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ccrB typing tool: an online resource for staphylococci ccrB sequence typing.
Published in:
Journal of Antimicrobial Chemotherapy (JAC), 2008, v. 61, n. 4, p. 959, doi. 10.1093/jac/dkn021
By:
- Duarte C. Oliveira;
- Mauro Santos;
- Catarina Milheiriço;
- João A. Carriço;
- Susana Vinga;
- Arlindo L. Oliveira;
- Hermínia de Lencastre
Publication type:
Article
Food Safety in the Age of Next Generation Sequencing, Bioinformatics, and Open Data Access.
Published in:
Frontiers in Microbiology, 2017, p. 1, doi. 10.3389/fmicb.2017.00909
By:
- Taboada, Eduardo N.;
- Graham, Morag R.;
- Carriço, João A.;
- Van Domselaar, Gary
Publication type:
Article
Highly Specific Blood-Brain Barrier Transmigrating Single-Domain Antibodies Selected by an In Vivo Phage Display Screening.
Published in:
Pharmaceutics, 2021, v. 13, n. 10, p. 1598, doi. 10.3390/pharmaceutics13101598
By:
- Aguiar, Sandra Isabel;
- Dias, Joana N. R.;
- André, Ana Santos;
- Silva, Marta Lisete;
- Martins, Diana;
- Carrapiço, Belmira;
- Castanho, Miguel;
- Carriço, João;
- Cavaco, Marco;
- Gaspar, Maria Manuela;
- Nobre, Rui Jorge;
- Pereira de Almeida, Luís;
- Oliveira, Soraia;
- Gano, Lurdes;
- Correia, João D. G.;
- Barbas 3rd, Carlos;
- Gonçalves, João;
- Neves, Vera;
- Aires-da-Silva, Frederico
Publication type:
Article
Two multi-fragment recombination events resulted in the β-lactam-resistant serotype 11A-ST6521 related to Spain9V-ST156 pneumococcal clone spreading in southwestern Europe, 2008 to 2016.
Published in:
Eurosurveillance (15607917), 2020, v. 25, n. 16, p. 42, doi. 10.2807/1560-7917.ES.2020.25.16.1900457
By:
- González-Díaz, Aida;
- Machado, Miguel P.;
- Càmara, Jordi;
- Yuste, José;
- Varon, Emmanuelle;
- Domenech, Miriam;
- Del Grosso, María;
- Marimón, José María;
- Cercenado, Emilia;
- Larrosa, Nieves;
- Quesada, María Dolores;
- Fontanals, Dionisia;
- El-Mniai, Assiya;
- Cubero, Meritxell;
- Carriço, João A.;
- Martí, Sara;
- Ramirez, Mario;
- Ardanuy, Carmen
Publication type:
Article
Plasmid ATLAS: plasmid visual analytics and identification in high-throughput sequencing data.
Published in:
Nucleic Acids Research, 2019, v. 47, n. D1, p. D188, doi. 10.1093/nar/gky1073
By:
- Jesus, Tiago F;
- Ribeiro-Gonçalves, Bruno;
- Silva, Diogo N;
- Bortolaia, Valeria;
- Ramirez, Mário;
- Carriço, João A
Publication type:
Article
PHYLOViZ Online: web-based tool for visualization, phylogenetic inference, analysis and sharing of minimum spanning trees.
Published in:
Nucleic Acids Research, 2016, v. 44, n. W1, p. W246, doi. 10.1093/nar/gkw359
By:
- Ribeiro-Gonçalves, Bruno;
- Francisco, Alexandre P.;
- Vaz, Cátia;
- Ramirez, Mário;
- Carriço, João André
Publication type:
Article
Data integration gets 'Sloppy'.
Published in:
2006
By:
- Almeida, Jonas S.;
- Chuming Chen;
- Gorlitsky, Robert;
- Stanislaus, Romesh;
- Aires-de-Sousa, Marta;
- Eleutério, Pedro;
- Carriço, João;
- Maretzek, António;
- Bohn, Andreas;
- Chang, Allen;
- Fan Zhang;
- Mitra, Rahul;
- Mills, Gordon B.;
- Xiaoshu Wang;
- Deus, Helena F.
