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Bibliography

Publications of the year

Doctoral Dissertations and Habilitation Theses

  • 1C. Villiers.

    L’import de l’adénosine monophosphate cyclique chez Escherichia coli, Université Joseph Fourier, Grenoble, 2013.

Articles in International Peer-Reviewed Journals

  • 2V. 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 ]

    http://hal.inria.fr/hal-00924044
  • 3G. Baptist, C. Pinel, C. Ranquet, J. Izard, D. Ropers, H. De Jong, J. Geiselmann.

    A genome-wide screen for identifying all regulators of a target gene, in: Nucleic Acids Research, 2013, vol. 41, no 17.

    http://hal.inria.fr/hal-00857345
  • 4S. Berthoumieux, M. Brilli, D. Kahn, H. De Jong, E. Cinquemani.

    On the identifiability of metabolic network models, in: Journal of Mathematical Biology, 2013, vol. 67, no 6-7, pp. 1795-1832. [ DOI : 10.1007/s00285-012-0614-x ]

    http://hal.inria.fr/hal-00762620
  • 5S. Berthoumieux, H. De Jong, G. Baptist, C. Pinel, C. Ranquet, D. Ropers, J. Geiselmann.

    Shared control of gene expression in bacteria by transcription factors and global physiology of the cell, in: Molecular Systems Biology, January 2013, vol. 9, no 1, 634 p. [ DOI : 10.1038/msb.2012.70 ]

    http://hal.inria.fr/hal-00793352
  • 6C. Chaouiya, D. Bérenguier, S. Keating, A. Naldi, M. van Iersel, N. Rodriguez, A. Dräger, F. Büchel, T. Cokelaer, B. Kowal, B. Wicks, E. Gonçalves, J. Dorier, M. Page, P. Monteiro, A. von Kamp, I. Xenarios, H. De Jong, M. Hucka, S. Klamt, D. Thieffry, N. Le Novère, J. Saez-Rodriguez, T. Helikar.

    SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools, in: BMC Systems Biology, 2013, vol. 7, no 1, 135 p. [ DOI : 10.1186/1752-0509-7-135 ]

    http://hal.inria.fr/hal-00926033
  • 7O. 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 ]

    http://hal.inria.fr/hal-00926632
  • 8O. Dudin, S. Lacour, J. Geiselmann.

    Expression dynamics of RpoS/Crl-dependent genes in Escherichia coli, in: Research in Microbiology, 2013.

    http://hal.inria.fr/hal-00857366
  • 9P. 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. [ DOI : 10.1111/1758-2229.12112 ]

    http://hal.inria.fr/hal-00926634
  • 10M. 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. [ DOI : 10.1074/mcp.M113.032672 ]

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

International Conferences with Proceedings

  • 11A. Carta, E. Cinquemani.

    State estimation for gene networks with intrinsic and extrinsic noise: a case study on E.coli arabinose uptake dynamics, in: ECC13 - European Control Conference - 2013, Zurich, Switzerland, 2013.

    http://hal.inria.fr/hal-00818902
  • 12A. Gonzalez, J. Uhlendorf, J. Schaul, E. Cinquemani, G. Batt, G. Ferrari-Trecate.

    Identification of biological models from single-cell data: a comparison between mixed-effects and moment-based inference, in: ECC - 12th European Control Conference - 2013, Zurich, Switzerland, 2013.

    http://hal.inria.fr/hal-00831641
  • 13V. Zulkower, J.-L. Gouzé, H. De Jong.

    Quantitative comparison of one-step and two-step models of gene expression, in: Journées Ouvertes Biologie, Informatique et Mathématiques (JOBIM'13), Toulouse, France, 2013.

    http://hal.inria.fr/hal-00927205

Scientific Books (or Scientific Book chapters)

  • 14J. 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 ]

    http://hal.inria.fr/hal-00926635

Internal Reports

  • 15V. Acary, H. De Jong, B. Brogliato.

    Numerical Simulation of Piecewise-Linear Models of Gene Regulatory Networks Using Complementarity Systems, Inria, January 2013, no RR-8207, 42 p.

    http://hal.inria.fr/hal-00778412
  • 16A. Gonzalez, J. Uhlendorf, J. Schaul, E. Cinquemani, G. Batt, G. Ferrari-Trecate.

    Identification of biological models from single-cell data: a comparison between mixed-effects and moment-based inference, Inria, April 2013, no RR-8288.

    http://hal.inria.fr/hal-00817582

Scientific Popularization



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