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--- people:jcarrico [2009/08/25 16:27]
jcarrico
+++ people:jcarrico [2009/09/03 17:01]
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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]], 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]]
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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>
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