Curriculum Vitae
Updated July 2010

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Personal Information

Name Paulo Costa Carvalho
Nationality Brazilian
E-mail 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)
Major in pattern recognition.  My final GPA was 3.0 out of 3.0

Thesis theme : Computational Proteomics / Pattern Recognition
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. Young Talent in Life Science 2009.
  2. Google Award for excellence in the PhD academic program / issued by Google university programs on December 2008.
  3. Fellowship awarded by CAPES (Brazilian Federal Agency for Support and Evaluation of Graduate Programs) to perform PhD research in Scripps from 2008 - 2009
  4. Best Work Award, I Symposium in Oncobiology at UFRJ, 2007
  5. Scholarship awarded during PhD by the “National Council for Scientific and Technological Development (CNPq)”, 2007-2010
  6. Scholarship awarded during MSc by the Oswaldo Cruz Institute, 2005-2006
  7. Award entitled “Best scientific work Oswaldo Cruz Institute 2005” at the Fiocruz bi-annual graduate scientific meeting

Societies

  1. Member of the International Society for Computational Biology (ISCB)
  2. Member of the Brazilian Society for Mass Spectrometry (BrMass).

Patents

  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 

  1. Moresco JJ, Carvalho PC, Yates JR III, Identifying components of protein complexes in C. elegans using co-immunoprecipitation and mass spectrometry, Journal of Proteomics, to appear.

  2. 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.

  3. 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

  4. 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.

  5. 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.

  6. 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.

  7. 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, Anal. Chem., 81 (5), pp 1996–2003, 2009.

  8. 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.

  9. 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.

  10. 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 .

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

  13. 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

  14. 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

  15. 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

  16. 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

  17. 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

  18. 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.

  19. 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.

  20. 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”

  21. 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, to appear.

  2. 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

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

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

  3. 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.

  4. A novel strategy for diferential proteomics by spectral counting and statistical learning, Sociedade Brasileira de Bioquímica e Biologia Molecular, Salvador BH, 2007

  5. Medical diagnosis through electrospray mass spectrometry and bioinformatics, Molecular Medicine, Creta 2005

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

  7. Rossle SC, Carvalho PC, Dardarene LE, Bisch PM: Development of a computational environment for protein structure prediction and functional analysis, Segundo Workshop Brasileiro de Bioinformática, 2003. v.1. p.57 – 63 Macaé / RJ

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)

Posters / Proceedings presented in Scientific Meetings

1. 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

1.    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

2.     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

3.     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

4.     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

5.     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

6.     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.

7.     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.

8.     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.

9.     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.

10.     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

11.     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

12.  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

13.  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

14.  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.

Experience as a reviewer

  1. 1 manuscript for Journal of Proteome Research
  2. 8 manuscripts reviewed for Bioinformatics
  3. 4 manuscript reviewed for Analytical Chemistry
  4. 1 manuscript reviewed for Briefings in 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

Licensed Softwares

  1. Carvalho PC, Gloria RV, Miranda AB, Degrave WM.
    Squid - a simple bioinformatics grid, 2005

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

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

Academics / Complementary

2001 – 2001

Short course in gas turbines, General Electric, GE, Brazil

2001 – 2001

Six Sigma - GreenBelt at GEAE - Ohio

2001 – 2001

Short course in ISO 9001 – for engineering services. General Electric Aircraft Engines, GEAE, Brazil

2002 – 2002

Short course in Genomic and post-genomic era in Medicine. National Academy of Medicine, ANM, Brazil

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, Brazil ,  2004

2004 – 2004

University extension course in Bioinformatics with major in Genomics, National Laboratory for Scientific Computation, LNCC, Petropolis, Brazil , 2004, Scholarship awarded by LNCC

2004 – 2004

University extension course in Bioinformatics with major in Proteomics, National Laboratory for scientific computation, LNCC/RJ, Brazil , 2004, – by LNCC

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

  1. Assistant professor for the course in Bioinformatics applied to Insects Genomes, September 6 - 17 2004, Instituto Oswaldo Cruz
  2. Collaborator of the graduate course in Introduction to Molecular Biology - Federal University of Rio de Janeiro 14/06/2004 – 25/06/2004