Curriculum Vitae
Updated on January 2016

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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, 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

Full papers published in peer reviewed journals

63. Paulo C Carvalho, Diogo B Lima, Felipe V Leprevost1,3, Marlon D M Santos, Juliana S G Fischer, Priscila F Aquino, James J Moresco, John R Yates III, Valmir C Barbosa, Integrated analysis of shotgun proteomic data with PatternLab for proteomics 4.0, Nature Protocols 11 (2016), 102–117

62. John T. Melchior, Ryan G. Walker, Jamie Morris, Martin K. Jones, Jere P. Segrest, Diogo B. Lima, Paulo C Carvalho, Fabio C Gozzo, Mark Castleberry, Thomas B. Thompson, and W. Sean Davidson An evaluation of the Crystal Structure of C-Terminus Truncated Apolipoprotein A-I in Solution Reveals Structural Dynamics Related to Lipid Binding, Journal of Biological Chemistry, in press, 2016

61. Mohibullah Shah, Fabiano M Teixeira, Emanoella L Soares, Arlete A Soares, Paulo Costa Carvalho, Gilberto B Domont, Robert W Thornburg, Fabio C S Noegueira, Francisco A P Campos Time-course proteome analysis of developing extrafloral nectaries of Ricinus communis Proteomics, in press, 2016.

60. Rafael D. Melani, Gabriel D.T. Araujo, Paulo C. Carvalho, Livia Goto, Fábio C.S. Nogueira, Magno Junqueira, Gilberto B. Domont, Seeing beyond the tip of the iceberg: A deep analysis of the venome of the Brazilian Rattlesnake, Crotalus durissus terrificus, EuPA Open Proteomics, 8, 144-156, doi:10.1016/j.euprot.2015.05.006, 2015

59. Chapeaurouge A, Reza MA, Mackessy SP, Carvalho PC, Valente RH, Teixeira-Ferreira A, Perales J, Lin Q, Kini RM., Interrogating the Venom of the Viperid Snake Sistrurus catenatus edwardsii by a Combined Approach of Electrospray and MALDI Mass Spectrometry PLoS One. 8;10(5), doi: 10.1371/journal.pone.0092091, 2015

58. Aline G Santana, Paulo C Carvalho, Nilson IT Zanchin and Tatiana ACB Souza, A Method for Purifying Native Transthyretin from Human Plasma, Biochem Pharmacol, in press, 2015.

57. Mohibullah Shah, Emanoella Lima Soares, Paulo C. Carvalho, Arlete Aparecida Soares, Gilberto B. Domont, Fabio C.S. Nogueira, and Francisco A.P. Campos, Proteomic Analysis of the Endosperm Ontogeny of Jatropha curcas L. Seeds Journal of Proteome Research,14(6):2557-68. doi: 10.1021/acs.jproteome.5b00106, 2015.

56. Fabiana Greyce Oliveira Almeida, Priscila Ferreira de Aquino, Afonso Duarte Leão de Souza, Antonia Queiroz Lima de Souza, Sonia do Carmo Vinhote, Thaís Messias Mac-Cormick, Marcelo Soares da Mota Silva, Sidney Raimundo Silva Chalub, Juliana de Saldanha da Gama Fischer, Paulo Costa Carvalho, Maria da Gloria da Costa Carvalho, Colorectal cancer DNA methylation patterns from patients in Manaus, Brazil Biol Res; 48(1): 50, 2015

55. Fischer JSG, Santos, MDM, Marchini FK, Barbosa, VC, Carvalho, PC, Zanchin NIT, A scoring model for phosphopeptide site localization and its impact on the question of whether to use MSA. Journal of Proteomics, Ahead of Print, 2015.

54. Lima DB, Lima TB, Balbuena, TS, Neves-Ferreira AGC, Barbosa VC; Gozzo FC, Carvalho PC. SIM-XL: A powerful and user-friendly tool for peptide cross-linking analysis. Journal of Proteomics Ahead of print, 2015.

53. Lima DB, Lima TB, Balbuena, TS, Neves-Ferreira AGC, Barbosa VC; Gozzo FC, Carvalho PC. Using SIM-XL to identify and annotate cross-linked peptides analyzed by mass spectrometry. Nature Protocol Exchange, doi:10.1038/protex.2015.015, 2015.

52. Giselle Villa Flor Brunoro, Marcelle Almeida Caminha, André Teixeira da Silva Ferreira, Felipe da Veiga Leprevost, Paulo Costa Carvalho, Jonas Peralesa, Richard Hemmi Valente, Rubem Figueiredo Sadok Menna-Barreto, Reevaluating the Trypanosoma cruzi proteomic map: the shotgun description of bloodstream trypomastigotes, Journal of Proteomics v.6 58-65, 2015.

51. Felipe V. Leprevost, Richard H. Valente, Diogo L. Borges, Jonas Perales, Rafael Melani, John R. Yates III, Valmir C.Barbosa, Magno Junqueira, and Paulo C.Carvalho, PepExplorer: a similarity-driven tool for analyzing de novo sequencing results, Molcular and Cellular Proteomics 13(9):2480-9, 2014

50. Soares Emanoella, Shah Mohibullah, Soares Arlete, Costa José, Carvalho Paulo, Domont Gilberto, Nogueira Fábio, Campos Francisco, Proteome analysis of the inner integument from developing seeds of Jatropha curcas L, Journal of Proteome Research,;13(8):3562-70, 2014.

