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Proteogenomics: concepts, applications and computational strategies.
Nesvizhskii AI. Nesvizhskii AI. Nat Methods. 2014 Nov;11(11):1114-25. doi: 10.1038/nmeth.3144. Nat Methods. 2014. PMID: 25357241 Free PMC article. Review.
Quantitative proteomic landscape of metaplastic breast carcinoma pathological subtypes and their relationship to triple-negative tumors.
Djomehri SI, Gonzalez ME, da Veiga Leprevost F, Tekula SR, Chang HY, White MJ, Cimino-Mathews A, Burman B, Basrur V, Argani P, Nesvizhskii AI, Kleer CG. Djomehri SI, et al. Among authors: nesvizhskii ai. Nat Commun. 2020 Apr 7;11(1):1723. doi: 10.1038/s41467-020-15283-z. Nat Commun. 2020. PMID: 32265444 Free PMC article.
Protein identification by tandem mass spectrometry and sequence database searching.
Nesvizhskii AI. Nesvizhskii AI. Methods Mol Biol. 2007;367:87-119. doi: 10.1385/1-59745-275-0:87. Methods Mol Biol. 2007. PMID: 17185772 Review.
Comprehensive analysis of proteins of pH fractionated samples using monolithic LC/MS/MS, intact MW measurement and MALDI-QIT-TOF MS.
Yoo C, Patwa TH, Kreunin P, Miller FR, Huber CG, Nesvizhskii AI, Lubman DM. Yoo C, et al. Among authors: nesvizhskii ai. J Mass Spectrom. 2007 Mar;42(3):312-34. doi: 10.1002/jms.1163. J Mass Spectrom. 2007. PMID: 17206599 Free PMC article.
Investigating MS2/MS3 matching statistics: a model for coupling consecutive stage mass spectrometry data for increased peptide identification confidence.
Ulintz PJ, Bodenmiller B, Andrews PC, Aebersold R, Nesvizhskii AI. Ulintz PJ, et al. Among authors: nesvizhskii ai. Mol Cell Proteomics. 2008 Jan;7(1):71-87. doi: 10.1074/mcp.M700128-MCP200. Epub 2007 Sep 13. Mol Cell Proteomics. 2008. PMID: 17872894
Analysis and validation of proteomic data generated by tandem mass spectrometry.
Nesvizhskii AI, Vitek O, Aebersold R. Nesvizhskii AI, et al. Nat Methods. 2007 Oct;4(10):787-97. doi: 10.1038/nmeth1088. Nat Methods. 2007. PMID: 17901868 Review.
False discovery rates and related statistical concepts in mass spectrometry-based proteomics.
Choi H, Nesvizhskii AI. Choi H, et al. Among authors: nesvizhskii ai. J Proteome Res. 2008 Jan;7(1):47-50. doi: 10.1021/pr700747q. Epub 2007 Dec 8. J Proteome Res. 2008. PMID: 18067251
Humoral response profiling reveals pathways to prostate cancer progression.
Taylor BS, Pal M, Yu J, Laxman B, Kalyana-Sundaram S, Zhao R, Menon A, Wei JT, Nesvizhskii AI, Ghosh D, Omenn GS, Lubman DM, Chinnaiyan AM, Sreekumar A. Taylor BS, et al. Among authors: nesvizhskii ai. Mol Cell Proteomics. 2008 Mar;7(3):600-11. doi: 10.1074/mcp.M700263-MCP200. Epub 2007 Dec 11. Mol Cell Proteomics. 2008. PMID: 18077443
Statistical validation of peptide identifications in large-scale proteomics using the target-decoy database search strategy and flexible mixture modeling.
Choi H, Ghosh D, Nesvizhskii AI. Choi H, et al. Among authors: nesvizhskii ai. J Proteome Res. 2008 Jan;7(1):286-92. doi: 10.1021/pr7006818. Epub 2007 Dec 14. J Proteome Res. 2008. PMID: 18078310
Semisupervised model-based validation of peptide identifications in mass spectrometry-based proteomics.
Choi H, Nesvizhskii AI. Choi H, et al. Among authors: nesvizhskii ai. J Proteome Res. 2008 Jan;7(1):254-65. doi: 10.1021/pr070542g. Epub 2007 Dec 27. J Proteome Res. 2008. PMID: 18159924
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