Curriculum Vitae
Updated on July 2017

 

Paulo Costa Carvalho - CV

Paulo holds a PhD in systems engineering and computer science from the Federal University of Rio de Janeiro and is a former member of the John R. Yates Laboratory at the Scripps Research Institute, California, EUA. Among his awards, we highlight the Google Award for Academic Excellence and the Young Biochemistry Scientist Award given by the Brazilian society for biochemistry and molecular biology (SBBq). In 2012 he earned a position as a research scientist in proteomics at Fiocruz, Brazil’s federal consortium of research institutes under the Ministry of Health. Paulo has published over 80 papers of which several of his first / last author papers are in distinguished journals such as Bioinformatics, Analytical Chemistry, Molecular and Cellular Proteomics, Nature Protocols, and Nature Methods. In 2014 he became accredited into the highly competitive group of researchers officially sponsored by Brazil’s Research Council, owing to the high quality of his publications in the fields of proteomics and computational mass spectrometry (pesquisador de produtividade CNPq).  Paulo is a member of the faculty at the Federal University of Rio de Janeiro and Carlos Chagas Institute, Fiocruz, where he teaches computational proteomics at the graduate level. Paulo is founding member of the Brazilian Society for Proteomics and is part of its scientific committee.  In October 2014, Paulo was nominated as an executive editor of the Journal of Proteomics (IF 3.9) which is the official journal of the European Proteomics Association. Recently, in 2016, he became part of the Features Panel of the prestigious Analytical Chemistry (IF 5.8) journal.

Academics

2012 - Present

Research scientist at the Carlos Chagas Institute, Fiocruz, Paraná, Brazil in the field of experimental and computational proteomics, professor of the graduate course "Analyzing proteomic data", and professor at the Chemistry Institute of the Federal University of Rio de Janeiro. I also serve as an executive editor for Journal of Proteomics since November / 2014.

2010 - 2011

Post-doc at the Laboratory for Toxinology at the Oswaldo Cruz Institute.

2006 - 2010

PhD student at the systems engineering and computer science program, COPPE, Federal University of Rio de Janeiro (UFRJ)
Major in pattern recognition.  My final GPA was 3.0 out of 3.0

I spent 1 year and 7 months in the John Yates III lab at The Scripps Research Institute in California as part of a "sandwich" PhD program.

Thesis title : A computational environment for proteomics.
Advisor: Valmir Carneiro Barbosa, Co-advisor: John R. Yates, III, Scholarship: CNPq

2004 - 2006

Masters in Molecular and Cellular Biology with major in Bioinformatics - Instituto Oswaldo Cruz, - RJ Brasil

Title: Pattern recognition in proteomic data for medical diagnosis
Advisors: Wim Maurits Degrave (Oswaldo Cruz Institute) and Gilberto Barbosa Domont (Federal University of Rio de Janeiro)
Scholarship: Instituto-Oswaldo-Cruz

2002 - 2003

Student in Bioinformatics. Federal University of Rio de Janeiro – Carlos Chagas Filho Biophysics Institute – Brazil

1995 - 2000

Bachelors: Mechanichal Engineering: Pontifícia Universidade Católica do Rio de Janeiro, PUC - RIO, Brasil

1981 - 1993

High School: American School of Rio de Janeiro, EARJ, Brasil, graduated in 93.2

 


Awards & Scholarships

  1. Features Panel member in Analytical Chemistry, 2016
  2. "Highly productive scientist award" from the Brazilian National Council for Research, (Pesquisador de produtividade Nivel 2 - CNPq), March 2014
  3. Honorable mention in poster "An algorithm for generating a representative protein sequence database to facilitate proteomic analysis of unsequenced organisms.", together with his undergrad Student Marlon Mariano Dias during the bi-anual meeting of the Brazilian Society for Proteomics (BrProt II), December 2014.
  4. Honorable mention in the "Premio CAPES tese de doutorado 2011" as one of the top 3 PhD thesis in computer science in Brazil, June 2012.
  5. Best poster award in the MSc category with my MSc student Diogo Borges at the I Meeting of the Brazilian Proteomics Society, 2012,
  6. Best poster award in the PhD category with my PhD student Priscila Aquino at the I Meeting of the Brazilian Proteomics Society, 2012
  7. Best poster award in the Proteomics category, IV BrMass (Meeting of the Brazilian Society for Mass Spectrometry) , December 2011
  8. Young proteomic award (1st place), IV Proteomic Forum of Rio de Janeiro, November 4th 2010.
  9. Young Talent in Life Science 2009.
  10. Google Award for excellence in the PhD academic program / issued by Google university programs on December 2008.
  11. Fellowship awarded by CAPES (Brazilian Federal Agency for Support and Evaluation of Graduate Programs) to perform PhD research in Scripps from 2008 - 2009
  12. Best Work Award, I Symposium in Oncobiology at UFRJ, 2007
  13. Scholarship awarded during PhD by the “National Council for Scientific and Technological Development (CNPq)”, 2007-2010
  14. Scholarship awarded during MSc by the Oswaldo Cruz Institute, 2005-2006
  15. Award entitled “Best scientific work Oswaldo Cruz Institute 2005” at the Fiocruz bi-annual graduate scientific meeting

Societies

  1. Founder and member of the scientific advisory board of the Brazilian Society for Proteomics
  2. Member of the International Society for Computational Biology (ISCB)
  3. Member of the Brazilian Society for Mass Spectrometry (BrMass); is currently vice-president of the scientific council.

Patent requests

  1. Carvalho MGC, Carvalho PC, Kit for diagnosis of HPV integration in infected cells, 2004
  2. Carvalho PC , Carvalho MGC, Degrave WM., Lilla, S., De Nucci, G., Fonseca Neto R, Spector, N, Musacchio J, Domont GB. Method for feature selection in mass spectra data, 2006
  3. DiagnoProt, 2017

Full papers published in peer reviewed journals

1. SILVA, ANDRÉ R F ; LIMA, DIOGO B ; PEÑA, ALEJANDRO ; DURAN, ROSARIO ; BATTHYANY, CARLOS ; AQUINO, PRISCILA F ; LEAL, JULIANA C ; RODRIGUEZ, JIMMY E ; Domont, Gilberto B ; SANTOS, MARLON D M ; CHAMOT-ROOKE, JULIA ; Barbosa, Valmir C ; Carvalho, Paulo C . DiagnoProt: a tool for discovery of new molecules by mass spectrometry. Bioinformatics (Oxford. Print), v. AOP, p. AOP, 2017.

