Curriculum Vitae
Updated May 2013

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Personal Information

Name Paulo Costa Carvalho
Nationality Brazilian
E-mail paulo at pcarvalho.com

Academics

2012-Present

I am a research scientist at the Carlos Chagas Institute, Fiocruz, Paraná, Brazil in the field of experimental and computational proteomics and professor of the graduate course "Analyzing proteomic data".

04/10 - 12/11

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

03/06 - 03/10

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 enviornment for proteomics.
Advisor: Valmir Carneiro Barbosa, Co-advisor: John R. Yates, III, Scholarship: CNPq

03/04 - 03/06

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. 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.
  2. Best poster award in the MSc category with my MSc student Diogo Borges at the I Meeting of the Brazilian Proteomics Society, 2012,
  3. Best poster award in the PhD category with my PhD student Priscila Aquino at the I Meeting of the Brazilian Proteomics Society, 2012
  4. Best poster award in the Proteomics category, IV BrMass (Meeting of the Brazilian Society for Mass Spectrometry) , December 2011
  5. Young proteomic award (1st place), IV Proteomic Forum of Rio de Janeiro, November 4th 2010.
  6. Young Talent in Life Science 2009.
  7. Google Award for excellence in the PhD academic program / issued by Google university programs on December 2008.
  8. Fellowship awarded by CAPES (Brazilian Federal Agency for Support and Evaluation of Graduate Programs) to perform PhD research in Scripps from 2008 - 2009
  9. Best Work Award, I Symposium in Oncobiology at UFRJ, 2007
  10. Scholarship awarded during PhD by the “National Council for Scientific and Technological Development (CNPq)”, 2007-2010
  11. Scholarship awarded during MSc by the Oswaldo Cruz Institute, 2005-2006
  12. 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).

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

Full papers published in peer reviewed journals 

40. Leprevost FV, Borges D, Crestani J, Perez-Riverol Y, Zanchin N, Barbosa VC, Carvalho PC. Pinpointing differentially expressed domains in complex protein mixtures with the cloud service of PatternLab for Proteomics, submitted, 2013. 

39. Fischer JSG, Canedo NHS, Gonçalves KMS, Chimelli MC, França M, Leprevost FV, Aquino PF, Carvalho PC, Carvalho MGC.  Proteome analysis of formalin-fixed paraffinn-embedd tissues from a primary gastric melanoma and its meningeal metastasis: a case report. Current Topics in Medicinal Chemistry, To appear, 2013.

38. Borges D, Perez-Riverol Y, Nogueira FCS, Domont GB, Noda J, Leprevost FV, Besada V, França FMG, Barbosa VC, Sanchez A, Carvalho PC.  Effectively addressing complex proteomic search spaces with peptide spectrum matching. Bioinformatics, Ahead of print, 2013.

37. Perez-Riverol Yasset, Sanchez A, Noda J, Borges D, Carvalho PC, Wang R, Vizcaíno JA, Betancourt LH, Ramos Y, Duarte G,  Nogueira FCS, Gonzales LJ, Padron G, Tabb DL, Hermjakob H, Domont GB, Besada V, HI-bone: A scoring system for identifying phenylisothiocyanate-derivatized peptides based on precursor mass and High Intensity fragment ions. Analytical Chemistry, Ahead of print, 2013.

36. Yates JR III, Sung KRP, Delahunty CM, Xu T, Savas JN, Cociorva D, Carvalho PC, Toward objective evaluation of proteomic algorithms., Nature Methods, (9) pp 445-456, 2012.

35. Aquino PF, Fischer JSG, Neves-Ferreira AGC, Perales J, Domont GB, Araujo GDT, Barbosa, VC, Viana J, Chalub SRS, Souza AQL, Carvalho MGC, Souza ADL, Carvalho PC, Are gastric cancer resection margin proteomic profiles more similar to those from controls or tumors? Journal of Proteome Research, 7;11(12):5836-42, 2012.

34. Carvalho PC, Fischer JSG, Yates JR III, Barbosa VC, PatternLab: From mass spectra to label-free differential shotgun proteomics., Current Protocols in Bioinformatics, Chapter 13:Unit13.19, 2012

 33. Nicolau CA, Teixeira-Ferreira A, Carvalho PC, Junqueira M, Perales, J, Neves-Ferreira AGC; Valente RH, Proteopeptidome determination of Bothrops jararaca venom: an innovative approach in snake venomics., Toxicon, (60) pp. 211-212, 2012.

