AF

Ana Teresa Freitas

Current PhD Students Completed

Publications

2018

Using Machine Learning to Improve the Prediction of Functional Outcome in Ischemic Stroke Patients

Miguel Monteiro, Ana Catarina Fonseca, Ana T. Freitas, Teresa Pinho e Melo, Alexandre P. Francisco, José M. Ferro, Arlindo L. Oliveira

IEEE/ACM Transactions on Computational Biology and Bioinformatics journal summary

2013

The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation inSaccharomyces 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 Teresa Freitas, Isabel Sá‐Correia

Nucleic Acids Research journal summary

2012

TAPYR: An efficient high-throughput sequence aligner for re-sequencing applications

Francisco Fernandes, Paulo G. S. da Fonseca, Luís M. S.Russo, Arlindo L. Oliveira, Ana T. Freitas

EMBnet journal journal summary

2011

Improved Model Checking Techniques for State Space Analysis of Gene Regulatory Networks

Helio Pais, Kenneth L. McMillan, Ellen Sentovich, Ana T. Freitas, Arlindo L. Oliveira

IGI Global eBooks book summary

Quantitative Modeling the Saccharomyces cerevisiae FLR1 Regulatory Network Using an S-System Formalism

Dulce Calçada, Susana Vinga, Ana T. Freitas, Arlindo L. Oliveira

conference summary

Using systems biology approaches to study a multidrug resistance network

Paulo Jorge Dias, Catarina Costa, Isabel Sá‐Correia, Miguel C. Teixeira, Pedro T. Monteiro, Arlindo L. Oliveira, Ana T. Freitas

conference summary

QUANTITATIVE MODELING OF THESACCHAROMYCES CEREVISIAEFLR1 REGULATORY NETWORK USING AN S-SYSTEM FORMALISM

Dulce Calçada, Susana Vinga, Ana T. Freitas, Arlindo L. Oliveira

Journal of Bioinformatics and Computational Biology journal summary

Qualitative modelling and formal verification of the FLR1 gene mancozeb response in Saccharomyces cerevisiae

Pedro T. Monteiro, Paulo Jorge Dias, Delphine Ropers, Arlindo L. Oliveira, I. Sá-Correia, Miguel C. Teixeira, Ana T. Freitas

IET Systems Biology journal summary

Efficient alignment of pyrosequencing reads for re-sequencing applications

Francisco Fernandes, Paulo GS da Fonseca, Luís M. S.Russo, Arlindo L. Oliveira, Ana T. Freitas

BMC Bioinformatics journal summary

2010

Computational modeling and analysis of the yeast FLR1 regulatory network in mancozeb-challenged cells

Pedro T. Monteiro, Paulo Jorge Dias, Delphine Ropers, Arlindo L. Oliveira, Isabel Sá‐Correia, Miguel C. Teixeira, Ana T. Freitas

HAL (Le Centre pour la Communication Scientifique Directe) preprint summary

Using graph modularity analysis to identify transcription factor binding sites

Alexandre P. Francisco, Sophie Schbath, Ana T. Freitas, Arlindo L. Oliveira

preprint summary

Refining current knowledge on the yeast FLR1 regulatory network by combined experimental and computational approaches

Miguel C. Teixeira, Paulo Jorge Dias, Pedro T. Monteiro, Adrien Sala, Arlindo L. Oliveira, Ana T. Freitas, Isabel Sá‐Correia

Molecular BioSystems journal summary

YEASTRACT: providing a programmatic access to curated transcriptional regulatory associations in Saccharomyces cerevisiae through a web services interface

D. Abdulrehman, Pedro T. Monteiro, Miguel C. Teixeira, Nuno P. Mira, Artur B. Lourenço, Sandra C. dos Santos, Tânia R. Cabrito, Alexandre P. Francisco, Sara C. Madeira, R. S. Aires, Arlindo L. Oliveira, Isabel Sá‐Correia, Ana T. Freitas

Nucleic Acids Research journal summary

2009

The regulatory network underlying the transcriptional up-regulation of the FRL1 gene in mancozeb stressed yeast cells: qualitative modeling and simulation

Pedro T. Monteiro, Paulo Jorge Dias, Delphine Ropers, Arlindo L. Oliveira, Ana T. Freitas, Isabel Sá‐Correia, Miguel C. Teixeira

HAL (Le Centre pour la Communication Scientifique Directe) preprint summary

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

Lecture notes in computer science book

An analysis of the positional distribution of DNA motifs in promoter regions and its biological relevance

Ana Casimiro, Susana Vinga, Ana T. Freitas, Arlindo L. Oliveira

BMC Bioinformatics journal summary

2007

Bioinformatics: A New Approach for the Challenges of Molecular Biology

Arlindo L. Oliveira, Ana T. Freitas, Isabel Sá‐Correia

book

YEASTRACT-DISCOVERER: new tools to improve the analysis of transcriptional regulatory associations in Saccharomyces cerevisiae

Pedro T. Monteiro, Nuno D. Mendes, Miguel C. Teixeira, Sofia d'Orey, Sandra Tenreiro, Nuno P. Mira, Helio Pais, Alexandre P. Francisco, Alexandra M. Carvalho, Artur B. Lourenço, Isabel Sá‐Correia, Arlindo L. Oliveira, Ana T. Freitas

Nucleic Acids Research journal summary

2006

Additional materials and results for MUSA

Nuno D. Mendes, Ana Casimiro, Pedro M. Santos, Arlindo L. Oliveira, Ana T. Freitas

conference

MUSA: a parameter free algorithm for the identification of biologically significant motifs

Nuno D. Mendes, Ana Casimiro, Pedro M. Santos, Isabel Sá‐Correia, Arlindo L. Oliveira, Ana T. Freitas

Bioinformatics journal summary

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 Transactions on Computational Biology and Bioinformatics journal summary

2005

A HIGHLY SCALABLE ALGORITHM FOR THE EXTRACTION OF CIS-REGULATORY REGIONS

Alexandra M. Carvalho, Ana T. Freitas, Arlindo L. Oliveira, Marie‐France Sagot

preprint summary

2004

Efficient Extraction of Structured Motifs Using Box-Links

Alexandra M. Carvalho, Ana T. Freitas, Arlindo L. Oliveira, Marie-France Sagot

Lecture notes in computer science book

A parallel algorithm for the extraction of structured motifs

Alexandra M. Carvalho, Arlindo L. Oliveira, Ana T. Freitas, Marie‐France Sagot

preprint summary

2003

Implicit Resolution of the Chapman-Kolmogorov Equations for Sequential Circuits: An Application in Power Estimation

Ana T. Freitas, Arlindo L. Oliveira

2003 Design, Automation and Test in Europe Conference and Exhibition conference summary