Delphine Ropers

Curriculum vitae

My work lies at the interface of bioinformatics, mathematical biology, biochemistry, and (micro)biology. I am passionate about mathematical modelling for the interpretation of experimental data and the inference of complex biological processes. First, as a PhD student, I combined experiments and mathematical modelling to decipher the regulation of alternative splicing of the human immunodeficiency virus mRNA. Then, as a post-doctoral and junior researcher at Inria, I worked as a computational biologist on modelling the molecular processes that control bacterial growth. I am now a senior researcher (DR2) at Inria – Univ Grenoble Alpes, an adjunct professor at Univ Grenoble Alpes (professeur attaché) and the head of the MICROCOSME team. I am also a member of the Laboratoire Interdisciplinaire de Physique at Université Grenoble Alpes.

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Research interests

• Mathematical modelling of biological systems: dynamical models (ODE and PLDE), constraint-based models, parameter estimation from heterogeneous experimental data
• Metabolic network reconstruction
• Analysis of gene expression and metabolism in bacteria
• Systems biology of microorganisms
• Applications in biotechnology and health

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Research projects

• HyLife (2023-2026): Microbial risks associated to hydrogen underground storage in Europe, Clean Energy Transition Partnership Joint Call
  
• RECOM (2023-2027): Competition of RNAs for RNase E, a mechanism regulating their degradation and the energy and carbon metabolism in the cell, ANR
• RIB-ECO (RIBonucleotide ECOnomy) – Engineering RNA life cycle to optimize economy of microbial energy: Application to the bioconversion of biomass-derived carbon sources, ANR Bioéconomie : technologies spécifiques et approches systèmes (2018-2022)
• MuSE – MUlti-Omics and Metabolic models integration to study growth transition in Escherichia coli, IXXI/BioSyl (2018-2020)
• MEMIP: Mixed‐Effects Models of Intracellular Processes : Methods, Tools and Applications, ANR Société de l’information et de la communication (2017- 2021)
• Maximic: Optimal control of microbial cells by natural and synthetic strategies (2017-2021), ANR
• PhD funding for Thibault Etienne:”Integrative analysis of the coodination between mRNA stability and cell physiology in the bacterium Escherichia coli” (2016-2019)
• RESET: Arrest and restart of the gene expression machinery in bacteria: from mathematical models to biotechnological applications (2012-2017), Investissements d’Avenir, Bioinformatique
• CJS INRA-Inria (PhD thesis Manon Morin): Fonction du système de régulation post-transcriptionnel CSR dans la dynamique de l’adaptation métabolique chez la bactérie modèle Escherichia coli (2012-2015)
• GemCO: Model reduction, experimental validation, and control for the gene expression machinery in E. coli (2010-2013), ANR Blanc
• ColAge: Natural and engineering solutions to the control of bacterial growth and aging (2009-2013), Large-Scale Initiative Action INRIA-INSERM
• MetaGenoReg: Towards an understanding of the interrelations between metabolic and gene regulation: E. coli carbon metabolism as a test case (2006-2010), ANR Biologie systémique (BIOSYS)
• EC-MOAN: Scalable modeling and analysis techniques to study emergent cell behavior: Understanding the E. coli stress response (2007-2009), NEST-2005-2 PATHFINDER
• COBIOS: Engineering and control of biological systems: A new way to tackle complex diseases and biotechnological innovation (2007-2009), NEST-2005-2 PATHFINDER
• Experimental verification of the predictions of a model of the E. coli nutritional stres response (2005-2007), CPER
• Hygeia: Hybrid systems for biochemical network modeling and analysis (2005-2007), NEST-2003-1 ADVENTURE
• BacAttract: Theoretical and experimental analysis of the attractors of genetic regulatory networks: Global regulation of transcription in Escherichia coli and Synechocystis PCC 6803 (2003-2006), ACI IMPBio
• GDyn: Dynamic analysis of genetic regulatory networks (2002-2004), Action de Recherche Coopérative INRIA

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Courses
I have given master courses in Bioinformatics and Systems Biology, in particular on the modelling and simulation of biochemical networks, at the Université Grenoble-Alpes (Master in Health engineering: 1st year Science and Management of Biotechnologies, 2nd year AI4OneHealth), at the Institut National des Sciences Appliquées (INSA) in Toulouse, at the school of engineering in Physics, Applied Physics, Electronics & Materials Science (Phelma, 1st year Master in Biomedical engineering) in Grenoble, and in the Ph.D. Program in Computational Biology of the Instituto Gulbenkian de Ciencia in Lisbon (Portugal).

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Organizational activities

I was on the steering committee of the Seminar on Modeling in the Life Sciences SEMOVI (2007-2019), on the scientific board of the Complex Systems Institute (IXXI, 2007-2015), and was a member of the Inria Evaluation Committee (2015-2019). I am “référent chercheur” (ombudsman) for Inria – Université Grenoble Alpes.

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Selected publications

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

2022

• T.A. Etienne, C. Roux, E. Cinquemani, L. Girbal, M. Cocaign-Bousquet, D. Ropers. A nonlinear mixed-effects approach for the mechanistic interpretation of time-series transcriptomics data. Submitted (manuscript).

