Delphine Ropers

Delphine Ropers
INRIA Grenoble – Rhône-Alpes
655 avenue de l’Europe, Montbonnot
38334 Saint-Ismier cedex, France
Tel. +33 4 76 61 53 72
Delphine.Ropers@inria.fr
Secretary: Catherine Bessiere
Tel. +33 4 76 61 53 61

Curriculum vitae

I received a B.Sc. in Biochemistry and a M.Sc. in Microbiology, Enzymology, and Nutrition from the University of Nancy. In the course of this training, I developed a strong interest for pluridisciplinarity and I decided to develop my research activites in the fields of molecular biology and bioinformatics.

In 1998, I started my PhD thesis in the Laboratory of RNA Maturation and Molecular Enzymology headed by Christiane Branlant (Centre National de la Recherche Scientifique – Université Nancy I), while collaborating with the group of Alexander Bockmayr at Inria Nancy – Grand Est. I studied, both by experiments and mathematical modeling, the alternative splicing of the human immunodeficiency virus type 1 mRNA.

After having obtained my PhD in 2003, I joined Inria Grenoble – Rhône-Alpes as a post-doctoral researcher in the HELIX research group. In 2006, I have been recruited as a research scientist (chargé de recherche) at Inria. Now in the Ibis research group, I work on the mathematical modeling of biochemical regulatory networks in bacteria, in particular, the model bacterium Escherichia coli.

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Research interests

Systems biology:

  • Mathematical modeling of biochemical networks: dynamical models (ODE and PLDE), constraint-based models, parameter estimation from heterogeneous experimental data
  • Analysis of gene expression and metabolism in bacteria: carbon starvation and osmotic stress response in Escherichia coli
  • Applications in biotechnology and food safety

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Research projects

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Courses
I have given master courses in Bioinformatics and Systems Biology, in particular on the modeling and simulation of biochemical networks, at the Université Grenoble-Alpes, at the Institut National des Sciences Appliquées (INSA) in Toulouse, at the school of engineering in Physics, Applied Physics, Electronics & Materials Science (Phelma) 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

In the framework of the French working group VICANNE, I organized with Hidde de Jong a meeting on integrated models of gene regulation and metabolism in Grenoble (May 2004). I organized with Eugenio Cinquemani a workshop on Identification and Control of Biological Interaction Networks (February 2011). I have been on the program committee of the Journées Ouvertes Biologie Informatique Mathématiques (JOBIM) 2007, 2008, and 2010, in the steering committee of the Seminar on Modeling in the Life Sciences SEMOVI (2007-), and in the scientific board of the Complex Systems Institute (IXXI, 2007-2015). I am a member of the Inria Evaluation Committee (2015-) and “référent chercheur” for the research centre Inria Grenoble – Rhône-Alpes.

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Selected publications

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

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

2012

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

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

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

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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