Assistant Professor at the CSE Dept, IST, Tech Univ of Lisbon. Researcher of the KDBIO group, INESC-ID. Collaborator of the UMMI, IMM, Fac of Medicine, Univ of Lisbon.
Doctorate (PhD) in Computer Science and Engineering. Master of Science (MSc) in Applied Mathematics. Licentiate (five year degree) in Applied Mathematics and Computer Science.
INESC-ID, Rua Alves Redol 9, 1000-029 Lisboa, PORTUGAL. Tel. (+351) 21 310 0272, Fax. (+351) 21 314 5843.aplf@{ist.utl,inesc-id}.pt (PGP public key)
PHYLOViZ, joint work with C. Vaz, P. T. Monteiro, J. A. Carriço, M. Ramirez and J. Melo-Cristino.
3rd International Workshop on Complex Networks (CompleNet 2012), Program Committee member.
TFRank: network-based prioritization of regulatory associations underlying transcriptional responses, by J. P. Gonçalves, A. P. Francisco, N. P. Mira, M. C. Teixeira, I. Sá-Correia, A. L. Oliveira, and S. C. Madeira. Bioinformatics, 2011. Online tool and documentation.
Mining query log graphs towards a query folksonomy, by A. P. Francisco, R. Baeza-Yates, and A. L. Oliveira. Concurrency and Computation: Practice and Experience, 2011. A preliminary version was released as INESC-ID Technical Report 36/2010.
YEASTRACT: Providing a programmatic access to curated transcriptional regulatory associations in Saccharomyces cerevisiae through a web services interface, by D. Abdulrehman, P. T. Monteiro, M. C. Teixeira, N. P. Mira, A. B. Lourenço, S. C. dos Santos, T. R. Cabrito, A. P. Francisco, S. C. Madeira, R. S. Aires, A. L. Oliveira, I. Sá-Correia, and A. T. Freitas. Nucleic Acids Research, 39(suppl 1):D136-D140, 2011. Website.
Fully generalized graph cores, by A. P. Francisco and A. L. Oliveira. In Complex Networks, Communications in Computer and Information Science, 116:22-34, 2010.
On community detection in very large networks, by A. P. Francisco and A. L. Oliveira. In Complex Networks, Communications in Computer and Information Science, 116:208-216, 2010. Algorithm implementation.
Mining large query induced graphs towards a hierarchical query folksonomy, by A. P. Francisco, R. Baeza-Yates, and A. L. Oliveira. In String Processing and Information Retrieval, Lecture Notes in Computer Science, 6393:238-243, 2010.
Fourteenth International Conference on Research in Computational Molecular Biology (RECOMB 2010), Organizing Committee member.
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).
Clique analysis of query log graphs, by A. P. Francisco, R. Baeza-Yates and A. L. Oliveira. In String Processing and Information Retrieval, Lecture Notes in Computer Science, 5280:188-199, 2008.
Identification of transcription factor binding sites in promoter regions by modularity analysis of the motif co-occurrence graph, by A. P. Francisco, A. L. Oliveira and A. T. Freitas. In Bioinformatics Research and Applications, Lecture Notes in Computer Science, 4983:220-231, 2008. A preliminary version was released as INESC-ID Technical Report 15/2007.
YEASTRACT-DISCOVERER: new tools to improve the analysis of transcriptional regulatory associations in Saccharomyces cerevisiae, by P. T. Monteiro, N. D. Mendes, M. C. Teixeira, S. d'Orey, S. Tenreiro, N. P. Mira, H. Pais, A. P. Francisco, A. M. Carvalho, A. B. Lourenço, I. Sá-Correia, A. L. Oliveira and A. T. Freitas. Nucleic Acids Research 36(suppl 1):D132-D136, 2008. Website.
Circuits of finite memory retrospective operators, by A. P. Francisco and J. F. Costa. In Second St.Petersburg Days of LOGIC and COMPUTABILITY, 2003. Paper and extended version.