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.
• 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.
• D. Ropers. Modelling biochemical reaction networks in bacteria – From data to models and back, HDR (habilitation), Ecole Doctorale E2M2, Université Claude Bernard, Lyon I (manuscript).

2020

• T.A. Etienne, M. Cocaign-Bousquet, D. Ropers. Competitive effects in bacterial mRNA decay. Journal of Theoretical Biology, 504:110333.
• M. Morin, B. Enjalbert, D. Ropers, L. Girbal, and M. Cocaign-Bousquet. Genome-wide stabilization of mRNA during a ‘feast-to-famine’ growth transition in Escherichia coli. mSphere, 5(3):e00276-20.

2019

• S. Pinhal, D. Ropers, J. Geiselmann, H. de Jong. Acetate metabolism and the inhibition of bacterial growth by acetate. Journal of Bacteriology, 201:e00147-19.

2018

• A. Kremling, J. Geiselmann, D. Ropers, H. de Jong. An ensemble of mathematical models shoing diauxic growth behaviour. BMC Systems Biology, 12:82.
• S. Casagranda, S. Touzeau, D. Ropers, J.-L. Gouzé. Principal process analysis of biological models. BMC Systems Biology, 12(1):68.
• 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.

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, 14:20170502.
• 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.
• A. Métris, S.M. George, D. Ropers. Piecewise linear approximations to model the dynamics of adapation to osmotic stress by food-borne pathogens. International Journal of Food Microbiology, 240:63-74.
• H. de Jong, J. Geiselmann, D. Ropers. Resource reallocation in bacteria by reengineering the gene expression machinery. Trends in Microbiology, 25(6):480-493.
• 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. Special issue ISMB/ECCB 2017.

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 et A. Métris. Osmotic stress response to NaCl in Escherichia coli: qualitative modeling and simulation data, Data in Brief, 9: 606-612.

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
• 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
• S. Casagranda, D. Ropers, J.-L. Gouzé (2015), Model reduction and process analysis of biological models. Proceedings of 23rd Mediterranean Conference on Control and Automation (MED 2015)
• S. Bourgoin-Voillard, C. Durmort, J. Geiselmann, A. Le Gouëllec, D. Ropers, M. Sève. La cellule procaryote en biotechnologies in Les biotechnologies en santé – Tome 1 : Introduction aux biotechnologies en santé. Coordonnateurs : S.  Bourgoin-Voillard, W. Rachidi, M. Sève. Ed. Lavoisier, 2015

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
•  I. Belgacem, E. Grac, D. Ropers, J.-L. Gouzé, Stability analysis of a reduced transcription-translation model of RNA polymerase, Proceedings of CDC 14, Dec 2014, Los Angeles, CA, United States.
• I. Belgacem, E. Grac, D. Ropers, J.-L. Gouzé, Proceedings of 21st International Symposium on Mathematical Theory of Networks and Systems, Jul 2014, pp 1383-1386, Groningen, Netherlands.

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, 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. Molecular Systems Biology, 9:634, 2013. Editors’ choice in Science

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 E. 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 and Protocols, Methods in Molecular Biology, Humana Press, Springer, New York, 2012, 439-462

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
• P.T. Monteiro, P.J. Dias, D. Ropers, A.L. Oliveira, I. Sá-Correia, M.C. Teixeira and A.T. Freitas (2011), Qualitative modeling and formal verification of the FLR1 gene mancozeb response in Saccharomyces cerevisiae, IET Systems Biology, 5(5) : 308-316.
• D. Ropers (2011), 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 VIH-1, Editions Universitaires Européennes, Saarbrücken (Germany), ISBN 978-613-1-56368-3.

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
• 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

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 and Synthetic Biology, Wiley & Sons, Hoboken NJ, 2009, 235-271
• F. Corblin, S. Tripodi, E. Fanchon, D. Ropers, L. Trilling (2009), A declarative constraint-based method for analyzing discrete genetic regulatory networks, BioSystems, 98(2):91-104.
• G. Khoury, L. Ayadi, J.-M. Sailou, S. Sanglier, D. Ropers, C. Branlant (2009), New actors in regulation of HIV-1 tat mRNA production, Retrovirology, 6(Suppl 2) :P46.
• D. Ropers, V. Baldazzi, H. de Jong (2009), Reduction of a kinetic model of the carbon starvation response in Escherichia coli, in Proceedings of the 15th IFAC Symposium on System Identification, SYSID 2009.
• J.-M. Saliou, C.F. Bourgeois, L. Ayadi-Ben Mena, D. Ropers, S. Jacquenet, V. Marchand, J. Stévenin and C. Branlant (2009), Role of RNA structure and protein factors in the control of HIV-1 splicing, Frontiers in Biosciences, 14:2714-2729.

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, 2008. Special issue ECCB-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.), Proceedings of 18th European Conference on Artificial Intelligence (ECAI 2008), IOS Press, Amsterdam, 2008, 229-233
• H. de Jong, R. Mateescu, D. Ropers, J. Geiselmann (2008), De la cellule à la puce, La Recherche, no. 419, Les cahiers de l’INRIA, I-II.

