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Bibliography

Publications of the year

Articles in International Peer-Reviewed Journals

  • 1V. Acary, H. De Jong, B. Brogliato.

    Numerical simulation of piecewise-linear models of gene regulatory networks using complementarity systems, in: Physica D: Nonlinear Phenomena, February 2014, vol. 269, pp. 103-119. [ DOI : 10.1016/j.physd.2013.11.013 ]

    https://hal.inria.fr/hal-00924044
  • 2O. Dudin, J. Geiselmann, H. Ogasawara, A. Ishihama, S. Lacour.

    Repression of flagellar genes in exponential phase by CsgD and CpxR, two crucial modulators of Escherichia coli biofilm formation, in: Journal of Bacteriology, 2014, vol. 196, no 3. [ DOI : 10.1128/JB.00938-13 ]

    https://hal.inria.fr/hal-00926632
  • 3A. Kremling, J. Geiselmann, D. Ropers, H. De Jong.

    Understanding carbon catabolite repression in Escherichia coli using quantitative models, in: Trends in Microbiology, 2015, forthcoming.

    https://hal.inria.fr/hal-01103556
  • 4P. Landini, T. Egli, J. Wolf, S. Lacour.

    SigmaS, a major player in the response to environmental stresses in Escherichia coli: role, regulation and mechanisms of promoter recognition, in: Environmental Microbiology Reports, 2014, vol. 6, no 1, pp. 1-13. [ DOI : 10.1111/1758-2229.12112 ]

    https://hal.inria.fr/hal-00926634
  • 5U. H. P. Nguyen, D. Grekov, J. Geiselmann, V. Stambouli, M. Weidenhaupt, D. Delabouglise.

    Anodic deposit from respiration metabolic pathway of Escherichia coli, in: Electrochimica Acta, 2014, vol. 130, pp. 200-205. [ DOI : 10.1016/j.electacta.2014.03.019 ]

    https://hal.archives-ouvertes.fr/hal-01067524
  • 6M. A. Rapsomaniki, E. Cinquemani, N. N. Giakoumakis, P. Kotsantis, J. Lygeros, Z. Lygerou.

    Inference of protein kinetics by stochastic modeling and simulation of fluorescence recovery after photobleaching experiments, in: Bioinformatics, September 2014, forthcoming. [ DOI : 10.1093/bioinformatics/btu619 ]

    https://hal.inria.fr/hal-01096966
  • 7D. Stefan, C. Pinel, S. Pinhal, E. Cinquemani, J. Geiselmann, H. De Jong.

    Inference of quantitative models of bacterial promoters from time-series reporter gene data, in: PLoS Computational Biology, 2015, vol. 11, no 1, e1004028.

    https://hal.inria.fr/hal-01097632
  • 8M. Trauchessec, M. Jaquinod, A. Bonvalot, V. Brun, C. Bruley, D. Ropers, H. De Jong, J. Garin, G. Bestel-Corre, M. Ferro.

    Mass spectrometry-based workflow for accurate quantification of E. coli enzymes: how proteomics can play a key role in metabolic engineering, in: Mol Cell Proteomics, January 2014, vol. 13, no 4, pp. 954-968. [ DOI : 10.1074/mcp.M113.032672 ]

    https://hal.inria.fr/hal-00947196

International Conferences with Proceedings

  • 9I. Belgacem, E. Grac, D. Ropers, J.-L. Gouzé.

    A coupled transcription-translation mathematical model of RNA polymerase, in: 21st International Symposium on Mathematical Theory of Networks and Systems, Groningen, Netherlands, July 2014.

    https://hal.inria.fr/hal-00966559
  • 10I. Belgacem, E. Grac, D. Ropers, J.-L. Gouzé.

    Stability analysis of a reduced transcription-translation model of RNA polymerase, in: Proceedings of the 53rd IEEE Conference on Decision and Control, Los Angeles, CA, United States, December 2014.

    https://hal.inria.fr/hal-01091674
  • 11N. Giordano, F. Mairet, J.-L. Gouzé, J. Geiselmann, H. De Jong.

    Dynamic optimisation of resource allocation in microorganisms, in: 21st International Symposium on Mathematical Theory of Networks and Systems (MTNS 2014), Groningen, Netherlands, July 2014.

    https://hal.inria.fr/hal-01079299

Conferences without Proceedings

  • 12V. Acary, H. De Jong, B. Brogliato.

    Numerical simulation of piecewise-linear models of gene regulatory networks using complementarity systems (Extended Abstract), in: MTNS 2014 - 21st International Symposium on Mathematical Theory of Networks and Systems, Groningen, Netherlands, July 2014.

    https://hal.inria.fr/hal-01103557

Scientific Books (or Scientific Book chapters)

  • 13J. Geiselmann.

    Systems biology and metabolic engineering in bacteria, in: Systems Biology of Metabolic and Signaling Networks : Energy, Mass and Information Transfer, M. A. Aon, V. Saks, U. Schlattner (editors), Springer Series in Biophysics, Springer, 2014, vol. 16, pp. 351-367. [ DOI : 10.1007/978-3-642-38505-6_13 ]

    https://hal.inria.fr/hal-00926635
  • 14L. Maruthi, I. Tkachev, A. Carta, E. Cinquemani, P. Hersen, G. Batt, A. Abate.

    Towards Real-Time Control of Gene Expression at the Single Cell Level: A Stochastic Control Approach, in: Computational Methods in Systems Biology, Lecture Notes in Computer Science, Springer International Publishing, 2014, vol. 8859, pp. 155-172. [ DOI : 10.1007/978-3-319-12982-2_12 ]

    https://hal.inria.fr/hal-01096959


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