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Last update:: 17 - November - 2011

my websites

Comparing Partitions - a web site usefull for finding correspondences between diferent partitions on a dataset, namely the application of different typing methods to a collection of bacterial isolates

PHYLOViZ - Phylogenetic inference and data visualization for sequence based typing methods

goeBURST - a globally optimized implementation of the eBURST algorithm.

ccrB typing - infering SCCmec type through the sequencing of ccrB gene.

Molecular Microbiology and Infection Unit - my research group wiki



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Biography

Full Name: João André Nogueira Custódio Carriço
Degree: Applied Chemistry, Biotechnology - FCT/UNL
               PhD in Biology:"New perspectives in Microbial Typing"
Email: jcarrico_at_fm.ul.pt (replace _at_ by @)
Work phone:+ 351 21 799 94 58 ext 47212

Current Position

Researcher
Molecular Microbiology and Infection Unit, Instituto de Medicina Molecular
Instituto de Microbiologia,Faculdade de Medicina de Lisboa, Universidade de Lisboa

Invited Researcher
Knowledge Discovery and Bioinformatics group (KDBIO)
Instituto de Engenharia de Sistemas e Computadores: Investigação e Desenvolvimento (INESC-ID), Location:Google Earth KMZ


Research Interests

Biology : Population Evolutionary Genetics, Molecular Epidemiology, Microbial Typing methods
Mathematics : Mathematical Modeling of Biological System Dynamics, Univariate/Multivariate Data Analysis
Informatics : , Data Mining, Database Management: Postgresql,MySQL, Linked Data and Semantic Web, Web-Based Interfaces: PHP and HTML/CSS, RESTful webservices.