Publication type:
Letter
EFSA and ECDC technical report on the collection and analysis of whole genome sequencing data from food‐borne pathogens and other relevant microorganisms isolated from human, animal, food, feed and food/feed environmental samples in the joint ECDC‐EFSA molecular typing database
Published in:
EFSA Supporting Publications, 2019, v. 16, n. 5, p. N.PAG, doi. 10.2903/sp.efsa.2019.EN-1337
By:
- Walle, Ivo;
- Guerra, Beatriz;
- Cavalieri, Vincenzo;
- Borges, Vitor;
- André Carriço, João;
- Cochrane, Guy;
- Dallman, Tim;
- Franz, Eelco;
- Karpíšková, Renata;
- Litrup, Eva;
- Mistou, Michel‐Yves;
- Morabito, Stefano;
- Mossong, Joèl;
- Alm, Erik;
- Barrucci, Federica;
- Bianchi, Chiara;
- Costa, Giancarlo;
- Kotila, Saara;
- Mangone, Iolanda;
- Palm, Daniel
Publication type:
Article
Beta-hemolytic Streptococcus dysgalactiae strains isolated from horses are a genetically distinct population within the Streptococcus dysgalactiae taxon.
Published in:
Scientific Reports, 2016, p. 31736, doi. 10.1038/srep31736
By:
- Pinho, Marcos D.;
- Erol, Erdal;
- Ribeiro-Gonçalves, Bruno;
- Mendes, Catarina I.;
- Carriço, João A.;
- Matos, Sandra C.;
- Preziuso, Silvia;
- Luebke-Becker, Antina;
- Wieler, Lothar H.;
- Melo-Cristino, Jose;
- Ramirez, Mario
Publication type:
Article
LMAS: evaluating metagenomic short de novo assembly methods through defined communities.
Published in:
GigaScience, 2023, v. 12, n. 1, p. 1, doi. 10.1093/gigascience/giac122
By:
- Mendes, Catarina Inês;
- Vila-Cerqueira, Pedro;
- Motro, Yair;
- Moran-Gilad, Jacob;
- Carriço, João André;
- Ramirez, Mário
Publication type:
Article
Increasing macrolide resistance among Streptococcus agalactiae causing invasive disease in non-pregnant adults was driven by a single capsular-transformed lineage, Portugal, 2009 to 2015.
Published in:
Eurosurveillance (15607917), 2018, v. 23, n. 21, p. 1, doi. 10.2807/1560-7917.ES.2018.23.21.1700473
By:
- Lopes, Elísia;
- Fernandes, Tânia;
- Machado, Miguel P.;
- Carriço, João André;
- Melo-Cristino, José;
- Ramirez, Mário;
- Martins, Elisabete R.
Publication type:
Article
Not Seeing the Forest for the Trees: Size of the Minimum Spanning Trees (MSTs) Forest and Branch Significance in MST-Based Phylogenetic Analysis.
Published in:
PLoS ONE, 2015, v. 10, n. 3, p. 1, doi. 10.1371/journal.pone.0119315
By:
- Teixeira, Andreia Sofia;
- Monteiro, Pedro T.;
- Carriço, João A;
- Ramirez, Mário;
- Francisco, Alexandre P.
Publication type:
Article
The Use of Machine Learning Methodologies to Analyse Antibiotic and Biocide Susceptibility in <i>Staphylococcus aureus</i>.
Published in:
PLoS ONE, 2013, v. 8, n. 2, p. 1, doi. 10.1371/journal.pone.0055582
By:
- Coelho, Joana Rosado;
- Carriço, João André;
- Knight, Daniel;
- Martínez, Jose-Luis;
- Morrissey, Ian;
- Oggioni, Marco Rinaldo;
- Freitas, Ana Teresa
Publication type:
Article
Evaluation of Jackknife and Bootstrap for Defining Confidence Intervals for Pairwise Agreement Measures.
Published in:
PLoS ONE, 2011, v. 6, n. 5, p. 1, doi. 10.1371/journal.pone.0019539
By:
- Severiano, Ana;
- Carriço, João A.;
- Robinson, D. Ashley;
- Ramirez, Mário;
- Pinto, Francisco R.
Publication type:
Article
EURISWEB - Web-based epidemiological surveillance of antibiotic-resistant pneumococci in Day Care Centers.
Published in:
BMC Medical Informatics & Decision Making, 2003, v. 3, n. 1, p. 9, doi. 10.1186/1472-6947-3-9
By:
- Silva, Sara;
- Gouveia-Oliveira, Rodrigo;
- Maretzek, António;
- Carriço, João;
- Gudnason, Thorolfur;
- Kristinsson, Karl G.;
- Ekdahl, Karl;
- Brito-Avô, António;
- Tomasz, Alexander;
- Sanches, Ilda Santos;
- de Lencastre, Hermínia;
- Almeida, Jonas
Publication type:
Article
Technical and Economic Assessment of a 450 W Autonomous Photovoltaic System with Lithium Iron Phosphate Battery Storage.
