Paulo Costa Carvalho

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Valmir C. BarbosaProfessor, Federal University of Rio de JaneiroVerified email at cos.ufrj.br
Juliana FischerInstituto Carlos ChagasVerified email at tecpar.br
John YatesErnest W. Hahn Professor @ The Scripps Research InstituteVerified email at scripps.edu
Diogo Borges LimaLeibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)Verified email at fmp-berlin.de
Maria da Gloria da Costa Carvalhoprofessora, universidade federal do rio de janeiro, pesquisadora CNPqVerified email at gcarvalho.org
Gilberto DomontEmeritus Professor, Universidade Federal do Rio de JaneiroVerified email at iq.ufrj.br
Jonas PeralesPesquisador Titular Fundação Oswaldo CruzVerified email at ioc.fiocruz.br
Richard Hemmi ValenteToxinology Laboratory - FIOCRUZVerified email at ioc.fiocruz.br
Marlon Dias Mariano SantosCarlos Chagas Institute, Fiocruz - Paraná, BrazilVerified email at tecpar.br
Priscila AquinoPesquisador em saúde pública, Fundação Oswaldo Cruz, Instituto Lêonidas e Maria DeaneVerified email at amazonia.fiocruz.br
Felipe da Veiga LeprevostPrincipal Scientist, GenentechVerified email at gene.com
Fábio César Sousa NogueiraProfessor, IQ, UFRJVerified email at ufrj.br
Fabio Cesar GozzoProfessor de Química, Universidade Estadual de CampinasVerified email at iqm.unicamp.br
Tao XuCorteva AgriscienceVerified email at corteva.com
Wim DegravePesquisador Titular, Instituto Oswaldo Cruz, FiocruzVerified email at fiocruz.br
Magno junqueiraAssociate Professor Institute of Chemistry Federal University of Rio de Janeiro - BrazilVerified email at iq.ufrj.br
Rosario DuranInsitut Pasteur de Montevideo/ Instituto de Investigaciones Biológicas Clemente EstableVerified email at pasteur.edu.uy
Yasset Perez-RiverolTeam Coordinator, Proteomics Resources, EMBL-EBI, UKVerified email at ebi.ac.uk
Julia Chamot-RookeCNRS - Institut PasteurVerified email at pasteur.fr
Francisco A.P. CamposDepartamento de Bioquímica e Biologia Molecular, Universidade Federal do CearáVerified email at ufc.br

Paulo Costa Carvalho

Carlos Chagas Institute, Fiocruz - Paraná, Brazil

Verified email at pcarvalho.com - Homepage

computational mass spectrometry machine learning proteomics


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PYR/PYL/RCAR family members are major in‐vivo ABI1 protein phosphatase 2C‐interacting proteins in Arabidopsis N Nishimura, A Sarkeshik, K Nito, SY Park, A Wang, PC Carvalho, S Lee, ... The Plant Journal 61 (2), 290-299, 2010	525	2010
Integrated analysis of shotgun proteomic data with PatternLab for proteomics 4.0 PC Carvalho, DB Lima, FV Leprevost, MDM Santos, JSG Fischer, ... Nature Protocols 11 (1), 102-117, 2016	244	2016
PatternLab for proteomics: a tool for differential shotgun proteomics PC Carvalho, JSG Fischer, EI Chen, JR Yates, VC Barbosa BMC bioinformatics 9 (1), 1-14, 2008	149	2008
Search engine processor: filtering and organizing peptide spectrum matches PC Carvalho, JSG Fischer, T Xu, D Cociorva, TS Balbuena, RH Valente, ... Proteomics 12 (7), 944-949, 2012	125	2012
XDIA: improving on the label-free data-independent analysis PC Carvalho, X Han, T Xu, D Cociorva, M da Gloria Carvalho, ... Bioinformatics 26 (6), 847-848, 2010	116	2010
Identifying differences in protein expression levels by spectral counting and feature selection PC Carvalho, J Hewel, VC Barbosa, JR Yates III Genetics and molecular research: GMR 7 (2), 342, 2008	111	2008
Improvements in proteomic metrics of low abundance proteins through proteome equalization using ProteoMiner prior to MudPIT BR Fonslow, PC Carvalho, K Academia, S Freeby, T Xu, A Nakorchevsky, ... Journal of proteome research 10 (8), 3690-3700, 2011	106	2011
SIM-XL: A powerful and user-friendly tool for peptide cross-linking analysis DB Lima, TB de Lima, TS Balbuena, AGC Neves-Ferreira, VC Barbosa, ... Journal of proteomics 129, 51-55, 2015	93	2015
YADA: a tool for taking the most out of high-resolution spectra PC Carvalho, T Xu, X Han, D Cociorva, VC Barbosa, JR Yates III Bioinformatics 25 (20), 2734-2736, 2009	89	2009
Platelet proteome reveals novel pathways of platelet activation and platelet-mediated immunoregulation in dengue MRO Trugilho, ED Hottz, GVF Brunoro, A Teixeira-Ferreira, PC Carvalho, ... PLoS pathogens 13 (5), e1006385, 2017	88	2017
Improving the TFold test for differential shotgun proteomics PC Carvalho, JR Yates III, VC Barbosa Bioinformatics 28 (12), 1652-1654, 2012	81	2012
PatternLab: from mass spectra to label‐free differential shotgun proteomics PC Carvalho, JSG Fischer, T Xu, JR Yates III, VC Barbosa Current protocols in bioinformatics 40 (1), 13.19. 1-13.19. 18, 2012	74	2012
Identifying components of protein complexes in C. elegans using co-immunoprecipitation and mass spectrometry JJ Moresco, PC Carvalho, JR Yates III Journal of proteomics 73 (11), 2198-2204, 2010	73	2010
On best practices in the development of bioinformatics software FV Leprevost, VC Barbosa, EL Francisco, Y Perez-Riverol, PC Carvalho Frontiers in genetics 5, 199, 2014	71	2014
On best practices in the development of bioinformatics software FV Leprevost, VC Barbosa, EL Francisco, Y Perez-Riverol, PC Carvalho Frontiers in genetics 5, 199, 2014	71	2014
An in-depth snake venom proteopeptidome characterization: Benchmarking Bothrops jararaca CA Nicolau, PC Carvalho, ILM Junqueira-de-Azevedo, A Teixeira-Ferreira, ... Journal of Proteomics 151, 214-231, 2017	62	2017
Single-step inline hydroxyapatite enrichment facilitates identification and quantitation of phosphopeptides from mass-limited proteomes with MudPIT BR Fonslow, SM Niessen, M Singh, CCL Wong, T Xu, PC Carvalho, ... Journal of proteome research 11 (5), 2697-2709, 2012	59	2012
Reevaluating the Trypanosoma cruzi proteomic map: The shotgun description of bloodstream trypomastigotes GVF Brunoro, MA Caminha, AT da Silva Ferreira, F da Veiga Leprevost, ... Journal of Proteomics 115, 58-65, 2015	54	2015
Characterization of homodimer interfaces with cross-linking mass spectrometry and isotopically labeled proteins DB Lima, JT Melchior, J Morris, VC Barbosa, J Chamot-Rooke, ... Nature protocols 13 (3), 431-458, 2018	51	2018
PepExplorer: a similarity-driven tool for analyzing de novo sequencing results FV Leprevost, RH Valente, DB Lima, J Perales, R Melani, JR Yates, ... Molecular & Cellular Proteomics 13 (9), 2480-2489, 2014	43	2014

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