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D. Ropers · SciRah

Researcher profile · Semantic Scholar

D. Ropers

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D. Ropers — researcher profile on SciRah

h-index: 24
Works: 73
Citations: 2,352

Most-cited papers

Validation of qualitative models of genetic regulatory networks by model checking: analysis of the nutritional stress response in Escherichia coli
Grégory Batt, D. Ropers, H. de Jong, J. Geiselmann +3 more
2005Intelligent Systems in Molecular Biology439 citations
Semantic Scholar
Acetate Metabolism and the Inhibition of Bacterial Growth by Acetate
Stéphane Pinhal, D. Ropers, J. Geiselmann, H. de Jong
2019Journal of Bacteriology214 citations Open access
Semantic Scholar
Qualitative simulation of the carbon starvation response in Escherichia coli.
D. Ropers, H. de Jong, Michel Page, D. Schneider +1 more
2006Bio Systems155 citations
Semantic Scholar
Shared control of gene expression in bacteria by transcription factors and global physiology of the cell
S. Berthoumieux, H. de Jong, Guillaume Baptist, Corinne Pinel +3 more
2013Molecular Systems Biology124 citations Open access
Semantic Scholar
Understanding carbon catabolite repression in Escherichia coli using quantitative models.
A. Kremling, J. Geiselmann, D. Ropers, H. de Jong
2015Trends in Microbiology121 citations
Semantic Scholar
Temporal logic patterns for querying dynamic models of cellular interaction networks
Pedro T. Monteiro, D. Ropers, R. Mateescu, A. T. Freitas +1 more
2008European Conference on Computational Biology101 citations Open access
Semantic Scholar
Conserved stem-loop structures in the HIV-1 RNA region containing the A3 3' splice site and its cis-regulatory element: possible involvement in RNA splicing.
S. Jacquenet, D. Ropers, Patricia S. Bilodeau, L. Damier +3 more
2001Nucleic Acids Research87 citations Open access
Semantic Scholar
A synthetic growth switch based on controlled expression of RNA polymerase
Jérôme Izard, Cindy D. C. Gomez Balderas, D. Ropers, Stéphan Lacour +5 more
2015Molecular Systems Biology84 citations Open access
Semantic Scholar
Experimental and computational validation of models of fluorescent and luminescent reporter genes in bacteria
H. de Jong, Caroline Ranquet, D. Ropers, Corinne Pinel +1 more
2010BMC Systems Biology83 citations Open access
Semantic Scholar
Differential Effects of the SR Proteins 9G8, SC35, ASF/SF2, and SRp40 on the Utilization of the A1 to A5 Splicing Sites of HIV-1 RNA*
D. Ropers, L. Ayadi, R. Gattoni, S. Jacquenet +3 more
2004Journal of Biological Chemistry79 citations Open access
Semantic Scholar
The Carbon Assimilation Network in Escherichia coli Is Densely Connected and Largely Sign-Determined by Directions of Metabolic Fluxes
V. Baldazzi, D. Ropers, Y. Markowicz, D. Kahn +2 more
2010PLoS Comput. Biol.67 citations Open access
Semantic Scholar
Mathematical modelling of microbes: metabolism, gene expression and growth
H. de Jong, Stefano Casagranda, N. Giordano, E. Cinquemani +3 more
2017Journal of the Royal Society Interface59 citations Open access
Semantic Scholar
Biochemical and NMR Study on the Competition between Proteins SC35, SRp40, and Heterogeneous Nuclear Ribonucleoprotein A1 at the HIV-1 Tat Exon 2 Splicing Site*
Houda Hallay, N. Locker, L. Ayadi, D. Ropers +2 more
2006Journal of Biological Chemistry59 citations Open access
Semantic Scholar
A declarative constraint-based method for analyzing discrete genetic regulatory networks
Fabien Corblin, S. Tripodi, E. Fanchon, D. Ropers +1 more
2009Biosyst.51 citations
Semantic Scholar
The post‐transcriptional regulatory system CSR controls the balance of metabolic pools in upper glycolysis of Escherichia coli
