Curriculum Vitae
Updated December 2011
Personal Information
| Name | Paulo Costa Carvalho |
| Nationality | Brazilian |
| paulo at pcarvalho.com |
Academics
04/10 - present |
Post-doc at the Laboratory for Toxinology at the Oswaldo Cruz Institute. Working with computational proteomics. |
03/06 - 03/10 |
PhD student at the systems engineering and computer science program, COPPE, Federal University of Rio de Janeiro (UFRJ) 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. |
03/04 - 03/06 |
Masters in
Molecular and Cellular Biology with major in Bioinformatics - Instituto Oswaldo Cruz, - RJ Brasil |
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
Societies
Patent requests
Full papers published in peer reviewed journals
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, submitted.
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, ahead of print (DOI: 10.1021/pr2005296)
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
Abstracts published in indexed journals
Book Chapters
Carvalho PC, Yates JR III, Barbosa VC, Analyzing shotgun proteomics data with PatternLab for proteomics, Current Protocols in Bioinformatics, to appear.
FOURNIER, M. V., CARVALHO, P.
C., MAGEE, D. D., CARVALHO, M.G.C.
Section 3: Biomarkers and
Clinical Proteomics In: BioArrays: From
Basics to Diagnostics ed. : Humana Press, 2007 - Buy from Amazon
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
Media
"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)
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.
Posters / Short Communications in Proceedings of Scientific Meetings
18. SEPro: a tool for maximizing peptide sequence matches. Carvalho PC, Fischer JSG, Xu T, Cociorva D, Balbuena ST, Valente RH, Perales J, Yates JR III, Barbosa VC, In: BrMass IV - Meeting of the Brazilian Society for Mass Spectrometry, Campinas, December 2011.
17.Nicolau, C.A. ; Texeira-Ferreira, A. ; Beghini, D.G. ; Carvalho, P. C. ; JUNQUEIRA, M.; Perales, J. ; VALENTE, RH. OFFGEL technology for snake venom peptidomics - Bothropos Jararaca. In: Brazilian Society for Biochemistry (SBBq), 2011, Foz do Iguaçu. XL, 2011.
16. Han X, Carvalho PC, Xu T, Cociorva D, Carvalho MGC, Barbosa VC, Yates JR III, Extended Data-Independent Aquisition (XDIA): Improving on the label-free data-independent analysis, ASMS 2010
15. Crestani J, Carvalho PC, Fischer JSG, Liao L, Yates JR, III, Vainstein MH, Proteomics of Copper Deprivation in Cryptococcus gatti using 2D-PAGE and MudPIT, 110th General Meeting of the American Society for Microbiology, San Diego - California, 2010
14. 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. ASMS, Philadelphia, 2009
13. Carvalho PC, Fischer JSG, Chen EI, Barbosa VC, Yates JR, III, PatternLab: An integrated approach for analyzing spectral counting data, La Jolla Proteomics Conference, from Experiment to Computing, UCSD, San Diego CA, 2008
12. Carvalho PC, Fischer JSG, Domont GB, Carvalho MGC, Hewel J, Yates JR III, Barbosa VC, A novel strategy for diferential proteomics by spectral counting and statistical learning, Sociedade Brasileira de Bioquímica e Biologia Molecular, Salvador BH, 2007
11. Carvalho PC, Carvalho MGC, Degrave W, Lilla S, De Nucci G, Fonseca R, Spector N, Musacchio J, Domont GB, Maximum divergence analysis for MS data mining, American Association for Cancer Research annual meeting 2006, Washington DC, USA., Maio 2006
10. Carvalho PC, Carvalho MGC, Degrave W, Lilla S, De Nucci G, Fonseca R, Spector N, Musacchio J, Domont GB, Towards a cancer-free serum standard through electrospray mass spectrometry and bioinformatics Human Plasma Organisation, Munich, Germany, Setembro 2005
9. Carvalho PC, Carvalho MGC, Degrave W, Lilla S, De Nucci G, Fonseca R, Spector N, Musacchio J, Domont GB, Diagnosing Hodgkins disease by support vector machines and serum global proteomic profile obtained with ESI-MS. Sociedade Brasileira de Bioquimica e Biologia Molecular, Aguas de Lindoia - SP. 2005.
8. Leopoldino AM, Junqueira M, Domont GB, Carvalho PC, Azevedo JR, Tajara WF Clonagem, expressão e purificação da quinase dependente de ciclina 9 (CDK9) humana, Sociedade Brasileira de Genética, São Paulo / 2004.
7. Carvalho PC, De Nucci G, Carvalho MGC, Spector N, Degrave W, Musacchio J, Domont GB, Pattern Analysis of Sera from Healthy Controls and Hodgkins Disease Patients Obtained by Q-TOF Mass Spectrometry. American Association for Cancer Research - Advances in Proteomics in Cancer Research Conference Proceedings.(Miami / EUA), 2004.
