D. Ropers

发表

Qualitative simulation of the carbon starvation response in Escherichia coli.

D. Schneider, M. Page, J. Geiselmann, 2006, Bio Systems.

Competitive effects in bacterial mRNA decay.

D. Ropers, M. Cocaign-Bousquet, Thibault A Etienne, 2020, Journal of theoretical biology.

Shared control of gene expression in bacteria by transcription factors and global physiology of the cell

J. Geiselmann, D. Ropers, H. de Jong, 2013, Molecular systems biology.

Understanding carbon catabolite repression in Escherichia coli using quantitative models.

J. Geiselmann, A. Kremling, D. Ropers, 2015, Trends in microbiology.

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.

D. Ropers, C. Branlant, S. Jacquenet, 2001, Nucleic acids research.

Qualitative Analysis of Genetic Regulatory Networks in Bacteria

Pedro T. Monteiro, H. D. Jong, M. Page, 2011 .

KOALAB: A new method for regulatory motif search. Illustration on alternative splicing regulation in HIV-1

D. Ropers, D. Eveillard, Abdelhalim Larhlimi, 2004 .

Resource Reallocation in Bacteria by Reengineering the Gene Expression Machinery.

Johannes Geiselmann, Delphine Ropers, Hidde de Jong, 2017, Trends in microbiology.

Mathematical modelling of microbes: metabolism, gene expression and growth

Eugenio Cinquemani, Jean-Luc Gouzé, Stefano Casagranda, 2017, Journal of The Royal Society Interface.

Correction: The Carbon Assimilation Network in Escherichia coli Is Densely Connected and Largely Sign-Determined by Directions of Metabolic Fluxes

J. Geiselmann, D. Kahn, D. Ropers, 2010, PLoS Computational Biology.

Genomewide Stabilization of mRNA during a “Feast-to-Famine” Growth Transition in Escherichia coli

D. Ropers, M. Cocaign-Bousquet, L. Girbal, 2020, mSphere.

Resource allocation accounts for the large variability of rate-yield phenotypes across bacterial strains

J. Gouzé, T. Gedeon, D. Ropers, 2022, bioRxiv.

Reduction and Stability Analysis of a Transcription–Translation Model of RNA Polymerase

J. Gouzé, D. Ropers, I. Belgacem, 2018, Bulletin of mathematical biology.

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*

D. Ropers, E. Guittet, C. Branlant, 2006, Journal of Biological Chemistry.

A genome-wide screen for identifying all regulators of a target gene

J. Geiselmann, D. Ropers, H. de Jong, 2013, Nucleic acids research.

Qualitative modelling and formal verification of the FLR1 gene mancozeb response in Saccharomyces cerevisiae.

Arlindo L. Oliveira, Pedro T. Monteiro, Miguel C. Teixeira, 2011, IET systems biology.

Importance of Metabolic Coupling for the Dynamics of Gene Expression Following a Diauxic Shift in E. coli

H. D. Jong, J. Geiselmann, D. Kahn, 2011 .

Piecewise linear approximations to model the dynamics of adaptation to osmotic stress by food-borne pathogens.

D. Ropers, S. George, A. Métris, 2017, International journal of food microbiology.

Reduction of a Kinetic Model of the Carbon Starvation Response in Escherichia coli

H. D. Jong, D. Ropers, V. Baldazzi, 2009 .

A coupled transcription-translation mathematical model of RNA polymerase

J. Gouzé, D. Ropers, I. Belgacem, 2014 .

Mass Spectrometry-based Workflow for Accurate Quantification of Escherichia coli Enzymes: How Proteomics Can Play a Key Role in Metabolic Engineering*

J. Garin, D. Ropers, H. de Jong, 2014, Molecular & Cellular Proteomics.

Temporal logic patterns for querying dynamic models of cellular interaction networks

Radu Mateescu, Hidde de Jong, Pedro T. Monteiro, 2008, ECCB.

Experimental and computational validation of models of fluorescent and luminescent reporter genes in bacteria

Hidde de Jong, Corinne Pinel, Johannes Geiselmann, 2010, BMC Systems Biology.

Estimation of time-varying growth, uptake and excretion rates from dynamic metabolomics data

Eugenio Cinquemani, Hidde de Jong, Delphine Ropers, 2017, Bioinform..

A multi-scale constraint programming model of alternative splicing regulation

Alexander Bockmayr, Hidde de Jong, Christiane Branlant, 2004, Theor. Comput. Sci..

