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
Twitter: @jacarrico

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. Teixeira AS, Monteiro PT, Carriço JA, Ramirez M, Francisco AP Not Seeing the Forest for the Trees: Size of the Minimum Spanning Trees (MSTs) Forest and Branch Significance in MST-Based Phylogenetic Analysis. PLoS One. 2015 Mar 23;10(3):e0119315. doi: 10.1371/journal.pone.0119315. eCollection 2015.Available Online
  2. Coelho LP, Pato C, Friães A, Neumann A, von Köckritz-Blickwede M, Ramirez M, Carriço JA. Automatic determination of NET (neutrophil extracellular traps) coverage in fluorescent microscopy images Bioinformatics. 2015 Mar 19. pii: btv156. [Epub ahead of print]Pubmed Abstract
  3. Vaz C, Francisco AP, Silva M, Jolley KA, Bray JE, Pouseele H, Rothganger J, Ramirez M, Carriço JA. TypOn: the microbial typing ontology. J Biomed Semantics. 2014 Oct 18;5(1):43. doi: 10.1186/2041-1480-5-43. eCollection 2014.Available Online
  4. Branquinho R, Meirinhos-Soares L, Carriço JA, Pintado M, Peixe LV. Phylogenetic and clonality analysis of Bacillus pumilus isolates uncovered a highly heterogeneous population of different closely related species and clones FEMS Microbiol Ecol. 2014 Dec;90(3):689-98. doi: 10.1111/1574-6941.12426. Epub 2014 Oct 6.Pubmed Abstract
  5. Branquinho R, Sousa C, Osório H, Meirinhos-Soares L, Lopes J, Carriço JA, Busse HJ, Abdulmawjood A, Klein G, Kämpfer P, Pintado ME, Peixe LV. Bacillus invictae sp. nov., isolated from a health product Int J Syst Evol Microbiol. 2014 Nov;64(Pt 11):3867-76. doi: 10.1099/ijs.0.067850-0. Epub 2014 Aug 29.Pubmed Abstract
  6. Silva-Costa C, Carriço JA, Ramirez M, Melo-Cristino J. Scarlet fever is caused by a limited number of Streptococcus pyogenes lineages and is associated with the exotoxin genes ssa, speA and speC. Pediatr Infect Dis J. 2014 Mar;33(3):306-10. doi: 10.1097/INF.0000000000000088Pubmed Abstract
  7. Coelho JR, Carriço JA, Knight D, Martinez J-L, Morrissey I,Oggioni MR, Freitas AT The Use of Machine Learning Methodologies to Analyse Antibiotic and Biocide Susceptibility in Staphylococcus aureus PLoS ONE 8(2): e55582. doi:10.1371/journal.pone.0055582 Available online
  8. Carriço JA*, Sabat AJ, Friedrich AW, Ramirez M, on behalf of the ESCMID Study Group for Epidemiological Markers (ESGEM). Bioinformatics in bacterial molecular epidemiology and public health: databases, tools and the next-generation sequencing revolution. Euro Surveill. 2013;18(4):pii=20382Available online
  9. Francisco, A.P., C. Vaz, P. T. Monteiro, J. Melo-Cristino, M. Ramirez, and J. A. Carriço* PHYLOViZ: Phylogenetic inference and data visualization for sequence based typing methods. .BMC Bioinformatics, 13:87 PubMed Abstract
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. 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
  30. 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
  31. 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
  32. 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. What bioinformatic tools should I use for analysis of high-throughput sequencing data for molecular diagnostics? (M022). 25th European Congress of Clinical Microbiology and Infectious Diseases (ECCMID), Copenhagen, Denmark, 25-28th April (Meet The Expert Session)
  2. Integrating phylogenetic inference and metadata visualization for NGS data: PHYLOViZ (WS20-Typing of Bacterial Pathogens in 2014: Expanding Scope of NGS).114th American Society of Microbiology General Meeting (ASM2014), Boston, USA, 17-20 May
  3. How to compare Typing Techniques: Do’s and Don’t’s (WS20-Typing of Bacterial Pathogens in 2014: Expanding Scope of NGS).114th American Society of Microbiology General Meeting (ASM2014), Boston, USA, 17-20 May
  4. Whole Genome Analysis of the first Vancomycin resistant Staphylococcus aureus (VRSA) isolated in Europe . (O112). 24th European Congress of Clinical Microbiology and Infectious Diseases (ECCMID), Barcelona, Spain, 10-13th May.
  5. NGSOnto - Keeping track of the NGS pipeline process using an ontology approach and its application on molecular epidemiology. 10th International Meeting on Microbial Epidemiological Markers (IMMEM-10), Paris, France 2-5 October 2013
  6. Statistical Analysis of typing methods: do’s and don’t’s 22nd European Congress of Clinical Microbiology and Infectious Diseases (ECCMID), ESGEM Educational Workshop: “Making sense out of molecular typing data in 2012: current gold standards and interpretation”, London, United Kingdom, 31 March - 3 April 2012
  7. Microbial Typing Ontology Münster Medical Genomics Conference: Rapid Next-Generation-Sequencing Conference for Public Health and Clinical Microbiology, Münster, Germany, March 8-9,2012
  8. Keynote panel for “Rapid NGS for Public Health Preparedness & Clinical Microbiology: Bioinformatics, Legal, and Social Issues” , Molecular Medicine TriConference 2012, San Francisco, CA, USA, February 13-19 2012
  9. 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.
  10. An Ontology and a REST API for Sequence based Microbial Typing Data, X Jornadas de Bioinformática, Málaga, October 27-29, 2010
  11. 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
  12. 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
  13. Bacterial clone definition using microbial typing methods: Advantages and caveats, Microbiotec 2009,Vilamoura, Portugal, November 28-30, 2009
  14. Exploring the relationship of strains characterized by sequence based typing methods using goeBURST algorithm, Microbiotec 2009,Vilamoura, Portugal, November 28-30, 2009
  15. www.comparingpartitions.info - a web-tool for the quantitative assessment of classification agreement, Jornadas de Bioinformática 2009, Lisboa, Portugal, 3-6 November, 1009
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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

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