Nombre de documents

49

CV de Delphine Ropers


Rapport7 documents

  • Valentina Baldazzi, Delphine Ropers, Johannes Geiselmann, Daniel Kahn, Hidde De Jong. Importance of metabolic coupling for the dynamics of gene expression following a diauxic shift in E. coli. [Research Report] RR-7617, INRIA. 2011. <inria-00593109>
  • Pedro T. Monteiro, Delphine Ropers, Radu Mateescu, Ana T. Freitas, Hidde De Jong. Temporal Logic Patterns for Querying Dynamic Models of Cellular Interaction Networks. [Research Report] RR-6470, INRIA. 2008. <inria-00260980v3>
  • Grégory Batt, Delphine Ropers, Hidde De Jong, Michel Page, Johannes Geiselmann. Symbolic Reachability Analysis of Genetic Regulatory Networks using Qualitative Abstractions. [Research Report] RR-6136, INRIA. 2007. <inria-00133991v2>
  • Grégory Batt, Hidde De Jong, Johannes Geiselmann, Michel Page, Delphine Ropers, et al.. Symbolic Reachability Analysis of Genetic Regulatory Networks using Qualitative Abstraction. [Research Report] RR-5362, INRIA. 2004, pp.37. <inria-00070641>
  • Delphine Ropers, Hidde De Jong, Michel Page, Dominique Schneider, Johannes Geiselmann. Qualitative Simulation of the Nutritional Stress Response in Escherichia coli. [Research Report] RR-5412, INRIA. 2004, pp.39. <inria-00070594>
  • Damien Eveillard, Delphine Ropers, Hidde De Jong, Christiane Branlant, Alexander Bockmayr. A Multi-Site Constraint Programming Model of Alternative Splicing Regulation. [Research Report] RR-4830, INRIA. 2003. <inria-00071756>
  • Damien Eveillard, Delphine Ropers, Hidde De Jong, Christiane Branlant, Alexander Bockmayr. Modeling the effects of SR proteins on alternative splicing. [Intern report] A02-R-117 || eveillard02b, 2002, 8 p. <inria-00101060>

