Rocha M - Search Results

1

Exploring synergies between plant metabolic modelling and machine learning.

Sampaio M, Rocha M, Dias O. Sampaio M, et al. Among authors: rocha m. Comput Struct Biotechnol J. 2022 Apr 16;20:1885-1900. doi: 10.1016/j.csbj.2022.04.016. eCollection 2022. Comput Struct Biotechnol J. 2022. PMID: 35521559 Free PMC article. Review.

2

Reconstructing genome-scale metabolic models with merlin.

Dias O, Rocha M, Ferreira EC, Rocha I. Dias O, et al. Among authors: rocha m, rocha i. Nucleic Acids Res. 2015 Apr 30;43(8):3899-910. doi: 10.1093/nar/gkv294. Epub 2015 Apr 6. Nucleic Acids Res. 2015. PMID: 25845595 Free PMC article.

3

Genome-Wide Semi-Automated Annotation of Transporter Systems.

Dias O, Gomes D, Vilaca P, Cardoso J, Rocha M, Ferreira EC, Rocha I. Dias O, et al. Among authors: rocha m, rocha i. IEEE/ACM Trans Comput Biol Bioinform. 2017 Mar-Apr;14(2):443-456. doi: 10.1109/TCBB.2016.2527647. Epub 2016 Feb 11. IEEE/ACM Trans Comput Biol Bioinform. 2017. PMID: 26887005 Free article.

4

Reconstructing High-Quality Large-Scale Metabolic Models with merlin.

Dias O, Rocha M, Ferreira EC, Rocha I. Dias O, et al. Among authors: rocha m, rocha i. Methods Mol Biol. 2018;1716:1-36. doi: 10.1007/978-1-4939-7528-0_1. Methods Mol Biol. 2018. PMID: 29222747

5

Predicting promoters in phage genomes using PhagePromoter.

Sampaio M, Rocha M, Oliveira H, Dias O. Sampaio M, et al. Among authors: rocha m. Bioinformatics. 2019 Dec 15;35(24):5301-5302. doi: 10.1093/bioinformatics/btz580. Bioinformatics. 2019. PMID: 31359029

6

SamPler - a novel method for selecting parameters for gene functional annotation routines.

Cruz F, Lagoa D, Mendes J, Rocha I, Ferreira EC, Rocha M, Dias O. Cruz F, et al. Among authors: rocha m, rocha i. BMC Bioinformatics. 2019 Sep 5;20(1):454. doi: 10.1186/s12859-019-3038-4. BMC Bioinformatics. 2019. PMID: 31488049 Free PMC article.

7

A review of methods for the reconstruction and analysis of integrated genome-scale models of metabolism and regulation.

Cruz F, Faria JP, Rocha M, Rocha I, Dias O. Cruz F, et al. Among authors: rocha m, rocha i. Biochem Soc Trans. 2020 Oct 30;48(5):1889-1903. doi: 10.1042/BST20190840. Biochem Soc Trans. 2020. PMID: 32940659 Review.

8

UPIMAPI, reCOGnizer and KEGGCharter: Bioinformatics tools for functional annotation and visualization of (meta)-omics datasets.

Sequeira JC, Rocha M, Alves MM, Salvador AF. Sequeira JC, et al. Among authors: rocha m. Comput Struct Biotechnol J. 2022 Apr 9;20:1798-1810. doi: 10.1016/j.csbj.2022.03.042. eCollection 2022. Comput Struct Biotechnol J. 2022. PMID: 35495109 Free PMC article.

9

merlin, an improved framework for the reconstruction of high-quality genome-scale metabolic models.

Capela J, Lagoa D, Rodrigues R, Cunha E, Cruz F, Barbosa A, Bastos J, Lima D, Ferreira EC, Rocha M, Dias O. Capela J, et al. Among authors: rocha m. Nucleic Acids Res. 2022 Jun 24;50(11):6052-6066. doi: 10.1093/nar/gkac459. Nucleic Acids Res. 2022. PMID: 35694833 Free PMC article.

10

The first multi-tissue genome-scale metabolic model of a woody plant highlights suberin biosynthesis pathways in Quercus suber.

Cunha E, Silva M, Chaves I, Demirci H, Lagoa DR, Lima D, Rocha M, Rocha I, Dias O. Cunha E, et al. Among authors: rocha m, rocha i. PLoS Comput Biol. 2023 Sep 20;19(9):e1011499. doi: 10.1371/journal.pcbi.1011499. eCollection 2023 Sep. PLoS Comput Biol. 2023. PMID: 37729340 Free PMC article.

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