6. Carvalho PC, Gloria RV, Tavares DM, Catanho M, Capriles PVSZ, Guimaraes ACR, Miranda AB, Degrave WM, Squid - A Simple Bioinformatics Grid, Segunda Escola de Modelagem Molecular em Sistemas Biológicos - LNCC, Petrópolis,. 2004.
5. Catanho M, Basilio A,. Carvalho PC, Degrave, W. MYCDB – Banco de dados de genes micobacterianos, IV Bienal de Pesquisa da Fundação Oswaldo Cruz, Dezembro de 2004
4. Henriques C; Souza RA; Lima LM; Carvalho PC; Godinho JL, Coutinho L; Degrave W. Análise da Disctribuição de D-prolina nas frações celulares de T.cruzi, IV Bienal de Pesquisa da Fundação Oswaldo Cruz, Rio de Janeiro, 2004
3. Carvalho PC, Carvalho MGC, Degrave W, Lilla S, De Nucci G, Spector, N, Musacchio J, Domont GB, Evidenciação de prováveis marcadores moleculares para a doença de Hodgkin localizada e disseminada em soro de pacientes. 38 Congresso Brasileiro de Patologia Clinica / Medicina Laboratorial, São Paulo 2004
2. Carvalho PC, Carvalho MGC, Degrave W, Abordagem de Bioinformática para Genotipagem Viral usando como modelo o Vírus do Papiloma Humano (HPV), Resumos de Temas Livres. , 2003. p.34 – 34 37 Congresso Brasileiro de Patologia Clinica / Medicina Laboratorial, Rio de Janeiro, 2003
1. Rossle SC, Carvalho PC, Ansuattigui JW, Bisch PM, Mhol3D: Ambiete Computacional para a aplicação de Metodos de Modelagem por Homologia em Genômica Estrutural, VI Jornada Científica - II Conferência Carlos Chagas Filho 40 anos da Pós-Graduação do Instituto de Biofísica Carlos Chagas Filho, IBCCF/UFRJ 2003.
Reviewer of the following journals:
Professional Experience
Licensed Softwares
Other meetings attended
1. HUPO USA 2009 (Human Plasma Organization)
2. American Society for Mass Spectrometry (ASMS) 2008
3. La Jolla Proteomics Conference, from Experiment to Computing, 2008.
4. American Association for Cancer Research Anual Meeting (2006)
5. BrMass Meeting / Campinas November 2005
6. Federal University of Rio de Janeiro's 1st meeting of Chemistry graduate students
7. Graduate scientific meeting Fiocruz 2005
8. International Congress of Bioinformatics – Angra dos Reis, Hotel do Frade, - Brazil 2004
9. II Workshop in Molecular Modeling and Biology, LNCC, Brazil 2004.
10. II Brazilian Workshop in Bioinformatics, Macaé, Brazil 2003.
11. IV Jornada Científica - II Conferência Carlos Chagas Filho 40 anos da Pós-Graduação do Instituto de Biofísica Carlos Chagas Filho, 2003
12. 37 Brazilian Congress of clinical pathology and laboratorial medicine, 2003.
13. II Brazilian Meeting of DNA Forensics Encontro Nacional de DNA Forense, 2002.
14. 36 Brazilian Congress of clinical pathology and laboratorial medicine, 2002.
Languages
Understands |
English (Fluent) , Portuguese (Fluent), Spanish (good) |
Speaks |
English (Fluent) , Portuguese (Fluent), Spanish (medium) |
Reads |
English (Fluent) , Portuguese (Fluent), Spanish (good) |
Writes |
English (Fluent) , Portuguese (Fluent), Spanish (poor) |
Programming Languages
Academics / Complementary
2001 – 2001 |
Short course in gas turbines, General Electric, GE,
|
2001 – 2001 |
Six Sigma - GreenBelt at GEAE - Ohio |
2001 – 2001 |
Short course in ISO 9001 – for engineering services. General Electric
Aircraft Engines, GEAE,
|
2002 – 2002 |
Short course in Genomic and post-genomic era in Medicine. National Academy
of Medicine, ANM,
|
2003 – 2003 |
Short course in forensics mathematics. Federal University of Rio de Janeiro, UFRJ, Rio De Janeiro, Brazil |
2004 – 2004 |
University extension course in Introduction to Proteomics. Federal University of Rio de Janeiro, UFRJ, Rio De Janeiro, Brazil |
2004 – 2004 |
University extension course in Artificial Intelligence. National Laboratory for Scientific
Computation, LNCC, Petropolis,
|
2004 – 2004 |
University extension course in Bioinformatics with major in Genomics,
National Laboratory for Scientific Computation, LNCC, Petropolis,
|
2004 – 2004 |
University extension course in Bioinformatics with major in Proteomics,
National Laboratory for scientific computation, LNCC/RJ,
|
2006 – 2006 |
International Course of Mass Spectrometry applied to Proteomics, Held by the Rio de Janeiro Proteomics Network and Ministrated by Dr. Peter Roepstorff |
Other relevant information