32 Aquino, PF, Carvalho PC, Fischer JSG, Chalub A, Souza ADL, Carvalho MGC. Epstein-Barr virus DNA associated with gastric adenocarcinoma and adjacent non-cancerous mucosa in patients from Manaus, Brazil, Genetics and Molecular Research, 11(4):4442-6, 2012

31. Carvalho PC, Yates JR III, Barbosa VC, Improving the TFold test for differential shotgun proteomics, Bioinformatics, 15;28(12):1652-4, 2012.

30. Fonslow BR, Niessen SM, Wong CC, Xu T, Carvalho PC, Park SK, Yates JR III, Single-step inline hydroxyapatite enrichment for identification and quantitation of higher peptide phosphorylation states with MudPIT, Journal of Proteome Research, 11(5):2697-709, 2012.

29. Junqueira M, Carvalho PC, Tools and challenges for diversity driven proteomics in Brazil, Proteomics, 12(17): 2601-6, 2012.

28. Carvalho PC, Fischer JSG, Xu T, Cociorva D, Balbuena T, Valente RH, Perales J, Yates JR III, Barbosa VC, Search Engine Processor: filtering and organizing PSMs, Proteomics, 12(7):944-949, 2012.

27. Crestani J, Carvalho PC, Han X, Seixas A, Broetto L, Fischer JSG, Staats CC, Schrank A, Yates JR III, Vainstein MH, Proteomic profiling of the influence of iron availability on Cryptococcus gattii, Journal of Proteome Research, 11 (1), pp 189–205, 2012

26. Barboza R, Cociorva D, Xu T, Barbosa VC, Perales J, Valente RH, França FM, Yates JR III, Carvalho PC, Can the False Discovery Rate be Misleading?, Proteomics, Oct;11(20):4105-8, 2011

25. Fonslow BR, Carvalho PC, Academia K, Freeby S, Xu T, Nakorchevsky A, Paulus A, Yates JR III, Improvements in Proteomic Metrics of Low Abundance Proteins through Proteome Equalization Using ProteoMiner Prior to MudPIT, Journal of Proteome Research,10(8):3690-700, 2011

24. Rebello KM, Barroso JSL, Mota EM, Carvalho PC, Perales J, Lenzi HL, Neves-Ferreira AGC, Comprehensive proteomic profiling of adult Angiostrongylus costaricensis, a human parasitic nematode, Journal of Proteomics, 24;74(9):1545-5, 2011.

23. Carvalho PC, Fischer JSG, Perales JEA, Yates JR III, Barbosa VC, Bareinboim E, A statistical approach for analyzing marginal cases in shotgun proteomics, Bioinformatics, 27: 275-276, 2011.

22. CarvalhoPC*, Fischer JSG*, Fonseca CO, Liao L, Degrave WM, Carvalho MGC, Yater JR, Domont GB, A chemo-resistant protein expression pattern of glioblastoma cells (A172) to perillyl alcohol, Journal of Proteome Research, 10(1):153-160, 2011

21. Moresco JJ, Carvalho PC, Yates JR III, Identifying components of protein complexes in C. elegans using co-immunoprecipitation and mass spectrometry, Journal of Proteomics, 73(11):2198-204, 2010.

20. Carvalho PC, Yates, JR III, Barbosa VC, Analyzing shotgun proteomic data with PatternLab for proteomics, Current Protocols in Bioinformatics, 13.13.1-13.13.15, 2010.

19. Carvalho PC, Han X, Xu T, Cociorva D, Carvalho MGC, Barbosa VC, Yates, JR III, XDIA: Improving on the label-free data-independent analysis, Bioinformatics., 26: pp. 847-848, 2010

18. Fischer JSG, Lujian Liau, Carvalho PC, Barbosa VC, Domont GB, Carvalho MGC, Yates JR, III. Dynamic proteomic analysis of the membrane enriched fraction of glioblastoma cells (A172) exposed to perillyl alcohol. Journal of Proteomics, 73 (2010), 1018–1027.

17. Nishimura N, Sarkeshik A, Nito K, Park S, Wang A, Carvalho PC, Lee S, Cutler SR, Chory J, Yates, JR III, and Schroeder JI, Identification of PYR/PYL/RACR family members as major in vivo ABI1 protein phosphatase 2C-interacting proteins in Arabidopsis. Plant Journal, 61(2):290-9, 2010.

