Identification of Transcription Factor Binding Sites in Promoter Regions by Modularity Analysis of the Motif Co-occurrence Graph. - Alexandre P. Francisco; Arlindo L. Oliveira; Ana T. Freitas (ISBRA, 2008)

Clique Analysis of Query Log Graphs. - Alexandre P. Francisco; Ricardo Baeza-Yates; Arlindo L. Oliveira (SPIRE, 2008)

YEASTRACT-DISCOVERER: new tools to improve the analysis of transcriptional regulatory associations in Saccharomyces cerevisiae. - Pedro T. Monteiro 001; Nuno D. Mendes; Miguel C. Teixeira; Sofia d'Orey; Sandra Tenreiro; Nuno P. Mira; Hélio Pais; Alexandre P. Francisco; Alexandra M. Carvalho; Artur B. Lourenço; Isabel Sá-Correia; Arlindo L. Oliveira; et al. (Nucleic Acids Res., 2008)

Global optimal eBURST analysis of multilocus typing data using a graphic matroid approach. - Alexandre P. Francisco; Miguel M. F. Bugalho; Mário Ramirez; João A. Carriço (BMC Bioinform., 2009)

Using graph modularity analysis to identify transcription factor binding sites. - Alexandre P. Francisco; Sophie Schbath; Ana T. Freitas; Arlindo L. Oliveira (BIBM Workshops, 2010)

Fully Generalized Graph Cores. - Alexandre P. Francisco; Arlindo L. Oliveira (CompleNet, 2010)

On Community Detection in Very Large Networks. - Alexandre P. Francisco; Arlindo L. Oliveira (CompleNet, 2010)

An Ontology and a REST API for Sequence Based Microbial Typing Data. - João Almeida; João Tiple; Mário Ramirez; José Melo-Cristino; Cátia Vaz; Alexandre P. Francisco; João A. Carriço (JBI, 2010)

Mining Large Query Induced Graphs towards a Hierarchical Query Folksonomy. - Alexandre P. Francisco; Ricardo Baeza-Yates; Arlindo L. Oliveira (SPIRE, 2010)

Baiacu: A Tool for the Visual Analysis of the Saccharomyces Cerevisiae Regulatory Network. - Ricardo Santos Aires; João A. Carriço; Alexandre P. Francisco; Sara C. Madeira (PACBB, 2011)

TFRank: network-based prioritization of regulatory associations underlying transcriptional responses. - Joana P. Gonçalves; Alexandre P. Francisco; Nuno P. Mira; Miguel C. Teixeira; Isabel Sá-Correia; Arlindo L. Oliveira; Sara C. Madeira (Bioinform., 2011)

YEASTRACT: providing a programmatic access to curated transcriptional regulatory associations in Saccharomyces cerevisiae through a web services interface. - Dário Abdulrehman; Pedro T. Monteiro 001; Miguel C. Teixeira; Nuno P. Mira; Artur B. Lourenço; Sandra Costa dos Santos; Tânia Rodrigues Cabrito; Alexandre P. Francisco; Sara C. Madeira; Ricardo Santos Aires; Arlindo L. Oliveira; Isabel Sá-Correia; et al. (Nucleic Acids Res., 2011)

Pattern matching through Chaos Game Representation: bridging numerical and discrete data structures for biological sequence analysis. - Susana Vinga; Alexandra M. Carvalho; Alexandre P. Francisco; Luís M. S. Russo; Jonas S. Almeida (Algorithms Mol. Biol., 2012)

PHYLOViZ: phylogenetic inference and data visualization for sequence based typing methods. - Alexandre P. Francisco; Cátia Vaz; Pedro T. Monteiro 001; José Melo-Cristino; Mário Ramirez; João A. Carriço (BMC Bioinform., 2012)

Mining query log graphs towards a query folksonomy. - Alexandre P. Francisco; Ricardo Baeza-Yates; Arlindo L. Oliveira (Concurr. Comput. Pract. Exp., 2012)

Real-Time Integration of Building Energy Data. - Diogo Anjos; Paulo Carreira 001; Alexandre P. Francisco (BigData Congress, 2014)

Evaluating the Impact of Anonymization on Large Interaction Network Datasets. - Mário J. Silva; Pedro Rijo; Alexandre P. Francisco (PSBD@CIKM, 2014)

