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Bibliography

Major publications by the team in recent years
  • 1V. Baldazzi, D. Ropers, Y. Markowicz, D. Kahn, J. Geiselmann, H. de Jong.

    The carbon assimilation network in Escherichia coli is densely connected and largely sign-determined by directions of metabolic fluxes, in: PloS Computational Biology, 2010, vol. 6, no 6, e1000812 p.
  • 2G. 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, 11 p.

    http://hal.inria.fr/hal-00857345
  • 3G. Batt, M. Page, I. Cantone, G. Goessler, P. Monteiro, H. de Jong.

    Efficient parameter search for qualitative models of regulatory networks using symbolic model checking, in: Bioinformatics, 2010, vol. 26, no 18, pp. i603-i610.
  • 4S. 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, pp. i186-i195.
  • 5S. 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
  • 6S. 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, 11 p. [ DOI : 10.1038/msb.2012.70 ]

    http://hal.inria.fr/hal-00793352
  • 7J. Izard, C. Gomez-Balderas, D. Ropers, S. Lacour, X. Song, Y. Yang, A. B. Lindner, J. Geiselmann, H. De Jong.

    A synthetic growth switch based on controlled expression of RNA polymerase, in: Molecular Systems Biology, November 2015, vol. 11, no 11, 16 p.

    https://hal.inria.fr/hal-01247993
  • 8A. Llamosi, A. Gonzalez, C. Versari, E. Cinquemani, G. Ferrari-Trecate, P. Hersen, G. Batt.

    What population reveals about individual cell identity: Single-cell parameter estimation of models of gene expression in yeast, in: PLoS Computational Biology, 2015, forthcoming.

    https://hal.inria.fr/hal-01248298
  • 9C. Peano, J. Wolf, J. Demol, E. Rossi, L. Petiti, G. de Bellis, J. Geiselmann, T. Egli, S. Lacour, P. Landini.

    Characterization of the Escherichia coli σ(S) core regulon by Chromatin Immunoprecipitation-sequencing (ChIP-seq) analysis, in: Scientific Reports, 2015, vol. 5, 15 p. [ DOI : 10.1038/srep10469 ]

    https://hal.inria.fr/hal-01217828
  • 10R. Porreca, E. Cinquemani, J. Lygeros, G. Ferrari-Trecate.

    Identification of genetic network dynamics with unate structure, in: Bioinformatics, 2010, vol. 26, no 9, pp. 1239-1245.
  • 11M. 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, 2015, vol. 31, no 3, pp. 355-362. [ DOI : 10.1093/bioinformatics/btu619 ]

    https://hal.inria.fr/hal-01096966
  • 12R. 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.
  • 13D. 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
  • 14V. Zulkower, M. Page, D. Ropers, J. Geiselmann, H. De Jong.

    Robust reconstruction of gene expression profiles from reporter gene data using linear inversion, in: Bioinformatics, 2015, vol. 31, no 12, pp. i71-i79. [ DOI : 10.1093/bioinformatics/btv246 ]

    https://hal.inria.fr/hal-01217800
Publications of the year

Doctoral Dissertations and Habilitation Theses

  • 15M. Morin.

    Rôle du régulateur post-transcriptionnel CSR dans l’adaptation métabolique de la bactérie modèle Escherichia coli, Université de Toulouse, Toulouse, 2015.
  • 16S. Pinhal.

    Adaptation d’E. coli à la croissance sur acétate : une approche pluridisciplinaire, Université Grenoble Alpes, Grenoble, 2015.
  • 17V. Zulkower.

    Etude de la dynamique des mécanismes de la répression catabolique : des modèles mathématiques aux données expérimentales, Université Grenoble Alpes, Grenoble, 2015.

Articles in International Peer-Reviewed Journals

  • 18J. Izard, C. Gomez-Balderas, D. Ropers, S. Lacour, X. Song, Y. Yang, A. B. Lindner, J. Geiselmann, H. De Jong.