Communication dans un congrès14 documents

  • Stefano Casagranda, Delphine Ropers, Jean-Luc Gouzé. Model simplification and process analysis of biological models. The 5th International Symposium on Positive Systems (POSTA), Sep 2016, Rome, Italy. <hal-01412049>
  • Stefano Casagranda, Delphine Ropers, Jean-Luc Gouzé. Model reduction and process analysis of biological models. 2015 23th Mediterranean Conference on Control and Automation (MED), Jun 2015, Torremolinos, Spain. 2015, Proceedings of 23th Mediterranean Conference on Control and Automation (MED). <10.1109/MED.2015.7158908>. <hal-01239356>
  • Aline Métris, Susan George, Delphine Ropers, Jozsef Baranyi. A dynamic network analysis of the physiological state of foodborne pathogens: application to Escherichia coli during osmotic stress and comparison with Salmonella Typhimurium. 9th International Conference on Predictive Modelling in Food, 2015, Rio de Janeiro, Brazil. Procedia Food Science. <hal-01251307>
  • Ismail Belgacem, Edith Grac, Delphine Ropers, Jean-Luc Gouzé. Stability analysis of a reduced transcription-translation model of RNA polymerase. Proceedings of the 53rd IEEE Conference on Decision and Control, Dec 2014, Los Angeles, CA, United States. 2014. <hal-01091674>
  • Ismail Belgacem, Edith Grac, Delphine Ropers, Jean-Luc Gouzé. A coupled transcription-translation mathematical model of RNA polymerase. 21st International Symposium on Mathematical Theory of Networks and Systems, Jul 2014, Groningen, Netherlands. 2014. <hal-00966559>
  • Valentina Baldazzi, Delphine Ropers, Hans Geiselmann, Daniel Kahn, Hidde Jong. Importance of metabolic coupling for the dynamics of gene expression following a diauxic shift in E. coli. Proceedings of the 18th IFAC World Congress, 2011, Milan, Italy. pp.14851-14856, 2011. <hal-00793037>
  • Valentina Baldazzi, Delphine Ropers, Yves Markowicz, Daniel Kahn, Hans Geiselmann, et al.. The carbon assimilation network in Escherichia coli is densely connected and largely sign-determined by directions of metabolic fluxes. Actes des Journées Ouvertes Biologie, Informatique et Mathématiques (JOBIM 2010), 2010, Montpellier, France. pp.11-12, 2010. <hal-00793021>
  • Pedro T. Monteiro, Ana T. Freitas, Delphine Ropers, Radu Mateescu, Hidde Jong. Modeling and formal verification of biological regulatory networks: an integrative approach. Proceedings of the IEEE International Conference on Bioinformatics & Biomedicine (BIBM 2010). First Workshop on Knowledge Engineering, Discovery and Dissemination in Health (KEDDH10), 2010, Ottawa, Canada. 2010. <hal-00793023>
  • Pedro T. Monteiro, Paulo J. Dias, Delphine Ropers, Arlindo L. Oliveira, Isabel Sà-Correia, et al.. Computational modeling and analysis of the yeast FLR1 regulatory network in mancozeb-challenged cells. 11th International Conference on Systems Biology, ICSB 2010, 2010, Edinburgh, United Kingdom. pp.105, 2010. <hal-00793029>
  • Pedro T. Monteiro, P.J. Dias, Delphine Ropers, A.L. Oliveira, Ana T. Freitas, et al.. The regulatory network underlying the transcriptional up-regulation of the FRL1 gene in mancozeb stressed yeast cells: qualitative modeling and simulation. Proceedings of the Congresso Nacional MicroBiotec'09, 2009, Vilamoura, Portugal. 2009. <hal-00793018>
  • Delphine Ropers, Valentina Baldazzi, Hidde Jong. Reduction of a kinetic model of the carbon starvation response in Escherichia coli. Proceedings of the 15th IFAC Symposium on System Identification, SYSID 2009, 2009, Saint Malo, France. IEEE, 2009. <hal-00793014>
  • Pedro T. Monteiro, Delphine Ropers, Radu Mateescu, Ana T. Freitas, Hidde De Jong. Temporal Logic Patterns for Querying Qualitative Models of Genetic Regulatory Networks. M. Ghallab and C.D. Spyropoulos and N. Fakotakis and N. Avouris. 18th European Conference on Artificial Intelligence, Aug 2008, Patras, Greece. IOS Press, 2008. <inria-00357802>
  • Damien Eveillard, Abdelhalim Larhlimi, Delphine Ropers, Stéphanie Billaut, Sandrine Peyrefitte. KOALAB: A new method for regulatory motif search. Illustration on alternative splicing regulation in HIV-1. 5èmes Journées Ouvertes Biologie Informatique Mathématiques - JOBIM 2004, Jun 2004, Montréal, Canada, 2004. <inria-00000915>
  • Damien Eveillard, Delphine Ropers, Hidde De Jong, Christiane Branlant, Alexander Bockmayr. Multiscale modeling of alternative splicing regulation. Corrado Priami. International Workshop on Computational Methods in Systems Biology - CMSB'03, 2003, Rovereto, Italie, Springer-Verlag, 2602, pp.75-87, 2003, Lecture Notes in Computer Science. <inria-00099792>