49. Felipe V. Leprevost, Valmir C. Barbosa, Eduardo L. Francisco, Yasset Perez-Riverol, and Paulo C. Carvalho, On best practices in the development of bioinformatics software, Frontiers in Genetics, Jul 2;5:199, 2014.

48. Moreira CJC, Waniek PJ, Valente RH, Carvalho PC, Perales J, Feder D, Geraldo RB, Castro HC, Azambuja P, Ratcliffe NA, Mello CB Isolation and molecular characterization of a major hemolymph serpin from the triatomine, Panstrongylus megistus Parasites & vectors, 7(1) pp. 1-16, 2014.

47. Perez-Riverol Y and Carvalho PC, Editorial: Genomics and Proteomics behind Drug Design, Current Topics in Medicinal Chemistry, v. 14, pp. 343-343, 2014.

46. 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, v.14 pp. 382-387, 2014.

45. MARTINS-DE-SOUZA, DANIEL*; Carvalho, Paulo C*. ; SCHMITT, ANDREA ; JUNQUEIRA, MAGNO ; NOGUEIRA, FÁBIO C.S. ; TURCK, CHRISTOPH W; DOMONT GB. 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, v. 13(1) pp. 147-157, 2014.

44. Aquino PF, Lima DB, Fischer JSG, Melani RD, Nogueira FCS, Chalub SRS, Soares ER, Barbosa VC, Domont GB, and Carvalho PC, Exploring the proteomic landscape of a gastric cancer biopsy with the Shotgun Imaging Analyzer. Journal of Proteome Research, v. 13(1) pp. 314-320, 2014.

43. González-Caballero N, Rodriguez-Vega A, Dias-Lopes G, Valenzuela JG, Ribeiro JMC, Carvalho PC, Valente RH, Brazil RP, Cuervo P. Expression of the mevalonate pathway enzyme in the Lutzomyia longipalpis (Diptera: Psychodidae) sex pherormone gland demonstrated by an integrated proteomic approach. Journal of Proteomics, v. 96, pp. 117-132, 2014.

42. Fischer JSG, Carvalho PC, Canedo NHS, da S Gonçalves KM, Aquino PF, et al. Applications of Formalin Fixed Paraffin-Embedded Tissue Proteomics in the Study of Cancer. A Proteomics. 2014;1(1): 7.

41. Chaves, DFS, Carvalho PC, Lima DB, Nicastro H, Lorenzeti FM, Filho MS, Hirabara SM, Alves PHM, Moresco JJ, Yates JR, Lancha AH. Comparative proteomic analysis of the aging soleus and extensor digitorum longus rat muscles using TMT labeling and mass spectrometry, Journal of Proteome Research, v12(10) pp. 4532-4546, 2013.

40. Pinheiro CB, Shah M, Soares EL, Nogueira FCS, Carvalho PC, Junqueira M, Araujo DTA, Soares AA, Domont, GB, Campos FAP. Proteome Analysis of Plastids from Developing Seeds of Jatropha curcas L., Journal of Proteome Research, v.12(11) pp. 5137-5145, 2013

39. 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, Journal of Proteomics v. 89 pp. 179-182, 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 29 (10): 1343-1344, 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, 85 (7), pp 3515-3520, 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, Proteopeptidomedetermination 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. BrazilianJournal 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. 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. SIM-XL: a powerful and user-friendly tool for peptide cross-linking analysis, Pasteur Institute, Paris, France, April 2015
  2. Analyzing proteomes of unsequenced organisms : The B jararaca case., The Scripps Research Institute, La Jolla, California, USA, March 2014
  3. Analyzing proteomes of unsequenced organisms : The B jararaca case., Federal University of Ceará, Fortaleza - Brazil, February 2014
  4. Computational strategy for analyzing proteomes of unsequenced organisms, BrMass V meeting at Campinas - SP, December 2013
  5. Statistical Validation of proteomic data, Workshop on advanced topics in proteomics, Instituto Oswaldo Cruz, November 30th, 2013.
  6. From mass spectrometry to differential proteomics, Centro de estudos do Instituto Oswaldo Cruz, Rio de Janeiro - RJ - Brazil, on May 4th, 2012
  7. Advanced topics in mass spectrometry and bioinformatics applied to proteomics, BrMass IV workshop, Campinas, São Paulo, SP - Brazil, December 13th 2011
  8. Analyzing shotgun proteomic data with PatternLab for proteomics,Proteomic approaches for systems biology at Butantan Institute, São Paulo, SP, September 23, 2011
  9. 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
  10. 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
  11. 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
  12. PatternLab, a pipeline for shotgun proteomics, IV Forum de Proteomica do Rio de Janeiro, Rio de Janeiro, 2010
  13. Analyzing shotgun proteomic data. Sociedade Brasileira de Bioquímica e Biologia Molecular, Foz do Iguaçu, 2010.
  14. A next generation label-free strategy for analyzing complex peptide mixtures, BRMass III, Campinas, November 2009.
  15. 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.
  16. A novel strategy for diferential proteomics by spectral counting and statistical learning, Sociedade Brasileira de Bioquímica e Biologia Molecular, Salvador BH, 2007
  17. Medical diagnosis through electrospray mass spectrometry and bioinformatics, Molecular Medicine, Crete 2005
  18. 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)

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
  9. Brazilian Journal of Medical and Biological Research

Reviewer of the funding agencies:

  1. National Centre for Research and Development  (Poland).

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)