Park*, Joo Young Yoon, Sunho Lee, Eunok Paek*, Heejin Park, Hee-Jung Jung, and Sang-Won Lee. (2008) Isotopic peak intensity ratio based algorithm for determination of isotopic clusters and monoisotopic masses of polypeptides from high resolution mass spectrometric data. Analytical Chemistry, 80(19), 7294-7303. (SCI. Impact Factor: 5.287) https://doi.org/10.1021/ac800913b
   
• Seungjin Na, Eunok Paek*, and Cheolju Lee. (2008) CIFTER: automated charge state determination for peptide tandem mass spectra. Analytical Chemistry, 80(5), 1520-1528. (SCI. Impact Factor: 5.287) https://doi.org/10.1021/ac702038q
   
• Jawon Seo, Jaeho Jeong, Young Mi Kim, Narae Hwang Eunok Paek, and Kong-Joo Lee*. (2008) A strategy for comprehensive identification of post-translational modifications in cellular proteins, including low abundant modifications: application to glyceraldehyde-3-phosphate dehydrogenase. Journal of Proteome Research, 7(2), 587-602. (SCI. Impact Factor: 5.675) https://doi.org/10.1021/pr700657y
   
• Seungjin Na and Eunok Paek*. (2006) Quality assessment of tandem mass spectra based on cumulative intensity normalization. Journal of Proteome Research, 5(12), 3241-3248. (SCI. Impact Factor: 6.901) https://doi.org/10.1021/pr0603248
   
• Sangtae Kim, Seungjin Na, Ji Woong Sim, Heejin Park, Jaeho Jeong, Hokeun Kim, Younghwan Seo, Jawon Seo, Kong-Joo Lee, and Eunok Paek*. (2006) MODⁱ: a powerful and convenient web server for identifying multiple post-translational peptide modifications from tandem mass spectra. Nucleic Acids Research, 34, W258-W263. (SCI. Impact Factor: 7.552) https://doi.org/10.1093/nar/gkl245
   
• Kiho Hong, Junhyung Park, Jihoon Yang, and Eunok Paek*. (2005) Automatic extraction of proteins and their interactions from biological text. Lecture Notes in Artificial Intelligence, 3735, 322-329. (SCI. Impact Factor: 0.251) https://doi.org/10.1007/11563983_27
   
• Eunok Paek*, Jisook Park, and Kong-Joo Lee*. (2004) Multi-layered representation for cell-signaling pathways. Molecular and Cellular Proteomics, 3(10), 1009-1022. (SCI. Impact Factor: 8.316) https://doi.org/10.1074/mcp.M400039-MCP200
   

   

Domestic Journal
 

• Selenocysteine을 포함한 폴리펩티드의 단동위질량을 결정하는 알고리즘의 실험적 분석
  이선호, 김진욱*, 박근수, 백은옥, 박희진
  정보과학회논문지 : 컴퓨팅의 실제 및 레터, 2013, 19(5), 235-241.
   
• 동위원소에 의한 펩타이드 질량분포의 근사 계산방법과 펩타이드 중수소치환에의 적용
  이경훈, 백은옥*, 나승진
  정보과학회논문지: 소프트웨어 및 응용, 2012, 39(10), 824-832.
   
• 마코프 논리 기반의 시맨틱 문서 검색
  황규백, 봉성용, 구현서, 백은옥
  정보과학회논문지: 컴퓨팅의 실제 및 레터, 2010, 16(6), 663-666.
   
• 대량의 프로테옴 데이타를 효과적으로 해석하기 위한 기계학습 기반 시스템
  나승진, 백은옥*
  정보과학회논문지: 소프트웨어 및 응용, 2007, 34(10), 889-899.
   
• 와일드카드 문자를 포함하는 스트링 데이타 사이의 포함관계 확인을 위한 효율적인 알고리즘
  김도한, 박희진, 백은옥*
  정보과학회논문지: 시스템 및 이론, 2005, 32(9·10), 475-482.
   
• 세포 신호전달 경로 데이타베이스를 위한 데이타 모델링
  박지숙, 백은옥*, 이공주, 이상혁, 이승록, 양갑석
  정보과학회논문지: 데이타베이스, 2003, 30(12), 573-584.