TypOn: the microbial typing ontology. - Cátia Vaz; Alexandre P. Francisco; Mickael Silva; Keith A. Jolley; James E. Bray; Hannes Pouseele; Jörg Rothgänger; Mário Ramirez; João A. Carriço (J. Biomed. Semant., 2014)

The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae. - Miguel Cacho Teixeira; Pedro Tiago Monteiro 001; Joana Fernandes Guerreiro; Joana Pinho Gonçalves; Nuno Pereira Mira; Sandra Costa dos Santos; Tânia Rodrigues Cabrito; Margarida Palma; Catarina Costa; Alexandre Paulo Francisco; Sara Cordeiro Madeira; Arlindo Limede Oliveira; et al. (Nucleic Acids Res., 2014)

Quick Hypervolume. - Luís M. S. Russo; Alexandre P. Francisco (IEEE Trans. Evol. Comput., 2014)

Techniques for Brain Functional Connectivity Analysis from High Resolution Imaging. - A. C. Leitão; Alexandre Paulo Francisco; Rodolfo Abreu; Sandro Nunes; Juliana Rodrigues; Patrícia Figueiredo; Lawrence L. Wald; Marta Bianciardi; L. Miguel Silveira (CompleNet, 2015)

Betweenness centrality in Delay Tolerant Networks: A survey. - Naércio Magaia; Alexandre P. Francisco; Paulo Rogério Pereira; Miguel Correia 001 (Ad Hoc Networks, 2015)

Influence and Sentiment Homophily on Twitter Social Circles. - Hugo Lopes; Helena Sofia Pinto; Alexandre P. Francisco (CompleNet, 2016)

Spanning Edge Betweenness in Practice. - Andreia Sofia Teixeira; Francisco C. Santos; Alexandre P. Francisco (CompleNet, 2016)

Extending quick hypervolume. - Luís M. S. Russo; Alexandre P. Francisco (J. Heuristics, 2016)

PHYLOViZ Online: web-based tool for visualization, phylogenetic inference, analysis and sharing of minimum spanning trees. - Bruno Ribeiro-Gonçalves; Alexandre P. Francisco; Cátia Vaz; Mário Ramirez; João André Carriço (Nucleic Acids Res., 2016)

Evaluating the impact of k-anonymization on the inference of interaction networks. - Pedro Rijo; Alexandre P. Francisco; Mário J. Silva (Trans. Data Priv., 2016)

NGSPipes: Fostering Reproducibility and Scalability in Biosciences. - Bruno Dantas; Calmenelias Fleitas; Alexandre Almeida; João Forja; Alexandre P. Francisco; José Simão; Cátia Vaz (BCB, 2017)

Dynamic Phylogenetic Inference for Sequence-based Typing Data. - Alexandre P. Francisco; Marta Nascimento; Cátia Vaz (BCB, 2017)

Using Spark and GraphX to Parallelize Large-Scale Simulations of Bacterial Populations over Host Contact Networks. - Andreia Sofia Teixeira; Pedro T. Monteiro 001; João A. Carriço; Francisco C. Santos; Alexandre P. Francisco (ICA3PP, 2017)

Towards Distance-Based Phylogenetic Inference in Average-Case Linear-Time. - Maxime Crochemore; Alexandre P. Francisco; Solon P. Pissis; Cátia Vaz (WABI, 2017)

PHYLOViZ 2.0: providing scalable data integration and visualization for multiple phylogenetic inference methods. - Marta Nascimento; Adriano Sousa; Mário Ramirez; Alexandre P. Francisco; João A. Carriço; Cátia Vaz (Bioinform., 2017)

Gelly-Scheduling: Distributed Graph Processing for Network Service Placement. - Miguel E. Coimbra; Alexandre P. Francisco; Luís Veiga (CoRR, 2017)

Study on Resource Efficiency of Distributed Graph Processing. - Miguel E. Coimbra; Alexandre P. Francisco; Luís Veiga (CoRR, 2017)

Beyond NGS data sharing and towards open science. - Bruno Dantas; Calmenelias Fleitas; Alexandre P. Francisco; José Simão; Cátia Vaz (CoRR, 2017)