2. ALMEIDA, FABIANA GREYCE OLIVEIRA ; DE AQUINO, PRISCILA FERREIRA ; CHALUB, SIDNEY RAIMUNDO S. ; ARAUJO, GABRIEL DUARTE T. ; Domont, Gilberto B. ; DE SOUZA, AFONSO DUARTE L. ; Carvalho, Paulo C. ; FISCHER, JULIANA DE SALDANHA DA G. . Proteomic assessment of colorectal cancers and respective resection margins from patients of the Amazon state of Brazil. Journal of Proteomics (Print), v. 154, p. 59-68, 2017.

3. MONTEIRO, KARINA M. ; LORENZATTO, KARINA R. ; DE LIMA, JEFERSON C. ; DOS SANTOS, GUILHERME B. ; FÖRSTER, SABINE ; PALUDO, GABRIELA P. ; Carvalho, Paulo C. ; BREHM, KLAUS ; FERREIRA, HENRIQUE B. . Comparative proteomics of hydatid fluids from two Echinococcus multilocularis isolates. Journal of Proteomics, v. AOP, p. AOP, 2017.

4. TRUGILHO, MONIQUE RAMOS DE OLIVEIRA ; HOTTZ, EUGENIO DAMACENO ; BRUNORO, GISELLE VILLA FLOR ; TEIXEIRA-FERREIRA, ANDRÉ ; Carvalho, Paulo Costa ; SALAZAR, GUSTAVO ADOLFO ; ZIMMERMAN, GUY A. ; BOZZA, FERNANDO A. ; BOZZA, PATRÍCIA T. ; Perales, Jonas . Platelet proteome reveals novel pathways of platelet activation and platelet-mediated immunoregulation in dengue. PLoS Pathogens, v. 13, p. e1006385, 2017.

5. WOWK, PRYSCILLA FANINI ; ZARDO, MARIA LUISA ; MIOT, HALISSON TESSEROLI ; GOLDENBERG, SAMUEL ; Carvalho, Paulo Costa ; MÖRKING, PATRICIA ALVES . Proteomic profiling of extracellular vesicles secreted from Toxoplasma gondii. PROTEOMICS, v. AOP, p. 1600477, 2017.

6. TREVISAN-SILVA, DILZA ; BEDNASKI, ALINE V. ; FISCHER, JULIANA S.G. ; VEIGA, SILVIO S. ; BANDEIRA, NUNO ; GUTHALS, ADRIAN ; MARCHINI, FABRICIO K. ; LEPREVOST, FELIPE V. ; Barbosa, Valmir C. ; SENFF-RIBEIRO, ANDREA ; Carvalho, Paulo C. . A multi-protease, multi-dissociation, bottom-up-to-top-down proteomic view of the Loxosceles intermedia venom. Scientific Data, v. 4, p. 170090, 2017.

7. SHAH, MOHIBULLAH ; TEIXEIRA, FABIANO M. ; SOARES, EMANOELLA L. ; SOARES, ARLETE A. ; Carvalho, Paulo C. ; Domont, Gilberto B. ; THORNBURG, ROBERT W. ; NOGUEIRA, FÁBIO C. S. ; CAMPOS, FRANCISCO A. P. . Time-course proteome analysis of developing extrafloral nectaries of Ricinus communis. Proteomics (Weinheim. Print), v. 16, p. 629-633, 2016.

8. BORGES, MARCIA H. ; FIGUEIREDO, SUELY G. ; LEPREVOST, FELIPE V. ; DE LIMA, MARIA ELENA ; CORDEIRO, MARTA DO N. ; DINIZ, MARCELO R.V. ; MORESCO, JAMES ; Carvalho, Paulo C. ; Yates, John R. . Venomous extract protein profile of Brazilian tarantula Grammostola iheringi: searching for potential biotechnological applications. Journal of Proteomics (Print), v. 136, p. 35-47, 2016.

9. MELCHIOR, JOHN T. ; WALKER, RYAN G. ; MORRIS, JAMIE ; JONES, MARTIN K. ; SEGREST, JERE P. ; LIMA, DIOGO B. ; Carvalho, Paulo C. ; GOZZO, FABIO C. ; CASTLEBERRY, MARK ; THOMPSON, THOMAS B. ; DAVIDSON, W. SEAN . An Evaluation of the Crystal Structure of C-terminal Truncated Apolipoprotein A-I in Solution Reveals Structural Dynamics Related to Lipid Binding. Journal of Biological Chemistry (Online), v. 291, p. jbc.M115.706093, 2016.

10. LIMA, D. C. ; DUARTE, F. T. ; MEDEIROS, V. K. S. ; Carvalho, P. C. ; NOGUEIRA, F. C. S. ; ARAUJO, G. D. T. ; DOMONT, G. B. ; BATISTUZZO DE MEDEIROS, S. R. . GeLC-MS-based proteomics of Chromobacterium violaceum: comparison of proteome changes elicited by hydrogen peroxide. Scientific Reports, v. 6, p. 28174, 2016.

11. SANTANA, ALINE GUIMARÃES ; GRACHER, ANA HELENA PEREIRA ; RÜDIGER, ANDRÉ LUIS ; ZANCHIN, NILSON IVO TONIN ; Carvalho, Paulo Costa ; CIPRIANI, THALES RICARDO ; DE ARRUDA CAMPOS BRASIL DE SOUZA, TATIANA . Identification of potential targets for an anticoagulant pectin. Journal of Proteomics (Print), v. AOP, p. AOP, 2016.

12. NICOLAU, CAROLINA A. ; Carvalho, Paulo C. ; JUNQUEIRA-DE-AZEVEDO, INÁCIO L.M. ; TEIXEIRA-FERREIRA, ANDRÉ ; JUNQUEIRA, MAGNO ; Perales, Jonas ; NEVES-FERREIRA, ANA GISELE C. ; Valente, Richard H. . An in-depth snake venom proteopeptidome characterization: Benchmarking Bothrops jararaca. Journal of Proteomics (Print), v. AOP, p. AOP, 2016.

