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Can the false-discovery rate be misleading?
Barboza R, Cociorva D, Xu T, Barbosa VC, Perales J, Valente RH, França FM, Yates JR 3rd, Carvalho PC. Barboza R, et al. Among authors: barbosa vc. Proteomics. 2011 Oct;11(20):4105-8. doi: 10.1002/pmic.201100297. Epub 2011 Sep 6. Proteomics. 2011. PMID: 21834134 Free PMC article.
Effectively addressing complex proteomic search spaces with peptide spectrum matching.
Borges D, Perez-Riverol Y, Nogueira FC, Domont GB, Noda J, da Veiga Leprevost F, Besada V, França FM, Barbosa VC, Sánchez A, Carvalho PC. Borges D, et al. Among authors: barbosa vc. Bioinformatics. 2013 May 15;29(10):1343-4. doi: 10.1093/bioinformatics/btt106. Epub 2013 Feb 27. Bioinformatics. 2013. PMID: 23446294
Search engine processor: Filtering and organizing peptide spectrum matches.
Carvalho PC, Fischer JS, Xu T, Cociorva D, Balbuena TS, Valente RH, Perales J, Yates JR 3rd, Barbosa VC. Carvalho PC, et al. Among authors: barbosa vc. Proteomics. 2012 Apr;12(7):944-9. doi: 10.1002/pmic.201100529. Proteomics. 2012. PMID: 22311825 Free PMC article.
PepExplorer: a similarity-driven tool for analyzing de novo sequencing results.
Leprevost FV, Valente RH, Lima DB, Perales J, Melani R, Yates JR 3rd, Barbosa VC, Junqueira M, Carvalho PC. Leprevost FV, et al. Among authors: barbosa vc. Mol Cell Proteomics. 2014 Sep;13(9):2480-9. doi: 10.1074/mcp.M113.037002. Epub 2014 May 30. Mol Cell Proteomics. 2014. PMID: 24878498 Free PMC article.
Mixed-Data Acquisition: Next-Generation Quantitative Proteomics Data Acquisition.
Santos MDM, Camillo-Andrade AC, Kurt LU, Clasen MA, Lyra E, Gozzo FC, Batista M, Valente RH, Brunoro GVF, Barbosa VC, Fischer JSG, Carvalho PC. Santos MDM, et al. Among authors: barbosa vc. J Proteomics. 2020 Jun 30;222:103803. doi: 10.1016/j.jprot.2020.103803. Epub 2020 May 5. J Proteomics. 2020. PMID: 32387712
Analyzing marginal cases in differential shotgun proteomics.
Carvalho PC, Fischer JS, Perales J, Yates JR, Barbosa VC, Bareinboim E. Carvalho PC, et al. Among authors: barbosa vc. Bioinformatics. 2011 Jan 15;27(2):275-6. doi: 10.1093/bioinformatics/btq632. Epub 2010 Nov 11. Bioinformatics. 2011. PMID: 21075743 Free PMC article.
Improving the TFold test for differential shotgun proteomics.
Carvalho PC, Yates JR 3rd, Barbosa VC. Carvalho PC, et al. Among authors: barbosa vc. Bioinformatics. 2012 Jun 15;28(12):1652-4. doi: 10.1093/bioinformatics/bts247. Epub 2012 Apr 26. Bioinformatics. 2012. PMID: 22539673 Free PMC article.
61 results