Data Integration Issues in the Reconstruction of the Genome-Scale Metabolic Model of Zymomonas Mobillis. - José P. Pinto; Oscar Dias; Anália Lourenço; Sónia Carneiro; Eugénio C. Ferreira; Isabel Rocha; Miguel Rocha 001 (IWPACBB, 2008)

Metagenomic Analysis of the Saliva Microbiome with Merlin. - Pedro Barbosa; Oscar Dias; Joel P. Arrais; Miguel Rocha 001 (PACBB, 2014)

Genome-Wide Semi-Automated Annotation of Transporter Systems. - Oscar Dias; Daniel Gomes; Paulo Vilaça; João G. R. Cardoso; Miguel Rocha 001; Eugénio C. Ferreira; Isabel Rocha (IEEE ACM Trans. Comput. Biol. Bioinform., 2017)

Towards the Reconstruction of Integrated Genome-Scale Models of Metabolism and Gene Expression. - Fernando Cruz; Diogo Lima; José P. Faria; Miguel Rocha 001; Oscar Dias (PACBB, 2019)

Predicting Promoters in Phage Genomes Using Machine Learning Models. - Marta Sampaio; Miguel Rocha 001; Hugo Oliveira; Oscar Dias (PACBB, 2019)

Predicting promoters in phage genomes using PhagePromoter. - Marta Sampaio; Miguel Rocha 001; Hugo Oliveira; Oscar Dias (Bioinform., 2019)

SamPler - a novel method for selecting parameters for gene functional annotation routines. - Fernando Cruz; Davide Lagoa; João Mendes; Isabel Rocha; Eugénio C. Ferreira; Miguel Rocha 001; Oscar Dias (BMC Bioinform., 2019)

Towards the Reconstruction of the Genome-Scale Metabolic Model of Lactobacillus acidophilus La-14. - Emanuel Cunha; Ahmad A. Zeidan; Oscar Dias (PACBB, 2020)

Reconciliation of Regulatory Data: The Regulatory Networks of Escherichia coli and Bacillus subtilis. - Diogo Lima; Fernando Cruz; Miguel Rocha 001; Oscar Dias (PACBB, 2020)

Reconciliation of regulatory data: the regulatory networks of Escherichia coli and Bacillus subtilis. - Diogo Lima; Fernando Cruz; Miguel Rocha 001; Oscar Dias (Zenodo, 2020)

Towards a Multivariate Analysis of Genome-Scale Metabolic Models Derived from the BiGG Models Database. - Alexandre Oliveira; Emanuel Cunha; Fernando Cruz; João Capela; João Carlos Sequeira; Marta Sampaio; Oscar Dias (PACBB, 2021)

A kinetic model of the central carbon metabolism for acrylic acid production in Escherichia coli. - Alexandre Oliveira; Joana Rodrigues; Eugénio Campos Ferreira; Lígia R. Rodrigues; Oscar Dias (PLoS Comput. Biol., 2021)

Exploring Xylella fastidiosa's Metabolic Traits Using a GSM Model of the Phytopathogenic Bacterium. - Alexandre Oliveira; Emanuel Cunha; Miguel Silva; Cristiana Faria; Oscar Dias (PACBB, 2022)

Systematic assessment of template-based genome-scale metabolic models created with the BiGG Integration Tool. - Alexandre Oliveira; Emanuel Cunha; Fernando Cruz; João Capela; João Carlos Sequeira; Marta Sampaio; Cláudia Sampaio; Oscar Dias (J. Integr. Bioinform., 2022)

The first multi-tissue genome-scale metabolic model of a woody plant highlights suberin biosynthesis pathways in Quercus suber. - Emanuel Cunha; Miguel Silva; Inês Chaves; Hüseyin Demirci; Davide Lagoa; Diogo Lima; Miguel Rocha 001; Isabel Rocha; Oscar Dias (PLoS Comput. Biol., 2023)

TranSyT, an innovative framework for identifying transport systems. - Emanuel Cunha; Davide Lagoa; José P. Faria; Filipe Liu; Christopher S. Henry; Oscar Dias (Bioinform., 2023)

A diel multi-tissue genome-scale metabolic model of Vitis vinifera. - Marta Sampaio; Miguel Rocha 001; Oscar Dias (PLoS Comput. Biol., 2024)

BioISO: An Objective-Oriented Application for Assisting the Curation of Genome-Scale Metabolic Models. - Fernando Cruz; João Capela; Eugénio C. Ferreira; Miguel Rocha 001; Oscar Dias (IEEE ACM Trans. Comput. Biol. Bioinform., 2024)

PhageDPO: A machine-learning based computational framework for identifying phage depolymerases. - M. Fernanda Vieira; José Duarte; Rita Domingues; Hugo Oliveira; Oscar Dias (Comput. Biol. Medicine, 2025)

Comparative Assessment of Protein Large Language Models for Enzyme Commission Number Prediction. - João Capela; Maria Zimmermann-Kogadeeva; Aalt D. J. van Dijk; Dick de Ridder; Oscar Dias; Miguel Rocha 001 (BMC Bioinform., 2025)