13. DE AQUINO, PRISCILA F. ; Carvalho, Paulo Costa ; NOGUEIRA, FÁBIO C. S. ; da Fonseca, Clovis Orlando ; DE SOUZA SILVA, JÚLIO CESAR THOMÉ ; Carvalho, Maria da Gloria da Costa ; Domont, Gilberto B. ; ZANCHIN, NILSON I. T. ; Fischer, Juliana de Saldanha da Gama . A Time-Based and Intratumoral Proteomic Assessment of a Recurrent Glioblastoma Multiforme. Frontiers in Oncology, v. 6, p. AOP, 2016.

14. SANTOS, RENATA M. ; NOGUEIRA, FABIO C.S. ; BRASIL, ALINE A. ; Carvalho, Paulo C. ; LEPREVOST, FELIPE V. ; Domont, Gilberto B. ; ELEUTHERIO, ELIS C.A. . Quantitative proteomic analysis of the Saccharomyces cerevisiae industrial strains CAT-1 and PE-2. Journal of Proteomics (Print), v. AOP, p. AOP, 2016.

15. OLIVEIRA, CAMILA ; Carvalho, Paulo Costa ; ALVES, LYSANGELA RONALTE ; GOLDENBERG, SAMUEL . The Role of the Trypanosoma cruzi TcNRBD1 Protein in Translation. Plos One, v. 11, p. e0164650, 2016.

16. RABELO, KÍSSILA ; TRUGILHO, MONIQUE R.O. ; COSTA, SIMONE M. ; PEREIRA, BERNARDO A.S. ; DA C. MOREIRA, OTACÍLIO ; FERREIRA, ANDRÉ T.S. ; Carvalho, Paulo C. ; Perales, Jonas ; ALVES, ADA M.B. . The effect of the dengue non-structural 1 protein expression over the HepG2 cell proteins in a proteomic approach. Journal of Proteomics (Print), v. AOP, p. AOP, 2016.

17. RABELO, KÍSSILA ; TRUGILHO, MONIQUE R.O. ; COSTA, SIMONE M. ; FERREIRA, ANDRÉ T.S. ; Carvalho, Paulo C. ; Perales, Jonas ; ALVES, ADA M.B. . Dataset of proteins mapped on HepG2 cells and those differentially abundant after expression of the dengue non-structural 1 protein. Data in Brief, v. AOP, p. AOP, 2016.

18. CARVALHO, CARLOS EDUARDO ; MCCORMICK, THAÍS MESSIAS ; Carvalho, Paulo Costa ; Fischer, Juliana de Saldanha da Gama ; AQUINO, PRISCILA FERREIRA DE ; BRAVO NETO, GUILHERME PINTO ; CARVALHO, MARIA DA GLÓRIA DA COSTA . Considerations about gastric cancer proteomics. Revista do Colégio Brasileiro de Cirurgiões (Online), v. 43, p. 395-397, 2016.

19. DA SILVA MENEGASSO, ANALLY RIBEIRO ; PRATAVIEIRA, MARCEL ; de Saldanha da Gama Fischer, Juliana ; Carvalho, Paulo Costa ; ROAT, THAISA CRISTINA ; MALASPINA, OSMAR ; PALMA, MARIO SERGIO . Profiling the proteomics in honeybee worker brains submitted to the proboscis extension reflex. Journal of Proteomics (Print), v. 151, p. 131-134, 2016.

20. BORGES, DIOGO ; B. LIMA, DIOGO ; B. DE LIMA, TATIANI ; S. BALBUENA, TIAGO ; C. NEVES-FERREIRA, ANA GISELE ; C. BARBOSA, VALMIR ; C. GOZZO, FABIO ; C. CARVALHO, PAULO . Using SIM-XL to identify and annotate cross-linked peptides analyzed by mass spectrometry. Nature Protocol Exchange, v. AOP, p. AOP, 2015.

21. BRUNORO, GISELLE VILLA FLOR ; Carvalho, Paulo Costa ; FERREIRA, ANDRÉ TEIXEIRA DA SILVA ; Perales, Jonas ; VALENTE, RICHARD HEMMI ; DE MOURA GALLO, CLAUDIA VITÓRIA ; PAGNONCELLI, DANTE ; NEVES-FERREIRA, ANA GISELE DA COSTA . Proteomic profiling of nipple aspirate fluid (NAF): Exploring the complementarity of different peptide fractionation strategies. Journal of Proteomics (Print), v. 117, p. 86-94, 2015.

22. CHAPEAUROUGE, ALEX ; REZA, MD ABU ; MACKESSY, STEPHEN P. ; Carvalho, Paulo C. ; Valente, Richard H. ; TEIXEIRA-FERREIRA, ANDRÉ ; Perales, Jonas ; LIN, QINGSONG ; KINI, R. MANJUNATHA . Interrogating the Venom of the Viperid Snake Sistrurus catenatus edwardsii by a Combined Approach of Electrospray and MALDI Mass Spectrometry. Plos One, v. 10, p. e0092091, 2015.

23. MELANI, RAFAEL D. ; ARAUJO, GABRIEL D.T. ; Carvalho, Paulo C. ; GOTO, LIVIA ; NOGUEIRA, FÁBIO C.S. ; JUNQUEIRA, MAGNO ; Domont, Gilberto B. . Seeing beyond the tip of the iceberg: A deep analysis of the venome of the Brazilian Rattlesnake, Crotalus durissus terrificus. EuPA Open Proteomics, v. AOP, p. AOP, 2015.

24. ALMEIDA, FABIANA GREYCE OLIVEIRA ; DE AQUINO, PRISCILA FERREIRA ; DE SOUZA, AFONSO DUARTE LEÃO ; DE SOUZA, ANTONIA QUEIROZ LIMA ; DO CARMO VINHOTE, SONIA ; MAC-CORMICK, THAÍS MESSIAS ; DA MOTA SILVA, MARCELO SOARES ; CHALUB, SIDNEY RAIMUNDO SILVA ; de Saldanha da Gama Fischer, Juliana ; Carvalho, Paulo Costa ; da Gloria da Costa Carvalho, Maria . Colorectal cancer DNA methylation patterns from patients in Manaus, Brazil. Biological Research, v. 48, p. 50, 2015.

25. LEPREVOST, FELIPE DA VEIGA ; BARBOSA, V. C. ; Carvalho, Paulo C . Using PepExplorer to Filter and Organize De Novo Peptide Sequencing Results. Current Protocols in Bioinformatics, v. 13, p. 1-9, 2015.

