Chewie Nomenclature Server (chewie-NS): a deployable nomenclature server for easy sharing of core and whole genome MLST schemas von Mamede, Rafael, Vila-Cerqueira, Pedro, Silva, Mickael, Carriço, João A, Ramirez, Mário

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Distance-based phylogenetic inference from typing data: a unifying view von Vaz, Cátia, Nascimento, Marta, Carrico, Joao, Rocher, Tatiana, Francisco, Alexandre P.

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Analysis of Typing Methods for Epidemiological Surveillance of both Methicillin-Resistant and Methicillin-Susceptible Staphylococcus aureus Strains von Faria, Nuno A, Carrico, João A, Oliveira, Duarte C, Ramirez, Mário, de Lencastre, Hermínia

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Scarlet Fever Is Caused By a Limited Number of Streptococcus pyogenes Lineages and Is Associated with the Exotoxin Genes ssa, speA and speC von SILVA-COSTA, Catarina, CARRICO, Joao A, RAMIREZ, Mario, MELO-CRISTINO, Jose

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Large-Scale Simulations of Bacterial Populations Over Complex Networks von Teixeira, Andreia Sofia, Monteiro, Pedro T, Carriço, João A, Santos, Francisco C, Francisco, Alexandre P

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Polymerase Chain Reaction for the in vitro detection of the pESI plasmid associated with the globally circulating Salmonella Infantis outbreak strain von McMillan, Elizabeth A, Hiott, Lari M, Carrico, Joao Andre, Machado, Miguel P, Pouseele, Hannes, Jackson, Charlene R, Frye, Jonathan G

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Clinical and molecular epidemiology of Acinetobacter baumannii bloodstream infections in an endemic setting von Marchaim, Dror, Levit, Dana, Zigron, Roy, Gordon, Michal, Lazarovitch, Tsillia, Carrico, Joao A, Chalifa-Caspi, Vered, Moran-Gilad, Jacob

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PHYLOViZ 2.0: providing scalable data integration and visualization for multiple phylogenetic inference methods von Nascimento, Marta, Sousa, Adriano, Ramirez, Mário, Francisco, Alexandre P, Carriço, João A, Vaz, Cátia

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Prognostic Prediction through Biclustering-Based Classification of Clinical Gene Expression Time Series von Carreiro, André V., Anunciação, Orlando, Carriço, João A., Madeira, Sara C.

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PHYLOViZ: phylogenetic inference and data visualization for sequence based typing methods von Francisco, Alexandre P, Vaz, Cátia, Monteiro, Pedro T, Melo-Cristino, José, Ramirez, Mário, Carriço, Joäo A

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Global optimal eBURST analysis of multilocus typing data using a graphic matroid approach von Francisco, Alexandre P, Bugalho, Miguel, Ramirez, Mário, Carriço, João A

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Adjusted Wallace Coefficient as a Measure of Congruence between Typing Methods von SEVERIANO, Ana, PINTO, Francisco R, RAMIREZ, Mario, CARRICO, Joao A

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Analysis of Invasiveness of Pneumococcal Serotypes and Clones Circulating in Portugal before Widespread Use of Conjugate Vaccines Reveals Heterogeneous Behavior of Clones Expressin... von SA-LEAO, Raquel, PINTO, Francisco, AGUIAR, Sandra, NUNES, Sonia, CARRICO, Joao A, FRAZAO, Nelson, GONCALVES-SOUSA, Natacha, MELO-CRISTINO, José, DE LENCASTRE, Hermínia, RAMIREZ, Mário

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Critical steps in clinical shotgun metagenomics for the concomitant detection and typing of microbial pathogens von Couto, Natacha, Schuele, Leonard, Raangs, Erwin C., Machado, Miguel P., Mendes, Catarina I., Jesus, Tiago F., Chlebowicz, Monika, Rosema, Sigrid, Ramirez, Mário, Carriço, João A., Autenrieth, Ingo B., Friedrich, Alex W., Peter, Silke, Rossen, John W.

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Plasmid ATLAS: plasmid visual analytics and identification in high-throughput sequencing data von Jesus, Tiago F, Ribeiro-Gonçalves, Bruno, Silva, Diogo N, Bortolaia, Valeria, Ramirez, Mário, Carriço, João A

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Phylogenetic and clonality analysis of Bacillus pumilus isolates uncovered a highly heterogeneous population of different closely related species and clones von Branquinho, Raquel, Meirinhos-Soares, Luís, Carriço, João A., Pintado, Manuela, Peixe, Luísa V.

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Food Safety in the Age of Next Generation Sequencing, Bioinformatics, and Open Data Access von Taboada, Eduardo N, Graham, Morag R, Carriço, João A, Van Domselaar, Gary

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Distinct phenotypic and genomic signatures underlie contrasting pathogenic potential of Staphylococcus epidermidis clonal lineages von Espadinha, Diana, Sobral, Rita G., Mendes, Inês, Méric, Guillaume, Sheppard, Samuel K., Carrico, Joao, de Lencastre, Hermínia, Miragaia, Maria

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High Rates of Transmission of and Colonization by Streptococcus pneumoniae and Haemophilus influenzae within a Day Care Center Revealed in a Longitudinal Study von Sá-Leão, Raquel, Nunes, Sónia, Brito-Avô, António, Alves, Carla R, Carriço, João A, Saldanha, Joana, Almeida, Jonas S, Santos-Sanches, Ilda, de Lencastre, Hermíniade

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Not seeing the forest for the trees: size of the minimum spanning trees (MSTs) forest and branch significance in MST-based phylogenetic analysis von Teixeira, Andreia Sofia, Monteiro, Pedro, Carrico, Joao, Ramos de Almeida Ramirez, Mário Nuno, Francisco, Alexandre P.

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