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Bibliography

Major publications by the team in recent years
  • 1G. 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
  • 2S. 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.
  • 3S. 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.

    http://hal.inria.fr/hal-00762620
  • 4S. 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
  • 5J. 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
  • 6A. 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.

    https://hal.inria.fr/hal-01103556
  • 7C. 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
  • 8M. 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
  • 9D. 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
  • 10V. 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.

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

Articles in International Peer-Reviewed Journals

  • 11H. De Jong, J. Geiselmann, D. Ropers.

    Resource reallocation in bacteria by reengineering the gene expression machinery, in: Trends in Microbiology, 2017.

    https://hal.inria.fr/hal-01420729
  • 12N. Giordano, F. Mairet, J.-L. Gouzé, J. Geiselmann, H. De Jong.

    Dynamical allocation of cellular resources as an optimal control problem: Novel insights into microbial growth strategies, in: PLoS Computational Biology, March 2016, vol. 12, no 3, e1004802. [ DOI : 10.1371/journal.pcbi.1004802 ]

    https://hal.inria.fr/hal-01332394
  • 13A. 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, February 2016, vol. 12, no 2, e1004706. [ DOI : 10.1371/journal.pcbi.1004706 ]

    https://hal.inria.fr/hal-01248298
  • 14M. Morin, D. Ropers, F. Letisse, S. Laguerre, J.-C. J.-C. Portais, M. Cocaign-Bousquet, B. Enjalbert.

    The post-transcriptional regulatory system CSR controls the balance of metabolic pools in upper glycolysis of Escherichia coli, in: Molecular Microbiology, January 2016, vol. 100, no 4, pp. 686-700. [ DOI : 10.1111/mmi.13343 ]

    https://hal.inria.fr/hal-01418224
  • 15A. Métris, S. George, D. Ropers.

    Piecewise linear approximations to model the dynamics of adaptation to osmotic stress by food-borne pathogens, in: International Journal of Food Microbiology, 2017, vol. 240, pp. 63-74. [ DOI : 10.1016/j.ijfoodmicro.2016.06.022 ]

    https://hal.inria.fr/hal-01417975
  • 16D. Ropers, A. Métris.

    Data for the qualitative modeling of the osmotic stress response to NaCl in Escherichia coli, in: Data in Brief, September 2016, vol. 9, pp. 606-612. [ DOI : 10.1016/j.dib.2016.09.028 ]

    https://hal.inria.fr/hal-01417966

Invited Conferences

  • 17S. Casagranda, D. Ropers, J.-L. Gouzé.

    Model simplification and process analysis of biological models, in: The 5th International Symposium on Positive Systems (POSTA), Rome, Italy, September 2016.

    https://hal.inria.fr/hal-01412049

International Conferences with Proceedings

  • 18E. Cinquemani.

    On observability and reconstruction of promoter activity statistics from reporter protein mean and variance profiles, in: Fifth International workshop on Hybrid Systems Biology - HSB 2016, Grenoble, France, E. Cinquemani, A. Donzé (editors), Hybrid Systems Biology, Springer, October 2016, vol. 9957, pp. 147-163. [ DOI : 10.1007/978-3-319-47151-8 ]

    https://hal.inria.fr/hal-01399934
  • 19A. M. Gonzalez-Vargas, E. Cinquemani, G. Ferrari-Trecate.

    Validation Methods for Population Models of Gene Expression Dynamics, in: 6th IFAC Conference on Foundations of Systems Biology in Engineering - FOSBE 2016, Magdeburg, Germany, October 2016.

    https://hal.inria.fr/hal-01399921

Books or Proceedings Editing

  • 20E. Cinquemani, A. Donzé (editors)

    Hybrid Systems Biology: 5th International Workshop, HSB 2016, Grenoble, France, October 20-21, 2016, Proceedings, Lecture Notes in Bioinformatics, Springer, Grenoble, France, 2016, no 9957. [ DOI : 10.1007/978-3-319-47151-8 ]

    https://hal.inria.fr/hal-01399942

Internal Reports

  • 21A. M. Gonzalez-Vargas, E. Cinquemani, G. Ferrari-Trecate.

    Validation methods for population models of gene expression dynamics, Inria Grenoble - Rhône-Alpes, July 2016, no RR-8938, 17 p.

    https://hal.inria.fr/hal-01349030


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