2025
- A. Belcour, L. Megy, S. Stephant, C. Michel, S. Rad, P. Bombach, N. Dopffel, H. de Jong, D. Ropers. Predicting coarse-grained representations of biogeochemical cycles from metabarcoding data. Bioinformatics, 41(Issue Supplement_1):i49–i57. Special issue ISMB/ECCB 2025
- A. Pavlou , E. Cinquemani , C. Pinel , N. Giordano , M. van Melle-Gateau, I. Mihalcescu, J. Geiselmann, H. de Jong. Single-cell data reveal heterogeneity of investment in ribosomes across a bacterial population. Nature Communications, 16:285, 2025. Editor’s Highlight in Nature Communications, in the category Microbiology and infectious diseases.
2024
- R. Asswad, E. Cinquemani, J.-L. Gouzé. Kalman-based approaches for online estimation of bioreactor dynamics from fluorescent reporter measurements. Proceedings of the 22nd European Control Conference (ECC 2024), Stockholm, Sweden, June 25-28, 2024
- R. Asswad, W Djema, O. Bernard, J.-L Gouzé, E. Cinquemani. Optimization of microalgae biosynthesis via controlled algal-bacterial symbiosis. Proceedings of the 63rd IEEE Conference on Decision and Control (CDC 2024), IEEE CSS, Dec 2024, Milan, Italy
- T. Clavier, C. Pinel, H. de Jong, J. Geiselmann. Improving the genetic stability of bacterial growth control for long-term bioproduction. Biotechnology and Bioengineering,121(9):2808-2819, 2024
- F. Denoeud, …, J.M. Cock. Evolutionary genomics of the emergence of brown algae as key components of coastal ecosystems. Cell 187: 1-23, 2024
- N. Dopffel, B.A. Stepec, P. Bombach, K. Cerna, J. Riha, K. Kyaw, N. Paltrinieri, A. Oust, D. Ropers, S. Rad, S. Stephant, J. Tremosa (2024). Microbial risks associated with hydrogen underground storage in Europe. In 85th EAGE Annual Conference & Exhibition, Vol. 2024, No. 1, pp. 1-5. European Association of Geoscientists & Engineers.
- N. Dopffel, K. Cerna, S. Stephant, P. Bombach, K. Wunch, B. A. An-Stepec, A. Valiakhmetova, T. Boiadjieva-Scherzer, J. Tremosa, S. Rad, D. Ropers (2024). Microbial risks associated with hydrogen underground storage in Europe. In Solution Mining Research Institute Spring 2024 Technical Conference, 12p. 22-23 April 2024, Krakow, Poland.
- A. Marguet, C. Smadi. Parasite infection in a cell population: role of the partitioning kernel, Journal of Mathematical Biology, 89(14), 2024
- A. Marguet, C. Smadi. Spread of parasites affecting death and division rates in a cell population. Stochastic Processes and their Applications, 168:104262, 2024
- C. Medous. Spinal constructions for continuous type-space branching processes with interactions. Electronic Journal of Probability. 29: 1–46.
- E. Reginato, A. Marguet, E. Cinquemani, Inference of tree-structured auto-regressive models of gene expression parameters from generation-snapshot data, Proceedings of the 22nd European Control Conference (ECC 2024), Stockholm, Sweden, June 25-28, 2024
- B. Ruiz, A. Belcour, S. Blanquart, S. Buffet-Bataillon, I. Le Huërou-Luron. SPARTA: Interpretable functional classification of microbiomes and detection of hidden cumulative effects. PLoS Computational Biology 20(11): e1012577, 2024
- M. Zonnequin, A. Belcour, L. Delage, A. Siegel, S. Blanquart, C. Leblanc and G.V. Markov. Empirical evidence for metabolic drift in plant and algal lipid biosynthesis pathways. Frontiers in Plant Science. 15:1339132, 2024
2023
- V. Baldazzi, D. Ropers, J.-L. Gouzé, T. Gedeon, H. de Jong. Resource allocation accounts for the large variability of rate-yield phenotypes across bacterial strains. eLife, 12:e79815, 2023
- E. Cinquemani, L. Paulevé (Eds). Special Issue of the 19th International Conference on Computational Methods in Systems Biology. BMC Bioinformatics Supplements, 24(1), 2023
- H. de Jong, D. Giannari, D. Oyarzún, S. Waldherr, A. Yabo. Optimal cell behavior in time. In: Economic Principles in Cell Biology, 2023. Free, community-wide, on-line textbook
- O. Golan, H.J. Hindley, H. de Jong, M. Köbis, E. Pascual Garcia, A.Y. Weiße. Models of growing cells. In: Economic Principles in Cell Biology, 2023. Free, community-wide, on-line textbook
- C. Martínez, E. Cinquemani, H. de Jong, J.-L. Gouzé. Optimal protein production by a synthetic microbial consortium: Coexistence, distribution of labor, and syntrophy. Journal of Mathematical Biology, 87(1):23, 2023
2022
- V. Bansaye, B. Cloez, P. Gabriel, A. Marguet. A non-conservative Harris ergodic theorem. Journal of the London Mathematical Society, 2022
- A. Pavlou, E. Cinquemani, J. Geiselmann, H. de Jong. Maturation models of fluorescent proteins are necessary for unbiased estimates of promoter activity. Biophysical Journal, 121(21):4179-4188, 2022
- 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, 21(1):137-165, 2022
2021
- E. Cinquemani, L. Paulevé (Eds.). Computational Methods in Systems Biology. Proceedings of the 19th International Conference on Computational Methods in Systems Biology (CMSB). Lecture Notes in Bioinformatics (LNBI) 12881, Springer, 2021
- A. dos Reis de Souza, D. Efimov, A. Polyakov, J.-L. Gouzé, E. Cinquemani. State observation in microbial consortia: a case study on a synthetic producer-cleaner consortium. International Journal of Robust and Nonlinear Control (Special Issue on Control-Theoretic Approaches for Systems in the Life Sciences), 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, 10(11):2910-2926, 2021
- 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 expression models 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(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
For publications before 2015, please visit the personal web pages of the team members and the HAL repository.
