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Delphine Ropers

 

Research scientist INRIA

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INRIA Grenoble - Rhône-Alpes
655 avenue de l’Europe, Montbonnot
38334 Saint-Ismier cedex
France

Tel. +33 4 76 61 53 72
Fax +33 4 56 52 71 20
Delphine.Ropers@inri a.fr
Web page

Secretary (Carol LOQUET)
Tel. +33 4 76 61 53 63

 
 

Curriculum vitae

I received a B.Sc. in Biochemistry and a M.Sc. in Microbiology, Enzymology, and Nutrition from the Henri Poincaré University in 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 MODBIO research group at Loria (Institut National de Recherche en Informatique et en Automatique, research unit INRIA Lorraine), headed at that time by Alexander Bockmayr. I studied, both by experiments and mathematical modeling, the splicing regulation of the human immunodeficiency virus RNA.

After having obtained my PhD in 2003, I joined the research unit INRIA 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 continue working on the mathematical modeling of biochemical regulatory networks in bacteria, in particular, the model bacterium Escherichia coli.

Research interests
-  Systems biology : mathematical modeling of biological systems (qualitative and quantitative models), integration of heterogeneous experimental data
-  Analysis of gene expression and metabolism in bacteria, such as carbon starvation in Escherichia coli.

Participation in projects and collaborations
-  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
-  Hygeia : Hybrid Systems for Biochemical Network Modeling and Analysis (2005-2008), NEST-2003-1 ADVENTURE.
-  Experimental verification of the predictions of a model of the E. coli nutritional stress response (2005-2007), CPER.
-  EC-MOAN : Scalable Modeling and Analysis Techniques to Study Emergent Cell Behavior ; Understanding the E. coli Stress Response (2007-2010), NEST-2005-2 PATHFINDER.
-  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).
-  ColAge : Natural and engineering solutions to the control of bacterial growth and aging (2009-2013), Large-Scale Initiative Action INRIA-INSERM.
-  Gemco : Model reduction, experimental validation, and control for the gene expression machinery in E. coli (2010-2013)
-  RESET : Arrest and restart of the gene expression machinery in bacteria : from mathematical models to biotechnological applications (2012-2016), Investissements d’Avenir, Bioinformatique

Courses

I have given master courses in Bioinformatics and Systems Biology, in particular on the modeling and simulation of biochemical networks, at the Joseph Fourier University in Grenoble, 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).

Organizational and other 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 recently 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, and in the scientific board of the Complex Systems Institute (IXXI). Article in INRIA newsletter

Selected publications

2016

-  M. Morin, D. Ropers, F. Letisse, S. Laguerre, J.C. Portais, M. Cocaign-Bousquet, B. Enjalbert (2016), The post-transcriptional regulatory system CSR controls the balance of metabolic pools in upper glycolysis of Escherichia coli. Mol. Microbiol., in press.

2015

-  J. Izard, C.D. Gomez Balderas, D. Ropers, S. Lacour, X. Song, Y. Yang, A.B. Lindner, J. Geiselmann, H. de Jong (2015), A synthetic growth switch based on controlled expression of RNA polymerase. Mol Syst Biol, 11(11):840
-  A. Kremling, J. Geiselmann, D. Ropers, H. de Jong (2015), Understanding carbon catabolite repression in Escherichia coli using quantitative models. Trends in Microbiology, 23(2):99-109.
-  V. Zulkower, M. Page, D. Ropers, J. Geiselmann, H. de Jong (2015), Robust reconstruction of gene expression profiles from reporter gene data using linear inversion, Bioinformatics, accepted for publication. ISMB/ECCB 2015 special issue.
-  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).

2014

-  M. Trauchessec, M. Jaquinod, A. Bonvalot, V. Brun, C. Bruley, D. Ropers, H. de Jong, J. Garin, G. Bestel-Corre, M. Ferro (2014), 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) : 954-63.
-  I. Belgacem, E. Grac, D. Ropers, J.-L. Gouzé (2014), 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 (2014), 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 (2013), A genome-wide screen for identifying all regulators of a target gene, Nucleic Acids Research, 41(17) :e164.
-  S. Berthoumieux, H. de Jong, G. Baptist, C. Pinel, C. Ranquet, D. Ropers, J. Geiselmann (2013), Shared control of gene expression in bacteria by transcription factors and global physiology of the cell, Molecular Systems Biology, 9:634. Editors’ choice in Science

2012

-  V. Baldazzi, D. Ropers, J. Geiselmann, D. Kahn, H. de Jong (2012), Importance of metabolic coupling for the dynamics of gene expression following a diauxic shift in Escherichia coli, Journal of Theoretical Biology, 295 : 100-115.
-  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, J. van Helden, A. Toussaint, D. Thieffry (eds), Bacterial Molecular Networks : Methods and Protocols, Methods in Molecular Biology, Humana Press, Springer, New York, 439-462.

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.
-  V. Baldazzi, P.T. Monteiro, M. Page, D. Ropers, J. Geiselmann, H. de Jong (2011), Qualitative analysis of genetic regulatory networks in bacteria, W. Dubitzky, J. Southgate, H. Fuss (eds.), Understanding the Dynamics of Biological Systems : Lessons Learned from Integrative Systems Biology, Springer-Verlag, Berlin, pp 111-130.
-  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.
-  D. Ropers, V. Baldazzi, H. de Jong (2011), 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.