26. Carvalho, Paulo C.; PADRON, GABRIEL ; CALVETE, JUAN J. ; PEREZ-RIVEROL, YASSET . Computational proteomics: Integrating mass spectral data into a biological context. Journal of Proteomics (Print), v. 129, p. 1-2, 2015.

27. LIMA, DIOGO B. ; DE LIMA, TATIANI B. ; Balbuena, Tiago S. ; NEVES-FERREIRA, ANA GISELE C. ; Barbosa, Valmir C. ; GOZZO, FÁBIO C. ; Carvalho, Paulo C. . SIM-XL: A powerful and user-friendly tool for peptide cross-linking analysis. Journal of Proteomics (Print), v. 129, p. 51-55, 2015.

28. FISCHER, JULIANA DE S. DA G. ; DOS SANTOS, MARLON D.M. ; MARCHINI, FABRICIO K. ; Barbosa, Valmir C. ; Carvalho, Paulo C. ; ZANCHIN, NILSON I.T. . A scoring model for phosphopeptide site localization and its impact on the question of whether to use MSA. Journal of Proteomics (Print), v. 129, p. 42-50, 2015.

29. SANTANA, A. G. ; Carvalho, P.C. ; ZANCHIN, NILSON I.T. ; SOUZA, T. A. C. B. . A Method for Purifying Native Transthyretin from Human Plasma. Biochemistry & Pharmacology: Open Access, v. 4, p. 5, 2015.

30. SHAH, MOHIBULLAH ; SOARES, EMANOELLA L. ; Carvalho, Paulo C. ; SOARES, ARLETE A. ; Domont, Gilberto B. ; NOGUEIRA, FÁBIO C.S. ; CAMPOS, FRANCISCO A. P. . Proteomic Analysis of the Endosperm Ontogeny of Jatropha curcas L. Seeds. Journal of Proteome Research (Print), v. 14, p. 2557-2568, 2015.

31. Carvalho, Paulo C; LIMA, DIOGO B ; LEPREVOST, FELIPE V ; SANTOS, MARLON D M ; Fischer, Juliana S G ; AQUINO, PRISCILA F ; MORESCO, JAMES J ; Yates, John R ; Barbosa, Valmir C . Integrated analysis of shotgun proteomic data with PatternLab for proteomics 4.0. Nature Protocols (Print), v. 11, p. 102-117, 2015.

32. MOREIRA, CARLOS JC ; WANIEK, PETER J ; Valente, Richard H ; Carvalho, Paulo C ; Perales, Jonas ; FEDER, DENISE ; GERALDO, REINALDO B ; CASTRO, HELENA C ; AZAMBUJA, PATRICIA ; RATCLIFFE, NORMAN A ; MELLO, CÍCERO B . Isolation and molecular characterization of a major hemolymph serpin from the triatomine, Panstrongylus megistus. Parasites & Vectors, v. 7, p. 23, 2014.

33. Fischer, Juliana ; CANEDO, NATHALIE ; GONCALVES, KATIA ; CHIMELLI, LEILA ; FRANCA, MONIQUE ; LEPREVOST, FELIPE ; AQUINO, PRISCILA ; CARVALHO, PAULO ; CARVALHO, MARIA . Proteome Analysis of Formalin-Fixed Paraffin-Embedded Tissues from a Primary Gastric Melanoma and its Meningeal Metastasis: A Case Report. Current Topics in Medicinal Chemistry (Print), v. 14, p. 382-387, 2014.

34. PEREZ-RIVEROL, YASSET ; CARVALHO, PAULO . Editorial (Thematic Issue: Genomics and Proteomics behind Drug Design). Current Topics in Medicinal Chemistry (Print), v. 14, p. 343-343, 2014.

35. AQUINO, PRISCILA FERREIRA ; LIMA, DIOGO BORGES ; de Saldanha da Gama Fischer, Juliana ; MELANI, RAFAEL DONADÉLLI ; NOGUEIRA, FABIO C. S. ; CHALUB, SIDNEY R. S. ; SOARES, ELZALINA R. ; Barbosa, Valmir C. ; Domont, Gilberto B. ; Carvalho, Paulo C. . Exploring the Proteomic Landscape of a Gastric Cancer Biopsy with the Shotgun Imaging Analyzer. Journal of Proteome Research (Print), v. 13, p. 314-320, 2014.

36. MARTINS-DE-SOUZA, DANIEL ; Carvalho, Paulo C. ; SCHMITT, ANDREA ; JUNQUEIRA, MAGNO ; NOGUEIRA, FÁBIO C. S. ; TURCK, CHRISTOPH W. ; Domont, Gilberto B. . Deciphering the Human Brain Proteome: Characterization of the Anterior Temporal Lobe and Corpus Callosum As Part of the Chromosome 15-centric Human Proteome Project. Journal of Proteome Research (Print), v. 13, p. 147-157, 2014.

37. LEPREVOST, FELIPE DA VEIGA ; Barbosa, Valmir C. ; FRANCISCO, EDUARDO L. ; PEREZ-RIVEROL, YASSET ; Carvalho, Paulo C. . On best practices in the development of bioinformatics software. Frontiers in Genetics, v. 5, p. 199, 2014.

38. SOARES, EMANOELLA L. ; SHAH, MOHIBULLAH ; SOARES, ARLETE A. ; COSTA, JOSÉ HÉLIO ; Carvalho, Paulo C. ; Domont, Gilberto B. ; NOGUEIRA, FÁBIO C.S. ; CAMPOS, FRANCISCO A.P. . Proteome analysis of the inner integument from developing seeds of Jatropha curcas L.. Journal of Proteome Research (Print), v. AOP, p. 140710143825003, 2014.

39. LEPREVOST, F. V. ; VALENTE, R. H. ; LIMA, D. B. ; Perales, J. ; MELANI, R. ; Yates, J. R. ; BARBOSA, V. C. ; JUNQUEIRA, M. ; Carvalho, P. C. . PepExplorer: A Similarity-driven Tool for Analyzing de Novo Sequencing Results. Molecular & Cellular Proteomics, v. 13, p. 2480-2489, 2014.

