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-People:​jcarrico ​ +====== João André Carriço ====== 
-Teste File upload{{:people:​journclass2.pdf|}}+{{:jac2.png|}} 
 + 
 +===== Bio ===== 
 + 
 +**Full Name**: João André Nogueira Custódio Carriço\\ 
 +**Degrees**:​  
 +  * Applied Chemistry, Biotechnology - FCT/UNL\\ 
 +  * PhD in Biology:"​New perspectives in Microbial Typing"​\\ 
 +===== Current Position ===== 
 +**Assistant Researcher**\\  
 +[[http://​www.imm.fm.ul.pt/​web/​imm/​molecularmicrobiologyandinfection|Molecular Microbiology and Infection Unit]], [[http://​www.imm.fm.ul.pt/​web/​imm/​home|Instituto de Medicina Molecular]]\\ 
 +Instituto de Microbiologia,​[[http://​www.fm.ul.pt/​|Faculdade de Medicina de Lisboa]], [[http://​www.ul.pt/​|Universidade de Lisboa]]\\  
 + 
 +**Invited Researcher** \\ 
 +[[http://​kdbio.inesc-id.pt|Knowledge Discovery and Bioinformatics group (KDBIO)]]\\  
 +[[http://​www.inesc-id.pt|Instituto de Engenharia de Sistemas e Computadores:​ Investigação e Desenvolvimento (INESC-ID)]] 
 + 
 +===== Research Interests ===== 
 +**Biology** : Microbiology,​ Population Evolutionary Genetics, Molecular Epidemiology,​ Microbial Typing methods\\ 
 +**Mathematics** : Univariate/​Multivariate Statistics for Data Analysis, Graph theory, Resampling methods\\ 
 +**Informatics** : Matlab, Perl, Data Mining, Databases: Postgresql, Web-Based Interfaces: PHP and HTML/CSS, XML schemas.\\ 
 + 
 +===== Websites ===== 
 +[[http://​www.joaocarrico.info|Personal homepage]] - My homepage\\ 
 + 
 +[[http://​www.comparingpartitions.info|Comparing Partitions]] - a web site useful for finding correspondences between diferent partitions on a dataset, namely the application of different typing methods to a collection of bacterial isolates\\ 
 + 
 +[[http://​www.ccrbtyping.net|ccrB typing]] - infering SCCmec type through the sequencing of ccrB gene.\\ 
 + 
 +[[http://​goeburst.phyloviz.net/​|goeBURST]] - a globally optimized implementation of the eBURST algorithm for the analysis of MLST data. 
 + 
 +===== Contacts ===== 
 + 
 +**Emails**:  
 +  * jcarrico_at_fm.ul.pt (replace _at_ by @)\\ 
 +  * jcarrico_at_kdbio.inesc-id.pt (replace _at_ by @)\\ 
 +**Twitter**:​ 
 +  * jacarrico [[http://​twitter.com/​jacarrico|Twitter homepage]] 
 +   
 +<​html>​ 
 +<object classid="​clsid:​d27cdb6e-ae6d-11cf-96b8-444553540000"​ codebase="​http://​download.macromedia.com/​pub/​shockwave/​cabs/​flash/​swflash.cab#​version=9,​0,​124,​0"​ width="​290"​ height="​350"​ id="​TwitterWidget"​ align="​middle">​ 
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 +</​object>​ 
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 +===== Publications ===== 
 +<​html>​ 
 +<span id='​badgeCont338345'​ style='​width:​126px'><​script src='​http://​labs.researcherid.com/​mashlets?​el=badgeCont338345&​mashlet=badge&​showTitle=false&​className=a&​rid=A-7367-2008'></​script></​span>​ 
 + ​ <​ol>​ 
 + ​ <​li value="​18">​ Francisco AP, Bugalho M, Ramirez M, <​U>​Carrico JA.</​U>,​ <​B>​Global Optimal eBURST analysis of Multilocus typing data using a graphic matroid approach</​B>,​BMC Bioinformatics 2009, 10:​152doi:​10.1186/​1471-2105-10-152 <a href="​http://​www.biomedcentral.com/​1471-2105/​10/​152">​ Abstract</​a>​ 
