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pXg
( Software download )
pXg: Comprehensive Identification of Noncanonical MHC-I-Associated Peptides From De Novo Peptide Sequencing Using RNA-Seq Reads.
Seunghyuk Choi and Eunok Paek.
Molecular & Cellular Proteomics, 2024, 23(4), 1-13.
[ PMID: 38403075 ]
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CyGate
( Software download )
CyGate Provides a Robust Solution for Automatic Gating of Single Cell Cytometry Data.
Seungjin Na, Yujin Choo, Tae Hyun Yoon, and Eunok Paek.
Analytical Chemistry, 2023, 95(46), 16918-16926.
[ PMID: 37946317 ]
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DbyDeep
( Software download )
DbyDeep: Exploration of MS-Detectable Peptides via Deep Learning.
Juho Son, Seungjin Na, and Eunok Paek.
Analytical Chemistry, 2023, 95, 30, 11193-11200.
[ PMID: 37459568 ]
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Deephos
( Software download )
Deephos: predicted spectral database search for TMT-labeled phosphopeptides and its false discovery rate estimation.
Seungjin Na, Hyunjin Choi, and Eunok Paek.
Bioinformatics, 2022, 38(11), 2980-2987
[ PMID: 35441674 ]
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TIDD
( Software download )
TIDD: tool-independent and data-dependent machine learning for peptide identification.
Honglan Li, Seungjin Na, Kyu-Baek Hwang, and Eunok Paek.
BMC Bioinformatics, 2022, 23(1), 1-12.
[ PMID: 35354356 ]
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MutCombinator
( Software download )
MutCombinator: identification of mutated peptides allowing
combinatorial mutations using nucleotide-based graph
search.
Seunghyuk Choi and Eunok Paek.
Bioinformatics, 2020, 7, i203-i209.
[ PMID: 32657416 ]
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MODplus
( Software download )
MODplus: Robust and Unrestrictive Identification of
Post-Translational Modifications Using Mass Spectrometry.
Seunjin Na, Jihyung Kim and Eunok Paek.
Analytical Chemistry, 2019, 91, 17, 11324-11333.
[ PMID: 31365238 ]
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deMix
( Software download )
deMix: Decoding Deuterated Distributions from Heterogeneous
Protein States vis HDX-MS
Seungjin Na, Jae-Jin Lee, Jong Wha J. Joo, Kong-Joo Lee and
Eunok Paek.
Scientific Reports, 2019, 9, 3176.
[ PMID: 30816214 ]
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DDPSearch
Data-dependent scoring parameter optimization in MS-GF+ using spectrum quality filter.
Hyunjin Jo and Eunok Paek.
Journal of Proteome Research, 2018, 17(10), 3593-3598.
[ PMID: 30033731 ]
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ACTG
( Software download )
ACTG: novel peptide mapping onto gene models.
Seunghyuk Choi, Hyunwoo Kim, and Eunok Paek.
Bioinformatics, 2017, 33(8), 1218-1220.
[ PMID: 28031186 ]
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NextSearch
( Software download )
NextSearch: A Search Engine for Mass Spectrometry Data against
a Compact Nucleotide Exon Graph.
Hyunwoo Kim, Heejin Park, and Eunok Paek.
Journal of Proteome Research, 2015, 14(7), 2784-2791.
[ PMID: 26004133 ]
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MODa
( Software download )
Fast multi-blind modification search through tandem mass
spectrometry.
Seungjin Na, Nuno Bandeira, and Eunok Paek.
Molecular and Cellular Proteomics, 2012, 11, M111.010199.
[ PMID: 22186716 ]
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DBond
( Software download )
New algorithm for the identification of intact disulfide
linkages based on fragmentation characteristics in tandem mass
spectra.
Seonhwa Choi, Jaeho Jeong, Seungjin Na, Hyo Sun Lee, Hwa-Young
Kim, Kong-Joo Lee, and Eunok Paek.
Journal of Proteome Research, 2010, 9, 626-635.
[ PMID: 19902913 ]
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MODmap
Prediction of novel modifications by unrestrictive search of
tandem mass spectra.
Seungjin Na and Eunok Paek.
Journal of Proteome
Research, 2009, 8, 4418-4427.
[ PMID: 19658439 ]
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MODi
Unrestrictive identification of multiple post-translational
modifications from tandem mass spectrometry using an
error-tolerant algorithm based on an extended sequence tag
approach.
Seungjin Na, Jaeho Jeong, Heejin Park, Kong-Joo Lee, and Eunok
Paek.
Molecular and Cellular Proteomics, 2008, 7, 2452-2463.
[ PMID: 18701446 ]
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