Exploiting Computation-Friendly Graph Compression Methods. - Alexandre P. Francisco; Travis Gagie; Susana Ladra; Gonzalo Navarro 001 (CoRR, 2017)

Capturing Financial Volatility Through Simple Network Measures. - Pedro C. Souto; Andreia Sofia Teixeira; Alexandre P. Francisco; Francisco C. Santos (COMPLEX NETWORKS (2), 2018)

Order-Preserving Pattern Matching Indeterminate Strings. - Rui Henriques; Alexandre P. Francisco; Luís M. S. Russo; Hideo Bannai (CPM, 2018)

Exploiting Computation-Friendly Graph Compression Methods for Adjacency-Matrix Multiplication. - Alexandre P. Francisco; Travis Gagie; Susana Ladra; Gonzalo Navarro 001 (DCC, 2018)

Gelly-scheduling: distributed graph processing for service placement in community networks. - Miguel E. Coimbra; Mennan Selimi; Alexandre P. Francisco; Felix Freitag; Luís Veiga (SAC, 2018)

Linking and Cutting Spanning Trees. - Luís M. S. Russo; Andreia Sofia Teixeira; Alexandre P. Francisco (Algorithms, 2018)

Fast phylogenetic inference from typing data. - João A. Carriço; Maxime Crochemore; Alexandre P. Francisco; Solon P. Pissis; Bruno Ribeiro-Gonçalves; Cátia Vaz (Algorithms Mol. Biol., 2018)

GraphBolt: Streaming Graph Approximations on Big Data. - Miguel E. Coimbra; Renato Rosa; Sérgio Esteves; Alexandre P. Francisco; Luís Veiga (CoRR, 2018)

SpliceTAPyR - An Efficient Method for Transcriptome Alignment. - Andreia Sofia Teixeira; Francisco Fernandes; Alexandre P. Francisco (Int. J. Found. Comput. Sci., 2018)

Large-Scale Simulations of Bacterial Populations Over Complex Networks. - Andreia Sofia Teixeira; Pedro T. Monteiro 001; João A. Carriço; Francisco C. Santos; Alexandre P. Francisco (J. Comput. Biol., 2018)

Using Machine Learning to Improve the Prediction of Functional Outcome in Ischemic Stroke Patients. - Miguel Monteiro; Ana Catarina Fonseca; Ana Teresa Freitas; Teresa Pinho e Melo; Alexandre P. Francisco; José M. Ferro 001; Arlindo L. Oliveira (IEEE ACM Trans. Comput. Biol. Bioinform., 2018)

Distributed graphs: in search of fast, low-latency, resource-efficient, semantics-rich Big-Data processing. - Miguel E. Coimbra; Alexandre P. Francisco; Luís Veiga (CoRR, 2019)

On Dynamic Succinct Graph Representations. - Miguel E. Coimbra; Alexandre P. Francisco; Luís M. S. Russo; Guillermo de Bernardo; Susana Ladra; Gonzalo Navarro 001 (DCC, 2020)

Approximating Optimal Bidirectional Macro Schemes. - Luís M. S. Russo; Ana Sofia D. Correia; Gonzalo Navarro 001; Alexandre P. Francisco (DCC, 2020)

Sparsifying parity-check matrices. - Luís M. S. Russo; Tobias Dietz; José Rui Figueira; Alexandre P. Francisco; Stefan Ruzika (Appl. Soft Comput., 2020)

Incremental Multiple Longest Common Sub-Sequences. - Luís M. S. Russo; Alexandre P. Francisco; Tatiana Rocher (CoRR, 2020)

Hardness of Modern Games. - Diogo M. Costa; Alexandre P. Francisco; Luís M. S. Russo (CoRR, 2020)

Eliciting Fairness in Multiplayer Bargaining through Network-Based Role Assignment. - Andreia Sofia Teixeira; Francisco C. Santos; Alexandre P. Francisco; Fernando P. Santos (AAMAS, 2021)

Distance-based phylogenetic inference from typing data: a unifying view. - Cátia Vaz; Marta Nascimento; João A. Carriço; Tatiana Rocher; Alexandre P. Francisco (Briefings Bioinform., 2021)

Eliciting Fairness in N-Player Network Games through Degree-Based Role Assignment. - Andreia Sofia Teixeira; Francisco C. Santos; Alexandre P. Francisco; Fernando P. Santos (Complex., 2021)