Article dans une revue24 documents

  • Aline Métris, Susan George, Delphine Ropers. Piecewise linear approximations to model the dynamics of adaptation to osmotic stress by food-borne pathogens. International Journal of Food Microbiology, Elsevier, 2017, 240, pp.63-74. <http://www.sciencedirect.com/science/article/pii/S0168160516303154>. <10.1016/j.ijfoodmicro.2016.06.022>. <hal-01417975>
  • Hidde De Jong, Johannes Geiselmann, Delphine Ropers. Resource reallocation in bacteria by reengineering the gene expression machinery. Trends in Microbiology, Elsevier, 2017. <hal-01420729>
  • Manon Morin, Delphine Ropers, Fabien Letisse, Sandrine Laguerre, Jean-Charles Portais, et al.. The post-transcriptional regulatory system CSR controls the balance of metabolic pools in upper glycolysis of Escherichia coli. Molecular Microbiology, Wiley, 2016, 100 (4), pp.686-700. <http://onlinelibrary.wiley.com/doi/10.1111/mmi.13343/abstract?systemMessage=Wiley+Online+Library+will+be+unavailable+on+Saturday+17th+December+2016+at+09%3A00+GMT%2F+04%3A00+EST%2F+17%3A00+SGT+for+4hrs+due+to+essential+maintenance.Apologies+for+the+inconvenience>. <10.1111/mmi.13343>. <hal-01418224>
  • Delphine Ropers, Aline Métris. Data for the qualitative modeling of the osmotic stress response to NaCl in Escherichia coli. Data in Brief, 2016, 9, pp.606-612. <http://www.sciencedirect.com/science/article/pii/S235234091630600X>. <10.1016/j.dib.2016.09.028>. <hal-01417966>
  • Valentin Zulkower, Michel Page, Delphine Ropers, Johannes Geiselmann, Hidde De Jong. Robust reconstruction of gene expression profiles from reporter gene data using linear inversion. Bioinformatics, Oxford University Press (OUP), 2015, 31 (12), pp.i71-i79. <10.1093/bioinformatics/btv246>. <hal-01217800>
  • Andreas Kremling, Johannes Geiselmann, Delphine Ropers, Hidde De Jong. Understanding carbon catabolite repression in Escherichia coli using quantitative models. Trends in Microbiology, Elsevier, 2015, 23 (2), pp.99-109. <10.1016/j.tim.2014.11.002>. <hal-01103556>
  • Jérôme Izard, Cindy Gomez-Balderas, Delphine Ropers, Stephan Lacour, Xiaohu Song, et al.. A synthetic growth switch based on controlled expression of RNA polymerase. Molecular Systems Biology, EMBO Press, 2015, 11 (11), pp.840. <http://msb.embopress.org/content/11/11/840>. <hal-01247993>
  • Mathieu Trauchessec, Michel Jaquinod, Aline Bonvalot, Virginie Brun, Christophe Bruley, et al.. 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, American Society for Biochemistry and Molecular Biology, 2014, 13 (4), pp.954-968. <10.1074/mcp.M113.032672>. <hal-00947196>
  • Sara Berthoumieux, Hidde De Jong, Guillaume Baptist, Corinne Pinel, Caroline Ranquet, et al.. Shared control of gene expression in bacteria by transcription factors and global physiology of the cell. Molecular Systems Biology, EMBO Press, 2013, 9 (1), pp.634. <10.1038/msb.2012.70>. <hal-00793352>
  • Guillaume Baptist, Corinne Pinel, Caroline Ranquet, Jérôme Izard, Delphine Ropers, et al.. A genome-wide screen for identifying all regulators of a target gene. Nucleic Acids Research, Oxford University Press (OUP): Policy C - Option B, 2013, 41 (17), pp.e164. <http://nar.oxfordjournals.org/content/early/2013/07/26/nar.gkt655.full>. <10.1093/nar/gkt655>. <hal-00857345>
  • Valentina Baldazzi, Delphine Ropers, Johannes Geiselmann, Daniel Kahn, Hidde De Jong. Importance of metabolic coupling for the dynamics of gene expression following a diauxic shift in Escherichia coli. Journal of Theoretical Biology, Elsevier, 2012, 295, pp.100-115. <http://www.sciencedirect.com/science/article/pii/S0022519311005728>. <10.1016/j.jtbi.2011.11.010>. <hal-00762570>
  • Pedro T. Monteiro, P.J. Dias, Delphine Ropers, A.L. Oliveira, I. Sa-Correia, et al.. Qualitative modelling and formal verification of the FLR1 gene mancozeb response in Saccharomyces cerevisiae. IET Systems Biology, Institution of Engineering and Technology, 2011, 5, pp.308-316. <10.1049/iet-syb.2011.0001>. <hal-00793036>
  • Delphine Ropers, Valentina Baldazzi, Hidde 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, Institute of Electrical and Electronics Engineers, 2011, 8, pp.166-181. <10.1109/TCBB.2009.49>. <hal-00793034>
  • Frédéric Boyer, Bruno Besson, Guillaume Baptist, Jérôme Izard, Corinne Pinel, et al.. WellReader: a MATLAB program for the analysis of fluorescence and luminescence reporter gene data.. Bioinformatics, Oxford University Press (OUP), 2010, 26 (9), pp.1262-3. <10.1093/bioinformatics/btq016>. <hal-00562237>
  • Hidde De Jong, Caroline Ranquet, Delphine Ropers, Corinne Pinel, Johannes Geiselmann. Experimental and computational validation of models of fluorescent and luminescent reporter genes in bacteria.. BMC Systems Biology, BioMed Central, 2010, 4 (1), pp.55. <10.1186/1752-0509-4-55>. <hal-00784438>
  • Valentina Baldazzi, Delphine Ropers, Yves Markowicz, Daniel Kahn, Johannes Geiselmann, et al.. The carbon assimilation network in Escherichia coli is densely connected and largely sign-determined by directions of metabolic fluxes.. PLoS Computational Biology, Public Library of Science, 2010, 6 (6), pp.e1000812. <http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000812>. <10.1371/journal.pcbi.1000812>. <inria-00527140>
  • Jean-Michel Saliou, Cyril Bourgeois, L. Ayadi-Ben Mena, Delphine Ropers, S. Jacquenet, et al.. Role of RNA structure and protein factors in the control of HIV-1 splicing. Frontiers in Bioscience, Frontiers in Bioscience, 2009, 14, pp.2714-2729. <hal-00793011>
  • Fabien Corblin, Sebastien Tripodi, Eric Fanchon, Delphine Ropers, Laurent Trilling. A declarative constraint-based method for analyzing discrete genetic regulatory networks. BioSystems, Elsevier, 2009, 98, pp.91-104. <hal-00793012>
  • Georges Khoury, Lilia Ayadi, Jean-Michel Saliou, Sarah Sanglier, Delphine Ropers, et al.. New actors in regulation of HIV-1 mRNA production. Retrovirology, BioMed Central, 2009, 6, pp.46. <hal-00793013>
  • Pedro T. Monteiro, Delphine Ropers, Radu Mateescu, Ana T. Freitas, Hidde De Jong. Temporal Logic Patterns for Querying Dynamic Models of Cellular Interaction Networks. Bioinformatics, Oxford University Press (OUP), 2008, ECCB 2008 CONFERENCE PROCEEDINGS 22-26 SEPTEMBER 2008, CAGLIARI, ITALY, 24 (16), pp.i227-i233. <10.1093/bioinformatics/btn275>. <inria-00357805>
  • Hidde De Jong, Delphine Ropers, Radu Mateescu, Johannes Geiselmann. De la cellule à la puce. Les Cahiers de l'INRIA - La Recherche, INRIA, 2008, 419, pp.I-II. <hal-01178203>
  • Delphine Ropers, Hidde De Jong, Michel Page, Dominique Schneider, Johannes Geiselmann. Qualitative simulation of the carbon starvation response in Escherichia coli.. BioSystems, Elsevier, 2006, 84 (2), pp.124-52. <10.1016/j.biosystems.2005.10.005>. <hal-00171698>
  • Delphine Ropers, Hidde De Jong, Johannes Geiselmann, Radu Mateescu, Michel Page, et al.. Validation of qualitative models of genetic regulatory networks by model checking: analysis of the nutritional stress response in Escherichia coli.. Bioinformatics, Oxford University Press (OUP), 2005, 21 Suppl 1, pp.i19-28. <10.1093/bioinformatics/bti1048>. <hal-00171939>
  • Damien Eveillard, Delphine Ropers, Hidde De Jong, Christiane Branlant, Alexander Bockmayr. A multi-scale constraint programming model of alternative splicing regulation. Theoretical Computer Science, Elsevier, 2004, Special issue: computational systems biology, 325 (1), pp.3-24. <10.1016/j.tcs.2004.03.062>. <inria-00000916>