Publications in Peer Reviewed Journals

* Authors contributed equally to the work
  1. Carreiro, A.V., Anunciação, O. Carriço J.A., Madeira S.C.: (2011) Prognostic Prediction through Biclustering-Based Classification of Clinical Gene Expression Time Series. J Integr Bioinform. 2011 Sep 15;8(3):175. doi: 10.2390/biecoll-jib-2011-175.PubMed Abstract
  2. Severiano A., F. R. Pinto, M. Ramirez, and J. A. Carriço. 2011. Adjusted Wallace as a measure of congruence between typing methods. J Clin Microbiol. 2011 Nov;49(11):3997-4000. Epub 2011 Sep 14.. PubMed Abstract
  3. Severiano A, Carriço JA, Robinson DA, Ramirez M, Pinto FR (2011) Evaluation of Jackknife and Bootstrap for Defining Confidence Intervals for Pairwise Agreement Measures. PLoS ONE 6(5): e19539. doi:10.1371/journal.pone.0019539
  4. Sá-Leão R., F. Pinto, S. I. Aguiar, S. Nunes, J. A. Carriço, N. Frazão, N. Gonçalves-Sousa, J. Melo-Cristino, H. de Lencastre, and M. Ramirez. 2011. Invasiveness of pneumococcal serotypes and clones circulating in Portugal before widespread use of conjugate vaccines revealing heterogeneous behavior of clones expressing the same serotype. J Clin Microbiol. in press
  5. Alexandra S. Simões, Raquel Sá-Leão, Marc J. Eleveld, Débora A. Tavares, João A. Carriço, Hester J. Bootsma, and Peter W.M. Hermans Highly penicillin-resistant multidrug-resistant pneumococcus-like strains colonizing children in Oeiras, Portugal: genomic characteristics and implications for surveillance
  6. Francisco AP, Bugalho M, Ramirez M, Carriço JA., Global Optimal eBURST analysis of Multilocus typing data using a graphic matroid approach,BMC Bioinformatics 2009, 10:152doi:10.1186/1471-2105-10-152 Abstract
  7. Duarte C. Oliveira,Mauro Santos,Catarina Milheiriço, João A. Carriço, Susana Vinga, Arlindo L. Oliveira and Hermínia de Lencastre, ccrB typing tool: an online resource for stapylococci ccrB sequence typing,J Antimicrob Chemother. 2008 Apr;61(4):959-60. Epub 2008 Jan 27, doi:10.1093/jac/dkn021
  8. Nuno A. Faria*, João A. Carriço*, Duarte C. Oliveira, Mário Ramirez and Hermínia de Lencastre, Analysis of typing methods for epidemiological surveillance of both methicillin-resistant and susceptible Staphylococcus aureus,J Clin Microbiol. 2008 Jan;46(1):136-144. PubMed Abstract
  9. Miragaia, M., João A. Carriço, J. C. Thomas, I. Couto, 5, M. C. Enright, and and Hermínia de Lencastre, Comparison of molecular typing methods for characterization of Staphylococcus epidermidis: a proposal for clone definition ,J Clin Microbiol. 2008 Jan;46(1):118-129. PubMed Abstract
  10. Raquel Sá-Leão*, Sónia Nunes1,*, António Brito-Avô, Carla R. Alves, João A. Carriço, Joana Saldanha, Jonas S. Almeida, Ilda Santos-Sanches, and Hermínia de Lencastre, High dynamics of transmission and colonization by Streptococcus pneumoniae and Haemophilus influenzae within a day-care center revealed in a longitudinal study ,J Clin Microbiol. 2008 Jan;46(1):225-234. PubMed Abstract
  11. Francisco R. Pinto, João A. Carriço, Mário Ramirez and Jonas S Almeida,Ranked Adjusted Rand: integrating distance and partition information in a measure of clustering agreement, BMC Bioinformatics 2007, 8:44 (07 Feb 2007) Full paper
  12. Almeida JS, C Chen, R Gorlitsky, R Stanislaus, M Aires-de-Sousa, P Eleutério, JA Carriço, A Maretzek, A Bohn, A Chang, F Zhang, R Mitra, GB Mills, X Wang, HF Deus (2006) Data integration gets 'Sloppy'. Nature Biotechnology (9):1070-1071.Pubmed Abstract
  13. Carriço, J.A.; C. Silva-Costa; J. Melo-Cristino; F. R. Pinto; H. de Lencastre; J.S.Almeida; M.Ramirez, Illustration of a Common Framework for Relating Multiple Typing Methods by Application to Macrolide-Resistant Streptococcus pyogenes, J Clin Microbiol. 2006 Jul;44(7):2524-32 Pubmed Abstract
