Research Interests

  • Algorithms and data structures.
  • Data Science
  • Formal methods and models, as fundamental tools for systems modeling. Specification languages.
  • Applied mathematical logic.
  • Knowledge representation and reasoning.

Publications

    Google Scholar Profile
  • GrapeTree: Visualization of core genomic relationships among 100,000 bacterial pathogens, by Zhemin Zhou, Nabil-Fareed Alikhan, M. J. Sergeant, N. Luhmann, C. Vaz, A. P. Francisco, J. A. Carriço and M. Achtman. Genome Research, 2018.
  • 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.
  • Maxime Crochemore, Alexandre P Francisco, Solon P Pissis, Cátia Vaz. Towards distance-based phylogenetic inference in average-case linear-time. LIPIcs-Leibniz International Proceedings in Informatics (WABI 2017)
  • Alexandre P Francisco, Marta Nascimento, Cátia Vaz. Dynamic Phylogenetic Inference for Sequence-based Typing Data. Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics, 2017. https://doi.org/10.1145/3107411.3108214
  • Bruno Dantas, Calmenelias Fleitas, Alexandre Almeida, João Forja, Alexandre P Francisco, José Simão, Cátia Vaz. NGSPipes: Fostering Reproducibility and Scalability in Biosciences. Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics, 2017. https://doi.org/10.1145/3107411.3108213
  • Marta Nascimento, Adriano Sousa, Mário Ramirez, Alexandre P. Francisco, João Carriço, Cátia Vaz. PHYLOViZ 2.0: Providing scalable data integration and visualization for multiple phylogenetic inference methods, Bioinformatics, (2016).
  • Bruno Ribeiro-Gonçalves, Alexandre P. Francisco, Cátia Vaz, Mário Ramirez, João A. Carriço. PHYLOViZ Online: web-based tool for visualization, phylogenetic inference, analysis and sharing of minimum spanning trees, Nucl. Acids Res., Web Issue (2016) (http://nar.oxfordjournals.org/content/early/2016/04/29/nar.gkw359.full)
  • Bruno Dantas, Calmenelias Fleitas, Alexandre P. Francisco, José Simão. NGSPipes: From Specification to Automatic Deployment of NGS pipelines, INFORUM 2016 (http://inforum.org.pt/INForum2016/)
  • Bruno Dantas, Calmenelias Fleitas, Alexandre P Francisco, José Simão and Cátia Vaz Beyond NGS data sharing and towards open science (pdf), 2016, arXiv preprint arXiv:1701.03507
  • João Forja, Alexandre Almeida, Alexandre Francisco, José Simão e Cátia Vaz. NGS4Cloud: Cloud-based NGS Data Processing. Inforum, 2016 http://inforum.org.pt/INForum2016/).
  • Bruno Dantas, Calmenelias Fleitas, Alexandre Almeida, João Forja, Alexandre P Francisco, José Simão, Cátia Vaz. NGSPipes: Fostering Reproducibility and Scalability in Biosciences. Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics, 2017. https://doi.org/10.1145/3107411.3108213
  • C. Vaz, A. P Francisco, M. Silva, K. A Jolley, J. E. Bray, H. Pouseele, J. Rothgaenger, M. Ramirez and João A Carriço. TypOn: The Microbial Typing Ontology. Journal of Biomedical Semantics, 5:43 4, 2014
  • A. Domingos, H. Ferreira, P. Rijo, C. Vaz, and A. P. Francisco. Degrees of separation on a dynamic social network. In Mining and Learning with Graphs - Knowledge Discovery and Data Mining (MLG-KDD'13), ACM 2013.
  • C. Vaz and C. Ferreira. On the analysis of compensation correctness. Journal of Logic and Algebraic Programming, Elsevier, 2012. Volume 81, no5, pp 585-605, Elsevier.
  • Alexandre P Francisco, Cátia Vaz, Pedro T Monteiro, José Melo-Cristino, Mário Ramirez and João A Carriço. PHYLOViZ: phylogenetic inference and data visualization for sequence based typing methods. BMC Bioinformatics 2012. Volume 13, no 87.
  • J. Almeida, J. Tiple, M. Ramirez, J. Melo-Cristino, C. Vaz, A. P. Francisco, and J. A. Carriço. An ontology and a REST API for sequence based microbial typing data. In Bioinformatics for Personalized Medicine, Lecture Notes in Computer Science, 6620:21-28, 2012 (doi:10.1007/978-3-642-28062-7_3).
  • I. Lanese, C. Vaz and C. Ferreira. On the Expressive Power of Primitives for Compensation Handling.In 19th European Symposium on Programming, ESOP 2010. Volume 6012 of Lecture Notes in Computer Science (2010), pp 366-386, Springer.
  • C. Vaz and C. Ferreira. Towards Compensation Correctness in Interactive Systems. In 6th International Workshop on Web Services and Formal Methods, WS-FM 2009. Volume 6194 of Lecture Notes in Computer Science (2010), pp 161-177 Springer.
  • C. Vaz, C. Ferreira and A. Ravara. Dynamic Recovering of Long Running Transactions, In 4th International Symposium on Trustworthy Global Computing, TGC 2008, Barcelona, Spain. Lecture Notes in Computer Science 5474, pp 201-215, Springer.
  • C. Vaz, C. Ferreira and A. Ravara. Dynamic Recovering of Long Running Transactions, CITI Tec. Rep., 2008.
  • C. Vaz and C. Ferreira. Towards Automated Verification of Web Services , IADIS WWW/Internet 2007, Oct. 2007.
  • C. Vaz and C. Ferreira. Formal Verifycation of Workflow Patterns. INESC-ID Tec. Rep. 12/2007, Abril 2007. (pdf)
  • C. Vaz. Quantales with supports and applications to modal logic. Instituto Superior Técnico, 2004. MSc thesis. Supervised by P. Resende.
  • C. Vaz. Independence structures on quantales. Instituto Superior Técnico, 2002. Diploma thesis. Supervised by P. Resende.

Current Projects

Some ongoing projects that I am envolved are: NGSPhylo, BacGenTrack.