José Pedro Faria

PhD Student


  • 2015: PhD Program on Bioengineering, Universidade do Minho
  • 2010 - 2015: Modeling Microbes: New methods for integrated metabolic and regulatory network reconstruction

Recent Publications

  • Faria, José Pedro; Davis, James J.; Edirisinghe, Janaka N.; Taylor, Ronald C.; Weisenhorn, Pamela; Olson, Robert D.; Stevens, Rick L.; Rocha, Miguel; Rocha, Isabel; Best, Aaron A.; DeJongh, Matthew; Tintle, Nathan L.; Parrello, Bruce; Overbeek, Ross; Henry, Christopher S.
Computing and applying atomic regulons to understand gene expression and regulation
  • Frontiers in Microbiology, 7(1819), 1-14, 2016
Reconstruction of the regulatory network for Bacillus subtilis and reconciliation with gene expression data
  • Frontiers in Microbiology, 7(275), 1-11, 2016
  • Faria, J.P.; Edirisinghe, J.N.; Davis, J.J.; Disz, T.; Hausmann, A.; Henry, C.S.; Olson, R.; Overbeek, R.A.; Pusch, G.D.; Shukla, M.; Vonstein, V.; Wattam, A.R.
Enabling comparative modeling of closely related genomes: example genus Brucella
  • 3 Biotech, 5(1), 101-105, 2015
Genome-scale bacterial transcriptional regulatory networks: reconstruction and integrated analysis with metabolic models
  • Briefings in Bioinformatics, 15(4), 592-611, 2014
Analysis of the effect of reversibility constraints on the predictions of genome-scale metabolic models
  • Advances in Intelligent and Soft Computing, 74, 217-224, 2010
Full List