16. Carvalho PC, Xu T, Han X, Cociorva D, Barbosa VC, Yates JR, III. YADA: A tool for taking the most out of high resolution mass spectra. Bioinformatics, 25: 2734-2736, 2009.

15. Carvalho PC, Cociorva D, Wong C, Carvalho MGC, Barbosa VC, Yates JR, III. Charge Prediction Machine: A tool for inferring precursor charge states of Electron Transfer Dissociation tandem mass spectra, Analytical Chemistry, 81 (5), pp 1996–2003, 2009.

14. Carvalho PC, Fischer JSG, Chen EI, Domont GB, Carvalho MGC, Degrave WM, Yates JR III, Barbosa VC. GO Explorer: A gene-ontology tool to aid in the interpretation of spectral counting data in shotgun proteomics, Proteome Science 2009, 7:6., Flagged as highly accessed.

13. Carvalho PC, Fischer JSG, Chen E, Yates JR III, Barbosa VC. PatternLab for proteomics: a tool for differential shotgun proteomics, BMC Bioinformatics 9:316, 2008 - Flagged as highly accessed.

12. Carvalho PC, Junqueira M, Valente RH, Domont GB.  Caititu: a tool to graphically represent peptide sequence coverage and domain distribution, Journal of Proteomics, 71(2008) 486-489.

11. Fischer JSG, Carvalho PC, Neves Ferreira AG, Orlando C, Perales JHA, Carvalho MGC, Domont GB. Anti-thrombin is a prognostic biomarker candidate for patients with recurrent glioblastoma multiform under treatment with perillyl alcohol, Journal of Experimental and Therapeutics Oncology, 7:4 p.285-290, 2008 .

10. Carvalho PC, Hewel J, Barbosa VC, Yates JR III. Identifying differences in protein expression levels by spectral counts and feature selection, Genetics and Molecular Research 7 (2): 342-356, 2008

9. Carvalho PC, Fischer JSG, Barbosa VC, Carvalho MGC, Degrave W, Barbosa GD. Ellipsoid clustering machine: a front line to aid in disease diagnosis, RECIIS –R. Eletr. de Com. Inf. Inov. Saúde. Rio de Janeiro, v.1, n.2, Sup. 1, p. Sup309-Sup316, Jul-Dec, 2007

8. Carvalho PC, Carvalho MGC, Degrave W, Lilla S, De Nucci G, Fonseca R, Spector N, Musacchio J Domont GB. Differential protein expression patterns obtained by mass spectrometry can aid in the diagnosis of Hodgkins disease. Journal of Experimental Therapeutics and Oncology. v.6(2). p. 137-45, 2007

7. Carvalho PC, Freitas SS, Lima AB, Barros M, Bittencourt I, Degrave W, Cordovil I, Fonseca R, Neto RM, Cabello PH. Personalized diagnosis by cached solutions with hypertension as a study model. Genetics and Molecular Research, 5 (4): 856-867, 2006

6. Fischer JSG, Carvalho PC, Gattass CR, Paschoal ME, Silva MSM, Carvalho MGC.  Effect of perillyl alcohol and heat shock in human adenocarcinoma lung cells: Journal of Experimental and Therapeutics Oncology 2006 5(4) p 301-307

5. Carvalho PC, Fischer JSG, Degrave W, Carvalho MGC. Serum markers and mass spectrometry in the diagnosis of cancer (Review). Brazilian Journal of Pathology and Laboratorial Medicine, v. 46 n.6 p 431-446. 2006

4. Carvalho PC, Fischer JSG, Silva MSM, Musacchio J, Spector N, Degrave WM, Carvalho MGC. Detection of potential serum molecular markers for Hodgkin’s disease. Brazilian Journal of Pathology and Laboratorial Medicine. v.41; p.165 - 168, 2005.

3. Fischer JSG, Silva MSM, Paschoal ME, Gattass CR, Carvalho PC, Carvalho MGC.
Efeito do álcool perílico na expressão gênica de células de adenocarcinoma de pulmão humano. Brazilian Journal of Pneumology. V.31; p. 373-81, 2005.