40. LIMA, DANIEL C ; DUARTE, FÁBIO T ; MEDEIROS, VIVIANE ; LIMA, DIOGO B ; CARVALHO, PAULO ; BONATTO, DIEGO ; BATISTUZZO DE MEDEIROS, SILVIA R . The influence of iron on the proteomic profile of Chomobacterium violaceum. BMC Microbiology (Online), v. 14, p. 267, 2014.

41.Fischer, Juliana de Saldanha da Gama ; Carvalho, Paulo C. ; CANEDO, N. H. S. ; GONCALVES, K. M. S. ; AQUINO, PRISCILA FERREIRA ; ALMEIDA, B. ; PANNAIN, V. L. N. ; CARVALHO, M. G. C. . Applications of Formalin Fixed Paraffin-Embedded Tissue Proteomics in the Study of Cancer. Austin Proteomics, v. 1, p. 1-7, 2014.

42.BRUNORO, GISELLE VILLA FLOR ; CAMINHA, MARCELLE ALMEIDA ; DA SILVA FERREIRA, ANDRÉ TEIXEIRA ; DA VEIGA LEPREVOST, FELIPE ; Carvalho, Paulo Costa ; Perales, Jonas ; VALENTE, RICHARD HEMMI ; MENNA-BARRETO, RUBEM FIGUEIREDO SADOK . Reevaluating the Trypanosoma cruzi proteomic map: the shotgun description of bloodstream trypomastigotes. Journal of Proteomics (Print), v. AOP, p. AOP, 2014.

43.BORGES, D. ; PEREZ-RIVEROL, Y. ; NOGUEIRA, F. C. S. ; DOMONT, G. B. ; NODA, J. ; LEPREVOST, F. D. V. ; BESADA, V. ; FRANCA, F. M. G. ; BARBOSA, V. C. ; SANCHEZ, A. ; Carvalho, P. C. . Effectively addressing complex proteomic search spaces with peptide spectrum matching. Bioinformatics (Oxford. Print), v. EUP, p. EUP, 2013.

44.LEPREVOST, F.V. ; LIMA, D.B. ; CRESTANI, J. ; PEREZ-RIVEROL, Y. ; ZANCHIN, N. ; Barbosa, V.C. ; Carvalho, P.C. . Pinpointing differentially expressed domains in complex protein mixtures with the cloud service of PatternLab for Proteomics. Journal of Proteomics (Print), v. 89, p. 179-182, 2013.

45.PINHEIRO, CAMILA B. ; SHAH, MOHIBULLAH ; SOARES, EMANOELLA L. ; NOGUEIRA, FÁBIO C.S. ; Carvalho, Paulo C. ; JUNQUEIRA, MAGNO ; ARAÚJO, GABRIEL D. T. ; SOARES, ARLETE A ; Domont, Gilberto B. ; CAMPOS, FRANCISCO A.P. . Proteome Analysis of Plastids from Developing Seeds of Jatropha curcas L.. Journal of Proteome Research (Print), v. AOP, p. 130915105936003, 2013.

46.PEREZ-RIVEROL, YASSET ; SÁNCHEZ, ANIEL ; NODA, JESUS ; BORGES, DIOGO ; Carvalho, Paulo Costa ; WANG, RUI ; VIZCAÍNO, JUAN ANTONIO ; BETANCOURT, LÁZARO ; RAMOS, YASSEL ; DUARTE, GABRIEL ; NOGUEIRA, FABIO C.S. ; GONZÁLEZ, LUIS J. ; PADRÓN, GABRIEL ; TABB, DAVID L. ; HERMJAKOB, HENNING ; Domont, Gilberto B. ; BESADA, VLADIMIR . HI-Bone: A Scoring System for Identifying Phenylisothiocyanate-Derivatized Peptides Based on Precursor Mass and High Intensity Fragment Ions. Analytical Chemistry, v. 85, p. 3515-3520, 2013.

47.GONZÁLEZ-CABALLERO, NATALIA ; RODRÍGUEZ-VEGA, ANDRÉS ; DIAS-LOPES, GEOVANE ; VALENZUELA, JESUS G. ; RIBEIRO, JOSE M.C. ; Carvalho, Paulo Costa ; Valente, Richard H. ; BRAZIL, REGINALDO P. ; CUERVO, PATRICIA . Expression of the mevalonate pathway enzymes in the Lutzomyia longipalpis (Diptera: Psychodidae) sex pheromone gland demonstrated by an integrated proteomic approach. Journal of Proteomics (Print), v. 16, p. 117-132, 2013.

48.Crestani, Juliana ; Carvalho, Paulo Costa ; Han, Xuemei ; Seixas, Adriana ; Broetto, Leonardo ; Fischer, Juliana de Saldanha da Gama ; Staats, Charley Christian ; Schrank, Augusto ; Yates, John R. ; Vainstein, Marilene Henning . Proteomic Profiling of the Influence of Iron Availability on. Journal of Proteome Research (Print), v. 11, p. 189-205, 2012.

49.JUNQUEIRA, M. ; Carvalho, P. C. . Tools and challenges for diversity-driven proteomics in Brazil. Proteomics (Weinheim. Print), v. 12, p. 2601-2606, 2012.

50.Fonslow, Bryan R. ; Niessen, Sherry M. ; Singh, Meha ; Wong, Catherine C. L. ; Xu, Tao ; Carvalho, Paulo C. ; Choi, Jeong ; Park, Sung Kyu ; Yates, John R. . Single-Step Inline Hydroxyapatite Enrichment Facilitates Identification and Quantitation of Phosphopeptides from Mass-Limited Proteomes with MudPIT. Journal of Proteome Research (Print), v. NT, p. 120417132154005, 2012.

51.Carvalho, P. C.; Yates III, J. R. ; BARBOSA, V. C. . Improving the TFold test for differential shotgun proteomics. Bioinformatics (Oxford. Print), v. 28, p. 1652-1654, 2012.

52.Yates, John R ; Park, Sung Kyu Robin ; Delahunty, Claire M ; Xu, Tao ; Savas, Jeffrey N ; Cociorva, Daniel ; Carvalho, Paulo Costa . Toward objective evaluation of proteomic algorithms. Nature Methods, v. 9, p. 455-456, 2012.