  14. Mato R, Sanches IS, Simas C, Nunes S, Carrico JA, Sousa NG, Frazao N, Saldanha J, Brito-Avo A, Almeida JS, Lencastre HD.Natural History of Drug-Resistant Clones of Streptococcus pneumoniae Colonizing Healthy Children in Portugal.Microb Drug Resist. 2005 Winter;11(4):309-22. Pubmed Abstract
  15. Carriço, J.A. , F.R. Pinto, C. Simas, S. Nunes, N. G. Sousa, N. Frazão, H. de Lencastre, and J.S. Almeida. 2005. Assessment of band-based similarity coefficients for automatic Type/Subtype classification of microbial isolates analyzed by Pulsed-Field Gel Electrophoresis. J Clin Microbiol. 2005 Nov;43(11):5483-90. Pubmed Abstract
  16. Sousa N. G., R. Sá-Leão, M.I. Crisóstomo, C. Simas, S. Nunes, N. Frazão, J. Carriço, R. Mato, I. Santos-Sanches, and H. de Lencastre. 2005. Properties of novel international drug-resistant pneumococcal clones identified in day-care centers (DCCs) of Lisbon, Portugal. J Clin Microbiol. 2005 Sep;43(9):4696-703. Pubmed Abstract
  17. I. Serrano, J. Melo-Cristino, J. Carriço and M. Ramirez, Characterization of the genetic lineages responsible for pneumococcal invasive disease in Portugal,J Clin Microbiol. 2005 Apr;43(4):1706-15.Pubmed Abstract
  18. Nelson Frazão; António Brito-Avô; Carla Simas; Joana Saldanha; Rosario Mato; Sónia Nunes; Natacha Gonçalves Sousa; João Carriço; Jonas Almeida; Ilda Santos-Sanches; Hermínia de Lencastre, Effect of the 7-valent conjugate pneumococcal vaccine on carriage and drug resistance of Streptococcus pneumoniae in healthy children attending day-care centers in Lisbon Pediatr Infect Dis J. 2005 Mar;24(3):243-52.Pubmed Abstract
  19. Nunes S, R Sá-Leão, J Carriço, CR Alves, R Mato, A Brito Avô, J Saldanha, JS Almeida, I Santos Sanches, and H de Lencastre (2005) Trends in drug resistance, serotypes and molecular types of Streptococcus pneumoniae colonizing pre-school age children attending day care centers in Lisbon, Portugal – a summary of four years of annual surveillance.J. Clin. Microbiol. 2005;43 1285-1293   JCM abstract
  20. Sara Silva, Rodrigo Gouveia-Oliveira, Antonio Maretzek, Joao Carrico,Thorolfur Gudnason, Karl G Kristinsson, Karl Ekdahl, Antonio Brito-Avo, Alexander Tomasz, Ilda S Sanches, Herminia de Lencastre and Jonas S Almeida.Web-based epidemiological surveillance of antibiotic-resistant pneumococci in Day Care Centers BMC Medical Informatics and Decision Making 2003, 3:9  Abstract
  21. Maria Miragaia, Isabel Couto, Sandro F. F. Pereira, Karl G. Kristinsson, Henrik Westh, Jens O. Jarløv, João Carriço, Jonas Almeida, Ilda Santos Sanches and Hermínia de Lencastre.Molecular Characterization of Methicillin Resistant Staphylococcus epidermidis (MRSE) Clones: Evidence of Geographic Dissemination J Clin Microbiol 2002 Feb;40(2):430-8 Pubmed Abstract
  22. Almeida, Jonas S.; Carriço, João A. ;Maretzek, António; Fletcher, Madilyn; Noble, Peter; "Analysis of genomic sequences by Chaos Game Representation", Journal of Bioinformatics, Vol.17 n.5 2001 pages 429-437 Pubmed Abstract
  23. Santos Sanches, I., R. Mato, H. de Lencastre, A. Tomasz, CEM/NET collaborators: S. Nunes, C. R. Alves, M. Miragaia, J. Carriço,I. Couto, I. Bonfim, M. A. de Sousa, D. Oliveira, A. Gomes, M. Vaz, S.Fernandes, S. C. Verde, S. ávila, F. Antunes, R. Sá-Leão, J. Almeida,and International collaborators: O. Melter, M. Chung, M. C.Brandileone, E. Castañeda, I. Heitmann, M. Hortal, W. Hryniewicz, F.Jia, K. Kikuchi, K. G. Kristinsson, J. Liñares, A. Rossi, E. Z. Savov,J. Schindler, F. Solorzano-Santos, K. Totsuka, M. Venditti, P. Villari,H. Westh, J. S. Wu, and R. C. Zanella. 2000. Patterns of multidrug resistance among methicillin-resistant hospital isolates of coagulase-positive and coagulase-negative staphylococci collected in the international multicenter study RESIST in 1997 and 1998. Microb. Drug Resist. 6:199-211.Pubmed Abstract

