2021
- D. Ropers, Y. Couté, L. Faure, S. Ferré, D. Labourdette, A. Shabani, L. Trouilh, P. Vasseur, G. Corre, M. Ferro, M.-A. Teste, J. Geiselmann, H. de Jong. A multi-omics study of bacterial growth arrest in a synthetic biology application. ACS Synthetic Biology. To appear
- A. Yabo, J.B. Caillau, J.L. Gouzé, H. de Jong, F. Mairet. Dynamical analysis and optimization of a generalized resource allocation model of microbial growth. SIAM Journal on Applied Dynamical Systems. To appear
- C. Roux, T.A. Etienne, E. Hajnsdorf, D. Ropers, A.J. Carpousis, M. Cocaign-Bousquet, L. Girbal. The essential role of mRNA degradation in understanding and engineering E. coli metabolism. Biotechnology Advances, 107805, 2021.
- A. Marguet, E. Cinquemani. Identification of stochastic gene expressionmodels over lineage trees. Proceedings of the 19th IFAC symposium on System Identification, Padova, July 13-16, 2021.
- A. Marguet, C. Smadi. Long time behaviour of continuous-state nonlinear branching processes with catastrophes.Electronic Journal of Probability, 26, no. 95, 1-32, 2021.
- M. Chaves, H. de Jong. Qualitative modeling, analysis and control of synthetic regulatory circuits. In: F. Menolascine (ed.), Synthetic Gene Circuits: Methods and Protocols, Methods in Molecular Biology 2229, Humana Press, New York, 2021, 1-40
- F. Mairet, J.-L. Gouzé, H. de Jong. Optimal proteome allocation and the temperature dependence of microbial growth laws. npj Systems Biology and Applications, 7:14, 2021
2020
- T.A. Etienne, M. Cocaign-Bousquet, D. Ropers. Competitive effects in bacterial mRNA decay. Journal of Theoretical Biology, 504:110333, 2020
- M. Mauri, J.-L. Gouzé, H. de Jong, E. Cinquemani. Enhanced production of heterologous proteins by a synthetic microbial community: Conditions and trade-offs. PLoS Computational Biology, 16(4):e1007795, 2020
- M. Morin, B. Enjalbert, D. Ropers, L. Girbal, M. Cocaign-Bousquet. Genomewide stabilization of mRNA during a “feast-to-famine” growth transition in Escherichia coli. Msphere, 5(3):e00276-20, 2020
2019
- E. Cinquemani. Stochastic reaction networks with input processes: Analysis and application to gene expression inference. Automatica, 101:150-156, 2019
- E. Cinquemani, F. Mairet, I. Yegorov, H. de Jong, J.-L. Gouzé. Optimal control of bacterial growth for metabolite production: The role of timing and costs of control. Proceedings of the 17th European Control Conference (ECC 2019), Naples, Italy, 2019
- M. Hoffman, A. Marguet. Statistical estimation in a randomly structured branching population. Stochastic Processes and their Applications, 129, 12:5236-5277, 2019
- S. Leonard, S. Meyer, S. Lacour, W. Nasser, F. Hommais, S. Reverchon. APERO: a genome-wide approach for identifying bacterial small RNAs from RNA-Seq data, Nucleic Acids Research, 47(15):e88, 2019
- A. Marguet. A law of large numbers for branching Markov processes by the ergodicity of ancestral lineages. ESAIM: Probability and Statistics, 23:638–661, 2019
- A. Marguet. Uniform sampling in a structured branching population. Bernoulli 25(4A):2649-2695, 2019
- Y. Martin, M. Page, C. Blanchet, H. de Jong. WellInverter: A web application for the analysis of fluorescent reporter gene data. BMC Bioinformatics, 20(1):309, 2019
- S. Pinhal, D. Ropers, J. Geiselmann, H. de Jong. Acetate metabolism and the inhibition of bacterial growth by acetate. Journal of Bacteriology, 201(13):e00147-19, 2019
- I. Yegorov, F. Mairet, H. de Jong, J.-L. Gouzé. Optimal control of bacterial growth for the maximization of metabolite production. Journal of Mathematical Biology, 78(4):985–1032, 2019
- A. Marguet, M. Lavielle, E. Cinquemani. Inheritance and variability of kinetic gene expression parameters in microbial cells: Modelling and inference from lineage tree data. Bioinformatics, 35(14):i586-i595, 2019. Special issue ISMB/ECCB 2019
2018
- I. Belgacem, S. Casagranda, E. Grac, D. Ropers, J.L. Gouzé. Reduction and stability analysis of a transcription-translation model of RNA polymerase. Bulletin of Mathematical Biology, 80(2):294-318, 2018
