A
Alexandre P. Francisco
Researcher at Instituto Superior Técnico
Publications - 88
Citations - 3088
Alexandre P. Francisco is an academic researcher from Instituto Superior Técnico. The author has contributed to research in topics: Computer science & Population. The author has an hindex of 16, co-authored 77 publications receiving 2336 citations. Previous affiliations of Alexandre P. Francisco include University of Lisbon & INESC-ID.
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Global optimal eBURST analysis of multilocus typing data using a graphic matroid approach
TL;DR: GoeBURST is a globally optimized implementation of the eBURST algorithm, that identifies alternative patterns of descent for several bacterial species and can be applied to any multilocus typing data based on the number of differences between numeric profiles.
Journal ArticleDOI
PHYLOViZ: phylogenetic inference and data visualization for sequence based typing methods
Alexandre P. Francisco,Alexandre P. Francisco,Cátia Vaz,Pedro T. Monteiro,Pedro T. Monteiro,José Melo-Cristino,Mário Ramirez,João A. Carriço,João A. Carriço +8 more
TL;DR: PHYLOViZ is platform independent Java software that allows the integrated analysis of sequence-based typing methods, including SNP data generated from whole genome sequence approaches, and associated epidemiological data.
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GrapeTree : visualization of core genomic relationships among 100,000 bacterial pathogens
Zhemin Zhou,Nabil-Fareed Alikhan,Martin J. Sergeant,Nina Luhmann,Cátia Vaz,Alexandre P. Francisco,Alexandre P. Francisco,João A. Carriço,Mark Achtman +8 more
TL;DR: GrapeTree is a stand-alone package for investigating phylogenetic trees plus associated metadata and is also integrated into EnteroBase to facilitate cutting edge navigation of genomic relationships among bacterial pathogens.
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PHYLOViZ 2.0: providing scalable data integration and visualization for multiple phylogenetic inference methods
Marta Nascimento,Marta Nascimento,Adriano Sousa,Mário Ramirez,Alexandre P. Francisco,Alexandre P. Francisco,João A. Carriço,Cátia Vaz,Cátia Vaz +8 more
TL;DR: PHYLOViZ 2.0 is presented, an extension of PHYLoviZ tool, a platform independent Java tool that allows phylogenetic inference and data visualization for large datasets of sequence based typing methods, including Single Nucleotide Polymorphism (SNP) and whole genome/core genome Multilocus Sequence Typing (wg/cgMLST) analysis.
Journal ArticleDOI
The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae
Miguel C. Teixeira,Pedro T. Monteiro,Joana F. Guerreiro,Joana P. Gonçalves,Nuno P. Mira,Sandra C. dos Santos,Tânia R. Cabrito,Margarida Palma,Catarina Costa,Alexandre P. Francisco,Sara C. Madeira,Arlindo L. Oliveira,Ana T. Freitas,Isabel Sá-Correia +13 more
TL;DR: The YEASTRACT information system was revisited and new information was added on the experimental conditions in which those associations take place and on whether the TF is acting on its target genes as activator or repressor, allowing the selection of specific environmental conditions, experimental evidence or positive/negative regulatory effect.