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Global optimal eBURST analysis of multilocus typing data using a graphic matroid approach.
Francisco AP, Bugalho M, Ramirez M, Carriço JA. Francisco AP, et al. Among authors: carrico ja. BMC Bioinformatics. 2009 May 18;10:152. doi: 10.1186/1471-2105-10-152. BMC Bioinformatics. 2009. PMID: 19450271 Free PMC article.
Evaluation of jackknife and bootstrap for defining confidence intervals for pairwise agreement measures.
Severiano A, Carriço JA, Robinson DA, Ramirez M, Pinto FR. Severiano A, et al. Among authors: carrico ja. PLoS One. 2011;6(5):e19539. doi: 10.1371/journal.pone.0019539. Epub 2011 May 18. PLoS One. 2011. PMID: 21611165 Free PMC article.
Adjusted Wallace coefficient as a measure of congruence between typing methods.
Severiano A, Pinto FR, Ramirez M, Carriço JA. Severiano A, et al. Among authors: carrico ja. J Clin Microbiol. 2011 Nov;49(11):3997-4000. doi: 10.1128/JCM.00624-11. Epub 2011 Sep 14. J Clin Microbiol. 2011. PMID: 21918028 Free PMC article.
PHYLOViZ: phylogenetic inference and data visualization for sequence based typing methods.
Francisco AP, Vaz C, Monteiro PT, Melo-Cristino J, Ramirez M, Carriço JA. Francisco AP, et al. Among authors: carrico ja. BMC Bioinformatics. 2012 May 8;13:87. doi: 10.1186/1471-2105-13-87. BMC Bioinformatics. 2012. PMID: 22568821 Free PMC article.
Bioinformatics in bacterial molecular epidemiology and public health: databases, tools and the next-generation sequencing revolution.
Carriço JA, Sabat AJ, Friedrich AW, Ramirez M; ESCMID Study Group for Epidemiological Markers (ESGEM). Carriço JA, et al. Euro Surveill. 2013 Jan 24;18(4):20382. doi: 10.2807/ese.18.04.20382-en. Euro Surveill. 2013. PMID: 23369390 Review.
Automatic determination of NET (neutrophil extracellular traps) coverage in fluorescent microscopy images.
Coelho LP, Pato C, Friães A, Neumann A, von Köckritz-Blickwede M, Ramirez M, Carriço JA. Coelho LP, et al. Among authors: carrico ja. Bioinformatics. 2015 Jul 15;31(14):2364-70. doi: 10.1093/bioinformatics/btv156. Epub 2015 Mar 19. Bioinformatics. 2015. PMID: 25792554
Not seeing the forest for the trees: size of the minimum spanning trees (MSTs) forest and branch significance in MST-based phylogenetic analysis.
Teixeira AS, Monteiro PT, Carriço JA, Ramirez M, Francisco AP. Teixeira AS, et al. Among authors: carrico ja. PLoS One. 2015 Mar 23;10(3):e0119315. doi: 10.1371/journal.pone.0119315. eCollection 2015. PLoS One. 2015. PMID: 25799056 Free PMC article.
PHYLOViZ Online: web-based tool for visualization, phylogenetic inference, analysis and sharing of minimum spanning trees.
Ribeiro-Gonçalves B, Francisco AP, Vaz C, Ramirez M, Carriço JA. Ribeiro-Gonçalves B, et al. Among authors: carrico ja. Nucleic Acids Res. 2016 Jul 8;44(W1):W246-51. doi: 10.1093/nar/gkw359. Epub 2016 Apr 29. Nucleic Acids Res. 2016. PMID: 27131357 Free PMC article.
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