2. Carvalho PC, Gloria RV, Miranda AB, Degrave WM. Squid - a simple bioinformatics grid. BMC Bioinformatics, v.6, n.197, 2005.  “flagged as highly accessed according to BMC”

1. Rebello AS, Carvalho MGC, Rebello MCS, Carvalho PC, Fischer JSG, Carvalho JFO. Detecção molecular da reativação simultânea de VZV e HSV em paciente com história clínica de roseola infantum. Brazilian Journal of Pathology and Laboratorial Medicine. v.39, n.3, 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.

Abstracts published in indexed journals

  1. Domont GB, Carvalho PC, De Nucci G, Spector N, Lilla S., Carvalho MGC, Musacchio J, Toward a Cancer-free Serum Standard through Electrospray Mass Spectrometry and Bioinformatics. Molecular and Cellular Proteomics, v.4, p.S88 - , 2005

  2. Carvalho PC, De Nucci G, Spector N, Lilla S, Carvalho MGC, Musacchio J, Domont GB Medical Diagnosis through Electrospray Mass Spectrometry and Bioinformatics
    International Journal of Molecular Medicine, v.16: Supplement 1, October 2005

Book Chapters

  1. Carvalho PC, Yates JR III, Barbosa VC, Analyzing shotgun proteomics data with PatternLab for proteomics, Current Protocols in Bioinformatics, Current Protocols in Bioinformatics; Chapter 13.13. 2010.

  2. 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

  3. 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. From mass spectrometry to differential proteomics, Centro de estudos do Instituto Oswaldo Cruz, Rio de Janeiro - RJ - Brazil, on May 4th, 2012

  2. Advanced topics in mass spectrometry and bioinformatics applied to proteomics, BrMass IV workshop, Campinas, São Paulo, SP - Brazil, December 13th 2011

  3. Analyzing shotgun proteomic data with PatternLab for proteomics,Proteomic approaches for systems biology at Butantan Institute, São Paulo, SP, September 23, 2011

  4. 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

  5. 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
  6. 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

  7. PatternLab, a pipeline for shotgun proteomics, IV Forum de Proteomica do Rio de Janeiro, Rio de Janeiro, 2010

  8. Analyzing shotgun proteomic data. Sociedade Brasileira de Bioquímica e Biologia Molecular, Foz do Iguaçu, 2010.

  9. A next generation label-free strategy for analyzing complex peptide mixtures, BRMass III, Campinas, November 2009.

  10. 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.

  11. A novel strategy for diferential proteomics by spectral counting and statistical learning, Sociedade Brasileira de Bioquímica e Biologia Molecular, Salvador BH, 2007
  12. Medical diagnosis through electrospray mass spectrometry and bioinformatics, Molecular Medicine, Crete 2005

  13. Inteligência Artificial e Espectrometria de Massa na Medicina In: FESBE 2005,  Modulo temático proteoma cancer, Aguas de Lindoia, Anais da FESBE 2005. 

Media

"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)

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.", 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", 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, June 2011.

1. Candidate: Carlos Henrique Saraiva Garcia, Type:MSc, Title: "Identificação de proteínas da linhagem celular HCC1954", for the program of Biochemistry of the Federal University of Rio de Janeiro, November 2010.

Advisory of post-graduate students (MSc or PhD)

4. Felipe da Veiga Leprevost, PhD candidate at Fiocruz - PR, ongoing.

3. Diogo Borges Lima, Advisor during his MSc at the Systems Engineering and Computer Sciente at COPPE, Federal University of Rio de Janeiro - Brazil,
    Current PhD advisor at the Carlos Chagas Institute, Fiocruz - Paraná

2. Priscila Ferreira de Aquino, Advisor durint 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

Professional Experience

  1. General Electric Aircraft Engines – GEAE * Ohio / EUA and Petrópolis / Brazil
    2001 – 2002 - Worked as an engineer and performed reverse engineering from various turbine parts for creating new repair protocols

  2. Coflexip – COFLEXIP Offshore
    2001 – 2001 - Worked as an engineer designing accessories for flexible tubes that connect petroleum platforms with the ocean bed
  3. Pontificia Universidade Católica – Laboratory of Electromagnetism
    97.2 - Worked as a lab assistant in the Electromagnetism Physics laboratory

Programming Languages

  1. C# (Advanced)
  2. Perl - (Advanced)
  3. Java (Advanced)