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Sangtae Kim, Ph.D. - Publications

Affiliations: 
Computer Science and Engineering University of California, San Diego, La Jolla, CA 
Area:
Bioinformatics, proteomics, mass spectrometry
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24 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Choi Y, Jeong K, Shin S, Lee JW, Lee YS, Kim S, Kim SA, Jung J, Kim KP, Kim VN, Kim JS. MS1-level proteome quantification platform allowing maximally increased multiplexity for SILAC and chemical labeling. Analytical Chemistry. PMID 32167278 DOI: 10.1021/Acs.Analchem.9B05148  0.612
2018 Kim S, Scheffler K, Halpern AL, Bekritsky MA, Noh E, Källberg M, Chen X, Kim Y, Beyter D, Krusche P, Saunders CT. Strelka2: fast and accurate calling of germline and somatic variants. Nature Methods. PMID 30013048 DOI: 10.1038/S41592-018-0051-X  0.301
2018 Park J, Piehowski PD, Wilkins C, Zhou M, Mendoza J, Fujimoto GM, Gibbons BC, Shaw JB, Shen Y, Shukla AK, Moore RJ, Liu T, Petyuk VA, Tolić N, Paša-Tolić L, ... ... Kim S, et al. Author Correction: Informed-Proteomics: open-source software package for top-down proteomics. Nature Methods. PMID 29899368 DOI: 10.1038/S41592-018-0040-0  0.3
2017 Park J, Piehowski PD, Wilkins C, Zhou M, Mendoza J, Fujimoto GM, Gibbons BC, Shaw JB, Shen Y, Shukla AK, Moore RJ, Liu T, Petyuk VA, Tolić N, Paša-Tolić L, ... ... Kim S, et al. Informed-Proteomics: open-source software package for top-down proteomics. Nature Methods. PMID 28783154 DOI: 10.1038/Nmeth.4388  0.498
2017 Kyle JE, Crowell KL, Casey CP, Fujimoto GM, Kim S, Dautel SE, Smith RD, Payne SH, Metz TO. LIQUID: an-open source software for identifying lipids in LC-MS/MS-based lipidomics data. Bioinformatics (Oxford, England). PMID 28158427 DOI: 10.1093/Bioinformatics/Btx046  0.435
2017 Shen Y, Tolić N, Piehowski PD, Shukla AK, Kim S, Zhao R, Qu Y, Robinson E, Smith RD, Paša-Tolić L. High-resolution ultrahigh-pressure long column reversed-phase liquid chromatography for top-down proteomics. Journal of Chromatography. A. PMID 28077236 DOI: 10.1016/J.Chroma.2017.01.008  0.465
2016 Choi M, Eren-Dogu ZF, Colangelo CM, Cottrell JS, Hoopmann MR, Kapp EA, Kim S, Lam H, Neubert TA, Palmblad M, Phinney BS, Weintraub ST, MacLean B, Vitek O. ABRF Proteome Informatics Research Group (iPRG) 2015 Study: Detection of differentially abundant proteins in label-free quantitative LC-MS/MS experiments. Journal of Proteome Research. PMID 27990823 DOI: 10.1021/Acs.Jproteome.6B00881  0.49
2016 Madar IH, Ko SI, Kim H, Mun DG, Kim S, Smith RD, Lee SW. Multiplexed Post-Experimental Monoisotopic Mass Refinement (mPE-MMR) to increase sensitivity and accuracy in peptide identifications from tandem mass spectra of co-fragmentation. Analytical Chemistry. PMID 27966901 DOI: 10.1021/Acs.Analchem.6B03874  0.565
2015 Tabb DL, Wang X, Carr SA, Clauser KR, Mertins P, Chambers MC, Holman JD, Wang J, Zhang B, Zimmerman LJ, Chen X, Gunawardena HP, Davies SR, Ellis MJ, Li S, ... ... Kim S, et al. Reproducibility of differential proteomic technologies in CPTAC fractionated xenografts. Journal of Proteome Research. PMID 26653538 DOI: 10.1021/Acs.Jproteome.5B00859  0.401
2015 Ting YS, Egertson JD, Payne SH, Kim S, MacLean B, Käll L, Aebersold RH, Smith RD, Noble WS, MacCoss MJ. Peptide-Centric Proteome Analysis: An Alternative Strategy for the Analysis of Tandem Mass Spectrometry Data. Molecular & Cellular Proteomics : McP. PMID 26217018 DOI: 10.1074/Mcp.O114.047035  0.596