Published in:
Journal of Sustainable Development of Energy, Water & Environment Systems (JSDEWES), 2018, v. 6, n. 1, p. 129, doi. 10.13044/j.sdewes.d5.0191
By:
- Carriço, João;
- Fernandes, João;
- Fernandes, Carlos;
- Branco, Paulo
Publication type:
Article
Fast phylogenetic inference from typing data.
Published in:
Algorithms for Molecular Biology, 2018, v. 13, p. 1, doi. 10.1186/s13015-017-0119-7
By:
- Carriço, João A.;
- Crochemore, Maxime;
- Francisco, Alexandre P.;
- Pissis, Solon P.;
- Ribeiro-Gonçalves, Bruno;
- Vaz, Cátia
Publication type:
Article
Distance-based phylogenetic inference from typing data: a unifying view.
Published in:
Briefings in Bioinformatics, 2021, v. 22, n. 3, p. 1, doi. 10.1093/bib/bbaa147
By:
- Vaz, Cátia;
- Nascimento, Marta;
- Carriço, João A;
- Rocher, Tatiana;
- Francisco, Alexandre P
Publication type:
Article
A widespread family of polymorphic toxins encoded by temperate phages.
Published in:
BMC Biology, 2017, v. 15, p. 1, doi. 10.1186/s12915-017-0415-1
By:
- Jamet, Anne;
- Touchon, Marie;
- Ribeiro-Gonçalves, Bruno;
- Carriço, João André;
- Charbit, Alain;
- Nassif, Xavier;
- Ramirez, Mario;
- Rocha, Eduardo P. C.
Publication type:
Article
Clonal and serotype dynamics of serogroup 6 isolates causing invasive pneumococcal disease in Portugal: 1999-2012.
Published in:
PLoS ONE, 2017, v. 12, n. 2, p. 1, doi. 10.1371/journal.pone.0170354
By:
- Diamantino-Miranda, Jorge;
- Aguiar, Sandra Isabel;
- Carriço, João André;
- Melo-Cristino, José;
- Ramirez, Mário
Publication type:
Article
Analysis of genomic sequences by Chaos Game Representation.
Published in:
Bioinformatics, 2001, v. 17, n. 5, p. 429, doi. 10.1093/bioinformatics/17.5.429
By:
- Almeida, Jonas S.;
- Carriço, João A.;
- Maretzek, Antonio;
- Noble, Peter A.;
- Fletcher, Madilyn
Publication type:
Article
Author Correction: Critical steps in clinical shotgun metagenomics for the concomitant detection and typing of microbial pathogens.
Published in:
2019
By:
- 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.
Publication type:
Correction Notice
Critical steps in clinical shotgun metagenomics for the concomitant detection and typing of microbial pathogens.
Published in:
Scientific Reports, 2018, v. 8, n. 1, p. 1, doi. 10.1038/s41598-018-31873-w
By:
- 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.
Publication type:
Article
Heterogeneity of penicillin-non-susceptible group B streptococci isolated from a single patient in Germany.
Published in:
2020
By:
- van der Linden, Mark;
- Mamede, Rafael;
- Levina, Natascha;
- Helwig, Peter;
- Vila-Cerqueira, Pedro;
- Carriço, João André;
- Melo-Cristino, José;
- Ramirez, Mário;
- Martins, Elisabete R
Publication type:
journal article
PHYLOViZ 2.0: providing scalable data integration and visualization for multiple phylogenetic inference methods.
Published in:
Bioinformatics, 2017, v. 33, n. 1, p. 128, doi. 10.1093/bioinformatics/btw582
By:
- Nascimento, Marta;
- Sousa, Adriano;
- Ramirez, Mário;
- Francisco, Alexandre P.;
- Carriço, João A.;
- Vaz, Cátia
Publication type:
Article
Natural Occurrence of Escherichia coli -Infecting Bacteriophages in Clinical Samples.
Published in:
Frontiers in Microbiology, 2019, v. 10, p. 1, doi. 10.3389/fmicb.2019.02484
By:
- Pacífico, Cátia;
- Hilbert, Miriam;
- Sofka, Dmitrij;
- Dinhopl, Nora;
- Pap, Ildiko-Julia;
- Aspöck, Christoph;
- Carriço, João André;
- Hilbert, Friederike
Publication type:
Article
Distinct Phenotypic and Genomic Signatures Underlie Contrasting Pathogenic Potential of Staphylococcus epidermidis Clonal Lineages.
Published in:
Frontiers in Microbiology, 2019, p. 1, doi. 10.3389/fmicb.2019.01971
By:
- Espadinha, Diana;
- Sobral, Rita G.;
- Mendes, Catarina Inês;
- Méric, Guillaume;
- Sheppard, Samuel K.;
- Carriço, João A.;
- de Lencastre, Hermínia;
- Miragaia, Maria
Publication type:
Article

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