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Journal Articles
- 2024
[j9]Marta Sampaio
, Miguel Rocha, Oscar Días:
A diel multi-tissue genome-scale metabolic model of Vitis vinifera. PLoS Comput. Biol. 20(10): 1012506 (2024)- [j8]Fernando Cruz, João Capela, Eugénio C. Ferreira, Miguel Rocha, Oscar Días:
BioISO: An Objective-Oriented Application for Assisting the Curation of Genome-Scale Metabolic Models. IEEE ACM Trans. Comput. Biol. Bioinform. 21(2): 215-226 (2024) - 2023
- [j7]Emanuel Cunha, Davide Lagoa, José P. Faria, Filipe Liu, Christopher S. Henry, Oscar Días:
TranSyT, an innovative framework for identifying transport systems. Bioinform. 39(8) (2023) - [j6]Emanuel Cunha, Miguel Silva, Inês Chaves, Hüseyin Demirci, Davide Lagoa, Diogo Lima, Miguel Rocha, Isabel Rocha, Oscar Días:
The first multi-tissue genome-scale metabolic model of a woody plant highlights suberin biosynthesis pathways in Quercus suber. PLoS Comput. Biol. 19(9) (2023) - 2022
- [j5]Alexandre Oliveira, Emanuel Cunha, Fernando Cruz, João Capela, João Carlos Sequeira, Marta Sampaio, Cláudia Sampaio, Oscar Días:
Systematic assessment of template-based genome-scale metabolic models created with the BiGG Integration Tool. J. Integr. Bioinform. 19(3) (2022) - 2021
- [j4]Alexandre Oliveira, Joana Rodrigues, Eugénio Campos Ferreira, Lígia R. Rodrigues, Oscar Días:
A kinetic model of the central carbon metabolism for acrylic acid production in Escherichia coli. PLoS Comput. Biol. 17(3) (2021) - 2019
- [j3]Marta Sampaio, Miguel Rocha, Hugo Oliveira, Oscar Días:
Predicting promoters in phage genomes using PhagePromoter. Bioinform. 35(24): 5301-5302 (2019) - [j2]Fernando Cruz, Davide Lagoa, João Mendes, Isabel Rocha, Eugénio C. Ferreira, Miguel Rocha, Oscar Días:
SamPler - a novel method for selecting parameters for gene functional annotation routines. BMC Bioinform. 20(1): 454:1-454:11 (2019) - 2017
- [j1]Oscar Días, Daniel Gomes, Paulo Vilaça, João G. R. Cardoso, Miguel Rocha, Eugénio C. Ferreira, Isabel Rocha:
Genome-Wide Semi-Automated Annotation of Transporter Systems. IEEE ACM Trans. Comput. Biol. Bioinform. 14(2): 443-456 (2017)
Conference and Workshop Papers
- 2022
- [c8]Alexandre Oliveira, Emanuel Cunha, Miguel Silva, Cristiana Faria, Oscar Días:
Exploring Xylella fastidiosa's Metabolic Traits Using a GSM Model of the Phytopathogenic Bacterium. PACBB 2022: 79-88 - 2021
- [c7]Alexandre Oliveira, Emanuel Cunha, Fernando Cruz, João Capela, João Carlos Sequeira, Marta Sampaio, Oscar Días:
Towards a Multivariate Analysis of Genome-Scale Metabolic Models Derived from the BiGG Models Database. PACBB 2021: 136-144 - 2020
- [c6]Diogo Lima, Fernando Cruz, Miguel Rocha, Oscar Días:
Reconciliation of Regulatory Data: The Regulatory Networks of Escherichia coli and Bacillus subtilis. PACBB 2020: 155-165 - [c5]Emanuel Cunha, Ahmad A. Zeidan, Oscar Días:
Towards the Reconstruction of the Genome-Scale Metabolic Model of Lactobacillus acidophilus La-14. PACBB 2020: 205-214 - 2019
- [c4]Marta Sampaio, Miguel Rocha, Hugo Oliveira, Oscar Días:
Predicting Promoters in Phage Genomes Using Machine Learning Models. PACBB 2019: 105-112 - [c3]Fernando Cruz, Diogo Lima, José P. Faria, Miguel Rocha, Oscar Días:
Towards the Reconstruction of Integrated Genome-Scale Models of Metabolism and Gene Expression. PACBB 2019: 173-181 - 2014
- [c2]Pedro Barbosa, Oscar Días, Joel P. Arrais, Miguel Rocha:
Metagenomic Analysis of the Saliva Microbiome with Merlin. PACBB 2014: 191-199 - 2008
- [c1]José P. Pinto, Oscar Días, Anália Lourenço, Sónia Carneiro, Eugénio C. Ferreira, Isabel Rocha, Miguel Rocha:
Data Integration Issues in the Reconstruction of the Genome-Scale Metabolic Model of Zymomonas Mobillis. IWPACBB 2008: 92-101
Data and Artifacts
- 2020
- [d1]Diogo Lima, Fernando Cruz, Miguel Rocha, Oscar Días:
Reconciliation of regulatory data: the regulatory networks of Escherichia coli and Bacillus subtilis. Zenodo, 2020
Coauthor Index
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