Manon Morin, D. Ropers, F. Létisse, Sandrine Laguerre +3 more
2016Molecular Microbiology47 citations Open access
Semantic Scholar
Model Reduction Using Piecewise-Linear Approximations Preserves Dynamic Properties of the Carbon Starvation Response in Escherichia coli
D. Ropers, V. Baldazzi, H. de Jong
2011IEEE/ACM Transactions on Computational Biology & Bioinformatics43 citations
Semantic Scholar
Genetic network analyzer: a tool for the qualitative modeling and simulation of bacterial regulatory networks.
Grégory Batt, Bruno Besson, P. Ciron, H. de Jong +7 more
2012Methods in molecular biology41 citations
Semantic Scholar
Role of RNA structure and protein factors in the control of HIV-1 splicing.
Jean-Michel Saliou, Cyril F. Bourgeois, Lilia Ayadi-Ben Mena, D. Ropers +4 more
2009Frontiers in Bioscience33 citations Open access
Semantic Scholar
Strategies for dealing with incomplete information in the modeling of molecular interaction networks
H. de Jong, D. Ropers
2006Briefings Bioinform.30 citations Open access
Semantic Scholar
An ensemble of mathematical models showing diauxic growth behaviour
A. Kremling, J. Geiselmann, D. Ropers, H. de Jong
2018BMC Syst. Biol.29 citations Open access
Semantic Scholar
The Csr System Regulates Escherichia coli Fitness by Controlling Glycogen Accumulation and Energy Levels
Manon Morin, D. Ropers, E. Cinquemani, J. Portais +2 more
2017mBio28 citations Open access
Semantic Scholar
Resource Reallocation in Bacteria by Reengineering the Gene Expression Machinery.
H. de Jong, J. Geiselmann, D. Ropers
2017Trends in Microbiology25 citations
Semantic Scholar
Analysis and Verification of Qualitative Models of Genetic Regulatory Networks: A Model-Checking Approach
Grégory Batt, D. Ropers, H. de Jong, J. Geiselmann +3 more
2005International Joint Conference on Artificial Intelligence25 citations
Semantic Scholar
Genomewide Stabilization of mRNA during a “Feast-to-Famine” Growth Transition in Escherichia coli
Manon Morin, B. Enjalbert, D. Ropers, L. Girbal +1 more
2020Msphere23 citations Open access
Semantic Scholar
Qualitative Analysis and Verification of Hybrid Models of Genetic Regulatory Networks: Nutritional Stress Response in
Grégory Batt, D. Ropers, H. de Jong, J. Geiselmann +2 more
2005International Conference on Hybrid Systems: Computation and Control23 citations
Semantic Scholar
Importance of metabolic coupling for the dynamics of gene expression following a diauxic shift in Escherichia coli.
V. Baldazzi, D. Ropers, J. Geiselmann, D. Kahn +1 more
2012Journal of Theoretical Biology21 citations
Semantic Scholar
The essential role of mRNA degradation in understanding and engineering E. coli metabolism.
C. Roux, Thibault Étienne, E. Hajnsdorf, D. Ropers +3 more
2021Biotechnology Advances20 citations Open access
Semantic Scholar
Robust reconstruction of gene expression profiles from reporter gene data using linear inversion
Valentin Zulkower, Michel Page, D. Ropers, J. Geiselmann +1 more
2015Bioinform.20 citations Open access
Semantic Scholar
Mass Spectrometry-based Workflow for Accurate Quantification of Escherichia coli Enzymes: How Proteomics Can Play a Key Role in Metabolic Engineering*
M. Trauchessec, M. Jaquinod, Aline Bonvalot, V. Brun +6 more
2014Molecular & Cellular Proteomics20 citations Open access
Semantic Scholar
A multi-scale constraint programming model of alternative splicing regulation
D. Eveillard, D. Ropers, H. de Jong, C. Branlant +1 more
2004Theoretical Computer Science20 citations Open access
Semantic Scholar
WellReader: a MATLAB program for the analysis of fluorescence and luminescence reporter gene data
F. Boyer, Bruno Besson, Guillaume Baptist, Jérôme Izard +4 more
2010Bioinform.17 citations Open access
Semantic Scholar
