Publications

2020

  • Tony Ribeiro, Maxime Folschette, Laurent Trilling, Nicolas Glade, Katsumi Inoue, Morgan Magnin, and Olivier Roux. Les enjeux de l’inférence de modèles dynamiques des systèmes biologiquesà partir de séries temporelles, https://hal.archives-ouvertes.fr/hal-02634235, 2020.
    working paper or preprint
  • Emilie Allart, Joachim Niehren, and Cristian Versari. Abstracting Linear Equation Systems, https://hal.archives-ouvertes.fr/hal-02279942, 2020.
    working paper or preprint
  • Maxime Folschette, Vincent Legagneux, Arnaud Poret, Lokmane Chebouba, Carito Guziolowski, and Nathalie Théret. A pipeline to create predictive functional networks: application to the tumor progression of hepatocellular carcinoma. BMC Bioinformatics, 21(1) :18, 2020.

2019

  • Emilie Allart, Cristian Versari, and Joachim Niehren. Computing Difference Abstractions of Metabolic Networks Under Kinetic Constraints. In: CMSB 2019 - 17th International Conference on Computational Methods in Systems Biology, pp. 266–285, Springer, Trieste, Italy, 2019.

2018

  • Emilie Allart, Joachim Niehren, and Cristian Versari. Elementary Flux Modes Improve Gene Knockout Predictions. In: 12th European Symposium on Biochemical Engineering Science, , Lisbon, Portugal, 2018.
    Hal

2017

  • Debarun Dhali, François Coutte, Anthony Argüelles Arias, Sandrine S. Auger, Vladimir V. Bidnenko, Gabrielle Chataigné, Michael Lalk, Joachim Niehren, De Sousa Joana, Cristian Versari, and Philippe Jacques. Genetic engineering of the branched fatty acid metabolic pathway of Bacillus subtilis for the overproduction of surfactin C14 isoform. Biotechnology Journal, 12(7) :23, 2017.
  • Guillaume Madelaine. Exact and Structural Simplifications of Biological Reaction Networks, Theses, Université de Lille, February 2017.
  • Guillaume Madelaine, Elisa Tonello, Cédric Lhoussaine, and Joachim Niehren. Simplification of Reaction Networks, Confluence and Elementary Modes. Computation, 2017.
    Extended version of a conference paper at CMSB’2016
  • Cristian Versari, Szymon Stoma, Kirill Batmanov, Artémis Llamosi, Filip Mroz, Adam Kaczmarek, Matt Deyell, Cédric Lhoussaine, Pascal Hersen, and Gregory Batt. Long-term tracking of budding yeast cells in brightfield microscopy: CellStar and the Evaluation Platform. Journal of the Royal Society Interface, 14(127) :32, 2017.

2016

  • Guillaume Madelaine, Cédric Lhoussaine, Joachim Niehren, and Elisa Tonello. Structural simplification of chemical reaction networks in partial steady states. BioSystems, 149 :34–49, 2016.
    This is a journal extension of a paper published at the CMSB’2015 conference
  • Guillaume Madelaine, Elisa Tonello, Cédric Lhoussaine, and Joachim Niehren. Normalizing Chemical Reaction Networks by Confluent Structural Simplification. In: 14th International Conference on Computational Methods in Systems Biology (CMSB 2016), Springer, Cambridge, United Kingdom, 2016.
  • Joachim Niehren, Cristian Versari, Mathias John, François Coutte, and Philippe Jacques. Predicting Changes of Reaction Networks with Partial Kinetic Information. BioSystems, 149 :113–124, 2016.
  • Artémis Llamosi, Andres Gonzalez, Cristian Versari, Eugenio Cinquemani, Giancarlo Ferrari-Trecate, Pascal Hersen, and Gregory Batt. What population reveals about individual cell identity: Single-cell parameter estimation of models of gene expression in yeast. PLoS Computational Biology, 12(2) :e1004706, 2016.

2015

  • Guillaume Madelaine, Cédric Lhoussaine, and Joachim Niehren. Structural simplification of chemical reaction networks preserving deterministic semantics. In: Computational Methods in Systems Biology (CMSB), pp. 133–144, Springer, Nantes, France, 2015.
  • Joachim Niehren, Mathias John, Cristian Versari, François Coutte, and Philippe Jacques. Qualitative Reasoning about Reaction Networks with Partial Kinetic Information. In: Computational Methods for Systems Biology, pp. 157–169, , Nantes, France, 2015.
  • François Coutte, Joachim Niehren, Debarun Dhali, Mathias John, Cristian Versari, and Philippe Jacques. Modeling Leucine’s Metabolic Pathway and Knockout Prediction Improving the Production of Surfactin, a Biosurfactant from Bacillus Subtilis. Biotechnology Journal, 10(8) :1216–34, 2015.