- S. Casagranda, S. Touzeau, D. Ropers, J.-L. Gouzé. Principal process analysis of biological models. BMC Systems Biology, 12(1):68, 2018
- E. Cinquemani. Identifiability and reconstruction of biochemical reaction networks from population snapshot data. Processes, 6(9):136, 2018
- A. Kremling, J. Geiselmann, D. Ropers, H. de Jong. An ensemble of mathematical models showing diauxic growth behavior. BMC Systems Biology, 21(1):82, 2018
- D. Lucena, M. Mauri, F. Schmidt, B. Eckhardt, P. Graumann. Microdomain formation is a general property of bacterial membrane proteins and induces heterogeneity of diffusion patterns. BMC Biology, 16(1):97, 2018
2017
- E. Cinquemani, V. Laroute, M. Cocaign-Bousquet, H. de Jong, D. Ropers. Estimation of time-varying growth, uptake and excretion rates from dynamic metabolomics data. Bioinformatics, 33(14):i301-i310, 2017. Special issue ISMB/ECCB 2017
- H. de Jong, S. Casagranda, N. Giordano, E. Cinquemani, D. Ropers, J. Geiselmann, J.-L. Gouzé. Mathematical modeling of microbes: Metabolism, gene expression, and growth. Journal of the Royal Society Interface, 14(136):20170502
- H. de Jong, J. Geiselmann, D. Ropers. Resource reallocation in bacteria by reengineering the gene expression machinery. Trends in Microbiology, 25(6):480-493, 2017
- A. Métris, S.M. George, D. Ropers. Piecewise linear approximations to model the dynamics of adaptation to osmotic stress by food-borne pathogens. International Journal of Food Microbiology, 240:63-74, 2017
- M. 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. mBio, 8(5):e01628-17, 2017
2016
- E. Cinquemani, On observability and reconstruction of promoter activity statistics from reporter protein mean and variance profiles. Proceedings of the 5th International Workshop on Hybrid Systems Biology, Lecture Notes in Bioinformatics (LNBI) 9957, Springer-Verlag, Berlin, 2016
- N. 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. PLoS Computational Biology, 12(3): e1004802, 2016
- A.M. Gonzalez-Vargas, E.Cinquemani, G. Ferrari-Trecate, Validation methods for population models of gene expression dynamics. Proceedings of the 6th IFAC Conference on Foundations of Systems Biology in Engineering (FOSBE), Magdeburg, Germany, 2016
- 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. PLoS Computational Biology, 12(2):e1004706, 2016
- M. Morin, D. Ropers, F. Letisse, S. Laguerre, 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. Molecular Microbiology, 100(4):686-700, 2016
- D. Ropers, A Métris. Data for the qualitative modeling of the osmotic stress response to NaCl in Escherichia coli. Data in Brief, 9:606-612, 2016
2015
- E. Cinquemani. Reconstruction of promoter activity statistics from reporter protein population snapshot data. In: Proceedings of the 54th IEEE Conference on Decision and Control (CDC 2015), Osaka, Japan, 2015
- E. Cinquemani. Reconstructing statistics of promoter switching from reporter protein population snapshot data. In: Proceedings of the 4th International Workshop on Hybrid Systems Biology (HSB 2015), Madrid, Spain, 2015
- 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. Molecular Systems Biology, 11(11):840, 2015
- A. Kremling, J. Geiselmann, D. Ropers, H. de Jong. Understanding carbon catabolite repression in Escherichia coli using quantitative models. Trends in Microbiology, 23(2):99-109, 2015
- 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: Proceedings of the 9th International Conference on Predictive Modelling in Food, Rio de Janeiro, Brazil, Procedia Food Science, 2015
- 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 σS core regulon by Chromatin Immunoprecipitation-sequencing (ChIP-seq) analysis. Scientific Reports, 5:10469, 2015
- 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. Bioinformatics, 31(3):355-62, 2015
- 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. PLoS Computational Biology, 11(1) :e1004028, 2015
