Brinsmade, S.R., Kleijn, R.J., Sauer, U., Sonenshein, A.L., Regulation of CodY activity through modulation of intracellular branched-chain amino acid pools. J. Bacteriol. 192:24 (2010), 6357–6368.
Calzone, L., Fages, F., Soliman, S., BIOCHAM: an environment for modeling biological systems and formalizing experimental knowledge. Bioinformatics 22:14 (2006), 1805–1807.
Cousot, P., Cousot, R., Systematic Design of Program Analysis Frameworks. 1979, POPL, 269–282.
Coutte, F., Niehren, J., Dhali, D., John, M., Versari, C., Jacques, P., Modeling Leucine's metabolic pathway and knockout prediction improving the production of surfactin, a biosurfactant from Bacillus subtilis. Biotechnol. J. 10:8 (2015), 1216–1234.
Fages, F., Gay, S., Soliman, S., Inferring reaction systems from ordinary differential equations. Theor. Comput. Sci. 599 (2015), 64–78.
Feinberg, M., Chemical reaction network structure and the stability of complex isothermal reactors-I. The deficiency zero and deficiency one theorems. Chem. Eng. Sci. 42:10 (1987), 2229–2268.
Forbus, K.D., Qualitative reasoning. Tucker, A.B., (eds.) The Computer Science and Engineering Handbook, 1997, CRC Press, 715–733.
Grandoni, J.A., Zahler, S.A., Calvo, J.M., Transcriptional regulation of the ilv-leu operon of Bacillus subtilis. J. Bacteriol. 174:10 (1992), 3212–3219.
John, M., Nebut, M., Niehren, J., Knockout prediction for reaction networks with partial kinetic information. 14th International Conference on Verification, Model Checking, and Abstract Interpretation, 2013, 355–374.
Mäder, U., Hennig, S., Hecker, M., Homuth, G., Transcriptional organization and posttranscriptional regulation of the Bacillus subtilis branched-chain amino acid biosynthesis genes. J. Bacteriol. 186:8 (2004), 2240–2252.
Mäder, U., Schmeisky, A.G., Flórez, L.A., Stülke, J., Subtiwiki˘2014a comprehensive community resource for the model organism bacillus subtilis. Nucl. Acids Res., 2011 gkr923.
Molle, V., Nakaura, Y., Shivers, R.P., Yamaguchi, H., Losick, R., Fujita, Y., Sonenshein, A.L., Additional targets of the Bacillus subtilis global regulator CodY identified by chromatin immunoprecipitation and genome-wide transcript analysis. J. Bacteriol. 185:6 (2003), 1911–1922.
Nethercote, N., Stuckey, P.J., Becket, R., Brand, S., Duck, G.J., Tack, G., Minizinc: towards a standard CP modelling language. Bessiere, C., (eds.) 13th International Conference, CP 2007, 2007, Proceedings, Vol. 474 of LNCS Principles and Practice of Constraint Programming – CP 2007, 2007, Springer, 529–543.
Niehren, J., John, M., Versari, C., Coutte, F., Jacques, P., Qualitative reasoning about reaction networks with partial kinetic information. Computational Methods for Systems Biology, Nantes, France, 2015, 12.
Odersky, M., The evolution of scala: Ple’14 keynote. Urma, R., Orchard, D.A., Mycroft, A., (eds.) Proceedings of the 1st Workshop on Programming Language Evolution, PLE@ECOOP 2014, Uppsala, Sweden, July 28 2014, 2014, ACM, 4.
Orth, J.D., Thiele, I., Palsson, B.O., What is flux balance analysis?. Nat. Biotechnol. 28:3 (2010), 245–248.
Otero, J.M., Nielsen, J., Industrial systems biology. Industrial Biotechnology: Sustainable Growth and Economic Success, 2016 (in press).
Shivers, R.P., Sonenshein, A.L., Activation of the Bacillus subtilis global regulator CodY by direct interaction with branched-chain amino acids. Mol. Microbiol. 53:2 (2004), 599–611.
Sohn, S.B., Kim, T.Y., Park, J.M., Lee, S.Y., In silico genome-scale metabolic analysis of Pseudomonas putida kt2440 for polyhydroxyalkanoate synthesis, degradation of aromatics and anaerobic survival. Biotechnol. J. 5:7 (2010), 739–750.
Tojo, S., Satomura, T., Morisaki, K., Deutscher, J., Hirooka, K., Fujita, Y., Elaborate transcription regulation of the Bacillus subtilis ilv-leu operon involved in the biosynthesis of branched-chain amino acids through global regulators of CcpA, CodY and TnrA. Mol. Microbiol. 56:6 (2005), 1560–1573.
Villapakkam, A.C., Handke, L.D., Belitsky, B.R., Levdikov, V.M., Wilkinson, A.J., Sonenshein, A.L., Genetic and biochemical analysis of the interaction of Bacillus subtilis CodY with branched-chain amino acids. J. Bacteriol. 191:22 (2009), 6865–6876.