Squid - a simple bioinformatics grid. - Paulo C. Carvalho; Rafael V. Glória; Antonio Basílio de Miranda; Wim M. Degrave (BMC Bioinform., 2005)

PatternLab for proteomics: a tool for differential shotgun proteomics. - Paulo C. Carvalho; Juliana S. G. Fischer; Emily I. Chen; John R. Yates III; Valmir Carneiro Barbosa (BMC Bioinform., 2008)

YADA: a tool for taking the most out of high-resolution spectra. - Paulo C. Carvalho; Tao Xu; Xuemei Han; Daniel Cociorva; Valmir Carneiro Barbosa; John R. Yates III (Bioinform., 2009)

XDIA: improving on the label-free data-independent analysis. - Paulo C. Carvalho; Xuemei Han; Tao Xu; Daniel Cociorva; Maria da Gloria Carvalho; Valmir Carneiro Barbosa; John R. Yates III (Bioinform., 2010)

Analyzing marginal cases in differential shotgun proteomics. - Paulo C. Carvalho; Juliana S. G. Fischer; Jonas Perales; John R. Yates III; Valmir Carneiro Barbosa; Elias Bareinboim (Bioinform., 2011)

Improving the TFold test for differential shotgun proteomics. - Paulo C. Carvalho; John R. Yates III; Valmir Carneiro Barbosa (Bioinform., 2012)

Effectively addressing complex proteomic search spaces with peptide spectrum matching. - Diogo B. Lima; Yasset Pérez-Riverol; Fabio C. S. Nogueira; Gilberto B. Domont; Jesus Noda; Felipe da Veiga Leprevost; Vladimir Besada; Felipe M. G. França; Valmir Carneiro Barbosa; Aniel Sánchez; Paulo C. Carvalho (Bioinform., 2013)

DiagnoProt: a tool for discovery of new molecules by mass spectrometry. - André Ramos Fernandes Da Silva; Diogo B. Lima; Alejandro Leyva; Rosario Durán; Carlos Batthyany; Priscila F. Aquino; Juliana C. Leal; Jimmy E. Rodriguez; Gilberto B. Domont; Marlon D. M. Santos; Julia Chamot-Rooke; Valmir C. Barbosa; et al. (Bioinform., 2017)

TopoLink: evaluation of structural models using chemical crosslinking distance constraints. - Allan J. R. Ferrari; Milan A. Clasen; Louise U. Kurt; Paulo C. Carvalho; Fábio C. Gozzo; Leandro Martínez (Bioinform., 2019)

Top-Down Garbage Collector: a tool for selecting high-quality top-down proteomics mass spectra. - Diogo B. Lima; André Ramos Fernandes Da Silva; Mathieu Dupré; Marlon D. M. Santos; Milan A. Clasen; Louise U. Kurt; Priscila F. Aquino; Valmir C. Barbosa; Paulo C. Carvalho; Julia Chamot-Rooke (Bioinform., 2019)

Characterizing protein conformers by cross-linking mass spectrometry and pattern recognition. - Louise U. Kurt; Milan A. Clasen; Marlon D. M. Santos; Eduardo S. B. Lyra; Luana O. Santos; Carlos H. I. Ramos; Diogo B. Lima; Fábio C. Gozzo; Paulo C. Carvalho (Bioinform., 2021)

Increasing confidence in proteomic spectral deconvolution through mass defect. - Milan A. Clasen; Louise U. Kurt; Marlon D. M. Santos; Diogo B. Lima; Fan Liu; Fábio C. Gozzo; Valmir C. Barbosa; Paulo C. Carvalho (Bioinform., 2022)