- V. Zulkower, M. Page, D. Ropers, J. Geiselmann, H. de Jong. Robust reconstruction of gene expression profiles from reporter gene data using linear inversion. Bioinformatics, 31(12):i71-i79, 2015. Special issue ISMB/ECCB 2015
2014
- V. Acary, H. de Jong, B. Brogliato. Numerical simulation of piecewise-linear models of gene regulatory networks using complementarity systems. Physica D: Nonlinear Phenomena, 269:103-119, 2014
- I. Belgacem, E. Grac, D. Ropers, J.-L. Gouzé. Stability analysis of a reduced transcription-translation model of RNA polymerase. In: Proceedings of the 53rd IEEE Conference on Decision and Control (CDC 2014), Los Angeles, CA, 2014
- O. Dudin, J. Geiselmann, H. Ogasawara, A. Ishihama, S. Lacour. Repression of flagellar genes in exponential phase by CsgD and CpxR, two crucial modulators of Escherichia coli biofilm formation. Journal of Bacteriology, 196(3):707-715, 2014
- J. Geiselmann. Systems biology and metabolic engineering in bacteria. In: M.A. Aon, V. Saks, U. Schlattner (eds), Systems Biology of Metabolic and Signaling Networks: Energy, Mass and Information Transfer. Springer Series in Biophysics 16, Springer-Verlag, Berlin, 2014, 351-367
- P. Landini, T. Egli, J. Wolf, S. Lacour. SigmaS, a major player in the response to environmental stresses in Escherichia coli: role, regulation and mechanisms of promoter recognition. Environmental Microbiology Reports, 6(1):1-13, 2014
- L.R.M. Maruthi, I. Tkachev, A. Carta, E. Cinquemani, P. Hersen, G. Batt, A. Abate. Towards real-time control of gene expression at the single cell level: A stochastic control approach. In: Proceedings of the 12th International Conference on Computational Methods in Systems Biology (CMSB 2014), LNCS 8859, Springer-Verlag, Berlin, 2014, 155-172
- M. Masseroli, B. Mons, E. Bongcam-Rudloff, S. Ceri, A. Kel, F. Rechenmann, F. Lisacek, P. Romano. Integrated Bio-Search: Challenges and trends for the integration, search and comprehensive processing of biological information. BMC Bioinformatics, 15(Suppl 1):S2, 2014
- M. Trauchessec, M. Jaquinod, A. Bonvalot, V. Brun, C. Bruley, D. Ropers, H. de Jong, J. Garin, G. Bestel-Corre, M. Ferro. Mass spectrometry-based workflow for accurate quantification of E. coli enzymes: how proteomics can play a key role in metabolic engineering. Molecular and Cellular Proteomics, 13(4):954-968, 2014
2013
- 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. Nucleic Acids Research, 41(17):e164, 2013
- S. Berthoumieux, M. Brilli, H. de Jong, D. Kahn, E. Cinquemani. On the identifiability of metabolic network models. Journal of Mathematical Biology, 67(6-7):1795-1832, 2013
- S. Berthoumieux, H. de Jong, G. Baptist, C. Pinel, C. Ranquet, D. Ropers, and J. Geiselmann. Shared control of gene expression in bacteria by transcription factors and global physiology of the cell. Molecular Systems Biology, 9:634, 2013. Editor’s choice in Science
- A. Carta, E. Cinquemani. State estimation for gene networks with intrinsic and extrinsic noise: a case study on E. coli arabinose uptake dynamics. In: Proceedings of 12th European Control Conference (ECC 2013), Zurich, 2013
- C. Chaouiya, D. Bérenguier, S.M. Keating, A. Naldi, M.P. van Iersel, N. Rodriguez, A. Dräger, F. Büchel, T. Cokelaer, B. Kowal, B. Wicks, E. Gonçalves, J. Dorier, M. Page, P.T. Monteiro, A. von Kamp, I. Xenarios, H. de Jong, M. Hucka, S. Klamt, D. Thieffry, N. Le Novère, J. Saez-Rodriguez, T. Helikar. SBML qualitative models : a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools. BMC Systems Biology, 7:135, 2013
- O. Dudin, S. Lacour, J. Geiselmann. Expression dynamics of RpoS/Crl-dependent genes in Escherichia coli. Research in Microbiology, 164(8):838-847, 2013
- A. Gonzalez, J. Uhlendorf, J. Schaul, E. Cinquemani, G. Batt, G. Ferrari-Trecate. Identification of biological models from single-cell data: a comparison between mixed-effects and moment-based inference. In: Proceedings of 12th European Control Conference (ECC 2013), Zurich
2012
- V. Baldazzi, N. Bertin, H. de Jong, M. Génard. Towards multi-scale plant models: integrating cellular networks. Trends in Plant Science, 17(12):728-736, 2012
