Publications

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

Time and Memory Efficient Lempel-Ziv Compression Using Suffix Arrays

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

arXiv (Cornell University) preprint summary

CONSTANT TIME CLASH DETECTION IN PROTEIN FOLDING

Miguel Bugalho, Arlindo L. Oliveira

Journal of Bioinformatics and Computational Biology journal summary

Efficient Biclustering Algorithms for Time Series Gene Expression Data Analysis

Sara C. Madeira, Arlindo L. Oliveira

Lecture notes in computer science book

On the Suitability of Suffix Arrays for Lempel-Ziv Data Compression

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

Communications in computer and information science book

On the Use of Suffix Arrays for Memory-Efficient Lempel-Ziv Data Compression

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

conference summary

Haplotype inference with pseudo-Boolean optimization

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

Annals of Operations Research journal

Approximate String Matching with Compressed Indexes

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

Algorithms journal summary

A polynomial time biclustering algorithm for finding approximate expression patterns in gene expression time series

Sara C. Madeira, Arlindo L. Oliveira

Algorithms for Molecular Biology journal summary

BiGGEsTS: integrated environment for biclustering analysis of time series gene expression data

Joana P. Gonçalves, Sara C. Madeira, Arlindo L. Oliveira

BMC Research Notes journal summary

Identification of Regulatory Modules in Time Series Gene Expression Data Using a Linear Time Biclustering Algorithm

Sara C. Madeira, Miguel C. Teixeira, Isabel Sá‐Correia, Arlindo L. Oliveira

IEEE/ACM Transactions on Computational Biology and Bioinformatics journal summary

2008

Cost effectiveness analysis of carotid doppler ultrasound examination in patients with significant left main coronary artery stenosis

Arlindo L. Oliveira, Márcio Sommer Bittencourt, Anthony Pereira, Luı́z Antonio Machado César, Luís Henrique Wolff Gowdak

Circulation journal

USING GRAMMATICAL INFERENCE TECHNIQUES TO LEARN ONTOLOGIES THAT DESCRIBE THE STRUCTURE OF DOMAIN INSTANCES

André L. Martins, H. Sofia Pinto, Arlindo L. Oliveira

Applied Artificial Intelligence journal summary

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

Generic ILP vs Specialized 0-1 ILP for Haplotype Inference

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

ePrints Soton (University of Southampton) conference summary

SUFFIX ARRAYS - A Competitive Choice for Fast Lempel-Ziv Compressions

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

conference summary

An Evaluation of the Impact of Side Chain Positioning on the Accuracy of Discrete Models of Protein Structures

Miguel Bugalho, Arlindo L. Oliveira

Lecture notes in computer science book

Haplotype Inference with Boolean Constraint Solving: An Overview

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

conference summary

Ontology Design Principles and Normalization Techniques in the Web

Xiaoshu Wang, Jonas S. Almeida, Arlindo L. Oliveira

Lecture notes in computer science book

Indexed Hierarchical Approximate String Matching

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

Lecture notes in computer science book

Clique Analysis of Query Log Graphs

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

Lecture notes in computer science book

Efficient Haplotype Inference with Combined CP and OR Techniques

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

Lecture notes in computer science book

Dynamic Fully-Compressed Suffix Trees

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

Lecture notes in computer science book

Models and Algorithms for Computing Minimum-Size Prime Implicants

Vasco Manquinho, Arlindo L. Oliveira, João Marques‐Silva

conference summary

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

ccrB typing tool: an online resource for staphylococci ccrB sequence typing

Duarte C. Oliveira, Marcelino Santos, Catarina Milheiriço, João André Carriço, Susana Vinga, Arlindo L. Oliveira, Hermı́nia de Lencastre

Journal of Antimicrobial Chemotherapy journal summary

Fully-Compressed Suffix Trees

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

Lecture notes in computer science book

A compressed self-index using a Ziv–Lempel dictionary

Luís M. S.Russo, Arlindo L. Oliveira

Information Retrieval journal

2007

Session details: Graph based retrieval (IR)

Arlindo L. Oliveira

conference summary

P1303 clfB typing in Staphylococcus aureus: online database for dis-play, clustering analysis and storage of clfB DNA sequences

Angelita dos Reis Gomes, João André Carriço, Susana Vinga, Arlindo L. Oliveira, Mihaela Zavolan, H. de Lencastre

International Journal of Antimicrobial Agents journal

Bioinformatics: A New Approach for the Challenges of Molecular Biology

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

book

Efficient and Tight Upper Bounds for Haplotype Inference by Pure Parsimony

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

ePrints Soton (University of Southampton) conference

Sensitivity to SEUs evaluation using probabilistic testability analysis at RTL

J. Fernandes, Marcelino Santos, Arlindo L. Oliveira, J.P. Teixeira, R. Velazco

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

IR-BASE: An Integrated Framework for the Research and Teaching of Information Retrieval Technologies

Pável Calado, Ana Cardoso-Cachopo, Arlindo L. Oliveira

Electronic workshops in computing journal summary

Approximate String Matching with Lempel-Ziv Compressed Indexes

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

Lecture notes in computer science book

Efficient and tight upper bounds for haplotype inference by pure parsimony using delayed haplotype selection

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

Lecture notes in computer science conference summary