2007

• D. Ropers, H. de Jong, J. Geiselmann. Modélisation de la réponse au stress nutritionnel de la bactérie Escherichia coli, Biofutur, 275:36-39, 2007
• D. Ropers, H. de Jong, J.-L. Gouzé, M. Page, D. Schneider, J. Geiselmann, Piecewise-linear models of genetic regulatory networks : Analysis of the carbon starvation response in Escherichia coli. Proceedings of ECMTB 2005, Mathematical Modeling of Biological Systems, Volume I. A. Deutsch, L. Brusch, H. Byrne, G. de Vries and H.-P. Herzel (eds), Birkhäuser, Boston, 83-96.
• G. Batt, H. de Jong, J. Geiselmann, J.-L. Gouzé, M. Page, D. Ropers, T. Sari, D. Schneider (2007), Analyse qualitative de la dynamique de réseaux de régulation génique par des modèles linéaires par morceaux, Technique et Science Informatique, 26(1-2):11-45.

2006

• D. Ropers, H. de Jong, M. Page, D. Schneider, J. Geiselmann. Qualitative simulation of the carbon starvation response in Escherichia coli. BioSystems, 84(2):124-152, 2006
• G. Batt, R. Casey, H. de Jong, J. Geiselmann, J.-L. Gouzé, M. Page, D. Ropers, T. Sari, D. Schneider. Qualitative analysis of the dynamics of genetic regulatory networks using piecewise-linear models. In: E. Pecou, S. Martinez, A. Maass (eds.), Mathematical and Computational Methods in Biology, Editions Hermann, Paris, 2006, 206-239
• H. de Jong, D. Ropers. Strategies for dealing with incomplete information in the modeling of molecular interaction networks. Briefings in Bioinformatics, 7(4):354-363, 2006
• H. de Jong, D. Ropers. Qualitative approaches towards the analysis of genetic regulatory networks. In: Z. Szallasi, V. Periwal, J. Stelling (eds), System Modeling in Cellular Biology: From Concepts to Nuts and Bolts, MIT Press, Cambridge, MA, 2006, 125-148
• H. Hallay, N. Locker, L. Ayadi, D. Ropers, E. Guittet, C. Branlant (2006), 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, Journal of Biological Chemistry, 281(48):37159-74.

2005

• G. Batt, D. Ropers, H. de Jong, J. Geiselmann, R. Mateescu, M. Page, D. Schneider. Analysis and verification of qualitative models of genetic regulatory networks : A model-checking approach. In: L.P. Kaelbling (ed.), Proceedings of the Nineteenth International Joint Conference on Artificial Intelligence (IJCAI-05), Morgan Kauffman, San Francisco, CA, 2005, 370-375
• G. Batt, D. Ropers, H. de Jong, J. Geiselmann, R. Mateescu, M. Page, D. Schneider. Validation of qualitative models of genetic regulatory networks by model checking: Analysis of the nutritional stress response in Escherichia coli. Bioinformatics, 21(Suppl 1) :i19-i28, 2005. Special issue ISMB-2005
• G. Batt, H. de Jong, J. Geiselmann, M. Page, D. Ropers, D. Schneider. Qualitative analysis and verification of hybrid models of genetic regulatory networks: Nutritional stress response in Escherichia coli. M. Morari, L. Thiele (eds), Hybrid Systems: Computation and Control (HSCC 2005), Lecture Notes in Computer Science 3414, Springer-Verlag, Berlin, 2005, 134-150
• H. de Jong, D. Ropers, C. Chaouiya, D. Thieffry. Modélisation, analyse et simulation de réseaux de régulation génique. Biofutur, 252:36-40, 2005

2004

• D. Eveillard, D. Ropers, H. de Jong, C. Branlant, A. Bockmayr. A multi-scale constraint programming model of alternative splicing regulation. Theoretical Computer Science, 135(1):3-24, 2004
•  D. Ropers, L. Ayadi, R. Gattoni, S. Jacquenet, L. Damier, C. Branlant, J. Stévenin (2004), 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, Journal of Biological Chemistry, 279(29) : 29963-29973.

2003

• D. Ropers (2003), Experimental study of the SR protein role in the splicing regulation of the HIV-1 virus RNA, responsible of the human immunodeficiency, and mathematical modeling of these regulations, PhD thesis in molecular biology, University Henri Poincaré, Nancy I.
• D. Eveillard, D. Ropers, H. de Jong, C. Branlant, A. Bockmayr (2003), Multiscale modeling of alternative splicing regulation, C. Priami (ed.), Computational Methods in Systems Biology, CMSB-03, Lecture Notes in Computer Science 2602, Springer-Verlag, Berlin, 75-87.

2001

• S. Jacquenet, D. Ropers, P. Bilodeau, L. Damier, A. Mougin, M. Stoltzfus, C. Branlant (2001), 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, Nucleic Acids Research, 29(2) : 464-478.

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