Piecewise-Linear Models of Genetic Regulatory Networks: Analysis of the Carbon Starvation Response in Escherichia coli

D. Schneider, H. D. Jong, J. Gouzé, 2007 .

Genetic network analyzer: a tool for the qualitative modeling and simulation of bacterial regulatory networks.

François Rechenmann, Pedro T. Monteiro, Johannes Geiselmann, 2012, Methods in molecular biology.

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, C. Branlant, S. Jacquenet, 2004, Journal of Biological Chemistry.

Role of RNA structure and protein factors in the control of HIV-1 splicing.

D. Ropers, V. Marchand, C. Branlant, 2009, Frontiers in bioscience.

The essential role of mRNA degradation in understanding and engineering E. coli metabolism.

D. Ropers, M. Cocaign-Bousquet, Thibault A Etienne, 2021, Biotechnology advances.

Acetate Metabolism and the Inhibition of Bacterial Growth by Acetate

Stéphane Pinhal, Johannes Geiselmann, Delphine Ropers, 2019, Journal of bacteriology.

Importance of metabolic coupling for the dynamics of gene expression following a diauxic shift in Escherichia coli.

Daniel Kahn, Valentina Baldazzi, Johannes Geiselmann, 2012, Journal of theoretical biology.

The Carbon Assimilation Network in Escherichia coli Is Densely Connected and Largely Sign-Determined by Directions of Metabolic Fluxes

Hidde de Jong, Daniel Kahn, Valentina Baldazzi, 2010, PLoS Comput. Biol..

A synthetic growth switch based on controlled expression of RNA polymerase

Johannes Geiselmann, Delphine Ropers, Hidde de Jong, 2015, Molecular systems biology.

Strategies for dealing with incomplete information in the modeling of molecular interaction networks

Hidde de Jong, Delphine Ropers, H. D. Jong, 2006, Briefings Bioinform..

Multiomics Study of Bacterial Growth Arrest in a Synthetic Biology Application.

J. Geiselmann, D. Ropers, H. de Jong, 2021, ACS synthetic biology.

Model Reduction Using Piecewise-Linear Approximations Preserves Dynamic Properties of the Carbon Starvation Response in Escherichia coli

Hidde de Jong, Valentina Baldazzi, Delphine Ropers, 2011, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Validation of qualitative models of genetic regulatory networks by model checking: analysis of the nutritional stress response in Escherichia coli

Radu Mateescu, Dominique Schneider, Hidde de Jong, 2005, ISMB.

The Csr System Regulates Escherichia coli Fitness by Controlling Glycogen Accumulation and Energy Levels

E. Cinquemani, D. Ropers, J. Portais, 2017, mBio.

A declarative constraint-based method for analyzing discrete genetic regulatory networks

Laurent Trilling, Eric Fanchon, Delphine Ropers, 2009, Biosyst..

An ensemble of mathematical models showing diauxic growth behaviour

Andreas Kremling, Hidde de Jong, Johannes Geiselmann, 2018, BMC Syst. Biol..

Principal process analysis of biological models

Jean-Luc Gouzé, Stefano Casagranda, Delphine Ropers, 2018, BMC Syst. Biol..

Model reduction and process analysis of biological models

Jean-Luc Gouzé, Stefano Casagranda, Delphine Ropers, 2015, 2015 23rd Mediterranean Conference on Control and Automation (MED).

The post‐transcriptional regulatory system CSR controls the balance of metabolic pools in upper glycolysis of Escherichia coli

D. Ropers, F. Létisse, J. Portais, 2016, Molecular microbiology.

Robust reconstruction of gene expression profiles from reporter gene data using linear inversion

Valentin Zulkower, Hidde de Jong, Johannes Geiselmann, 2015, Bioinform..

Qualitative Simulation of the Nutritional Stress Response in Escherichia coli

Dominique Schneider, Hidde de Jong, Johannes Geiselmann, 2003 .

Resource allocation accounts for the large variability of rate-yield phenotypes across bacterial strains

J. Gouzé, T. Gedeon, D. Ropers, 2023, bioRxiv.

Qualitative Analysis and Verification of Hybrid Models of Genetic Regulatory Networks: Nutritional Stress Response in

Dominique Schneider, Hidde de Jong, Grégory Batt, 2005, HSCC.

Role of RNA structure and protein factors in the control of HIV-1 splicing.

D. Ropers, V. Marchand, C. Branlant, 2009, Frontiers in bioscience.

Temporal Logic Patterns for Querying Qualitative Models of Genetic Regulatory Networks

Radu Mateescu, Hidde de Jong, Pedro T. Monteiro, 2008, ECAI.