José P. Faria

According to our database, José P. Faria authored at least 7 papers between 2010 and 2023.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2023

<i>TranSyT</i>, an innovative framework for identifying transport systems.

Emanuel Cunha, Davide Lagoa, José P. Faria, Filipe Liu, Christopher S. Henry, Oscar Días

Bioinform., August, 2023

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, Kelly C. Wrighton

Bioinform., April, 2023

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, Jeffrey A. Kimbrel, Patrik D'haeseleer, Sean R. McCorkle, Jay R. Bolton, Erik Pearson, Shane Canon, Elisha M. Wood-Charlson, Robert W. Cottingham, Adam P. Arkin, Christopher S. Henry

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.

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, Jeffrey A. Kimbrel, Patrik D'haeseleer, Sean R. McCorkle, Jay R. Bolton, Erik Pearson, Shane Canon, Elisha M. Wood-Charlson, Robert W. Cottingham, Adam P. Arkin, Christopher S. Henry

Nucleic Acids Res., 2021

2019

Towards the Reconstruction of Integrated Genome-Scale Models of Metabolism and Gene Expression.

Fernando Cruz, Diogo Lima, José P. Faria, Miguel Rocha, Oscar Días

Proceedings of the Practical Applications of Computational Biology and Bioinformatics, 2019

2014

Genome-scale bacterial transcriptional regulatory networks: reconstruction and integrated analysis with metabolic models.

José P. Faria, Ross A. Overbeek, Fangfang Xia, Miguel Rocha, Isabel Rocha, Christopher S. Henry

Briefings Bioinform., 2014

2010

Analysis of the Effect of Reversibility Constraints on the Predictions of Genome-Scale Metabolic Models.

José P. Faria, Miguel Rocha, Rick L. Stevens, Christopher S. Henry

Proceedings of the Advances in Bioinformatics, 2010