Selected Publications

In recent years Systems Biology has become a rich field of study, trying to encompass all the information that has become available thanks to the new high-throughput techniques of biologists. Fifteen years ago, a fundamental breakthrough was the publication of Kurt Kohn’s map of the cell cycle control in mammals. Its similarity with electronic circuits was crucial in both making it impossible for humans to comprehend fully, and in prompting the use of formal methods […]
Habilitation à diriger des recherches, Université Paris Sud - Orsay, December, 2016.

Biochemical reaction networks grow bigger and bigger, fed by the high-throughput data provided by biologists and bred in open repositories of models allowing merging and evolution. Nevertheless, since the available data is still very far from permitting the identification of the increasing number of kinetic parameters of such models, the necessity of structural analyses for describing the dynamics of chemical networks appears stronger every day. Using the structural information, notably from the stoichiometric matrix, of a biochemical reaction system, we state a more strict version of the famous Thomas’ necessary condition for multistability […]
Bulletin of Mathematical Biology, 75 (11):2289-2303, November, 2013.

Background We present a way to compute the minimal semi-positive invariants of a Petri net representing a biological reaction system, as resolution of a Constraint Satisfaction Problem. The use of Petri nets to manipulate Systems Biology models and make available a variety of tools is quite old, and recently analyses based on invariant computation for biological models have become more and more frequent, for instance in the context of module decomposition. Results In our case, this analysis brings both qualitative and quantitative information on the models, in the form of conservation laws, consistency checking, etc […]
Algorithms for Molecular Biology, 7 (1):15, December, 2012.

Other Recent Publications

More Publications

. Influence Networks compared with Reaction Networks: Semantics, Expressivity and Attractors. IEEE/ACM Transactions on Computational Biology and Bioinformatics, PP (99):1-14, 2018.

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. Probably Approximately Correct Learning of Regulatory Networks from Time-Series Data. In J. Feret, H. Koeppl, editor, CMSB’17 - 15th International Conference on Computational Methods for Systems Biology, pages 74-90, 2017.

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. Model-based Investigation of the Circadian Clock and Cell Cycle Coupling in Mouse Embryonic Fibroblasts: Prediction of RevErb-α Up-regulation During Mitosis. In Dynamics Days 2017 - XXXVII Dynamics Days Europe International Conference, 2017.

HAL

. Model-based investigation of the circadian clock and cell cycle coupling in mouse embryonic fibroblasts: Prediction of RevErb-α up-regulation during mitosis. BioSystems, 149:59–69, 2016.

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. Influence Systems vs Reaction Systems. In Ezio Bartocci, Pietro Lio, Nicola Paoletti, editor, CMSB’16: Proceedings of the fourteenth international conference on Computational Methods in Systems Biology, volume 9859 of Lecture Notes in Computer Science, pages 98-115, Springer-Verlag, 2016.

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Projects

ANR BioPSy

Hybrid Formal Modelling of Time for Circadian Clock Biology and Chronopharmacology

ANR HyClock

Hybrid Formal Modelling of Time for Circadian Clock Biology and Chronopharmacology

French-German PROCOPE Mobility Grant

O. Radulescu, Univ. Montpellier, France, Andreas Weber, Univ. Bonn, Germany

Teaching

I teach/taught in the following frameworks:

  • in the Paris Computer Science Masters (Research), I am in charge of the Constraint Programming course;

    Course notes will be updated along teaching:

    • class 1 - Introduction to CLP, operational semantics, examples
    • class 2 - CLP: fixpoint semantics
    • class 3 - CLP: logical semantics, CSP: solving by simplification and domain reduction
    • class 4 - CLP: the Warren Abstract Machine, CSP: Symmetries
    • class 5 - CLP: typing; CHR; Programming project discussion; MiniZinc and CLPZinc
    • class 6 - CC: examples, operational and denotational semantics
    • class 7 - CC: linear logic semantics; LCC
    • class 8 - LCC: logical semantics, links with CHR; EMoP: modules for LCC/CC/CLP
  • at Ecole Polytechnique, I was for several years teaching assistant for Java classes corresponding to the Informatique Fondamentale lessons of Jean-Jacques Levy.

See also the programming project for the MPRI classes and the subject of the 2015-2016 Exam.

I am also propose some internships on the dedicated page of the Lifeware team.

Recent Posts

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Nontransitive dice

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.ode to reaction model converter

This page allows you to convert a system of ordinary differential equations in the .ode format of XPPAUT to a reaction model.

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CellDesigner model to influence graph converter

This page allows you to convert a CellDesigner model to a supposedly meaningful influence model.

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Nicotine Is a COnstraint-based T and p-INvariant Extractor.

Besides being a famous alkaloid found in tobacco, Nicotine (Nicotine Is a COnstraint-based T and p-INvariant Extractor) is a (GNU Prolog) program that computes a Petri-net’s invariants by using Constraint Programming and has grown to encompass many other utilities.

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This is a set of reasonable guidelines for formatting Prolog programs, freely adapted from Caml guidelines and M. Covington’s Prolog coding guidelines. They aim at reflecting the consensus among the programmers of the Lifeware team. Nevertheless, all detailed notifications of possible errors or omissions will be noted with pleasure. To send your comments: Sylvain.Soliman@inria.fr.

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