Competitive effects in bacterial mRNA decay.
Thibault Étienne, M. Cocaign-Bousquet, D. Ropers
2020Journal of Theoretical Biology15 citations Open access
Semantic Scholar
A genome-wide screen for identifying all regulators of a target gene
Guillaume Baptist, Corinne Pinel, Caroline Ranquet, Jérôme Izard +3 more
2013Nucleic Acids Research15 citations Open access
Semantic Scholar
Temporal Logic Patterns for Querying Qualitative Models of Genetic Regulatory Networks
Pedro T. Monteiro, D. Ropers, R. Mateescu, A. T. Freitas +1 more
2008European Conference on Artificial Intelligence13 citations Open access
Semantic Scholar
Estimation of time-varying growth, uptake and excretion rates from dynamic metabolomics data
E. Cinquemani, V. Laroute, M. Cocaign-Bousquet, H. de Jong +1 more
2017Bioinform.12 citations Open access
Semantic Scholar
Resource allocation accounts for the large variability of rate-yield phenotypes across bacterial strains
V. Baldazzi, D. Ropers, J. Gouzé, Tomáš Gedeon +1 more
2023bioRxiv11 citations Open access
Semantic Scholar
Qualitative Analysis of Genetic Regulatory Networks in Bacteria
V. Baldazzi, Pedro T. Monteiro, Michel Page, D. Ropers +2 more
201111 citations
Semantic Scholar
Multiscale Modeling of Alternative Splicing Regulation
D. Eveillard, D. Ropers, H. de Jong, C. Branlant +1 more
2003Computational Methods in Systems Biology10 citations
Semantic Scholar
Reduction and Stability Analysis of a Transcription–Translation Model of RNA Polymerase
I. Belgacem, Stefano Casagranda, Edith Grac, D. Ropers +1 more
2018Bulletin of Mathematical Biology9 citations Open access
Semantic Scholar
Mathematical modeling of genetic regulatory networks: Stress responses in ıt Escherichia coli
D. Ropers, H. de Jong, Hans Geiselmann
20099 citations
Semantic Scholar
Symbolic Reachability Analysis of Genetic Regulatory Networks using Qualitative Abstraction
Grégory Batt, H. de Jong, J. Geiselmann, Michel Page +2 more
20079 citations
Semantic Scholar
Qualitative Simulation of the Nutritional Stress Response in Escherichia coli
D. Ropers, H. de Jong, Michel Page, D. Schneider +1 more
20039 citations
Semantic Scholar
Stability analysis of a reduced transcription-translation model of RNA polymerase
I. Belgacem, Edith Grac, D. Ropers, J. Gouzé
2014IEEE Conference on Decision and Control8 citations
Semantic Scholar
Qualitative modelling and formal verification of the FLR1 gene mancozeb response in Saccharomyces cerevisiae.
Pedro T. Monteiro, P. Dias, D. Ropers, Arlindo L. Oliveira +3 more
2011IET Systems Biology8 citations
Semantic Scholar
Model reduction and process analysis of biological models
Stefano Casagranda, D. Ropers, J. Gouzé
20152015 23rd Mediterranean Conference on Control and Automation (MED)6 citations Open access
Semantic Scholar
Multiomics Study of Bacterial Growth Arrest in a Synthetic Biology Application.
D. Ropers, Y. Couté, L. Faure, Sabrina Ferré +9 more
2021ACS Synthetic Biology5 citations
Semantic Scholar
Piecewise linear approximations to model the dynamics of adaptation to osmotic stress by food-borne pathogens.
A. Métris, S. George, D. Ropers
2017Journal of food microbiology5 citations
Semantic Scholar
Principal process analysis of biological models
Stefano Casagranda, S. Touzeau, D. Ropers, J. Gouzé
2018BMC Syst. Biol.3 citations Open access
Semantic Scholar
A coupled transcription-translation mathematical model of RNA polymerase
I. Belgacem, Edith Grac, D. Ropers, J. Gouzé
20143 citations
Semantic Scholar
Piecewise-Linear Models of Genetic Regulatory Networks: Analysis of the Carbon Starvation Response in Escherichia coli
D. Ropers, H. de Jong, J. Gouzé, Michel Page +2 more
20073 citations
Semantic Scholar

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