- V. Baldazzi, D. Ropers, J. Geiselmann, D. Kahn, H. de Jong. Importance of metabolic coupling for the dynamics of gene expression following a diauxic shift in Escherichia coli. Journal of Theoretical Biology, 295:100-115, 2012
- G. Batt, B. Besson, P.-E. Ciron, H. de Jong, E. Dumas, J. Geiselmann, R. Monte, P.T. Monteiro, M. Page, F. Rechenmann, D. Ropers. Genetic Network Analyzer: A tool for the qualitative modeling and simulation of bacterial regulatory networks. In: J. van Helden, A. Toussaint, D. Thieffry (eds), Bacterial Molecular Networks, Methods in Molecular Biology, Humana Press, Springer, New York, 2012, 439-462
- S. Berthoumieux, D. Kahn, H. de Jong, E. Cinquemani. Structural and practical identifiability of approximate metabolic network models. In: Proceedings of the 16th IFAC Symposium on System Identification, Brussels, 2012
- R. Porreca, E. Cinquemani, J. Lygeros, G. Ferrari-Trecate. Invalidation of the structure of genetic network dynamics : A geometric approach. International Journal of Robust and Nonlinear Control, 22(10):1140-1156, 2012. Special issue on System Identification for Biological Systems
2011
- V. Baldazzi, D. Ropers, J. Geiselmann, D. Kahn, H. de Jong. Importance of metabolic coupling for the dynamics of gene expression following a diauxic shift in Escherichia coli. In: Proceedings of the 18th IFAC World Congress (IFAC 2011), Milan, Italy, 2011, 14851-14856
- V. Baldazzi, P.T. Monteiro, M. Page, D. Ropers, J. Geiselmann, H. de Jong. Qualitative analysis of genetic regulatory networks in bacteria. In: W. Dubitzky, J. Southgate, H. Fuss (eds.), Understanding the Dynamics of Biological Systems: Lessons Learned from Integrative Systems Biology, Springer-Verlag, Berlin, 2011, 111-130
- S. Berthoumieux, M. Brilli, H. de Jong, D. Kahn, E. Cinquemani. Identification of metabolic network models from incomplete high-throughput datasets. Bioinformatics, 27(13):i186-i195, 2011. Special issue ISMB/ECCB 2011
- D. Chatterjee, E. Cinquemani, J. Lygeros. Maximizing the probability of attaining a target prior to extinction. Nonlinear Analysis: Hybrid Systems, 5(5):367-381, 2011
- E. Cinquemani, M. Agarwal, D. Chatterjee, J. Lygeros. Convexity and convex approximations of discrete-time stochastic control problems with constraints. Automatica, 47(9):2082-2087, 2011
- R. Mateescu, P. Monteiro, E. Dumas, H. de Jong. CTRL: Extension of CTL with regular expressions and fairness operators to verify genetic regulatory networks. Theoretical Computer Science, 412(26):2854-2883, 2011. Special issue CMSB 2008
- P.T. Monteiro, P.J. Dias, D. Ropers, A.L. Oliveira, I. Sá-Correia, M.C. Teixeira, A.T. Freitas. Qualitative modeling and formal verification of the FLR1 gene mancozeb response in Saccharomyces cerevisiae. IET Systems Biology, 5(5):308-316, 2011
- R. Porreca, E. Cinquemani, J. Lygeros, G. Ferrari-Trecate. Learning the structure of genetic network dynamics: A geometric approach. In: Proceedings of the 18th IFAC World Congress (IFAC 2011), Milan, Italy, 2011, 11654-11659
- D. Ropers. De la complexité génomique à la diversité protéique – Analyse par modélisation et expériences de la régulation de l’épissage alternatif de l’ARN du virus HIV-1. Editions Universitaires Européennes, Saarbrücken, Germany, 2011
- D. Ropers, V. Baldazzi, H. de Jong. Model reduction using piecewise-linear approximations preserves dynamic properties of the carbon starvation response in Escherichia coli. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 8(1):166-181, 2011
- 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. BMC Systems Biology, 5:191, 2011
2010
- 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. PLoS Computational Biology, 6(6):e1000812, 2010
- 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. Bioinformatics, 26(18):i603-i610, 2010. Special issue ECCB 2010
- F. Boyer, B. Besson, G. Baptist, J. Izard, C. Pinel, D. Ropers, J. Geiselmann, H. de Jong. WellReader: A MATLAB program for the analysis of fluorescence and luminescence reporter gene data. Bioinformatics, 26(9):1262-1263, 2010