53.Carvalho, Paulo C.; Balbuena, Tiago S. ; Yates, John R. ; Cociorva, Daniel ; Xu, Tao ; Perales, Jonas ; Fischer, Juliana S. G. ; Valente, Richard H. ; Barbosa, Valmir C. . Search engine processor: Filtering and organizing peptide spectrum matches. Proteomics (Weinheim. Print), v. 12, p. 944-949, 2012.

54.NICOLAU, CAROLINA A. ; TEIXEIRA-FERREIRA, ANDRÉ ; Carvalho, Paulo C. ; JUNQUEIRA, MAGNO ; Perales, Jonas ; NEVES, ANA GISELE -FERREIRA C. ; Valente, Richard H. . 227. Proteopeptidome Determination of Bothrops jararaca Venom: an Innovative Approach in Snake Venomics. Toxicon (Oxford), v. 60, p. 211-212, 2012.

55.DE AQUINO, P.F. ; Carvalho, P.C. ; DA GAMA FISCHER, J.S. ; DE SOUZA, A.Q.L. ; VIANA, J.S. ; CHALUB, S.R.S. ; DE SOUZA, A.D.L. ; CARVALHO, M.G.C. . Epstein-Barr virus DNA associated with gastric adenocarcinoma and adjacent non-cancerous mucosa in patients from Manaus, Brazil. Genetics and Molecular Research, v. 11, p. 4442-4446, 2012.

56.Carvalho, P. C.; FISCHER, J. S. G. ; Perales, J. ; Yates, J. R. ; BARBOSA, V. C. ; BAREINBOIM, E. . Analyzing marginal cases in differential shotgun proteomics. Bioinformatics (Oxford. Print), v. 27, p. 275-276, 2011.

57.de Saldanha da Gama Fischer, Juliana ; Costa Carvalho, Paulo ; da Fonseca, Clovis Orlando ; Liao, Lujian ; Degrave, Wim M. ; da Gloria da Costa Carvalho, Maria ; Yates, John R. ; Domont, Gilberto B. ; Carvalho, Paulo C . Chemo-Resistant Protein Expression Pattern of Glioblastoma Cells (A172) to Perillyl Alcohol. Journal of Proteome Research (Print), v. 10, p. 153-160, 2011.

58.Fonslow, Bryan R. ; Carvalho, Paulo C. ; Academia, Katrina ; Freeby, Steve ; Xu, Tao ; Nakorchevsky, Aleksey ; Paulus, Aran ; Yates, John R. . Improvements in Proteomic Metrics of Low Abundance Proteins through Proteome Equalization Using ProteoMiner Prior to MudPIT. Journal of Proteome Research (Print), v. 00, p. 110624111106081, 2011.

59.Rebello, Karina M. ; Barros, Juliana S.L. ; Mota, Ester M. ; Carvalho, Paulo C. ; Perales, Jonas ; Lenzi, Henrique L. ; Neves-Ferreira, Ana G.C. . Comprehensive proteomic profiling of adult Angiostrongylus costaricensis, a human parasitic nematode. Journal of Proteomics, v. 74, p. 1545-1559, 2011.

60.Barboza, Rodrigo ; Cociorva, Daniel ; Xu, Tao ; Barbosa, Valmir C. ; Perales, Jonas ; Valente, Richard H. ; França, Felipe M. G. ; Yates, John R. ; Carvalho, Paulo C. . Can the false-discovery rate be misleading?. Proteomics (Weinheim. Print), v. 11, p. 4105-4108, 2011.

61.Nishimura, Noriyuki ; Sarkeshik, Ali ; Nito, Kazumasa ; Park, Sang-Youl ; Wang, Angela ; Carvalho, Paulo C. ; Lee, Stephen ; Caddell, Daniel F. ; Cutler, Sean R. ; Chory, Joanne ; Yates, John R. ; Schroeder, Julian I. . PYR/PYL/RCAR family members are major in-vivo ABI1 protein phosphatase 2C-interacting proteins in Arabidopsis. Plant Journal, v. 61, p. 290-299, 2010.

62.Carvalho, P. C.; Han, X. ; Xu, T. ; COCIORVA, D. ; Carvalho, M. d. G. ; BARBOSA, V. C. ; Yates, J. R. . XDIA: improving on the label-free data-independent analysis. Bioinformatics (Oxford), v. 26, p. 847-848, 2010.

63.Fischer, Juliana de Saldanha da Gama ; Liao, Lujian ; Carvalho, Paulo C. ; Barbosa, Valmir C. ; Domont, Gilberto B. ; Carvalho, Maria da Gloria da Costa ; Yates III, John R. . Dynamic proteomic overview of glioblastoma cells (A172) exposed to perillyl alcohol. Journal of Proteomics, v. 73, p. 1018-1027, 2010.

64.Carvalho, P. C.; Yates III, John R. ; BARBOSA, V. C. . Analyzing shotgun proteomic data with PatternLab for proteomics. Current Protocols in Bioinformatics, v. 30, p. 13.13.1-13.13.1, 2010.

65.Moresco, James J. ; Carvalho, Paulo C. ; Yates III, John R. . Identifying components of protein complexes in C. elegans using co-immunoprecipitation and mass spectrometry. Journal of Proteomics, v. 73, p. 2198-2204, 2010.

66.Carvalho, Paulo C. ; Cociorva, Daniel ; Wong, Catherine C. L. ; Carvalho, Maria da Gloria da C. ; Barbosa, Valmir C. ; Yates, John R. ; Carvalho, Paulo C . Charge Prediction Machine: Tool for Inferring Precursor Charge States of Electron Transfer Dissociation Tandem Mass Spectra. Analytical Chemistry (Washington), v. 81, p. 1996-2003, 2009.

67.Carvalho, Paulo C; Fischer, Juliana S G ; Chen, Emily I ; Domont, Gilberto B ; Carvalho, Maria G C ; Degrave, Wim M ; Yates, John R ; Barbosa, Valmir C . GO Explorer: A gene-ontology tool to aid in the interpretation of spectral counting data in shotgun proteomics. Proteome Science, v. 7, p. 6, 2009.

68.Carvalho, P. C.; Xu, T. ; Han, X. ; COCIORVA, D. ; BARBOSA, V. C. ; Yates, J. R. . YADA: a tool for taking the most out of high-resolution spectra. Bioinformatics (Oxford), v. 25, p. 2734-2736, 2009.

69.Carvalho, P.C.; HEWEL, J. ; Barbosa, V.C. ; Yates III, J.R. . Identifying differences in protein expression levels by spectral counting and feature selection. Genetics and Molecular Research, v. 7, p. 342-356, 2008.

