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Bibliography

Publications of the year

Doctoral Dissertations and Habilitation Theses

  • 1W.-F. Wang.

    Finding missing genes in genetic regulatory networks, Université Joseph Fourier/National University of Taiwan, Grenoble/Taipeh, 2011.

Articles in International Peer-Reviewed Journal

  • 2V. Baldazzi, D. Ropers, J. Geiselmann, D. Kahn, H. de Jong.

    Importance of metabolic coupling for the dynamics of gene expression following a diauxic shift in Escherichia coli, in: Journal of Theoretical Biology, 2011, In press.
  • 3S. Berthoumieux, M. Brilli, H. de Jong, D. Kahn, E. Cinquemani.

    Identification of metabolic network models from incomplete high-throughput datasets, in: Bioinformatics, 2011, vol. 27, no 13, p. i186-i195.
  • 4D. Chatterjee, E. Cinquemani, J. Lygeros.

    Maximizing the probability of attaining a target prior to extinction, in: Nonlinear Analysis: Hybrid Systems, 2011, vol. 5, no 2, p. 367-381.
  • 5E. Cinquemani, M. Agarwal, D. Chatterjee, J. Lygeros.

    Convexity and convex approximations of discrete-time stochastic control problems with constraints, in: Automatica, 2011, vol. 47, no 9, p. 2082-2087.
  • 6P. Hokayem, E. Cinquemani, D. Chatterjee, F. Ramponi, J. Lygeros.

    Stochastic receding horizon control with output feedback and bounded control inputs, in: Automatica, 2011, In press.
  • 7R. Mateescu, P. Monteiro, E. Dumas, H. de Jong.

    CTRL: Extension of CTL with regular expressions and fairness operators to verify genetic regulatory networks, in: Theoretical Computer Science, 2011, vol. 412, no 26, p. 2854-2883.
  • 8P. Monteiro, P. Dias, D. Ropers, A. Oliveira, I. Sa-Correia, M. Teixeira, A. Freitas.

    Qualitative modelling and formal verification of the FLR1 gene mancozeb response in Saccharomyces cerevisiae, in: IET Systems Biology, 2011, vol. 5, no 5, p. 308-316.
  • 9R. Porreca, E. Cinquemani, J. Lygeros, G. Ferrari-Trecate.

    Invalidation of the structure of genetic network dynamics : A geometric approach, in: International Journal of Robust and Nonlinear Control, 2011, In press.
  • 10D. Ropers, V. Baldazzi, H. de Jong.

    Model reduction using piecewise-linear approximations preserves dynamic properties of the carbon starvation response in Escherichia coli, in: IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2011, vol. 8, no 1, p. 166-181.
  • 11R. Silva-Rocha, H. de Jong, J. Tamames, V. de Lorenzo.

    The logic layout of the TOL network of Pseudomonas putida pWW0 plasmid stems from a metabolic amplifier motif (MAM) that optimizes biodegradation of m-xylene, in: BMC Systems Biology, 2011, vol. 5, 191 p.

International Conferences with Proceedings

  • 12V. Baldazzi, D. Ropers, J. Geiselmann, D. Kahn, H. de Jong.

    Importance of metabolic coupling for the dynamics of gene expression following a diauxic shift in Escherichia coli, in: Proceedings of the 18th IFAC World Congress, Milan, Italy, 2011, p. 14851-14856.
  • 13R. Porreca, E. Cinquemani, J. Lygeros, G. Ferrari-Trecate.

    Learning the structure of genetic network dynamics : A geometric approach, in: Proceedings of the 18th IFAC World Congress, Milan, Italy, 2011, p. 11654-11659.

Scientific Books (or Scientific Book chapters)

  • 14V. Baldazzi, P. Monteiro, M. Page, D. Ropers, J. Geiselmann, H. de Jong.

    Qualitative analysis of genetic regulatory networks in bacteria, in: Understanding the Dynamics of Biological Systems: Lessons Learned from Integrative Systems Biology, New York, W. Dubitzky, J. Southgate, H. Fuss (editors), Springer, New York, 2011, p. 111-130.
  • 15G. Batt, B. Besson, P. Ciron, H. de Jong, E. Dumas, J. Geiselmann, R. Monte, P. Monteiro, M. Page, F. Rechenmann, D. Ropers.

    Genetic Network Analyzer: A tool for the qualitative modeling and simulation of bacterial regulatory networks, in: Bacterial Molecular Networks, New York, J. van Helden, A. Toussaint, D. Thieffry (editors), Humana Press, Springer, New York, 2012, p. 439-462.
  • 16D. Ropers.

    De la complexité génomique à la diversité protéique : Analyse par modélisation et expériences de la régulation de l'épissage alternatif de l'ARN du virus VIH-1, Editions Universitaires Européennes, Saarbrücken, Germany, 2011.

Internal Reports

  • 17S. Berthoumieux, M. Brilli, H. de Jong, D. Kahn, E. Cinquemani.

    Identification of metabolic network models from incomplete high-throughput datasets, INRIA, 2011, no RR-7524.

Scientific Popularization