Chapitre d'ouvrage3 documents

  • Grégory Batt, Bruno Besson, Pierre-Emmanuel Ciron, Hidde De Jong, Estelle Dumas, et al.. Genetic Network Analyzer: A Tool for the Qualitative Modeling and Simulation of Bacterial Regulatory Networks. Jacques van Helden, Ariane Toussaint, Denis Thieffry. Bacterial Molecular Networks Methods and Protocols, 804, Springer, pp.439-462, 2012, Methods in Molecular Biology,, 978-1-61779-361-5. <10.1007/978-1-61779-361-5_22>. <hal-00762122>
  • Valentina Baldazzi, Pedro T. Monteiro, Michel Page, Delphine Ropers, Hans Geiselmann, et al.. Qualitative analysis of genetic regulatory networks in bacteria. W. Dubitzky and J. Southgate and H. Fuss. Understanding the Dynamics of Biological Systems: Lessons Learned from Integrative Systems Biology, Springer, pp.111-130, 2011, 978-1-4419-7964-3. <10.1007/978-1-4419-7964-3_6>. <hal-00793038>
  • Delphine Ropers, Hidde Jong, Hans Geiselmann. Mathematical modeling of genetic regulatory networks: Stress responses in ıt Escherichia coli. P. Fu and M. Letterich and S. Panke. Systems Biology and Synthetic Biology, John Wiley & Sons, pp.235-271, 2009. <hal-00793019>

Ouvrage (y compris édition critique et traduction)1 document

  • Delphine Ropers. 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, pp.288, 2011. <hal-00793035>