Centre of Biological Engineering / Centro de Engenharia Biológica

2010 - 2015: Modeling Microbes: New methods for integrated metabolic and regulatory network reconstruction

1	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
2	Faria, José Pedro; Overbeek, Ross; Taylor, Ronald C; Conrad, Neal; Vonstein, Veronika; Goelzer, Anne; Fromion, Vincent; Rocha, Miguel; Rocha, Isabel; Henry, Christopher Scott Reconstruction of the regulatory network for Bacillus subtilis and reconciliation with gene expression data Frontiers in Microbiology, 7(275), 1-11, 2016
3	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
4	Faria, J.P.; Overbeek, R.; Xia, F.; Rocha, M.; Rocha, I.; Henry, C.S. Genome-scale bacterial transcriptional regulatory networks: reconstruction and integrated analysis with metabolic models Briefings in Bioinformatics, 15(4), 592-611, 2014
5	Rocha, M.; Faria, J.P.; Stevens, R.L.; Henry, C.S. 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

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