 + ​ <​li value="​17">​Duarte C. Oliveira,​Mauro Santos,​Catarina Milheiriço,​ João A. Carriço, Susana Vinga, Arlindo L. Oliveira and Herm&​iacute;​nia de Lencastre, <​b><​i>​ccrB</​i>​ typing tool: an online resource for stapylococci <​i>​ccrB</​i>​ sequence typing</​b>,​J Antimicrob Chemother. 2008 Apr;​61(4):​959-60. Epub 2008 Jan 27, doi:​10.1093/​jac/​dkn021 
 + 
 + <li value="​16">​Nuno A. Faria*, <​U>​Jo&​atilde;​o A. Carri&​ccedil;​o</​U>​*,​ Duarte C. Oliveira, M&​aacute;​rio Ramirez and Herm&​iacute;​nia de Lencastre, <​b>​Analysis of typing methods for epidemiological surveillance of both methicillin-resistant and susceptible <​i>​Staphylococcus aureus</​i></​b>,​J Clin Microbiol. 2008 Jan;​46(1):​136-144.<​a href="​http://​www.ncbi.nlm.nih.gov/​pubmed/​17989188?​ordinalpos=3&​itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum">​ PubMed Abstract</​a>​ 
 +  
 + </​li><​li value="​15">​ Miragaia, M., <​U>​Jo&​atilde;​o A. Carri&​ccedil;​o</​U>,​ J. C. Thomas, I. Couto, 5, M. C. Enright, and and Herm&​iacute;​nia de Lencastre, <b> Comparison of molecular typing methods for characterization of <​i>​Staphylococcus epidermidis</​i>:​ a proposal for clone definition </​b>,​J Clin Microbiol. ​ 2008 Jan;​46(1):​118-129. <a href="​http://​www.ncbi.nlm.nih.gov/​pubmed/​17989196?​ordinalpos=2&​itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum">​ PubMed Abstract</​a>​ 
 +  
 + </​li><​li value="​14">​Raquel S&​aacute;​-Le&​atilde;​o*,​ S&​oacute;​nia Nunes1,*, Ant&​oacute;​nio Brito-Av&​ocirc;,​ Carla R. Alves, <​U>​Jo&​atilde;​o A. Carri&​ccedil;​o</​U>,​ Joana Saldanha, Jonas S. Almeida, Ilda Santos-Sanches,​ and Herm&​iacute;​nia de  
 +Lencastre, <​b>​High dynamics of transmission and colonization by <​i>​Streptococcus pneumoniae</​i>​ and <​i>​Haemophilus influenzae</​i>​ within a day-care center revealed in a longitudinal study </​b>,​J Clin Microbiol. ​ 2008 Jan;​46(1):​225-234.  
 + <a href="​http://​www.ncbi.nlm.nih.gov/​pubmed/​18003797?​ordinalpos=1&​itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum">​ PubMed Abstract</​a>​ 
 + <li value="​13">​ 
 + Francisco R. Pinto, <​u>​Jo&​atilde;​o A. Carri&​ccedil;​o</​u>,​ M&​aacute;​rio Ramirez and Jonas S Almeida,<​b>​Ranked Adjusted Rand: integrating distance and partition information in a measure of clustering agreement</​b>,​ BMC Bioinformatics 2007, 8:44 (07 Feb 2007) <a href="​http://​www.biomedcentral.com/​1471-2105/​8/​44">​Full paper</​a>​ 
 + </​li>​ 
 +      <li value="​12">​ 
 +Almeida JS, C Chen, R Gorlitsky, R Stanislaus, M Aires-de-Sousa,​ P Eleut&​eacute;​rio,​ <u>JA Carri&​ccedil;​o</​u>,​ A Maretzek, A Bohn, A Chang, F Zhang, R Mitra, GB Mills, X Wang, HF Deus (2006) <​b>​Data integration gets '​Sloppy'</​b>​. Nature Biotechnology (9):​1070-1071.<​a href="​http://​www.ncbi.nlm.nih.gov/​entrez/​query.fcgi?​db=pubmed&​amp;​cmd=Retrieve&​amp;​dopt=AbstractPlus&​amp;​list_uids=16964209&​amp;​query_hl=3&​amp;​itool=pubmed_docsum">​Pubmed Abstract</​a>​ 
 + 