2010

-  V. Baldazzi, D. Ropers, Y. Markowicz, D. Kahn, J. Geiselmann, H. de Jong (2010), 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.
-  H. de Jong, C. Ranquet, D. Ropers, C. Pinel, J. Geiselmann (2010), Experimental and computational validation of models of fluorescent and luminescent reporter genes in bacteria, BMC Systems Biology, 4:55.
-  F. Boyer, B. Besson, G. Baptist, J. Izard, C. Pinel, D. Ropers, J. Geiselmann, H. de Jong (2010), A MATLAB program for the analysis of fluorescence and luminescence reporter gene data, Bioinformatics, 26(9):1262-1263.

2009

-  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

-  D. Ropers, H. de Jong, J. Geiselmann (2008), Mathematical modeling of genetic regulatory networks : Stress responses in Escherichia coli, In : P. Fu, M. Latterich, S. Panke, Systems and Synthetic Biology, Wiley-Intersciences, 235-271.
-  P.T. Monteiro, D. Ropers, R. Mateescu, A.T. Freitas, H. de Jong (2008), Temporal logic patterns for querying dynamic models of cellular interaction networks, Bioinformatics, 24(16) : i227-i233. Special issue ECCB-2008.
-  P.T. Monteiro, D. Ropers, R. Mateescu, A.T. Freitas, H. de Jong (2008), 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 (ECAI2008), IOS Press, Amsterdam, 229-233, 2008.
-  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.-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.
-  D. Ropers, H. de Jong, J. Geiselmann (2007), Modélisation de la réponse au stress nutritionnel de la bactérie Escherichia coli, Biofutur, 275:36-39.
-  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.
-  G. Batt, D. Ropers, H. de Jong, M. Page, J. Geiselmann (2007), Symbolic reachability analysis of genetic regulatory networks using qualitative abstractions, Technical Report INRIA, RR-6136.

2006

-  H. de Jong, D. Ropers (2006), Strategies for dealing with incomplete information in the modeling of molecular interaction networks, Briefings in Bioinformatics, 7(4):354-363.
-  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.
-  D. Ropers, H. de Jong, M. Page, D. Schneider, J. Geiselmann (2006), Qualitative simulation of the carbon starvation response in Escherichia coli. BioSystems, 84(2):124-152. Top 5 most cited articles.
-  G. Batt, R. Casey, H. de Jong, J. Geiselmann, J.-L. Gouzé, M. Page, D. Ropers, T. Sari, D. Schneider (2006), Qualitative analysis of the dynamics of genetic regulatory networks using piecewise-linear models. E. Pecou, S. Martinez, A. Maass (eds.), Mathematical and Computational Methods in Biology, Editions Hermann, Paris, 206-238.
-  H. de Jong, D. Ropers (2006), Qualitative approaches towards the analysis of genetic regulatory networks, Z. Szallasi, V. Periwal, J. Stelling (eds), System Modeling in Cellular Biology : From Concepts to Nuts and Bolts, MIT Press, Cambridge, MA, 125-148.

2005

-  G. Batt, D. Ropers, H. de Jong, J. Geiselmann, R. Mateescu, M. Page and D. Schneider (2005), 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, special issue ISMB-2005. Also in G. Perrière, A. Guénoche and C. Geourjon, eds., Working Notes of the Journées Ouvertes Biologie, Informatique et Mathématiques (JOBIM’05), 471-482, Lyon, France.
-  G. Batt, D. Ropers, H. de Jong, J. Geiselmann, R. Mateescu, M. Page, D. Schneider (2005), Analysis and verification of qualitative models of genetic regulatory networks : A model-checking approach. Proceedings of the Nineteenth International Joint Conference on Artificial Intelligence (IJCAI-05), Morgan Kauffman, San Francisco, CA., 370-375.
-  G. Batt, H. de Jong, J. Geiselmann, M. Page, D. Ropers, D. Schneider (2005), 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, 134-150.
-  H. de Jong, D. Ropers, C. Chaouiya, D. Thieffry (2005), Modélisation, analyse et simulation de réseaux de régulation génique, Biofutur, 252 : 36-40.

2004

-  D. Ropers, H. de Jong, M. Page, D. Schneider, J. Geiselmann (2004), Qualitative simulation of the nutritional stress response in Escherichia coli, INRIA RR-5412.
-  G. Batt, H. de Jong, J. Geiselmann, M. Page, D. Ropers, D. Schneider (2004), Symbolic reachability analysis of genetic regulatory networks using qualitative abstraction, INRIA RR-5362.
-  D. Eveillard, D. Ropers, H. de Jong, C. Branlant, A. Bockmayr (2004), A multi-scale constraint programming model of alternative splicing regulation, Theoretical Computer Science, 135(1) : 3-24.
-  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.
-  Eveillard D., Larhlimi A., Ropers D., Billaut S., Peyrefitte S. (2004), KOALAB : A new method for regulatory motif search. Illustration on alternative splicing regulation in HIV-1. Proceedings of the Journées Ouvertes Biologie Informatique Mathématiques, JOBIM 2004, Montreal, Canada.

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), A Multi-Site Constraint Programming Model of Alternative Splicing Regulation, INRIA RR-4830.
-  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.