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, n^o 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, n^o 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, n^o 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, n^o 1, 11 p. [ DOI : 10.1038/msb.2012.70 ]
  
  http://hal.inria.fr/hal-00793352
• 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, n^o 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, n^o 11, 16 p.
  
  https://hal.inria.fr/hal-01247993
• 7A. 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, n^o 2, pp. 99-109.
  
  https://hal.inria.fr/hal-01103556
• 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
• 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
• 10M. 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, n^o 3, pp. 355-362. [ DOI : 10.1093/bioinformatics/btu619 ]
  
  https://hal.inria.fr/hal-01096966
• 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, n^o 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, n^o 12, pp. i71-i79.
  
  https://hal.inria.fr/hal-01217800

Publications of the year

Doctoral Dissertations and Habilitation Theses

• 13S. Casagranda.
  
  Analysis and control of models of gene regulatory networks, Université Nice Sophia Antipolis, Nice, 2017.
• 14B. Chelli Ponce de Leon.
  
  Quantitative study of the effects of low DnaA concentrations in Escherichia coli, using the uhp pathway as an inducible expression system, Université Grenoble Alpes, Grenoble, 2017.
• 15N. Giordano.
  
  Microbial growth control in shifting environments: Theoretical and experimental study of resource allocation in Escherichia coli, Université Grenoble Alpes, Grenoble, 2017.

Articles in International Peer-Reviewed Journals

• 16I. 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, 2017, pp. 1-25, forthcoming. [ DOI : 10.1007/s11538-017-0372-4 ]
  
  https://hal.inria.fr/hal-01655367
• 17E. 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, n^o 14, pp. i301-i310. [ DOI : 10.1093/bioinformatics/btx250 ]
  
  https://hal.archives-ouvertes.fr/hal-01607919
• 18H. De Jong, S. Casagranda, N. Giordano, E. Cinquemani, D. Ropers, J. Geiselmann, J.-L. Gouzé.
  
  Mathematical modelling of microbes: metabolism, gene expression and growth, in: Journal of the Royal Society Interface, November 2017, vol. 14, n^o 136, pp. 1-14. [ DOI : 10.1098/rsif.2017.0502 ]
  
  https://hal.inria.fr/hal-01666954
• 19H. De Jong, J. Geiselmann, D. Ropers.
  
  Resource reallocation in bacteria by reengineering the gene expression machinery, in: Trends in Microbiology, 2017, vol. 25, n^o 6, pp. 480-493. [ DOI : 10.1016/j.tim.2016.12.009 ]
  
  https://hal.inria.fr/hal-01420729
• 20M. Morin, D. Ropers, E. Cinquemani, J.-C. Portais, B. Enjalbert, M. Cocaign-Bousquet.
  
  The Csr System Regulates Escherichia coli Fitness by Controlling Glycogen Accumulation and Energy Levels, in: mBio, October 2017, vol. 8, n^o 5, pp. 1-14. [ DOI : 10.1128/mBio.01628-17 ]
  
  https://hal.inria.fr/hal-01672038
• 21A. 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

International Conferences with Proceedings

• 22E. Cinquemani.
  
  Structural identification of biochemical reaction networks from population snapshot data, in: Proceedings of the 20th IFAC World Congress, Toulouse, France, IFAC, July 2017.
  
  https://hal.inria.fr/hal-01577565

Other Publications

• 23E. Cinquemani.
  
  Stochastic reaction networks with input processes: Analysis and applications to reporter gene systems, October 2017, https://arxiv.org/abs/1710.06259 - working paper or preprint. [ DOI : 10.06259 ]
  
  https://hal.inria.fr/hal-01672506