Search Results - "Paek, Eunok"

Fast Multi-blind Modification Search through Tandem Mass Spectrometry by Na, Seungjin, Bandeira, Nuno, Paek, Eunok

“…With great biological interest in post-translational modifications (PTMs), various approaches have been introduced to identify PTMs using MS/MS. Recent…”
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Software eyes for protein post-translational modifications by Na, Seungjin, Paek, Eunok

“…Post‐translational modifications (PTMs) are critical to almost all aspects of complex processes of the cell. Identification of PTMs is one of the biggest…”
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Integrated pharmaco-proteogenomics defines two subgroups in isocitrate dehydrogenase wild-type glioblastoma with prognostic and therapeutic opportunities by Oh, Sejin, Yeom, Jeonghun, Cho, Hee Jin, Kim, Ju-Hwa, Yoon, Seon-Jin, Kim, Hakhyun, Sa, Jason K., Ju, Shinyeong, Lee, Hwanho, Oh, Myung Joon, Lee, Wonyeop, Kwon, Yumi, Li, Honglan, Choi, Seunghyuk, Han, Jang Hee, Chang, Jong Hee, Choi, Eunsuk, Kim, Jayeon, Her, Nam-Gu, Kim, Se Hoon, Kang, Seok-Gu, Paek, Eunok, Nam, Do-Hyun, Lee, Cheolju, Kim, Hyun Seok

“…The prognostic and therapeutic relevance of molecular subtypes for the most aggressive isocitrate dehydrogenase 1/2 ( IDH ) wild-type glioblastoma (GBM) is…”
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TIDD: tool-independent and data-dependent machine learning for peptide identification by Li, Honglan, Na, Seungjin, Hwang, Kyu-Baek, Paek, Eunok

“…In shotgun proteomics, database search engines have been developed to assign peptides to tandem mass (MS/MS) spectra and at the same time post-processing (or…”
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Computational methods in mass spectrometry-based structural proteomics for studying protein structure, dynamics, and interactions by Na, Seungjin, Paek, Eunok

“…Mass spectrometry (MS) has made enormous contributions to comprehensive protein identification and quantification in proteomics. MS is also gaining momentum…”
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Comprehensive analysis of human protein N-termini enables assessment of various protein forms by Yeom, Jeonghun, Ju, Shinyeong, Choi, YunJin, Paek, Eunok, Lee, Cheolju

“…Various forms of protein (proteoforms) are generated by genetic variations, alternative splicing, alternative translation initiation, co- or post-translational…”
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Evaluating the effect of database inflation in proteogenomic search on sensitive and reliable peptide identification by Li, Honglan, Joh, Yoon Sung, Kim, Hyunwoo, Paek, Eunok, Lee, Sang-Won, Hwang, Kyu-Baek

“…Proteogenomics is a promising approach for various tasks ranging from gene annotation to cancer research. Databases for proteogenomic searches are often…”
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Isoform-specific regulation of Akt by PDGF-induced reactive oxygen species by Wani, Revati, Qian, Jiang, Yin, Leimiao, Bechtold, Erika, King, S. Bruce, Poole, Leslie B, Paek, Eunok, Tsang, Allen W, Furdui, Cristina M

“…Isoform-specific signaling of Akt, a major signaling hub and a prominent therapeutic target, remained poorly defined until recently. Subcellular distribution,…”
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Cataract-Associated New Mutants S175G/H181Q of βΒ2-Crystallin and P24S/S31G of γD-Crystallin Are Involved in Protein Aggregation by Structural Changes by Song, In-Kang, Na, Seungjin, Paek, Eunok, Lee, Kong-Joo

“…β/γ-Crystallins, the main structural protein in human lenses, have highly stable structure for keeping the lens transparent. Their mutations have been linked…”
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deMix: Decoding Deuterated Distributions from Heterogeneous Protein States via HDX-MS by Na, Seungjin, Lee, Jae-Jin, Joo, Jong Wha J., Lee, Kong-Joo, Paek, Eunok

