Publications
Static and discrete models (Task 2).
- Bordron P, Eveillard D, Rusu I. Integrated analysis of the gene neighbouring impact on bacterial metabolic networks. IET Syst Biol. 2011 Jul;5(4):261-8. (www)
- T. Tonon, D. Eveillard, S. Prigent, J. Bourdon, P. Potin, C. Boyen, and A. Siegel. Toward systems biology in brown algae to explore acclimation and adaptation to the shore environment. OMICS: A Journal of Integrative Biology 15(12), 2011 (www)
- Andres Aravena, Carito Guziolowski, Anne Siegel and Alejandro Maass. Using Mutual Information and Answer Set Programming to refine PWM based transcription regulation network . Preliminary results. JOBIM Conference. 2012
- Santiago Videla, Carito Guziolowski, Federica Eduati, Sven Thiele, Niels Grabe, Julio Saez-Rodriguez and Anne Siegel. Revisiting the Training of Logic Models of Protein Signaling Networks with a Formal Approach based on Answer Set Programming. CMSB 2012. London.
- A. Richard, A fixed point theorem for Boolean networks expressed in terms of forbidden subnetworks, AUTOMATA 2011 - 17th International Workshop on Cellular Automata and Discrete Complex Systems, DMTCS Proc AP., 1-16, 2012 (www)
- A. Richard, G. Rossignol, J.-P. Comet, G. Bernot, J. Guespin-Michel and A. Merieau. Boolean models of biosurfactants production in Pseudomonas fluorescens, PLoS ONE, 7(1):e24651, 2012 (www)
- A. Richard and P. Ruet, From kernels in directed graphs to fixed points and negative cycles in Boolean networks, Discrete Applied Mathematics, Accepted.
- S. Soliman, A stronger necessary condition for the multistationarity of chemical reaction networks, submitted 2013 preprint
- François Fages, Sylvain Soliman. From reaction models to influence graphs and back: a theorem. In Proceedings of Formal Methods in Systems Biology FMSB'08, Lecture Notes in Computer Science. Springer-Verlag, 2008.
Hybrid models (Task 3)
- Loïc Paulevé, Morgan Magnin, and Olivier Roux. Tuning Temporal Features within the Stochastic π-Calculus. IEEE Transactions on Software Engineering, 37(6):858-871, 2011
- Loïc Paulevé, Morgan Magnin, and Olivier Roux. Static analysis of biological regulatory networks dynamics using abstract interpretation. Mathematical Structures in Computer Science, 22(04):651-685, 2012.
- Maxime Folschette, Loïc Paulevé, Katsumi Inoue, Morgan Magnin, and Olivier Roux. Concretizing the process hitting into biological regulatory networks. In CMSB 2012.
- Andrieux G , Fattet L , Le Borgne M , Rimokh R , Théret N (2012) Dynamic Regulation of Tgf-B Signaling by Tif1 ? A Computational Approach. PLoS ONE 7(3) : e33761, 2012
- Aurélien Rizk, Grégory Batt, François Fages, Sylvain Soliman. Continuous Valuations of Temporal Logic Specifications with applications to Parameter Optimization and Robustness Measures. Theoretical Computer Science, 412(26):2827–2839, 2011.
- François Fages, Steven Gay, Sylvain Soliman. Inferring reaction models from ordinary differential equations. Submitted to Theoretical Computer Science, January 2013. (Prelilminary version in CMSB 2012).
- Aurélien Rizk, Grégory Batt, François Fages, Sylvain Soliman. A general computational method for robustness analysis with applications to synthetic gene networks. Bioinformatics, 12(25):il69–il78, 2009.
Population scale models (Task 4)
- Jérémie Bourdon & Damien Eveillard. Probabilistic Approaches for Investigating Biological Networks, in Algorithms in Computational Molecular Biology: Techniques, Approaches and Applications (eds M. Elloumi and A. Y. Zomaya), pp 893-913, John Wiley & Sons, Inc., Hoboken, NJ, USA, 2011.
- J. Bourdon, D. Eveillard, A. Siegel. Integrating quantitative knowledge into a qualitative gen regulatory network. PLoS Comput Biol 7(9), 2011, e1002157 (www)
Model reduction (Task 5)
- V. Noel, S. Vakulenko & O. Radulescu (2011): Algorithm for identification of piecewise smooth hybrid systems: application to eukaryotic cell cycle regulation. Lecture Notes in Computer Science 6833, pp. 225–236, doi:10.1007/978-3-642-23038-7_20.(Tâche 5)
- V.Noel, D.Grigoriev, S.Vakulenko, O.Radulescu (2012): Hybrid models of the cell cycle molecular machinery. Electronic Proceedings in Theoretical Computer Science 92: 88-105 (Tâche 5)
- Sylvain Soliman. Invariants and Other Structural Properties of Biochemical Models as a Constraint Satisfaction Problem (www) Algorithms for Molecular Biology, 7(15), 2012.
- V. Noel, D. Grigoriev, S. Vakulenko & O. Radulescu (2012): Tropical geometries and dynamics of biochemical networks. Application to hybrid cell cycle models. Electronic Notes in Theoretical Computer Science 284, pp. 75–91, doi:10.1016/j.entcs.2012.05.016 (Tâche 5)
- O.Radulescu, A.N.Gorban, A.Zinovyev, V.Noel (2012): Reduction of dynamical biochemical reaction networks in computational biology. Frontiers in Bioinformatics and Computational Biology 3, 00131, DOI=10.3389/fgene.2012.00131. (Tâche 5)
- Steven Gay, Sylvain Soliman, François Fages. A Graphical Method for Reducing and Relating Models in Systems Biology. Bioinformatics, 26(18):i575–i581, 2010.
