Publications by authors named "VC Barbosa"

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Shape complexity in cluster analysis.
Eduardo J Aguilar, Valmir C Barbosa

PLoS One· May 2023

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DiagnoMass: A proteomics hub for pinpointing discriminative spectral clusters.
Marlon D M Santos, Amanda C Camillo-Andrade, Diogo B Lima, Tatiana A C B Souza, Juliana de S da G Fischer, Valmir C Barbosa

J Proteomics· April 2023

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PatternLab V Handles Multiplex Spectra in Shotgun Proteomic Searches and Increases Identification.
Milan A Clasen, Marlon D M Santos, Louise Ulrich Kurt, Juliana Fischer, Amanda C Camillo-Andrade, Valmir C Barbosa

J Am Soc Mass Spectrom· April 2023

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Increasing confidence in proteomic spectral deconvolution through mass defect.
Milan A Clasen, Louise U Kurt, Marlon D M Santos, Diogo B Lima, Fan Liu, Valmir C Barbosa

Bioinformatics· November 2022

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Simple, efficient and thorough shotgun proteomic analysis with PatternLab V.
Marlon D M Santos, Diogo B Lima, Juliana S G Fischer, Milan A Clasen, Louise U Kurt, Valmir C Barbosa

Nat Protoc· July 2022

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Leveraging the partition selection bias to achieve a high-quality clustering of mass spectra.
André R F Silva, Diogo B Lima, Louise U Kurt, Mathieu Dupré, Julia Chamot-Rooke, Valmir C Barbosa

J Proteomics· August 2021

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Interspecies evolutionary dynamics mediated by public goods in bacterial quorum sensing.
Eduardo J Aguilar, Valmir C Barbosa, Raul Donangelo, Sergio R Souza

Phys Rev E· January 2021

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Mixed-Data Acquisition: Next-Generation Quantitative Proteomics Data Acquisition.
Marlon D M Santos, Amanda Caroline Camillo-Andrade, Louise U Kurt, Milan A Clasen, Eduardo Lyra, Valmir C Barbosa

J Proteomics· June 2020

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Top-Down Garbage Collector: a tool for selecting high-quality top-down proteomics mass spectra.
Diogo B Lima, André R F Silva, Mathieu Dupré, Marlon D M Santos, Milan A Clasen, Valmir C Barbosa

Bioinformatics· September 2019

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A quantitation module for isotope-labeled peptides integrated into PatternLab for proteomics.
Marlon D M Santos, Diogo B Lima, André R F Silva, Louise U Kurt, Milan A Clasen, Valmir C Barbosa

J Proteomics· June 2019

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Differential proteomic comparison of breast cancer secretome using a quantitative paired analysis workflow.
Giselle Villa Flor Brunoro, Paulo Costa Carvalho, Valmir C Barbosa, Dante Pagnoncelli, Claudia Vitória De Moura Gallo

BMC Cancer· April 2019

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Information-theoretic signatures of biodiversity in the barcoding gene.
Valmir C Barbosa

J Theor Biol· August 2018

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Characterization of homodimer interfaces with cross-linking mass spectrometry and isotopically labeled proteins.
Diogo B Lima, John T Melchior, Jamie Morris, Valmir C Barbosa, Julia Chamot-Rooke

Nat Protoc· March 2018

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A multi-protease, multi-dissociation, bottom-up-to-top-down proteomic view of the Loxosceles intermedia venom.
Dilza Trevisan-Silva, Aline V Bednaski, Juliana S G Fischer, Silvio S Veiga, Nuno Bandeira, Valmir C Barbosa

Sci Data· July 2017

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DiagnoProt: a tool for discovery of new molecules by mass spectrometry.
André R F Silva, Diogo B Lima, Alejandro Leyva, Rosario Duran, Carlos Batthyany, Valmir C Barbosa

Bioinformatics· June 2017

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Integrated analysis of shotgun proteomic data with PatternLab for proteomics 4.0.
Paulo C Carvalho, Diogo B Lima, Felipe V Leprevost, Marlon D M Santos, Juliana S G Fischer, Valmir C Barbosa

Nat Protoc· January 2016

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A scoring model for phosphopeptide site localization and its impact on the question of whether to use MSA.
Juliana de S da G Fischer, Marlon D M Dos Santos, Fabricio K Marchini, Valmir C Barbosa, Paulo C Carvalho

J Proteomics· November 2015

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SIM-XL: A powerful and user-friendly tool for peptide cross-linking analysis.
Diogo B Lima, Tatiani B de Lima, Tiago S Balbuena, Ana Gisele C Neves-Ferreira, Valmir C Barbosa

J Proteomics· November 2015

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Using PepExplorer to Filter and Organize De Novo Peptide Sequencing Results.
Felipe da Veiga Leprevost, Valmir C Barbosa, Paulo Costa Carvalho

Curr Protoc Bioinformatics· September 2015

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Early detection of epilepsy seizures based on a weightless neural network.
Kleber de Aguiar, Felipe M G Franca, Valmir C Barbosa, Cesar A D Teixeira

Annu Int Conf IEEE Eng Med Biol Soc· August 2015

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PepExplorer: a similarity-driven tool for analyzing de novo sequencing results.
Felipe V Leprevost, Richard H Valente, Diogo B Lima, Jonas Perales, Rafael Melani, Valmir C Barbosa

Mol Cell Proteomics· September 2014

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On best practices in the development of bioinformatics software.
Felipe da Veiga Leprevost, Valmir C Barbosa, Eduardo L Francisco, Yasset Perez-Riverol, Paulo C Carvalho

Front Genet· July 2014

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Exploring the proteomic landscape of a gastric cancer biopsy with the shotgun imaging analyzer.
Priscila Ferreira Aquino, Diogo Borges Lima, Juliana de Saldanha da Gama Fischer, Rafael Donadélli Melani, Fabio C S Nogueira, Valmir C Barbosa

J Proteome Res· January 2014

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Pinpointing differentially expressed domains in complex protein mixtures with the cloud service of PatternLab for Proteomics.
F V Leprevost, D B Lima, J Crestani, Y Perez-Riverol, N Zanchin, V C Barbosa

J Proteomics· August 2013

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The conduciveness of CA-rule graphs.
Valmir C Barbosa

Artif Life· July 2013

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