Wiki BioTempo- Publications

Static and discrete models (Task 2).

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.
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. 10th International Conference on Computational Methods in Systems Biology, LNCS 7605, pp. 342–361. Springer, Heidelberg (2012) (www)
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)
L. Paulevé and A. Richard. Static analysis of boolean networks based on interaction graphs: a survey. Proceedings of The Second International Workshop on Static Analysis and Systems Biology (SASB 2011), Electronic Notes in Theoretical Computer Science 284, 93-104, 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, 161(7-8):1106-1117, 2013 (www)
Jean-Paul Comet, Mathilde Noual, Adrien Richard, Julio Aracena, Laurence Calzone, Jacques Demongeot, Marcelle Kaufman, Aurélien Naldi, El Houssine Snoussi, Denis Thieffry. On Circuit Functionality in Boolean Networks. Bulletin of Mathematical Biology June 2013, Volume 75, Issue 6, pp 906-919 (www)
Tarek Melliti, Damien Regnault, Adrien Richard, Sylvain Sené. On the Convergence of Boolean Automata Networks without Negative Cycles. Cellular Automata and Discrete Complex Systems Lecture Notes in Computer Science Volume 8155, 2013, pp 124-138 (www)
J. Aracena, A. Richard, L. Salinas. Maximum number of fixed points in AND-OR-NOT networks. Journal of Computer and System Sciences, 80(7):1175-1190, 2014.
S. Laurent, A. Richard, O. Mulner-Lorillon, J. Morales, D. Flament, V. Glippa, J. Bourdon, P. Gosselin, A. Siegel, P. Cormier, R. Bellé. Modelisation of the regulation of protein synthesis following fertilization in sea urchin shows requirement of two processes: a destabilization of eIF4E:4E-BP complex and a great stimulation of the 4E-BP-degradation mechanism, both rapamycin-sensitive. Frontiers in Genetics, 5(117), 2014.
S. Soliman, A stronger necessary condition for the multistationarity of chemical reaction networks, Buletin of Mathematical Biology, in press 2013 preprint
P. Bordron, D. Eveillard, A. Maass, A. Siegel and S. Thiele: An ASP application in integrative biology: identification of functional gene units, In procedings, LPNMR - 12th Conference on Logic Programming and Nonmonotonic Reasoning - 2013 (2013)
Kaminski R., Schaub T, Siegel A and Videla S. Minimal Intervention Strategies in Logical Signaling Networks with Answer Set Programming. 29th International Conference on Logic Programming. To appear in the special issue of the journal Theory and Practice of Logic Programming, Cambridge University Press.
Guziolowski C., Videla S., Eduati F., Thiele S., Cokelaer T., Siegel A. and Saez-Rodriguez J. Exhaustively characterizing feasible logic models of a signaling network using Answer Set Programming. Bioinformatics, Oxford University Press (2013). (www)

Hybrid models (Task 3)

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.
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
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.
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
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).
Katherine Chiang, François Fages, Jie-Hong Jiang, and Sylvain Soliman. On the hybrid composition and simulation of heterogeneous biochemical models. In CMSB'13: Proceedings of the eleventh international conference on Computational Methods in Systems Biology, Lecture Notes in BioInformatics. Springer-Verlag, September 2013.
L. Paulevé, G. Andrieux, and H. Koeppl. Under-approximating cut sets for reachability in large scale automata networks. Computer Aided Verification, volume 8044 of LNCS, pages 69-84, 2013 (www)
Maxime Folschette, Loïc Paulevé, Morgan Magnin, and Olivier Roux. Under-approximation of reachability in multivalued asynchronous networks. In 4th International Workshop on Interactions between Computer Science and Biology (CS2Bio'13), 2013.
Loïc Paulevé, Courtney Chancellor, Maxime Folschette, Morgan Magnin, and Olivier Roux. Logical Modeling of Biological Systems, chapter Analyzing Large Network Dynamics with Process Hitting, In press. Wiley, 2014. (pdf)
An integrative modeling framework reveals plasticity of TGF-β signaling. Andrieux G, Le Borgne M, Théret N. BMC Syst Biol. 2014 Mar 12;8:30.

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)

Steven Gay, Sylvain Soliman, François Fages (2010). A Graphical Method for Reducing and Relating Models in Systems Biology. Bioinformatics, 26(18):i575–i581, 2010.
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.
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 (2012). 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.
V. Noel, D. Grigoriev, S. Vakulenko, O. Radulescu (2013). A hybrid mammalian cell cycle model, Electronic Proceedings in Theoretical Computer Science (2013) 125: 68-84
V. Noel, D. Grigoriev, S. Vakulenko, O. Radulescu (2013). Tropicalization and tropical equilibration of chemical reactions. In press, Contemporary Mathematics, "Tropical and Idempotent Mathematics and Applications", GL Litvinov and S. Sergeev, edts., AMS 2013.
Sylvain Soliman, François Fages, and Ovidiu Radulescu (2013). A constraint solving approach to tropical equilibration and model reduction. In Proceedings of the ninth Workshop on Constraint Based Methods for Bioinformatics WCB'13 , pp. 27-36, colocated with CP 2013.