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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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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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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Illustration of a Common Framework for Relating Multiple Typing Methods by Application to Macrolide-Resistant Streptococcus pyogenes von Carriço, J.A, Silva-Costa, C, Melo-Cristino, J, Pinto, F.R, de Lencastre, H, Almeida, J.S, Ramirez, M

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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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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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A primer on microbial bioinformatics for nonbioinformaticians von Carriço, J.A., Rossi, M., Moran-Gilad, J., Van Domselaar, G., Ramirez, M.

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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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Comparison of Molecular Typing Methods for Characterization of Staphylococcus epidermidis: Proposal for Clone Definition von Miragaia, M, Carriço, J.A, Thomas, J.C, Couto, I, Enright, M.C, de Lencastre, H

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Assessment of Band-Based Similarity Coefficients for Automatic Type and Subtype Classification of Microbial Isolates Analyzed by Pulsed-Field Gel Electrophoresis von Carriço, J. A, Pinto, F. R, Simas, C, Nunes, S, Sousa, N. G, Frazão, N, Lencastre, H. de, Almeida, J. S

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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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Dynamic susceptibility of dipolar coupled magnetic vortices von Jales, T. G. M., Martins, S. M. B., Carriço, A. S., Dantas, Ana L.

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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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Sample pooling methods for efficient pathogen screening: Practical implications von Furstenau, Tara N., Cocking, Jill H., Hepp, Crystal M., Fofanov, Viacheslav Y.

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Evaluation of jackknife and bootstrap for defining confidence intervals for pairwise agreement measures von Severiano, Ana, Carriço, João A, Robinson, D Ashley, Ramirez, Mário, Pinto, Francisco R

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Dipolar domain wall tuning in Fe@Py core-shell cylinders von Souza, R.M., Martins, S.M.S.B., Dantas, Ana L., Bezerra, D.H.D., Carriço, A.S.

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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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