2014 Kim S, Pevzner PA. MS-GF+ makes progress towards a universal database search tool for proteomics. Nature Communications. 5: 5277. PMID 25358478 DOI: 10.1038/Ncomms6277  0.731
2014 Liu X, Segar MW, Li SC, Kim S. Spectral probabilities of top-down tandem mass spectra. Bmc Genomics. 15: S9. PMID 24564718 DOI: 10.1186/1471-2164-15-S1-S9  0.513
2014 Meyer JG, Kim S, Maltby DA, Ghassemian M, Bandeira N, Komives EA. Expanding proteome coverage with orthogonal-specificity α-lytic proteases. Molecular & Cellular Proteomics : McP. 13: 823-35. PMID 24425750 DOI: 10.1074/Mcp.M113.034710  0.714
2014 Granholm V, Kim S, Navarro JC, Sjölund E, Smith RD, Käll L. Fast and accurate database searches with MS-GF+Percolator. Journal of Proteome Research. 13: 890-7. PMID 24344789 DOI: 10.1021/Pr400937N  0.642
2013 Jeong K, Kim S, Pevzner PA. UniNovo: a universal tool for de novo peptide sequencing. Bioinformatics (Oxford, England). 29: 1953-62. PMID 23766417 DOI: 10.1093/Bioinformatics/Btt338  0.738
2013 Mohimani H, Kim S, Pevzner PA. A new approach to evaluating statistical significance of spectral identifications. Journal of Proteome Research. 12: 1560-8. PMID 23343606 DOI: 10.1021/Pr300453T  0.663
2012 Jeong K, Kim S, Bandeira N. False discovery rates in spectral identification. Bmc Bioinformatics. 13: S2. PMID 23176207 DOI: 10.1186/1471-2105-13-S16-S2  0.726
2011 Jeong K, Kim S, Bandeira N, Pevzner PA. Gapped spectral dictionaries and their applications for database searches of tandem mass spectra. Molecular & Cellular Proteomics : McP. 10: M110.002220. PMID 21444829 DOI: 10.1074/Mcp.M110.002220  0.783
2010 Kim S, Mischerikow N, Bandeira N, Navarro JD, Wich L, Mohammed S, Heck AJ, Pevzner PA. The generating function of CID, ETD, and CID/ETD pairs of tandem mass spectra: applications to database search. Molecular & Cellular Proteomics : McP. 9: 2840-52. PMID 20829449 DOI: 10.1074/Mcp.M110.003731  0.776
2009 Kim S, Bandeira N, Pevzner PA. Spectral profiles, a novel representation of tandem mass spectra and their applications for de novo peptide sequencing and identification. Molecular & Cellular Proteomics : McP. 8: 1391-400. PMID 19254948 DOI: 10.1074/Mcp.M800535-Mcp200  0.755
2009 Kim S, Gupta N, Bandeira N, Pevzner PA. Spectral dictionaries: Integrating de novo peptide sequencing with database search of tandem mass spectra. Molecular & Cellular Proteomics : McP. 8: 53-69. PMID 18703573 DOI: 10.1074/Mcp.M800103-Mcp200  0.774
2008 Pevzner PA, Kim S, Ng J. Comment on "Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry". Science (New York, N.Y.). 321: 1040; author reply 1. PMID 18719266 DOI: 10.1126/Science.1155006  0.677
2008 Kim S, Gupta N, Pevzner PA. Spectral probabilities and generating functions of tandem mass spectra: a strike against decoy databases. Journal of Proteome Research. 7: 3354-63. PMID 18597511 DOI: 10.1021/Pr8001244  0.751
2006 Kim S, Na S, Sim JW, Park H, Jeong J, Kim H, Seo Y, Seo J, Lee KJ, Paek E. MODi: a powerful and convenient web server for identifying multiple post-translational peptide modifications from tandem mass spectra. Nucleic Acids Research. 34: W258-63. PMID 16845006 DOI: 10.1093/nar/gkl245  0.43
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