PUBLICATIONS


[partially updated June 2017]

Book Chapter

[PCFMR-2014] Loic Pauleve, Courtney Chancelor, Maxime Folschette, Morgan Magnin and Olivier Roux. “Analyzing Large Network Dynamics with Process Hitting“, in Logical Modeling of Biological Systems, pages 125-166. [ bib | pdf ].


Academic Journals

[Frontiers-2017] Zurah Bibi, Jamil Ahmad, Amnah Siddiqa, Rehan Z. Paracha, Tariq Saeed, Amjad Ali, Hussnain Ahmed Janjua, Shakir Ullah, Emna Ben Abdallah and Olivier Roux. “Formal Modeling of mTOR Associated Biological Regulatory Network Reveals Novel Therapeutic Strategy for the Treatment of CancerFrontiers in Physiology Systems Biology, Volume 8, June 2017. [ bib | paper | doi ].

[Algorithms-2017] Emna Ben Abdallah, Tony Ribeiro, Morgan Magnin, Olivier Roux and Katsumi Inoue. “Modeling Delayed Dynamics in Biological Regulatory Networks from Time Series DataJournal Algorithms – Special Issue Biological Networks, Volume 10, Number 1, Janvier 2017. [ bib | pdf | doi ].

[Biol.Syst.-2016] Amine Amar, Morgan Magnin, Olivier Roux, Elias Cueto and Francisco Chinesta. “Chemical Master Equation Empirical Moment ClosureBiological Systems Open Access, Volume 5, Number 155,  2016. [ bib | pdf | doi ].

[TCS-2015-bMaxime Folschette, Loïc Paulevé, Morgan Magnin and Olivier Roux. “Sufficient Conditions for Reachability in Automata Networks with Priorities”Theoretical Computer Science, Volume 608, Part 1, pp. 66–83, September 2015. Extended version of the article published in CS2Bio’13. [ bib | pdf | doi ].

[Entropy-2015] Francisco Chinesta, Morgan Magnin, Olivier Roux, Amine Ammar and Elias Cueto. “Kinetic Theory Modeling and Efficient Numerical Simulation of Gene Regulatory Networks Based on Qualitative Descriptions. Entropy, April 2015. [ bib | doi | free access ].

[TSI-2015Loïc Paulevé, Maxime Folschette, Morgan Magnin and Olivier Roux. “Analyses statiques de la dynamique des réseaux d’automates indéterministes”Technique et Science Informatiques, Volume 34, Number 4, pp. 463–484, 2015. [ link | pdf | doi ].

[Frontiers-2015S. H. K. Tareen, J. Ahmad and O. Roux.”Parametric linear hybrid automata for complex environmental systems modeling”. Frontiers in Environmental Science – section Environmental Informatics, July 2015. [ bib | pdf | doi ].

[TCS-2015-a] Maxime Folschette, Loïc Paulevé, Katsumi Inoue, Morgan Magnin and Olivier Roux. “Identification of biological regulatory networks from Process Hitting models. Theoretical Computer Science, Vol. 568, pp. 49-71, February 2015.[ bib | doi | pdf ].

[MSCS-2012] Loic Pauleve, 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. [ bib | doi ].

[TCSB-2011] Loic Pauleve, Morgan Magnin and Olivier Roux. “Refining Dynamics of Gene Regulatory Networks in a Stochastic π-calculus Framework. In Corrado Priami, Ralph-Johan Back, Ion Petre, and Erik de Vink, editors, Transactions on Computational Systems Biology XIII, volume 6575 of Lecture Notes in Computer Science, pages 171-191. Springer Berlin / Heidelberg, 2011. [ bib | doi | pdf ].

[IEEE_TSE-2011] Loic Pauleve, Morgan Magnin and Olivier Roux. “Tuning Temporal Features within the Stochastic π-calculus. IEEE Transactions on Software Engineering, 37(6):858-871, 2011. [ bib | doi ].