“…Characterization of protein structural changes in response to protein modifications, ligand or chemical binding, or protein-protein interactions is essential…”
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New Algorithm for the Identification of Intact Disulfide Linkages Based on Fragmentation Characteristics in Tandem Mass Spectra by Choi, Seonhwa, Jeong, Jaeho, Na, Seungjin, Lee, Hyo Sun, Kim, Hwa-Young, Lee, Kong-Joo, Paek, Eunok

“…Identifying the sites of disulfide bonds in a protein is essential for thorough understanding of a protein’s tertiary and quaternary structures and its…”
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Strategy for Comprehensive Identification of Post-translational Modifications in Cellular Proteins, Including Low Abundant Modifications: Application to Glyceraldehyde-3-phosphate Dehydrogenase by Seo, Jawon, Jeong, Jaeho, Kim, Young Mee, Hwang, Narae, Paek, Eunok, Lee, Kong-Joo

“…Post-translational modifications (PTMs) play key roles in the regulation of biological functions of proteins. Although some progress has been made in…”
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Unrestrictive Identification of Multiple Post-translational Modifications from Tandem Mass Spectrometry Using an Error-tolerant Algorithm Based on an Extended Sequence Tag Approach by Na, Seungjin, Jeong, Jaeho, Park, Heejin, Lee, Kong-Joo, Paek, Eunok

“…Identification of post-translational modifications (PTMs) is important to understanding the biological functions of proteins. MS/MS is a useful tool to…”
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Reinvestigation of aminoacyl-tRNA synthetase core complex by affinity purification-mass spectrometry reveals TARSL2 as a potential member of the complex by Kim, Kyutae, Park, Seong-Jun, Na, Seungjin, Kim, Jun Seok, Choi, Hyungwon, Kim, Yoon Ki, Paek, Eunok, Lee, Cheolju

“…Twenty different aminoacyl-tRNA synthetases (ARSs) link each amino acid to their cognate tRNAs. Individual ARSs are also associated with various non-canonical…”
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Estimating Influence of Cofragmentation on Peptide Quantification and Identification in iTRAQ Experiments by Simulating Multiplexed Spectra by Li, Honglan, Hwang, Kyu-Baek, Mun, Dong-Gi, Kim, Hokeun, Lee, Hangyeore, Lee, Sang-Won, Paek, Eunok

“…Isobaric tag-based quantification such as iTRAQ and TMT is a promising approach to mass spectrometry-based quantification in proteomics as it provides wide…”
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High-throughput peptide quantification using mTRAQ reagent triplex by Yoon, Joo Young, Yeom, Jeonghun, Lee, Heebum, Kim, Kyutae, Na, Seungjin, Park, Kunsoo, Paek, Eunok, Lee, Cheolju

“…Protein quantification is an essential step in many proteomics experiments. A number of labeling approaches have been proposed and adopted in mass spectrometry…”
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pXg: Comprehensive Identification of Noncanonical MHC-I–Associated Peptides From De Novo Peptide Sequencing Using RNA-Seq Reads by Choi, Seunghyuk, Paek, Eunok

“…Discovering noncanonical peptides has been a common application of proteogenomics. Recent studies suggest that certain noncanonical peptides, known as…”
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MutCombinator: identification of mutated peptides allowing combinatorial mutations using nucleotide-based graph search by Choi, Seunghyuk, Paek, Eunok

“…Abstract Motivation Proteogenomics has proven its utility by integrating genomics and proteomics. Typical approaches use data from next-generation sequencing…”
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DbyDeep: Exploration of MS-Detectable Peptides via Deep Learning by Son, Juho, Na, Seungjin, Paek, Eunok

“…Predicting peptide detectability is useful in a variety of mass spectrometry (MS)-based proteomics applications, particularly targeted proteomics. However,…”
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Deephos: predicted spectral database search for TMT-labeled phosphopeptides and its false discovery rate estimation by Na, Seungjin, Choi, Hyunjin, Paek, Eunok

“…Abstract Motivation Tandem mass tag (TMT)-based tandem mass spectrometry (MS/MS) has become the method of choice for the quantification of post-translational…”
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