Circuit partitioning techniques for power estimation using the full set of input correlations. - Ana T. Freitas; Arlindo L. Oliveira (ICECS, 2001)

Implicit Resolution of the Chapman-Kolmogorov Equations for Sequential Circuits: An Application in Power Estimation. - Ana T. Freitas; Arlindo L. Oliveira (DATE, 2003)

A parallel algorithm for the extraction of structured motifs. - Alexandra M. Carvalho; Arlindo L. Oliveira; Ana T. Freitas; Marie-France Sagot (SAC, 2004)

Efficient Extraction of Structured Motifs Using Box-Links. - Alexandra M. Carvalho; Ana T. Freitas; Arlindo L. Oliveira; Marie-France Sagot (SPIRE, 2004)

A highly scalable algorithm for the extraction of CIS-regulatory regions. - Alexandra M. Carvalho; Ana T. Freitas; Arlindo L. Oliveira; Marie-France Sagot (APBC, 2005)

MUSA: a parameter free algorithm for the identification of biologically significant motifs. - Nuno D. Mendes; Ana C. Casimiro; Pedro M. Santos 003; Isabel Sá-Correia; Arlindo L. Oliveira; Ana T. Freitas (Bioinform., 2006)

The YEASTRACT database: a tool for the analysis of transcription regulatory associations in Saccharomyces cerevisiae. - Miguel C. Teixeira; Pedro T. Monteiro 001; Pooja Jain; Sandra Tenreiro; Alexandra R. Fernandes; Nuno P. Mira; Marta Alenquer; Ana T. Freitas; Arlindo L. Oliveira; Isabel Sá-Correia (Nucleic Acids Res., 2006)

An Efficient Algorithm for the Identification of Structured Motifs in DNA Promoter Sequences. - Alexandra M. Carvalho; Ana T. Freitas; Arlindo L. Oliveira; Marie-France Sagot (IEEE ACM Trans. Comput. Biol. Bioinform., 2006)

Temporal Logic Patterns for Querying Qualitative Models of Genetic Regulatory Networks. - Pedro T. Monteiro 001; Delphine Ropers; Radu Mateescu 001; Ana T. Freitas; Hidde de Jong (ECAI, 2008)

Temporal logic patterns for querying dynamic models of cellular interaction networks. - Pedro T. Monteiro 001; Delphine Ropers; Radu Mateescu 001; Ana T. Freitas; Hidde de Jong (ECCB, 2008)

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)

An analysis of the positional distribution of DNA motifs in promoter regions and its biological relevance. - Ana C. Casimiro; Susana Vinga; Ana T. Freitas; Arlindo L. Oliveira (BMC Bioinform., 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)

CSA: An efficient algorithm to improve circular DNA multiple alignment. - Francisco Fernandes; Luísa Pereira; Ana T. Freitas (BMC Bioinform., 2009)

A service-oriented architecture for integrating the modeling and formal verification of genetic regulatory networks. - Pedro T. Monteiro 001; Estelle Dumas; Bruno Besson; Radu Mateescu 001; Michel Page; Ana T. Freitas; Hidde de Jong (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)

Semantic characterization of hypertrophic cardiomyopathy disease. - Catia M. Machado; Francisco M. Couto; Alexandra R. Fernandes; Susana Santos; Nuno Cardim; Ana T. Freitas (BIBM Workshops, 2010)

Modeling and formal verification of biological regulatory networks: An integrative approach. - Pedro T. Monteiro 001; Ana T. Freitas; Delphine Ropers; Radu Mateescu 001; Hidde de Jong (BIBM Workshops, 2010)

Unraveling Hypertrophic Cardiomyopathy Variability. - Catia M. Machado; Francisco M. Couto; Alexandra R. Fernandes; Susana Santos; Nuno Cardim; Ana T. Freitas (ERCIM News, 2010)

Quantitative Modeling the Saccharomyces cerevisiae FLR1 Regulatory Network Using an S-System Formalism. - Dulce Calçada; Susana Vinga; Ana T. Freitas; Arlindo L. Oliveira (HISB, 2011)

Efficient alignment of pyrosequencing reads for re-sequencing applications. - Francisco Fernandes; Paulo G. S. da Fonseca 002; Luís M. S. Russo; Arlindo L. Oliveira; Ana T. Freitas (BMC Bioinform., 2011)

Quantitative Modeling of the Saccharomyces cerevisiae Flr1 regulatory Network Using an S-System Formalism. - Dulce Calçada; Susana Vinga; Ana T. Freitas; Arlindo L. Oliveira (J. Bioinform. Comput. Biol., 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)

Toward a Translational Medicine Approach for Hypertrophic Cardiomyopathy. - Catia M. Machado; Francisco M. Couto; Alexandra R. Fernandes; Susana Santos; Ana T. Freitas (ITBAM, 2012)

Navigating the unexplored seascape of pre-miRNA candidates in single-genome approaches. - Nuno D. Mendes; Steffen Heyne; Ana T. Freitas; Marie-France Sagot; Rolf Backofen (Bioinform., 2012)

Parallel efficient aligner of pyrosequencing reads. - Miguel E. Coimbra; Francisco Fernandes; Luís M. S. Russo; Ana T. Freitas (EuroMPI, 2013)

Enrichment analysis applied to disease prognosis. - Catia M. Machado; Ana T. Freitas; Francisco M. Couto (J. Biomed. Semant., 2013)

slaMEM: efficient retrieval of maximal exact matches using a sampled LCP array. - Francisco Fernandes; Ana T. Freitas (Bioinform., 2014)

Data Management in Metagenomics: A Risk Management Approach. - Filipe Ferreira; Miguel E. Coimbra; Raquel Bairrão; Ricardo Viera; Ana T. Freitas; Luís M. S. Russo; José Borbinha (Int. J. Digit. Curation, 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)

The semantic web in translational medicine: current applications and future directions. - Catia M. Machado; Dietrich Rebholz-Schuhmann; Ana T. Freitas; Francisco M. Couto (Briefings Bioinform., 2015)

BioSurfDB: knowledge and algorithms to support biosurfactants and biodegradation studies. - Jorge S. Oliveira; Wydemberg Araújo; Ana Isabela Lopes Sales; Alaine de Brito Guerra; Sinara Carla da Silva Araújo; Ana Tereza Ribeiro de Vasconcelos; Lucymara F. Agnez-Lima; Ana Teresa Freitas (Database J. Biol. Databases Curation, 2015)

A Virtual Research Environment for the Oil and Gas Domain. - Jorge S. Oliveira; José Borbinha; Ana Teresa Freitas (ERCIM News, 2017)

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)

CSA-MEM: Enhancing Circular DNA Multiple Alignment Through Text Indexing Algorithms. - André Salgado; Francisco Fernandes; Ana Teresa Freitas (ISBRA, 2023)

Microbiome Classification in Colon Cancer Patients Using Chaos Game Representations and CNN Models. - Javier Montoya; Francisco Fernandes; Ana Teresa Freitas (IWBBIO (2), 2024)