 +      </​li><​li value="​11"><​u>​Carri&​ccedil;​o,​ J.A.</​u>;​ C. Silva-Costa;​ J. Melo-Cristino;​ F. R. Pinto; H. de Lencastre; J.S.Almeida;​ M.Ramirez, <​b>​Illustration of a Common Framework for Relating Multiple Typing Methods by Application to Macrolide-Resistant <​i>​Streptococcus pyogenes</​i></​b>,​ J Clin Microbiol. 2006 Jul;​44(7):​2524-32 <a href="​http://​www.ncbi.nlm.nih.gov/​entrez/​query.fcgi?​db=pubmed&​amp;​cmd=Retrieve&​amp;​dopt=Abstract&​amp;​list_uids=16825375&​amp;​query_hl=5&​amp;​itool=pubmed_docsum">​Pubmed Abstract</​a>​ 
 + 
 +      </​li><​li value="​10">​Mato R, Sanches IS, Simas C, Nunes S, <​u>​Carrico JA</​u>,​ Sousa NG, Frazao N, Saldanha J, Brito-Avo A, Almeida JS, Lencastre HD.<​b>​Natural History of Drug-Resistant Clones of Streptococcus pneumoniae Colonizing Healthy Children in Portugal.</​b>​Microb Drug Resist. 2005 Winter;​11(4):​309-22. <a href="​http://​www.ncbi.nlm.nih.gov/​entrez/​query.fcgi?​cmd=Retrieve&​amp;​db=pubmed&​amp;​dopt=Abstract&​amp;​list_uids=16359190&​amp;​query_hl=1">​Pubmed Abstract</​a>​ 
 + 
 +      </​li><​li value="​9">​ <​u>​Carri&​ccedil;​o,​ J.A.</​u>​ , F.R. Pinto, C. Simas, S. Nunes, N. G. Sousa, ​ N. Fraz&​atilde;​o,​ H. de Lencastre, and J.S. Almeida. 2005. <​b>​Assessment 
 +of band-based similarity coefficients for automatic Type/​Subtype 
 +classification of microbial isolates analyzed by Pulsed-Field Gel 
 +Electrophoresis.</​b>​ J Clin Microbiol. ​ 2005 Nov;​43(11):​5483-90. <a href="​http://​www.ncbi.nlm.nih.gov/​entrez/​query.fcgi?​cmd=Retrieve&​amp;​db=pubmed&​amp;​dopt=Abstract&​amp;​list_uids=16272474&​amp;​query_hl=3">​Pubmed Abstract</​a>​ 
 + 
 + 
 +    </​li><​li value="​8">​Sousa N. G., R. S&​aacute;​-Le&​atilde;​o,​ M.I. Cris&​oacute;​stomo,​ C. Simas, S. Nunes, N. Fraz&​atilde;​o,​ <u>J. Carri&​ccedil;​o</​u>,​ R. Mato, I. Santos-Sanches,​ and H. de Lencastre. 2005. <​b>​Properties of novel international drug-resistant pneumococcal clones identified in day-care centers (DCCs) of Lisbon, Portugal.</​b>​ J Clin Microbiol. 2005 Sep;​43(9):​4696-703. <a href="​http://​www.ncbi.nlm.nih.gov/​entrez/​query.fcgi?​cmd=Retrieve&​amp;​db=pubmed&​amp;​dopt=Abstract&​amp;​list_uids=16145129&​amp;​query_hl=3">​Pubmed Abstract</​a>​ 
 + 
 +    </​li><​li value="​7">​ I. Serrano, J. Melo-Cristino,​ <u>J. Carri&​ccedil;​o</​u>​ and M. Ramirez, <​b>​Characterization of the genetic lineages responsible for pneumococcal invasive disease in Portugal</​b>,​J Clin Microbiol. 2005 Apr;​43(4):​1706-15.<​a href="​http://​www.ncbi.nlm.nih.gov/​entrez/​query.fcgi?​cmd=Retrieve&​amp;​db=pubmed&​amp;​dopt=Abstract&​amp;​list_uids=15814989">​Pubmed Abstract</​a><​br>​ 
 +    </​li><​li value="​6">​Nelson Fraz&​atilde;​o;​ Ant&​oacute;​nio Brito-Av&​ocirc;;​ Carla Simas; Joana Saldanha; Rosario Mato; S&​oacute;​nia Nunes; Natacha Gon&​ccedil;​alves Sousa; <​u>​Jo&​atilde;​o Carri&​ccedil;​o</​u>;​ Jonas Almeida; Ilda Santos-Sanches;​ Herm&​iacute;​nia de Lencastre, <​b>​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</​b>​ Pediatr Infect Dis J. 2005 Mar;​24(3):​243-52.<​a href="​http://​www.ncbi.nlm.nih.gov/​entrez/​query.fcgi?​cmd=Retrieve&​amp;​db=pubmed&​amp;​dopt=Abstract&​amp;​list_uids=15750461">​Pubmed Abstract</​a>​ <​br></​li>​ 
