Publications

Our papers and reports on PHYLOViZ and related projects

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 Software package (superseded by PHYLOViZ, see above).

Student projects and theses

Works done by several students in collaboration with PHYLOViZ team.

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.