2014

  • Guillaume Madelaine, Cédric Lhoussaine, and Joachim Niehren. Attractor Equivalence: An Observational Semantics for Reaction Networks. In: First International Conference on Formal Methods in Macro-Biology, pp. 82–101, Springer-Verlag, Nouméa, New Caledonia, 2014.

2013

  • Mathias John, Mirabelle Nebut, and Joachim Niehren. Knockout Prediction for Reaction Networks with Partial Kinetic Information. In: 14th International Conference on Verification, Model Checking, and Abstract Interpretation, pp. 355–374, Springer, Rome, Italy, 2013.
  • Kirill Batmanov, Cristian Versari, and Michel Petitot. Réseaux de Pétri stochastiques comportant une seule place 1ere partie: régime stationnaire. 2013.
  • Cristian Versari and Gianluigi Zavattaro. Complex Functional Rates in the Modeling of Nano Devices. Electronic Notes in Theoretical Computer Science, 293 :3–15, 2013.

2012

  • Cristian Versari and Gianluigi Zavattaro. Complex Functional Rates in Rule-Based Languages for Biochemistry. Transactions on Computational Systems Biology, 7625(XIV) :123–150, 2012.
  • Mathias John, Hans-Jörg Schulz, Heidrun Schumann, Adelinde Uhrmacher, and Andrea Unger. Constructing and Visualizing Chemical Reaction Networks from Pi-Calculus Models. Formal Aspects of Computing, 2012.
  • Kirill Batmanov, Celine Kuttler, François Lemaire, Cédric Lhoussaine, and Cristian Versari. Symmetry-based model reduction for approximate stochastic analysis. In: Computational Methods in Systems Biology 2012 (CMSB 2012), pp. 49–68, Springer, London, United Kingdom, 2012.
  • Russ Harmer, Jean Krivine, Élise Laruelle, Cédric Lhoussaine, Guillaume Madelaine, and Mirabelle Nebut. Models of Tet-On System with Epigenetic Effects. In: Computational Methods in Systems Biology 2012 (CMSB 2012, Flashposter), p. 378, Springer, London, United Kingdom, 2012.
  • Kirill Batmanov, Celine Kuttler, Cédric Lhoussaine, and Yasushi Saka. Self-organized patterning by diffusible factors: roles of a community effect. Fundamenta Informaticae, 118(4) :419–461, 2012.

2011

  • Mathias John, Cédric Lhoussaine, Joachim Niehren, and Cristian Versari. Biochemical Reaction Rules with Constraints. In: 20th European Symposium on Programming Languages, pp. 338–357, Springer, Saarbrücken, Germany, 2011.
  • Yasushi Saka, Cédric Lhoussaine, Celine Kuttler, Ekkehard Ullner, and Marco Thiel. Theoretical basis of the community effect in development. BMC Systems Biology, 5 :54, 2011.

2010

  • Celine Kuttler, Cédric Lhoussaine, and Mirabelle Nebut. Rule-based modeling of transcriptional attenuation at the tryptophan operon. Transactions on Computational Systems Biology, XII :199–228, 2010.
    LNBI 5945
  • Mathias John, Cédric Lhoussaine, Joachim Niehren, and Adelinde Uhrmacher. The Attributed Pi Calculus with Priorities. Transactions on Computational Systems Biology, XII(5945) :13–76, 2010.
  • Samuel Alexandre Vidal, Michel Petitot, François Boulier, François Lemaire, and Celine Kuttler. Models of stochastic gene expression and Weyl algebra. Lecture Notes in Computer Science, :pages, 2010.
  • Samuel Alexandre Vidal, Michel Petitot, François Boulier, François Lemaire, and Celine Kuttler. Models of stochastic gene expression and Weyl algebra. In: Algebraic and Numeric Biology (ANB 2010), pp. 76–97, Springer, Hagenberg, Austria, 2010.

2009

  • Celine Kuttler, Cédric Lhoussaine, and Mirabelle Nebut. Rule-based modeling of transcriptional attenuation at the tryptophan operon. In: Winter Simulation Conference, pp. 920–931, , Austin, Texas, USA, United States, 2009.
  • Mathias John, Cédric Lhoussaine, and Joachim Niehren. Dynamic Compartments in the Imperative Pi Calculus. In: Computational Methods in Systems Biology, 7th International Conference, pp. 235–250, Spinger, Bologna, Italy, 2009.