Tony Ribeiro, Maxime Folschette, Morgan Magnin, and Katsumi Inoue. Learning any memory-less discrete semantics for dynamical systems represented by logic programs. Machine Learning, 2021.
Tony Ribeiro, Maxime Folschette, Morgan Magnin, and Katsumi Inoue. Polynomial Algorithm For Learning From Interpretation Transition. In: 1st International Joint Conference on Learning \& Reasoning, , (virtual), Greece, 2021.
Guillaume Beslon, Vincent F Liard, and Jonathan Rouzaud-Cornabas. The Complexity Ratchet. In: CCS 2021 - International Conference on Complex Systems, , Lyon, France, 2021.
Omar IKEN, Maxime Folschette, and Tony Ribeiro. Automatic Modeling of Dynamical Interactions Within Marine Ecosystems. In: 1st International Joint Conference on Learning \& Reasoning, , (virtual), Greece, 2021.
Emilie Allart, Joachim Niehren, and Cristian Versari. Exact Boolean Abstraction of Linear Equation Systems. Computation, 9(11) :32, 2021.
Emilie Allart, Joachim Niehren, and Cristian Versari. Reaction Networks to Boolean Networks, https://hal.archives-ouvertes.fr/hal-02279942, 2021.
working paper or preprint
Emilie Allart, Joachim Niehren, and Cristian Versari. Computing Difference Abstractions of Linear Equation Systems. Theoretical Computer Science, 2021.
This is an extension of a previous publication, see hal-02302463v1.
Danilo Dursoniah, Maxime Folschette, Cédric Lhoussaine, Rebecca Goutchtat, François Pattou, and Violeta Raverdy. Limits of a Glucose-Insulin Model to Investigate Intestinal Absorption in Type 2 Diabetes. In: IARIA (ed.) BIOTECHNO 2021 : The Thirteenth International Conference on Bioinformatics, Biocomputational Systems and Biotechnologies, pp. 4–7, IARIA, Valencia, Spain, 2021.
Ariane Théatre, Carolina Cano-Prieto, Marco Bartolini, Yoann Laurin, Magali Deleu, Joachim Niehren, Tarik Fida, Saïcha Gerbinet, Mohammad Alanjary, Marnix H Medema, Angélique Léonard, Laurence Lins, Ana Arabolaza, Hugo Gramajo, Harald Gross, and Philippe Jacques. The surfactin-like lipopeptides from Bacillus spp.: natural biodiversity and synthetic biology for a broader application range. Frontiers in Bioengineering and Biotechnology, 2021.
Emilie Allart. Abstractions de différences exactes de réseaux de réactions : Améliorer la précision de prédiction de changements de systèmes biologiques, Theses, Université de Lille, January 2021.
Marie Lefebvre, Alban Gaignard, Maxime Folschette, Jérémie Bourdon, and Carito Guziolowski. Large-scale regulatory and signaling network assembly through linked open data. Database - The journal of Biological Databases and Curation, 2021 :baaa113, 2021.
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. Simplifications Exactes et Structurelles de Réseaux de Réactions Biologiques, 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.
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
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.
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.
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.
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.
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.
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.