Analysis of genomic sequences by Chaos Game Representation. - Jonas S. Almeida; João A. Carriço; António Maretzek; Peter A. Noble; Madilyn Fletcher (Bioinform., 2001)

EURISWEB - Web-based epidemiological surveillance of antibiotic-resistant pneumococci in Day Care Centers. - Sara Silva; Rodrigo Gouveia-Oliveira; António Maretzek; João A. Carriço; Thorolfur Gudnason; Karl G. Kristinsson; Karl Ekdahl; António Brito-Avô; Alexander Tomasz; Ilda Santos Sanches; Hermínia de Lencastre; Jonas S. Almeida (BMC Medical Informatics Decis. Mak., 2003)

Ranked Adjusted Rand: integrating distance and partition information in a measure of clustering agreement. - Francisco R. Pinto; João A. Carriço; Mário Ramirez; Jonas S. Almeida (BMC Bioinform., 2007)

Global optimal eBURST analysis of multilocus typing data using a graphic matroid approach. - Alexandre P. Francisco; Miguel M. F. Bugalho; Mário Ramirez; João A. Carriço (BMC Bioinform., 2009)

An Ontology and a REST API for Sequence Based Microbial Typing Data. - João Almeida; João Tiple; Mário Ramirez; José Melo-Cristino; Cátia Vaz; Alexandre P. Francisco; João A. Carriço (JBI, 2010)

Baiacu: A Tool for the Visual Analysis of the Saccharomyces Cerevisiae Regulatory Network. - Ricardo Santos Aires; João A. Carriço; Alexandre P. Francisco; Sara C. Madeira (PACBB, 2011)

Biclustering-Based Classification of Clinical Expression Time Series: A Case Study in Patients with Multiple Sclerosis. - André Valério Carreiro; Orlando Anunciação; João A. Carriço; Sara C. Madeira (PACBB, 2011)

Prognostic Prediction through Biclustering-Based Classification of Clinical Gene Expression Time Series. - André Valério Carreiro; Orlando Anunciação; João André Carriço; Sara Cordeiro Madeira (J. Integr. Bioinform., 2011)

PHYLOViZ: phylogenetic inference and data visualization for sequence based typing methods. - Alexandre P. Francisco; Cátia Vaz; Pedro T. Monteiro 001; José Melo-Cristino; Mário Ramirez; João A. Carriço (BMC Bioinform., 2012)

TypOn: the microbial typing ontology. - Cátia Vaz; Alexandre P. Francisco; Mickael Silva; Keith A. Jolley; James E. Bray; Hannes Pouseele; Jörg Rothgänger; Mário Ramirez; João A. Carriço (J. Biomed. Semant., 2014)

Automatic determination of NET (neutrophil extracellular traps) coverage in fluorescent microscopy images. - Luís Pedro Coelho; Catarina Pato; Ana Friães; Ariane Neumann; Maren von Köckritz-Blickwede; Mário Ramirez; João André Carriço (Bioinform., 2015)

PHYLOViZ Online: web-based tool for visualization, phylogenetic inference, analysis and sharing of minimum spanning trees. - Bruno Ribeiro-Gonçalves; Alexandre P. Francisco; Cátia Vaz; Mário Ramirez; João André Carriço (Nucleic Acids Res., 2016)

Using Spark and GraphX to Parallelize Large-Scale Simulations of Bacterial Populations over Host Contact Networks. - Andreia Sofia Teixeira; Pedro T. Monteiro 001; João A. Carriço; Francisco C. Santos; Alexandre P. Francisco (ICA3PP, 2017)

PHYLOViZ 2.0: providing scalable data integration and visualization for multiple phylogenetic inference methods. - Marta Nascimento; Adriano Sousa; Mário Ramirez; Alexandre P. Francisco; João A. Carriço; Cátia Vaz (Bioinform., 2017)

Fast phylogenetic inference from typing data. - João A. Carriço; Maxime Crochemore; Alexandre P. Francisco; Solon P. Pissis; Bruno Ribeiro-Gonçalves; Cátia Vaz (Algorithms Mol. Biol., 2018)

Large-Scale Simulations of Bacterial Populations Over Complex Networks. - Andreia Sofia Teixeira; Pedro T. Monteiro 001; João A. Carriço; Francisco C. Santos; Alexandre P. Francisco (J. Comput. Biol., 2018)

Plasmid ATLAS: plasmid visual analytics and identification in high-throughput sequencing data. - Tiago F. Jesus; Bruno Ribeiro-Gonçalves; Diogo N. Silva; Valeria Bortolaia; Mário Ramirez; João A. Carriço (Nucleic Acids Res., 2019)

Distance-based phylogenetic inference from typing data: a unifying view. - Cátia Vaz; Marta Nascimento; João A. Carriço; Tatiana Rocher; Alexandre P. Francisco (Briefings Bioinform., 2021)

Chewie Nomenclature Server (chewie-NS): a deployable nomenclature server for easy sharing of core and whole genome MLST schemas. - Rafael Mamede; Pedro Vila-Cerqueira; Mickael Silva; João A. Carriço; Mário Ramirez (Nucleic Acids Res., 2021)