70.CARVALHO, PC; JUNQUEIRA, M. ; VALENTE, RH ; DOMONT, G. B. . Caititu: A tool to graphically represent peptide sequence coverage and domain distribution. Journal of Proteomics, v. 71, p. 486-489, 2008.

71.CARVALHO, PC; Fischer, Juliana SG ; Chen, Emily I ; Yates, John R ; Barbosa, Valmir C . PatternLab for proteomics: a tool for differential shotgun proteomics. BMC Bioinformatics, v. 9, p. 316, 2008.

72.FISCHER, J. S. G. ; Carvalho, Paulo C ; NEVES FERREIRA, A. G. ; ORLANDO, C. ; Perales JHA ; m.g.c.carvalho ; DOMONT, G. B. . Anti-thrombin is a prognostic biomarker candidate for patients with recurrent glioblastoma multiform under treatment with perillyl alcohol. Journal of Experimental Therapeutics & Oncology, v. 7, p. 285-290, 2008.

73.CARVALHO, PC; m.g.c.carvalho ; DEGRAVE, W. M. ; LILLA, S. ; NUCCI, G. ; FONSECA NETO, R. ; Spector, N ; MUSACCHIO, J. ; DOMONT, G. B. . Differential protein expression patterns obtained by mass spectrometry can aid in the diagnosis of Hodgkins disease. Journal of Experimental Therapeutics & Oncology, v. 6, p. 137-145, 2007.

74.CARVALHO, PC; FISCHER, J. S. G. ; BARBOSA, V. C. ; DEGRAVE, W. M. ; m.g.c.carvalho ; DOMONT, G. B. . Ellipsoid clustering machine: a front line to aid in disease diagnosis. RECIIS. Electronic Journal of Communication Information and Innovation in Health (English edition. Online), v. 1, p. 308-315, 2007.

75.FISCHER, J. S. G. ; CARVALHO, PC ; GATTASS, C. R. ; M.E.M. Paschoal ; SILVA, M. S. M. E. ; m.g.c.carvalho . Effect of perillyl alcohol and heat shock in human adenocarcinoma lung cells. Journal of Experimental Therapeutics & Oncology, v. 5, p. 301-307, 2006.

76.CARVALHO, PC; FREITAS, S. S. ; DEGRAVE, W. M. ; FONSECA NETO, R. ; CABELLO, P. H. . Personalized diagnosis by cached solutions with hypertension as a study model. Genetics and Molecular Research, v. 5, p. 856-867, 2006.

77.Carvalho, Paulo Costa; Fischer, Juliana de Saldanha da Gama ; Degrave, Wim M. ; Carvalho, Maria da Gloria da Costa . Marcadores séricos e espectrometria de massa no diagnóstico do câncer. Jornal Brasileiro de Patologia e Medicina Laboratorial (Impresso), v. 42, p. 431-436, 2006.

78.Carvalho, Paulo C; Glória, Rafael V ; de Miranda, Antonio B ; Degrave, Wim M . Squid - a simple bioinformatics grid. BMC Bioinformatics, v. 6, n.197, p. 197, 2005.

79.Carvalho, Paulo Costa; Fischer, Juliana de Saldanha da Gama ; SILVA, MARCELO SOARES DA MOTA E ; MUSACCHIO, JULIANE ; SPECTOR, NELSON ; DEGRAVE, WIM MAURITS ; Carvalho, Maria da Gloria da Costa . Detecção de potenciais marcadores moleculares séricos da doença de Hodgkin. Jornal Brasileiro de Patologia e Medicina Laboratorial (Impresso), v. 41, p. 165-168, 2005.

80.Fischer, Juliana de Saldanha da Gama ; SILVA, MARCELO SOARES DA MOTA E ; PASCHOAL, MARCOS EDUARDO ; GATTASS, CERLI ROCHA ; Carvalho, Paulo Costa ; Carvalho, Maria da Gloria da Costa . Efeito do álcool perílico na expressão gênica de células de adenocarcinoma de pulmão humano. Jornal Brasileiro de Pneumologia (Impresso), v. 31, p. 511-515, 2005.

81.REBELLO, ANDRÉ SOARES ; CARVALHO, MARIA DA GLÓRIA DA COSTA ; REBELLO, MARIA CHRISTINA SOARES ; Fischer, Juliana ; Carvalho, Paulo Costa ; CARVALHO, JOSÉ FRANCISCO DE OLIVEIRA . Detecção molecular da reativação simultânea de VZV e HSV em paciente com história clínica de roseola infantum. Jornal Brasileiro de Patologia e Medicina Laboratorial (Impresso), v. 39, p. 207-209, 2003.

 

Full papers published in conference proceedings

  1. Rossle SC, Carvalho PC, Dardarene LE, Bisch PM Development of a computational environment for protein structure prediction and functional analysis Anais do Segundo Workshop Brasileiro de Bioinformática, 2003. v.1. p.57 – 63 Macaé / RJ ** This work is also known as MholLine or Mhol3D - Click here for the full conference proceedings.

Book Chapters

  1. Fournier MV., Carvalho PC, Magee DD., Carvalho MGC. Section 3: Biomarkers and Clinical Proteomics In: BioArrays: From Basics to Diagnostics ed. : Humana Press, 2007 - Buy from Amazon

  2. Carvalho MGC,  Carvalho PC, Rebello MCS, Reação em cadeia pela polimerase In: Marcia Ramos e silva. (Org.). Semiologia e Métodos especiais em Dermatologia. Rio de Janeiro: Editora Atheneu, 2007. This book was awarded with the " Prêmio Jabuti 2009 for Life Sciences

