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  • The Inria's Research Teams produce an annual Activity Report presenting their activities and their results of the year. These reports include the team members, the scientific program, the software developed by the team and the new results of the year. The report also describes the grants, contracts and the activities of dissemination and teaching. Finally, the report gives the list of publications of the year.

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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.
  • 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, 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
  • 4E. Cinquemani, V. Laroute, M. Bousquet, H. De Jong, D. Ropers.

    Estimation of time-varying growth, uptake and excretion rates from dynamic metabolomics data, in: Bioinformatics, 2017, vol. 33, no 14, pp. i301-i310. [ DOI : 10.1093/bioinformatics/btx250 ]

    https://hal.archives-ouvertes.fr/hal-01607919
  • 5N. 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 p. [ DOI : 10.1371/journal.pcbi.1004802 ]

    https://hal.inria.fr/hal-01332394
  • 6J. 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
  • 7A. 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 p.

    https://hal.inria.fr/hal-01248298
  • 8M. 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. 4, 15 p. [ DOI : 10.1111/mmi.13343 ]

    https://hal.inria.fr/hal-01418224
  • 9M. Morin, D. Ropers, F. Letisse, S. Laguerre, J.-C. J.-C. Portais, M. Cocaign-Bousquet, B. Enjalbert.

    The Csr system regulates Escherichia coli fitness by controlling glycogen accumulation and energy levels, in: mBio, 2017, vol. 8, no 5, pp. 1-14.

    https://hal.inria.fr/hal-01672038
  • 10C. 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
  • 11D. 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
  • 12V. 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

  • 13I. Belgacem, S. Casagranda, E. Grac, D. Ropers, J.-L. Gouzé.

    Reduction and stability analysis of a transcription-translation model of RNA polymerase, in: Bulletin of Mathematical Biology, 2018, vol. 80, no 2, pp. 294-318. [ DOI : 10.1007/s11538-017-0372-4 ]

    https://hal.inria.fr/hal-01655367
  • 14S. Casagranda, S. Touzeau, D. Ropers, J.-L. Gouzé.

    Principal process analysis of biological models, in: BMC Systems Biology, 2018, vol. 12, 68 p. [ DOI : 10.1186/s12918-018-0586-6 ]

    https://hal.inria.fr/hal-01818033
  • 15E. Cinquemani.

    Identifiability and Reconstruction of Biochemical Reaction Networks from Population Snapshot Data, in: Processes, August 2018, vol. 6, no 9, pp. 1-24. [ DOI : 10.3390/pr6090136 ]

    https://hal.inria.fr/hal-01909765
  • 16E. Cinquemani.

    Stochastic reaction networks with input processes: Analysis and application to gene expression inference, in: Automatica, 2018, pp. 1-9.

    https://hal.inria.fr/hal-01925923
  • 17A. Kremling, J. Geiselmann, D. Ropers, H. De Jong.

    An ensemble of mathematical models showing diauxic growth behaviour, in: BMC Systems Biology, December 2018, vol. 12, no 1, pp. 1-16. [ DOI : 10.1186/s12918-018-0604-8 ]

    https://hal.inria.fr/hal-01893978
  • 18D. Lucena, M. Mauri, F. Schmidt, B. Eckhardt, P. L. Graumann.

    Microdomain formation is a general property of bacterial membrane proteins and induces heterogeneity of diffusion patterns, in: BMC Biology, December 2018, vol. 16, no 1. [ DOI : 10.1186/s12915-018-0561-0 ]

    https://hal.inria.fr/hal-01966627
  • 19A. Marguet.

    Uniform sampling in a structured branching population, in: Bernoulli, 2019, https://arxiv.org/abs/1609.05678.

    https://hal.archives-ouvertes.fr/hal-01362366
  • 20I. Yegorov, F. Mairet, H. De Jong, J.-L. Gouzé.

    Optimal control of bacterial growth for the maximization of metabolite production, in: Journal of Mathematical Biology, October 2018, pp. 1-48. [ DOI : 10.1007/s00285-018-1299-6 ]

    https://hal.inria.fr/hal-01929475

Other Publications