Fast phylogenetic inference from typing data, by J. A. Carriço, M. Crochemore, A. P. Francisco, S. P. Pissis, B. Ribeiro‑Gonçalves and C. Vaz. Algorithms for Molecular Biology, 13:4, 2018.
Using Spark and GraphX to parallelize large-scale simulations of bacterial populations over host contact networks, by A. S. Teixeira, P. T. Monteiro, J. A. Carriço, F. C. Santos and A. P. Francisco. In Algorithms and Architectures for Parallel Processing: 17th International Conference, ICA3PP 2017, 591-600, 2017.
Towards distance-based phylogenetic inference in average-case linear-time, by M. Crochemore, A. P. Francisco, S. P. Pissis and C. Vaz. In 17th International Workshop on Algorithms in Bioinformatics (WABI 2017), Leibniz International Proceedings in Informatics (LIPIcs), 88(9):1-14, 2017.
Dynamic phylogenetic inference for sequence-based typing data, by A. P. Francisco, M. Nascimento and C. Vaz. In Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics, 604-604, 2017.
PHYLOViZ 2.0: Providing scalable data integration and visualization for multiple phylogenetic inference methods, by M. Nascimento, A. Sousa, M. Ramirez A. P. Francisco, J. A. Carriço and C. Vaz. Bioinformatics, 2016. Website and preprint.
PHYLOViZ Online: web-based tool for visualization, phylogenetic inference, analysis and sharing of minimum spanning trees, by B. Ribeiro-Gonçalves, A. P. Francisco, C. Vaz, M. Ramirez and J. A. Carriço. Nucleic Acids Research, 2016. Website.PHYLOViZ Online: Web-based phylogenetic data analysis and visualization for allelic profiles and SNP data, by B. Gonçalves, A. P. Francisco, C. Vaz, M. Ramirez, and J. A. Carriço. In 11th International Meeting on Microbial Epidemiological Markers (IMMEM XI), 2016.
Not seeing the forest for the trees: Size of the minimum spanning trees (MSTs) forest and branch significance in MST-based phylogenetic analysis, by A. S. Teixeira, P. T. Monteiro, M. Ramirez, J. A. Carriço, and A. P. Francisco. PLoS One, 10(3):e0119315, 2015. Code and data.
TypOn: The Microbial Typing Ontology, by C. Vaz, A. P. Francisco, M. Silva, K. A. Jolley, J. E. Bray, H. Pouseele, J. Rothgaenger, M. Ramirez, and J. A. Carriço. Journal of Biomedical Semantics, 2014. Website. TypOn is also available at BioPortal. [pdf]
Topological representation of the within-species evolutionary structure of bacterial populations: the SLV graph, by P. T. Monteiro, A. P. Francisco, M. Ramirez, and J. A. Carriço. INESC-ID Technical Report 16/2014.
PHYLOViZ: Phylogenetic inference and data visualization for sequence based typing methods, by A. P. Francisco, C. Vaz, P. T. Monteiro, J. Melo-Cristino, M. Ramirez, and J. A. Carriço. BMC Bioinformatics, 13:87, 2012. PHYLOViZ website. Source code is also available at Bitbucket.
An ontology and a REST API for sequence based microbial typing data, by J. Almeida, J. Tiple, M. Ramirez, J. Melo-Cristino, C. Vaz, A. P. Francisco, and J. A. Carriço. In Bioinformatics for Personalized Medicine, Lecture Notes in Computer Science, 6620:21-28, 2012. Ontology website.
Global optimal eBURST analysis of multilocus typing data using a graphic matroid approach, by A. P. Francisco, M. F. Bugalho, M. Ramirez, and J. A. Carriço. BMC Bioinformatics, 10:152, 2009. Software package (superseded by PHYLOViZ, see above).
Large scale and dynamic phylogenetic inference from epidemic data, by M. Nascimento. MSc thesis, Instituto Superior Técnico, Universidade de Lisboa, 2017.
Visualização e algoritmos de clustering para análise filogenética, by A. Sousa and M. Nascimento. BSc thesis, Instituto Superior de Engenharia de Lisboa, 2015.
A framework for bacterial evolution simulation, by V. Ribeiro. MSc thesis, Instituto Superior Técnico, Universidade de Lisboa, 2012.
sLink, by C. Crisóstomo. BSc thesis, Instituto Superior de Engenharia de Lisboa, 2012.
RESTful Multilocus Sequence Typing Information System, by J. Almeida and J. Tiple. BSc thesis, Instituto Superior de Engenharia de Lisboa, 2010.
Framework de integração e visualização de dados biológicos, by D. Silva and L. Abel. BSc thesis, Instituto Superior de Engenharia de Lisboa, 2009.