Oral presentations in meetings

  1. PatternLab for proteomics in the Brazilian Society for Mass Spectrometry, 2106
  2. SIM-XL: a powerful and user-friendly tool for peptide cross-linking analysis, Pasteur Institute, Paris, France, April 2015
  3. Analyzing proteomes of unsequenced organisms : The B jararaca case., The Scripps Research Institute, La Jolla, California, USA, March 2014
  4. Analyzing proteomes of unsequenced organisms : The B jararaca case., Federal University of Ceará, Fortaleza - Brazil, February 2014
  5. Computational strategy for analyzing proteomes of unsequenced organisms, BrMass V meeting at Campinas - SP, December 2013
  6. Statistical Validation of proteomic data, Workshop on advanced topics in proteomics, Instituto Oswaldo Cruz, November 30th, 2013.
  7. From mass spectrometry to differential proteomics, Centro de estudos do Instituto Oswaldo Cruz, Rio de Janeiro - RJ - Brazil, on May 4th, 2012
  8. Advanced topics in mass spectrometry and bioinformatics applied to proteomics, BrMass IV workshop, Campinas, São Paulo, SP - Brazil, December 13th 2011
  9. Analyzing shotgun proteomic data with PatternLab for proteomics,Proteomic approaches for systems biology at Butantan Institute, São Paulo, SP, September 23, 2011
  10. Challenges in analyzing shotgun proteomic data, Workshop entitled "From Omics to Systems Biology", XXX Thematic Workshop CAT / cepid, Butantan Institute, São Paulo, SP, September 22, 2011
  11. Can the false discovery rate provide misleading results when analyzing shotgun proteomic data?, Conference for the Brazilian Society for Genetics (SBG), Aguas de Lindoia - SP, September 2nd, 2011
  12. Computational strategies and challenges for analyzing shotgun proteomic data, Seminars from the Center of Biotecnology of the Federal University of Rio Grande do Sul, Rio Grande do Sul, July 2011
  13. PatternLab, a pipeline for shotgun proteomics, IV Forum de Proteomica do Rio de Janeiro, Rio de Janeiro, 2010
  14. Analyzing shotgun proteomic data. Sociedade Brasileira de Bioquímica e Biologia Molecular, Foz do Iguaçu, 2010.
  15. A next generation label-free strategy for analyzing complex peptide mixtures, BRMass III, Campinas, November 2009.
  16. A strategy to automatically infer precursor charge states of electron transfer dissociation tandem mass spectra. Sociedade Brasileira de Bioquímica e Biologia Molecular, São Paulo, 2009.
  17. A novel strategy for diferential proteomics by spectral counting and statistical learning, Sociedade Brasileira de Bioquímica e Biologia Molecular, Salvador BH, 2007
  18. Medical diagnosis through electrospray mass spectrometry and bioinformatics, Molecular Medicine, Crete 2005
  19. Inteligência Artificial e Espectrometria de Massa na Medicina In: FESBE 2005,  Modulo temático proteoma cancer, Aguas de Lindoia, Anais da FESBE 2005

Media

"Most Influential Authors in Computational Proteomics" Yasset Riverol - Computational Proteomics Blog, October 2013

"Tecnologia pode tornar Brasil cometitivo em proteômica", Planeta COPPE, July 2012

" Juntando as peças do quebra-cabeças", Ciência Hoje, June 2010.

" Ferramenta computacional a serviço da oncologia", Onconews, 2010

PodCast about the Charge Prediction Machine manuscript, Analytical Chemistry, Feb. 2009

PatternLab for differential shotgun proteomics, Journal of Proteome Research, 2008

"Engenharia da computação a serviço da Oncobiologia", Onconews, 2007

"Inteligencia Proteica", FAPESP News Agency (01/13/2006)

 

Participation in examination of dissertations / thesis (for MSc or PhD)

7. Candidate: Mohibullah Shah, Type: PhD, Title, "Proteome Analysis of developing seeds of Jatropha curacas L. (Euphorbiaceae)", Federal University of Ceará, Fortaleza, Brazil, 2014

6. Candidate: Claire da Silva Santos, Type: PhD, Title, "Avaliação do papel das células T CD8+ e análise proteômica nas biópsias de pacientes com leishmaniose cutânea localizada infectados por L. braziliensis.", Fiocruz - BA, 2013

5. Candidate: Paulo Ornellas de Souza, Type: MSc, Title, "Carcinoma epidermóide invasivo de pênis: subexpressão dos fragmentos C3 e C4 A/B do sistema complemento detectado no plasma pela plataforma proteômica ClinProt / MALDI / TOF", UERJ, August 2013

4. Candidate: Karen Soares Trinta, Type: PhD, Title "Análise Proteômica do Plasma de Pacientes com Hepatite C em Diferentes Fases da Infecção e Evolução da Doença.", Fiocruz, September 2012

3. Candidate: Juliana Crestani, Type: PhD, Title: "Influência da alteração dos níveis de ferro e cobre na fisiologia e patogenicidade de Cryptococcus gattii: uma visão proteômica", UFRGS, July 2011.

2. Candidate: Caio Ribeiro de Souza, Type: MSc, Title: "Redes neurais sem-peso aplicadas a categorização de mutações de resistencia de HIV-1", for the program of Systems Engineering and Computer Science of the Federal University of Rio de Janeiro, UFRJ, June 2011.

1. Candidate: Carlos Henrique Saraiva Garcia, Type:MSc, Title: "Identificação de proteínas da linhagem celular HCC1954", UFRJ, November 2010.

Supervisor of MSc and PhD students (MSc or PhD)

5. Milan Clasen, MSc studend, Fiocruz, (2017 -Ongoing)

4. Felipe da Veiga Leprevost, PhD candidate at Fiocruz - PR, (2015 concluded).

3. Diogo Borges Lima, Advisor during his MSc at the Systems Engineering and Computer Science at COPPE, Federal University of Rio de Janeiro – Brazil (2013 - concluded),
 PhD advisor at the Carlos Chagas Institute, Fiocruz – Paraná (2016 - concluded).

2. Priscila Ferreira de Aquino, Advisor during her MSc in Biochemistry, Federal University of the Amazon - Brazil (concluded),
   Current PhD candidate at the Institute of Chemistry, UFRJ, ongoing.

1. Rodrigo de Moura Barboza, MSc in Systems Engineering and Computer Science at COPPE, Federal University of Rio de Janeiro - Brazil , concluded in 2011

Reviewer of the following journals:

  1. Nature Methods
  2. Journal of Proteome Research
  3. Bioinformatics
  4. Analytical Chemistry
  5. Plos One
  6. Briefings in Bioinformatics
  7. Rapid Communications in Mass Spectrometry
  8. BMC Bioinformatics
  9. Brazilian Journal of Medical and Biological Research

Reviewer of the funding agencies:

  1. National Centre for Research and Development  (Poland).
  2. Brazilian National Council for Research (CNPq)