Curriculum Vitae
Updated on June 2021


Paulo Costa Carvalho - CV

Paulo Costa Carvalho 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 (h-index 174) Laboratory at the Scripps Research Institute, California, EUA. Among his awards, we highlight the Google Award for Academic Excellence, the CAPES award for having his PhD thesis as one of the most prominent in Brazil, and, more recently, the Institute Pasteur Talent Award (2019). He is currently the head of the Laboratory for Structural and Computational Proteomics at Fiocruz Paraná; at Fiocruz, Paulo serves as a professor at the graduate level and mentors MSc and PhD students. Paulo published over 120 papers of which several of his first/last author ones being in journals such as Bioinformatics, 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 (pesquisador de produtividade CNPq). Paulo is a founding member of the Brazilian Society for Proteomics and a member of its scientific committee.  In October 2014, Paulo was nominated as an executive editor of the Journal of Proteomics which is the official journal of the European Proteomics Association.  Paulo has earned several national and international grants; some examples are CNPq Universal, Papes Jovem Cientista, Fiocruz Inova, and Microsoft Research. He also coordinates projects with the industry, examples being with Nitto Aveccia (USA), Nova Analítica (Brazil), and O Boticario (Brazil).


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. Institut Pasteur Talent Award (2019)
  2. Fleury Award – For the innovations described in DiagnoProt patent, 2018
  3. Features Panel member in Analytical Chemistry, 2016
  4. "Highly productive scientist award" from the Brazilian National Council for Research, (Pesquisador de produtividade Nivel 2 - CNPq), March 2014
  5. 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.
  6. 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.
  7. Best poster award in the MSc category with my MSc student Diogo Borges at the I Meeting of the Brazilian Proteomics Society, 2012,
  8. Best poster award in the PhD category with my PhD student Priscila Aquino at the I Meeting of the Brazilian Proteomics Society, 2012
  9. Best poster award in the Proteomics category, IV BrMass (Meeting of the Brazilian Society for Mass Spectrometry) , December 2011
  10. Young proteomic award (1st place), IV Proteomic Forum of Rio de Janeiro, November 4th 2010.
  11. Young Talent in Life Science 2009.
  12. Google Award for excellence in the PhD academic program / issued by Google university programs on December 2008.
  13. Fellowship awarded by CAPES (Brazilian Federal Agency for Support and Evaluation of Graduate Programs) to perform PhD research in Scripps from 2008 - 2009
  14. Best Work Award, I Symposium in Oncobiology at UFRJ, 2007
  15. Scholarship awarded during PhD by the “National Council for Scientific and Technological Development (CNPq)”, 2007-2010
  16. Scholarship awarded during MSc by the Oswaldo Cruz Institute, 2005-2006
  17. Award entitled “Best scientific work Oswaldo Cruz Institute 2005” at the Fiocruz bi-annual graduate scientific meeting


  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

5 selected publications out of 103.  For a full list of publications please refer to:  or


1.      LIMA, DIOGO B ; MELCHIOR, JOHN T ; MORRIS, JAMIE ; Barbosa, Valmir C ; CHAMOT-ROOKE, JULIA; FIORAMONTE, MARIANA ; SOUZA, TATIANA A C B ; Fischer, Juliana S G ; GOZZO, FABIO C ; DAVIDSON, W SEAN; Carvalho, Paulo C ;. Characterization of homodimer interfaces with cross-linking mass spectrometry and isotopically labeled proteins. Nature Protocols, v. 13, p. 431-458, 2018.

2.      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.

3.      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

4.      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..


5.      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.

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

Supervisor of MSc and PhD students (MSc or PhD)

9 Marlon Dias Mariano dos Santos, PhD student (2019 - )

8 Milan Clasen, PhD student (2019 -)

7 Louise Kurt, MSc student (2018 - )

6. Marlon dias Mariano dos Santos, MSc student (2018 – 2019)

5. Milan Clasen, MSc student, Fiocruz, (2017 -2019)

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)