[BMC-2010] Jonathan Fromentin, Damien Eveillard, and Olivier Roux. ”Hybrid modeling of biological networks : Mixing temporal and qualitative properties”. BMC Systems Biology, Vol. 4, 2010. [ bib | doi ]

[IJDBM-2010] Jamil Ahmad and Olivier Roux. “Invariance kernel of Biological Regulatory Networks“. International Journal of Data Mining and Bioinformatics (IJDMB), Vol. 4, No. 5, pp. 553 – 570, 2010. [ bib | doi ]

[Biosystems-2009] Jamil Ahmad, Jérémie Bourdon, Damien Eveillard, Jonathan Fromentin, Olivier Roux and Christine Sinoquet. “Temporal constraints of a gene regulatory network: refining a qualitative simulation”. Biosystems, Vol. 98, Issue 3, 2009. [ bib | doi ]

[IJBRA-2008] Jamil Ahmad, Olivier Roux, Gilles Bernot, Jean-Paul Comet and Adrien Richard: “Analysing Formal Models of Genetic Regulatory Networks with Delays: Applications to lambda phage and T-cell activation systems“. International Journal of Bioinformatics Research and Applications (IJBRA). 4(3):240-262, 2008. Inderscience Publisher, ISSN (Paper): 1744-5485. [ bib | doi ]

[ComplexUs-2007] Jamil Ahmad, Gilles Bernot, Jean-Paul Comet, Didier Lime and Olivier Roux. “Hybrid Modelling and Dynamical Analysis of Gene Regulatory Networks with Delays“. ComPlexUs, 3(4):231-251, 2006 (Cover Date Nov. 2007). Karger Publisher. [ bib | doi ]

[TPLP-2006] Guillaume Gardey, Olivier (H.) Roux, and Olivier (F.) Roux. “State space computation and analysis of time Petri nets“. Theory and Practice of Logic Programming (TPLP), Special Issue on Specification Analysis and Verification of Reactive Systems, 6(3):301-320, 2006. Cambridge Press. [ bib | doi ]

[FI-2004] Franck Cassez, Claire Pagetti, and Olivier Roux. “A timed extension for AltaRica“. Fundamenta Informaticæ, 62(3-4):291-332, August 2004. [ bib ]

[JRTS-2001] Frédéric Herbreteau, Franck Cassez, and Olivier Roux. “Application of Partial-Order Methods to Reactive Systems with Event Memorization”. Journal of Real-Time Systems, 20(3):287-316, May 2001. Kluwer Academics. [ bib | doi ]

[FAC-1999] Olivier Roux, Vlad Rusu, and Franck Cassez. “Hybrid Verification of Reactive Systems”. Formal Aspects of Computing, 11(4):448-471, December 1999. Copyright Springer-Verlag. [ bib | doi ]

[TCS-1995] Franck Cassez and Olivier Roux. “Compilation of the Electre Reactive Language into Finite Transition Systems”. Theoretical Computer Science, 146(1-2):109-143, July 1995. Copyright Elsevier. [ bib | doi ]

[APII-1994] Olivier Roux and Vlad Rusu. “Translating from GRAFCET to the reactive language ELECTRE”. Automatique, Productique et Informatique Industrielle, 28(2):131-158, 1994. [ bib | doi ]

[TCS-1992] Jean Perraud Cassez and Olivier Roux and Marc Huou. “Operational semantics of a kernel of the language ELECTRE”. Theoretical Computer Science, 97(1):83-103, April 1992. Copyright Elsevier. [ bib | doi ]

[CJ-1986] Jean-Pierre Elloy and Olivier Roux. “Electre: A Language for Control Structuring in Real time”. The Computer Journal, 29(3):229-234, January 1986. Copyright Oxford Journals. [ bib | doi ]


International Conferences and Workshops (full-paper selection) (since 2003)

Edition of Conference Proceedings and Special Issue

[L1] — O. ROUX AND J. BOURDON, Computational Methods in Systems Biology – 13th International Conference, CMSB 2015, Nantes, France, September 16-18, 2015, Proceedings. Lecture Notes in Computer Science 9308, Springer 2015, ISBN 978-3-319-23400-7. (2015).

[NS1] — J. BOURDON AND O. ROUX, Biosystems, Volume 149, Pages 1-154 (November 2016), Selected papers from the Computational Methods in Systems Biology 2015 conference, Edited by Olivier Roux and Jérémie Bourdon. (2015).


Invited Conferences and talks

[Madrid-2012] Olivier Roux: ”A New Framework to Analyze Huge Biological Regulatory Network”, Systems Biology Europe / Track Informatics (Distinguished Faculty Speaker), Madrid, Spain, October 2012.