Publications in Peer Reviewed Conferences

  1. R. Aires, J. A. Carrico, A. P. Francisco, and S. C. Madeira Baiacu: A tool for the visual analysis of the saccharomyces cerevisiae regulatory network. In Practical Applications of Computational Biology & Bioinformatics, Advances in Intelligent and Soft Computing, 93 pp. 49-56. Springer, 2011
  2. A.V. Carreiro, O. Anunciacao, J.A. Carrico, S.C. Madeira. Biclustering-based Classication of Clinical Expression Time Series: A Case Study in Patients with Multiple Sclerosis. In: Proc. of the 5th International Conference on Practical Applications of Computational Biology & Bioinformatics (PACBB 2011) - Advances in Intelligent and Soft Computing, 93 pp. 229-239. Springer 2011
  3. J. Almeida, J. Tiple, M. Ramirez, J. Melo-Cristino, C. Vaz, A.P. Francisco, J.A.Carrico. An ontology and a REST API for sequence based microbial typing data. Proceedings of Xth Jornadas de Bioinformatica, Malaga, Spain 27-29 October 2010.
  4. A.P.Francisco, M. Bugalho, C. Vaz ,J. Melo-Cristino, M. Ramirez, J.A Carrico goeBURST software: a scalable platform for the data analysis, integration and visualization of sequence based typing methods data. Jornadas de Bioinformática, Lisboa, Portugal, 3-6 Novemer 2009.
  5. Carriço JA, A. Severiano, F.R. Pinto, J. Melo-Cristino, M. Ramirez. www.comparingpartitions.info - a web-tool for quantitative assessment of classification agreement. Jornadas de Bioinformática 2009, Lisboa, Portugal, 3-6 November 2009.
  6. João Carriço, Francisco Pinto, Mário Ramirez and Jonas Almeida fBURST: Enhancing eBURST with an information-theoretic similarity metric,BKDB2005 -Bioinformatics: Knowledge Discovery in Biology
  7. Tony Solomonides, Mohammed Odeh, Richard McClatchey,Jean-Marie Le Goff, João Carriço,Jonas Almeida.Conceptual Modelling of an Epidemiological Information System, IADIS International Conference e-Society 2003, ISBN:972-98947-0-1

Oral Presentations in Conferences, Meetings and Workshops

  1. Linked Data for Microbial Typing: Are we there yet?, Applied Bioinformatics & Public Health Microbiology Conference, Welcome Trust Genome Campus , Hinxton, Cambridge, United Kingdom, 1-3 June 2011.
  2. An Ontology and a REST API for Sequence based Microbial Typing Data, X Jornadas de Bioinformática, Málaga, October 27-29, 2010
  3. Increasing the confidence in the evaluation of congruence between microbial typing methods, 9th International Meeting on Microbial Epidemiological Markers - From genomes to tracing pathogens, Werningerode, Germany, September 1-4, 2010
  4. Phyloviz: an open-source platform for epidemiological data integration, analysis and visualization, 9th International Meeting on Microbial Epidemiological Markers - From genomes to tracing pathogens, Werningerode, Germany, September 1-4, 2010
  5. Bacterial clone definition using microbial typing methods: Advantages and caveats, Microbiotec 2009,Vilamoura, Portugal, November 28-30, 2009
  6. Exploring the relationship of strains characterized by sequence based typing methods using goeBURST algorithm, Microbiotec 2009,Vilamoura, Portugal, November 28-30, 2009
  7. www.comparingpartitions.info - a web-tool for the quantitative assessment of classification agreement, Jornadas de Bioinformática 2009, Lisboa, Portugal, 3-6 November, 1009
  8. goeBURST software: a scalable platform for the data analysis, integration and visualization of sequence based typing methods data,Jornadas de Bioinformática 2009, Lisboa, Portugal, 3-6 November, 2009
  9. OSTIS - Online Sequence-based typing Information System: A Flexible Online System for sequence-based typing methods , 8th international meeting on Microbial Epidemiological Markers, Zakopane, Poland, May 14-17, 2008
  10. Download Presentation Computer Assisted Analysis of Pulsed-field Gel Electrophoresis gels 40th ESCMID Postgraduate Education Course:Bacterial Molecular Typing – A Practical and Theoretical Course , Oeiras, 4 May 2007
  11. Quantitative Correspondence between Streptococcus pneumoniae typing methods results: how similar are Serotyping, Multi-Locus Sequence typing and Pulsed-Field Gel Electrophoresis type assignments? , 8th European Meeting on the Molecular Biology of the Pneumococcus (Europneumo) , Oeiras, 14 - 17 April
  12. Download Presentation Correspondence between typing methods results: a web-based quantitative analysis tool - 17th European Congress of Clinical Microbiology and Infectious Diseases (ECCMID) and 25th International Congress of Chemotherapy (ICC), Munich/Germany, 31 March - 3 April 2007
  13. The Project EURIS online database - Latest Advances in Molecular Fingerprinting Methods for Bacteria and the Construction of Computer Databases ENEMTI Symposium, Barcelona, 23 November 2002

Downloads

  • PhD Thesis pdf "New Perspectives in Microbial Typing"
    JAC's thesis(16MB)
  • Bionumerics Scripts for partition comparison:Webpage

Hobbies