    A synthetic growth switch based on controlled expression of RNA polymerase, in: Molecular Systems Biology, November 2015, vol. 11, no 11, 16 p.

    https://hal.inria.fr/hal-01247993
  • 19A. Kremling, J. Geiselmann, D. Ropers, H. De Jong.

    Understanding carbon catabolite repression in Escherichia coli using quantitative models, in: Trends in Microbiology, 2015, vol. 23, no 2, pp. 99-109. [ DOI : 10.1016/j.tim.2014.11.002 ]

    https://hal.inria.fr/hal-01103556
  • 20A. Llamosi, A. Gonzalez, C. Versari, E. Cinquemani, G. Ferrari-Trecate, P. Hersen, G. Batt.

    What population reveals about individual cell identity: Single-cell parameter estimation of models of gene expression in yeast, in: PLoS Computational Biology, 2015, forthcoming.

    https://hal.inria.fr/hal-01248298
  • 21C. Peano, J. Wolf, J. Demol, E. Rossi, L. Petiti, G. de Bellis, J. Geiselmann, T. Egli, S. Lacour, P. Landini.

    Characterization of the Escherichia coli σ(S) core regulon by Chromatin Immunoprecipitation-sequencing (ChIP-seq) analysis, in: Scientific Reports, 2015, vol. 5, 15 p. [ DOI : 10.1038/srep10469 ]

    https://hal.inria.fr/hal-01217828
  • 22M. 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, 2015, vol. 31, no 3, pp. 355-362. [ DOI : 10.1093/bioinformatics/btu619 ]

    https://hal.inria.fr/hal-01096966
  • 23D. 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. [ DOI : 10.1371/journal.pcbi.1004028 ]

    https://hal.inria.fr/hal-01097632
  • 24V. Zulkower, M. Page, D. Ropers, J. Geiselmann, H. De Jong.

    Robust reconstruction of gene expression profiles from reporter gene data using linear inversion, in: Bioinformatics, 2015, vol. 31, no 12, pp. i71-i79. [ DOI : 10.1093/bioinformatics/btv246 ]

    https://hal.inria.fr/hal-01217800

Invited Conferences

  • 25H. De Jong, J. Geiselmann.

    Fluorescent reporter genes and the analysis of bacterial regulatory networks, in: Hybrid Systems Biology: Proceedings of the Second International Workshop, HSB 2013, and Third International Workshop, HSB 2014, Vienna, Austria, O. Maler, A. Halász, T. Dang, C. Piazza (editors), Lecture Notes in Bioinformatics, Springer-Verlag, 2015, vol. 7699, pp. 1-24. [ DOI : 10.1007/978-3-319-27656-4_2 ]

    https://hal.inria.fr/hal-01247997

International Conferences with Proceedings

  • 26S. Casagranda, D. Ropers, J.-L. Gouzé.

    Model reduction and process analysis of biological models, in: 2015 23th Mediterranean Conference on Control and Automation (MED), Torremolinos, Spain, Proceedings of 23th Mediterranean Conference on Control and Automation (MED), June 2015. [ DOI : 10.1109/MED.2015.7158908 ]

    https://hal.inria.fr/hal-01239356
  • 27E. Cinquemani.

    Reconstructing statistics of promoter switching from reporter protein population snapshot data, in: Fourth International Workshop on Hybrid Systems Biology, Madrid, Spain, September 2015, forthcoming.

    https://hal.archives-ouvertes.fr/hal-01218004
  • 28E. Cinquemani.

    Reconstruction of promoter activity statistics from reporter protein population snapshot data, in: 54th IEEE Conference on Decision and Control, Osaka, Japan, December 2015, forthcoming.

    https://hal.archives-ouvertes.fr/hal-01218010
  • 29A. Métris, S. George, D. Ropers, J. Baranyi.

    A dynamic network analysis of the physiological state of foodborne pathogens: application to Escherichia coli during osmotic stress and comparison with Salmonella Typhimurium, in: 9th International Conference on Predictive Modelling in Food, Rio de Janeiro, Brazil, Procedia Food Science, 2015.

    https://hal.inria.fr/hal-01251307


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