[Luxembourg-2012] Olivier Roux: ”Hybrid and Algebraic Modeling of Biological Systems for the Analysis of their Timing Features”, Luxembourg University invited seminar (Thomas Sauter and Jun Pang), Luxembourg, April 2012,

[Paris-2009] Olivier Roux: “Using the Stochastic π-Calculus Framework for Temporal Parameters Inference in Gene Regulatory Networks“. International Workshop on Timing and Stochasticity in Petri nets and other models of concurrency (TiSTo), a satellite event of Petri Nets 2009. Keynote 2 : (invited speaker), Paris, France, June 2009.

[Konstanz-2009] Olivier Roux: “Hybrid Modelling of biological systems for the accurate analysis of their timing features“. In Konstanz University invited seminar (Stefan Leue), Konstanz, Germany, July 2009.

[Berlin-2007] Olivier Roux: “Analysing Gene regulatory Networks by both Constraint Programming and Model-Checking“. In MPG-CNRS joint Workshop on Systems Biology, (WSB’07), Berlin, Germany, 24-26 September 2007.


International Conferences

[C1] — E. BEN ABDALLAH, T. RIBEIRO, M. MAGNIN, O. ROUX and K. INOUE. Inference of delayed biological regulatory networks from time series data. CMSB 2016 – 14th conference on Computational Methods for Systems Biology, volume 9859 of Lecture Notes in Bioinformatics. Springer, University of Cambridge (UK), September 2016. (2016).

[C’6] — E. BEN ABDALLAH, T. RIBEIRO, M. MAGNIN, O. ROUX and K. INOUE. Challenge in Computational Biology: Gene Expression Data Analysis. 2nd Challenge in Computational Biology: Gene Expression Data Analysis. Genomics and Computational Biology, Institute of Molecular Biology, Mainz, Germany, (December 2016).

[C’7] — L. FIPPO FITIME, O. ROUX, C. GUZIOLOWSKI and L. PAULEVE. Identification of Bifurcations in Biological Regulatory Networks using Answer-Set Programming , Constraint-Based Methods for Bioinformatics – 12th International Workshop, WCB 2016, Toulouse, France, September 5-9, 2016. Revised Selected Papers. Workshop satellite de CP’06. (2016).

[C2] — E. BEN ABDALLAH, M. FOLSCHETTE, O. ROUX, and M. MAGNIN. Exhaustive analysis of dynamical properties of biological regulatory networks with answer set programming, in Bioinformatics and Biomedicine (BIBM), 2015 IEEE International Conference on, pp. 281–285. (2015).

[C3] — L. FIPPO FITIME, C. SCHUSTER, P. ANGEL, O. ROUX, and C. GUZIOLOWSKI. Integrating Time-Series Data in Large-Scale Discrete Cell-Based Models , Hybrid Systems Biology: Fourth International Workshop, HSB 2015, Madrid, Spain, September 4-5, 2015. Volume 9271 of the series Lecture Notes in Computer Science. pp 75-95. (2015)

[C4] — G. BERNOT, J.P. COMET, and O. ROUX, A Genetically Modified Hoare Logic that Identifies the Parameters of a Gene Network. 13th International Conference. CMSB 2015, Nantes, France, September 16-18, 2015, Proceedings. Lecture Notes in Computer Science 9308, Springer. pp. 8-12. (2015).

[C’8] — L. FIPPO FITIME, A. BEICA, O. ROUX, and C. GUZIOLOWSKI. Integrating Time-Series Data on Large-Scale Cell-Based Models: application to skin differentiation. Thematic School on Advances in Systems and Synthetic Biology, aSSB’14, Evry, France, March 24-28, 2014. Revised Selected Papers , pages 57–72. (2014).

[CMSB-2013] Courtney Chancellor, Francisco Chinesta, Olivier Roux, Amine Ammar and Morgan Magnin. “ Linking Discrete and Stochastic Models: the Chemical Master Equation as a bridge between Process Hitting and PGD . In Computational Methods in Systems Biology (CMSB 2013), LNCS n°8130, Wien (Austria), September 2013. [ bib | doi ].

[CS2Bio-2013] M. Folschette, L. Paulevé, M. Magnin, and O. Roux. “Under-approximation of Reachability in Multivalued Asynchronous Networks. In 4th International Workshop on Interactions between Computer Science and Biology (CS2Bio’13), Electronic Notes in Theoretical Computer Science, Firenze (Italy), June 2013. [ bib | doi ].

[CMSB-2012] M. Folschette, L. Paulevé, K. Inoue, M. Magnin, and O. Roux. “Concretizing the Process Hitting into Biological Regulatory Networks. In D. Gilbert and M. Heiner, editors, Computational Methods in Systems Biology (CMSB’2012), Lecture Notes in Computer Science, 166-186. Springer Berlin Heidelberg, London, United Kingdom, October 2012. [ bib | doi ].