Evolution of collective fairness in complex networks through degree-based role assignment. - Andreia Sofia Teixeira; Francisco C. Santos; Alexandre P. Francisco; Fernando P. Santos (CoRR, 2021)

Small Longest Tandem Scattered Subsequences. - Luís M. S. Russo; Alexandre P. Francisco (Sci. Ann. Comput. Sci., 2021)

An analysis of the graph processing landscape. - Miguel E. Coimbra; Alexandre P. Francisco; Luís Veiga (J. Big Data, 2021)

A practical succinct dynamic graph representation. - Miguel E. Coimbra; Joana Hrotkó; Alexandre P. Francisco; Luís M. S. Russo; Guillermo de Bernardo; Susana Ladra; Gonzalo Navarro 001 (Inf. Comput., 2022)

Order-preserving pattern matching indeterminate strings. - Luís M. S. Russo; Diogo M. Costa; Rui Henriques; Hideo Bannai; Alexandre P. Francisco (Inf. Comput., 2022)

VeilGraph: incremental graph stream processing. - Miguel E. Coimbra; Sérgio Esteves; Alexandre P. Francisco; Luís Veiga (J. Big Data, 2022)

Graph Compression for Adjacency-Matrix Multiplication. - Alexandre P. Francisco; Travis Gagie; Dominik Köppl; Susana Ladra; Gonzalo Navarro 001 (SN Comput. Sci., 2022)

Correction to: Graph Compression for Adjacency-Matrix Multiplication. - Alexandre P. Francisco; Travis Gagie; Dominik Köppl; Susana Ladra; Gonzalo Navarro 001 (SN Comput. Sci., 2022)

Cache-oblivious Hilbert Curve-based Blocking Scheme for Matrix Transposition. - João Nuno Ferreira Alves; Luís Manuel Silveira Russo; Alexandre P. Francisco (ACM Trans. Math. Softw., 2022)

A Novel Triangular Space-Filling Curve for Cache-Oblivious In-Place Transposition of Square Matrices. - João Nuno Ferreira Alves; Luís M. S. Russo; Alexandre P. Francisco; Siegfried Benkner (IPDPS, 2023)

On Finding Optimal (Dynamic) Arborescences. - Joaquim Espada; Alexandre P. Francisco; Tatiana Rocher; Luís M. S. Russo; Cátia Vaz (Algorithms, 2023)

phyloDB: A framework for large-scale phylogenetic analysis. - Bruno Lourenço; Cátia Vaz; Miguel E. Coimbra; Alexandre P. Francisco (CoRR, 2023)

Phylogenetic tree distance computation over succinct representations. - António Pedro Branco; Cátia Vaz; Alexandre P. Francisco (CoRR, 2023)

Computing RF Tree Distance over Succinct Representations. - António Pedro Branco; Cátia Vaz; Alexandre P. Francisco (Algorithms, 2024)

A modular and scalable web platform for computational phylogenetics. - Nyckollas Brandão; André Jesus; André Páscoa; Alexandre P. Francisco; Mário Ramirez; Cátia Vaz (CoRR, 2024)

Accelerating Graph Neural Networks with a Novel Matrix Compression Format. - João Nuno Ferreira Alves; Samir Moustafa; Siegfried Benkner; Alexandre P. Francisco; Wilfried N. Gansterer; Luís M. S. Russo (CoRR, 2024)

phyloDB: A framework for large-scale phylogenetic analysis of sequence based typing data. - Bruno Lourenço; Cátia Vaz; Miguel E. Coimbra; Alexandre P. Francisco (SoftwareX, 2024)

A multi-objective mixed integer linear programming model for thesis defence scheduling. - João Almeida; Daniel Santos 003; José Rui Figueira; Alexandre P. Francisco (Eur. J. Oper. Res., 2024)

Accelerating Graph Neural Networks Using a Novel Computation-Friendly Matrix Compression Format. - João Nuno Ferreira Alves; Samir Moustafa; Siegfried Benkner; Alexandre P. Francisco; Wilfried N. Gansterer; Luís M. S. Russo (IPDPS, 2025)

Survey: Graph Databases. - Miguel E. Coimbra; Lucie Svitáková; Alexandre P. Francisco; Luís Veiga (CoRR, 2025)