Analysis of the Effect of Reversibility Constraints on the Predictions of Genome-Scale Metabolic Models. - José P. Faria; Miguel Rocha 001; Rick L. Stevens; Christopher S. Henry (IWPACBB, 2010)

Genome-scale bacterial transcriptional regulatory networks: reconstruction and integrated analysis with metabolic models. - José P. Faria; Ross A. Overbeek; Fangfang Xia; Miguel Rocha 001; Isabel Rocha; Christopher S. Henry (Briefings Bioinform., 2014)

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)

The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes. - Samuel M. D. Seaver; Filipe Liu; Qizhi Zhang; James G. Jeffryes; José P. Faria; Janaka N. Edirisinghe; Michael B. Mundy; Nicholas Chia; Elad Noor; Moritz Emanuel Beber; Aaron A. Best; Matthew DeJongh; et al. (Nucleic Acids Res., 2021)

The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes (Corrigendum). - Samuel M. D. Seaver; Filipe Liu; Qizhi Zhang; James G. Jeffryes; José P. Faria; Janaka N. Edirisinghe; Michael B. Mundy; Nicholas Chia; Elad Noor; Moritz Emanuel Beber; Aaron A. Best; Matthew DeJongh; et al. (Nucleic Acids Res., 2021)

kb_DRAM: annotation and metabolic profiling of genomes with DRAM in KBase. - Michael Shaffer; Mikayla A. Borton; Ben Bolduc; José P. Faria; Rory M. Flynn; Parsa Ghadermazi; Janaka N. Edirisinghe; Elisha M. Wood-Charlson; Christopher S. Miller; Siu Hung Joshua Chan; Matthew B. Sullivan; Christopher S. Henry; et al. (Bioinform., 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)