 +    <li value="​5">​Nunes S, R S&​aacute;​-Le&​atilde;​o,​ <u>J Carri&​ccedil;​o</​u>,​ CR Alves, R Mato, A Brito Av&​ocirc;,​ J Saldanha, JS Almeida, I Santos Sanches, and H de Lencastre (2005) <​b>​Trends 
 +in drug resistance, serotypes and molecular types of Streptococcus 
 +pneumoniae colonizing pre-school age children attending day care 
 +centers in Lisbon, Portugal &#8211; a summary of four years of annual 
 +surveillance.</​b>​J. Clin. Microbiol. 2005;43 1285-1293 &​nbsp;&​nbsp;<​a href="​http://​jcm.asm.org/​cgi/​content/​abstract/​43/​3/​1285?​etoc">​JCM abstract</​a><​br></​li>​ 
 +   
 +    <li value="​4">​Sara Silva, Rodrigo Gouveia-Oliveira,​ Antonio Maretzek, <​u>​Joao Carrico</​u>,​Thorolfur 
 +Gudnason, Karl G Kristinsson,​ Karl Ekdahl, Antonio Brito-Avo, Alexander 
 +Tomasz, Ilda S Sanches, Herminia de Lencastre and Jonas S Almeida.<​b>​Web-based epidemiological surveillance of antibiotic-resistant pneumococci in Day Care Centers</​b>​ BMC Medical Informatics and Decision Making 2003, 3:​9&​nbsp;&​nbsp;<​a href="​http://​www.biomedcentral.com/​1472-6947/​3/​9/​abstract">​Abstract</​a><​br></​li>​ 
 +    <li value="​3">​Maria Miragaia, Isabel Couto, Sandro F. F. Pereira, Karl G. Kristinsson,​ Henrik Westh, Jens O. Jarl&​oslash;​v,​ <​u>​Jo&​atilde;​o Carri&​ccedil;​o</​u>,​ Jonas Almeida, Ilda Santos Sanches and Herm&​iacute;​nia de Lencastre.<​b>​Molecular 
 +Characterization of Methicillin Resistant Staphylococcus epidermidis 
 +(MRSE) Clones: Evidence of Geographic Dissemination</​b> ​ J Clin Microbiol 2002 Feb;​40(2):​430-8 <a href="​http://​www.ncbi.nlm.nih.gov/​entrez/​query.fcgi?​cmd=Retrieve&​amp;​db=PubMed&​amp;​list_uids=11825953&​amp;​dopt=Abstract">​Pubmed Abstract</​a><​br></​li>​ 
 +    <li value="​2">​Almeida,​ Jonas S.; <​u>​Carri&​ccedil;​o,​ Jo&​atilde;​o A.</​u>​ ;Maretzek, Ant&​oacute;​nio;​ Fletcher, Madilyn; Noble, Peter; <​b>"​Analysis of genomic sequences by Chaos Game Representation"</​b>,​ Journal of Bioinformatics,​ Vol.17 n.5 2001 pages 429-437 ​ <a href="​http://​www.ncbi.nlm.nih.gov/​entrez/​query.fcgi?​cmd=Retrieve&​amp;​db=PubMed&​amp;​list_uids=11331237&​amp;​dopt=Abstract">​Pubmed Abstract</​a><​br></​li>​ 
 +    <li value="​1">​Santos Sanches, I., R. Mato, H. de Lencastre, A. Tomasz, CEM/NET collaborators:​ S. Nunes, C. R. Alves, M. Miragaia, <u>J. Carri&​ccedil;​o</​u>,​I. 
 +Couto, I. Bonfim, M. A. de Sousa, D. Oliveira, A. Gomes, M. Vaz, 
 +S.Fernandes,​ S. C. Verde, S. &​aacute;​vila,​ F. Antunes, R. S&​aacute;​-Le&​atilde;​o,​ J. 
 +Almeida,and International collaborators:​ O. Melter, M. Chung, M. 
 +C.Brandileone,​ E. Casta&​ntilde;​eda,​ I. Heitmann, M. Hortal, W. Hryniewicz,​ 
 +F.Jia, K. Kikuchi, K. G. Kristinsson,​ J. Li&​ntilde;​ares,​ 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. <​b>​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.</​b>​ Microb. Drug Resist. 6:​199-211.<​a href="​http://​www.ncbi.nlm.nih.gov/​entrez/​query.fcgi?​cmd=Retrieve&​amp;​db=PubMed&​amp;​list_uids=11144420&​amp;​dopt=Abstract">​Pubmed Abstract</​a><​br></​li>​ 
 +    </​ol>​ 
 +</​html>​
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