Publications

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

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

Efficient and Accurate Haplotype Inference by Combining Parsimony and Pedigree Information

Ana Graça, Inês Lynce, João Marques‐Silva, Arlindo L. Oliveira

Lecture notes in computer science book

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

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

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

conference

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

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

Sliding Window Update Using Suffix Arrays

Artur Ferreira, Arlindo L. Oliveira, Mário A. T. Figueiredo

conference

On Community Detection in Very Large Networks

Alexandre P. Francisco, Arlindo L. Oliveira

Communications in computer and information science book

Mining query log graphs towards a query folksonomy

Alexandre P. Francisco, Ricardo Baeza‐Yates, Arlindo L. Oliveira

Concurrency and Computation Practice and Experience journal

Fully Generalized Graph Cores

Alexandre P. Francisco, Arlindo L. Oliveira

Communications in computer and information science book

GRISOTTO: A greedy approach to improve combinatorial algorithms for motif discovery with prior knowledge

Alexandra M. Carvalho, Arlindo L. Oliveira

Algorithms for Molecular Biology journal

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

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

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

Bioinformatics journal

Discriminative Learning of Bayesian Networks via Factorized Conditional Log-Likelihood

Alexandra M. Carvalho, Teemu Roos, Arlindo L. Oliveira, Petri Myllymäki

Työväentutkimus Vuosikirja journal

Fully compressed suffix trees

Luís M. S.Russo, Gonzalo Navarro, Arlindo L. Oliveira

ACM Transactions on Algorithms journal

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

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

Using graph modularity analysis to identify transcription factor binding sites

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

preprint

Mining Large Query Induced Graphs towards a Hierarchical Query Folksonomy

Alexandre P. Francisco, Ricardo Baeza‐Yates, Arlindo L. Oliveira

Lecture notes in computer science book

Parallel and Distributed Compressed Indexes

Luís M. S.Russo, Gonzalo Navarro, Arlindo L. Oliveira

Lecture notes in computer science book

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

Haplotype Inference by Pure Parsimony: A Survey

Ana Graça, Inês Lynce, João Marques‐Silva, Arlindo L. Oliveira

Journal of Computational Biology journal

Apt-pbo

Paulo Trezentos, Inês Lynce, Arlindo L. Oliveira

conference

A Data Mining Approach for the Detection of High-Risk Breast Cancer Groups

Orlando Anunciação, Bruno Costa Gomes, Susana Vinga, Jorge Gaspar, Arlindo L. Oliveira, José Rueff

Advances in intelligent and soft computing book

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