- H. de Jong, C. Ranquet, D. Ropers, C. Pinel, J. Geiselmann. Experimental and computational validation of models of fluorescent and luminescent reporter genes in bacteria. BMC Systems Biology, 4:55, 2010
- R. Porreca, E. Cinquemani, J. Lygeros, G. Ferrari-Trecate. Identification of genetic network dynamics with unate structure. Bioinformatics, 26(9):1239-1245, 2010
2009
- V. Baldazzi, P. Paci, M. Bernaschi, F. Castiglione. Modeling lymphocyte homing and encounters in lymph nodes. BMC Bioinformatics, 10:387, 2009
- F. Corblin, S. Tripodi, E. Fanchon, D. Ropers, L. Trilling. A declarative constraint-based method for analyzing discrete genetic regulatory networks. Biosystems, 98(2):91-104, 2009
- G. Khoury, L. Ayadi, J.-M. Sailou, S. Sanglier, D. Ropers, C. Branlant. New actors in regulation of HIV-1 tat mRNA production. Retrovirology, 6(Suppl 2):P46, 2009
- P.T. Monteiro, E. Dumas, B. Besson, R. Mateescu, M. Page, A.T. Freitas, H. de Jong. A service-oriented architecture for integrating the modeling and formal verification of genetic regulatory networks. BMC Bioinformatics, 10:450, 2009
- H. de Jong. Vers la cellule virtuelle. DocSciences, 8:20-25, 2009
- D. Ropers, H. de Jong, J. Geiselmann. Mathematical modeling of genetic regulatory networks: Stress responses in Escherichia coli. In: P. Fu, M. Latterich, S. Panke (eds), Systems Biology and Synthetic Biology, John Wiley & Sons, Hoboken, NJ, 2009, 235-271
- J.-M. Saliou, C.F. Bourgeois, L. Ayadi-Ben Mena, D. Ropers, S. Jacquenet, V. Marchand, J. Stévenin, C. Branlant. Role of RNA structure and protein factors in the control of HIV-1 splicing. Frontiers in Biosciences, 14:2714-2729, 2009
2008
- G. Batt, H. de Jong, M. Page, J. Geiselmann. Symbolic reachability analysis of genetic regulatory networks using discrete abstractions. Automatica, 44(4):982-989, 2008
- H. de Jong. Qualitative modeling and simulation of bacterial regulatory networks. In: A. Uhrmacher, M. Heiner (eds.), In: Proceedings of the 6th International Conference on Computational Methods in Systems Biology (CMSB-08), LNCS 5307, Springer-Verlag, Berlin, 2008, 1
- H. de Jong, M. Page. Search for steady states of piecewise-linear differential equation models of genetic regulatory networks. ACM/IEEE Transactions on Computational Biology and Bioinformatics, 5(2):508-522, 2008
- H. de Jong, D. Ropers, R. Mateescu, J. Geiselmann. De la cellule à la puce. La Recherche, 419, 2008. Les cahiers de l’INRIA, I-II
- S. Drulhe, G. Ferrari-Trecate, H. de Jong. The switching threshold reconstruction problem for piecewise affine models of genetic regulatory networks. IEEE Transactions on Automatic Control & IEEE Transactions on Circuits and Systems I, 53(1):153-165, 2008. Joint special issue on Systems Biology
- R. Mateescu, P.T. Monteiro, E. Dumas, H. de Jong. Computation Tree Regular Logic for genetic regulatory networks. In: S. Cha, J.-Y. Choi, M. Kim, I. Lee, M. Viswanathan (eds.), In: Proceedings of the 6th International Symposium on Automated Technology for Verification and Analysis (ATVA-08), LNCS 5311, Springer-Verlag, Berlin, 48-63, 2008
- P.T. Monteiro, D. Ropers, R. Mateescu, A.T. Freitas, H. de Jong. Temporal logic patterns for querying qualitative models of genetic regulatory networks. In: M. Ghallab, C.D. Spyropoulos, N. Fakotakis, N. Avouris (eds.), In: Proceedings of 18th European Conference on Artificial Intelligence (ECAI-08), IOS Press, Amsterdam, 229-233, 2008
- P.T. Monteiro, D. Ropers, R. Mateescu, A.T. Freitas, H. de Jong. Temporal logic patterns for querying dynamic models of cellular interaction networks. Bioinformatics, 24(16):i227-i233. Special issue ECCB 2008
- R. Porreca, S. Drulhe, H. de Jong, G. Ferrari-Trecate. Structural identification of piecewise-linear models of genetic regulatory networks. Journal of Computational Biology, 15(10):1365-1380, 2008
For publications before 2008, please visit the personal web pages of the team members and the HAL repository.