[ECML-PKDD-2012] ”Abducing Biological Regulatory Networks from Process Hitting models”, Workshop on Learning and Discovery in Symbolic Systems Biology, Bristol, United Kingdom, Septembre 2012.

[SASB-2010] Loïc Paulevé, Morgan Magnin, and Olivier Roux. and Olivier Roux. “Abstract Interpretation of Dynamics of Biological Regulatory Networks. Proceedings of The First International Workshop on Static Analysis and Systems Biology (SASB’2010), Electronic Notes in Theoretical Computer Science, 272:43-56, 2011.

[CSBIO-2010] Jean-Paul Comet, Jonathan Fromentin, Gilles Bernot, Olivier Roux: ”A formal model for gene regulatory networks with time delays”, 1st International Conference on Computational Systems-Biology and Bioinformatics (CSBio’2010), Volume 115 of CCIS, pp. 1-13,  Best paper award, Bangkok, Thailand, November 3-5, 2010.

[SASB-2010] Loïc Paulevé, Morgan Magnin and Olivier Roux: ”Abstract Interpretation of Dynamics of Biological Regulatory Networks”. Proceedings of The First International Workshop on Static Analysis and Systems Biology (SASB’10). Electronic Notes in Theoretical Computer Science, 272 :43-56, 2011.

[BICOB-2009] Mylène Maurin, Morgan Magnin and Olivier Roux: “Modeling of Genetic Regulatory Network in Stochastic π-Calculus”. International Conference on Bioinformatics and Computational Biology (BICOB’09), LNBI, n ̊5462, Springer-Verlag,  New Orleans, USA (Louis.), April 2009.

[BIBM-2008] Jamil Ahmad and Olivier Roux: “Invariance Kernel of Biological Regulatory Networks“, IEEE International Conference on Bioinformatics and Biomedicine (BIBM’08), Philadelphia, PA, USA, Nov. 3‐5, 2008 .

[EMBC-2007] Jonathan Fromentin, Jean-Paul Comet, Pascale Le Gall and Olivier Roux: “Analysing Gene regulatory Networks by both Constraint Programming and Model-Checking“. In 29th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, (EMBC’07), pages 4595-4598, Lyon, France, 23-26 August 2007.

[WODES-2006] Guillaume Gardey, Olivier (F) Roux, and Olivier (H) Roux. “Safety Control Synthesis for Time Petri Nets“. In 8th International Worshop on Discrete Event Systems, (WODES’06), pages 222-228, Ann Arbor, Michigan, USA, July 2006. IEEE.

[IWBRA-2006] Jamil Ahmad, Adrien Richard, Gilles Bernot, Jean-Paul Comet, and Olivier Roux. “Delays in Biological Regulatory Networks (BRN)“. In International Workshop on Bioinformatics Research and Applications, (IWBRA’06), volume 3992 of Lecture Notes in Computer Science, pages 887–894, Reading, UK, May 2006. Springer. Copyright Springer-Verlag.

[FORMATS-2003] Guillaume Gardey, Olivier (H.) Roux, and Olivier (F.) Roux. “A zone-based method for computing the state space of a time Petri Net“. In Formal Modeling and Analysis of Timed Systems, (FORMATS’03), volume 2791 of Lecture Notes in Computer Science, pages 246-259, Marseille, France, September 2003. Springer. Copyright Springer-Verlag.

[BIOCONCUR-2003] Gilles Bernot, Franck Cassez, Jean-Paul Comet, Franck Delaplace, Céline Müller, Olivier Roux, and Olivier (H.) Roux. “Semantics of Biological Regulatory Networks“. In Vincent Danos and Cosimo Laneve, editors, Workshop on Concurrent Models in Molecular Biology (BioConcur 2003), Electronic Notes in Theoretical Computer Science, Marseille (France), September 2003. Elsevier’s ENTCS series. Copyright Elsevier.

[WTRTES-2003] Armelle Prigent and Olivier Roux. “Testing Real-Time Parameterized Systems“. In Workshop On Testing Real-Time and Embedded Systems (WTRTES 2003). Satellite Workshop of FM 2003, Pisa, Italy – September 13, 2003.
Also in Studia Informatica Universalis, volume 3, numero 2, April 2004.


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