Members
Overall Objectives
Research Program
Highlights of the Year
New Software and Platforms
New Results
Bilateral Contracts and Grants with Industry
Partnerships and Cooperations
Dissemination
Bibliography
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Bibliography

Major publications by the team in recent years
[1]
V. 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.
[2]
G. 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
[3]
G. 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.
[4]
S. 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.
[5]
S. 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
[6]
S. 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
[7]
J. 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
[8]
A. 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
[9]
C. 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
[10]
R. 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.
[11]
M. 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
[12]
R. 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.
[13]
D. 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
[14]
V. 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

[15]
M. Morin.
Rôle du régulateur post-transcriptionnel CSR dans l’adaptation métabolique de la bactérie modèle Escherichia coli, Université de Toulouse, Toulouse, 2015.
[16]
S. Pinhal.
Adaptation d’E. coli à la croissance sur acétate : une approche pluridisciplinaire, Université Grenoble Alpes, Grenoble, 2015.
[17]
V. 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

[18]
J. 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
[19]
A. 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
[20]
A. 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
[21]
C. 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
[22]
M. 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
[23]
D. 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
[24]
V. 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

[25]
H. 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

[26]
S. 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
[27]
E. 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
[28]
E. 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
[29]
A. 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