Sylvain Soliman

发表

Executable Disease Networks: Adding dynamics to molecular maps

Anna Niarakis, Marek Ostaszewski, Vidisha Singh, 2018 .

Apprentissage de r ` egles de r ´ eactions biochimiques ` a partir de propri ´ et ´ es en logique temporelle

Laurence Calzone, Sylvain Soliman, Nathalie Chabrier-Rivier, 2005 .

On a Continuous Degree of Satisfaction of Temporal Logic Formulae with Applications to Systems Biology

François Fages, Sylvain Soliman, Grégory Batt, 2008, CMSB.

Abstract interpretation and types for systems biology

François Fages, Sylvain Soliman, S. Soliman, 2008, Theor. Comput. Sci..

Closures and Modules Within Linear Logic Concurrent Constraint Programming

François Fages, Rémy Haemmerlé, Sylvain Soliman, 2007, FSTTCS.

Trace Simplifications preserving Temporal Logic Formulae with Case Study in a Coupled Model of the Cell Cycle and the Circadian Clock (Best Student Paper Prize)

Pauline Traynard, Sylvain Soliman, François Fages, 2014, CMSB 2014.

Inferring Reaction Models from ODEs

François Fages, Sylvain Soliman, Steven Gay, 2012, CMSB.

New Results - Abstract Interpretation for Systems Biology I: Hierarchy of Semantics

François Fages, Sylvain Soliman, 2007 .

Modelling of FSHR-induced Signalling Network

Frédérique Clément, Sylvain Soliman, Franccois Fages, 2008 .

Usage of bioinformatics tools and identification of information sources

Werner Nutt, Rolf Backofen, Sebastian Will, 2005 .

Software and Platforms - BIOCHAM, biochemical abstract machine

François Fages, Sylvain Soliman, François-Marie Floch, 2013 .

CMBSlib: A Library for Comparing Formalisms and Models of Biological Systems

François Fages, Sylvain Soliman, 2004, CMSB.

Recent Advances in Constraints, post-proceedings of 12th Annual ERCIM International Workshop on

Francesca Rossi, Sylvain Soliman, Franccois Fages, 2008 .

Continuous valuations of temporal logic specifications with applications to parameter optimization and robustness measures

François Fages, Sylvain Soliman, Grégory Batt, 2011, Theor. Comput. Sci..

Probably Approximately Correct Learning of Regulatory Networks from Time-Series Data

François Fages, Sylvain Soliman, Arthur Carcano, 2017, CMSB.

From models to metamodels

Sylvain Soliman, Franccois Fages, 2010 .

BIOCHAM: an environment for modeling biological systems and formalizing experimental knowledge

François Fages, Laurence Calzone, Sylvain Soliman, 2006, Bioinform..

CLPGUI: A Generic Graphical User Interface for Constraint Logic Programming

François Fages, Sylvain Soliman, Rémi Coolen, 2004, Constraints.

Modelling Biochemical Reaction Networks with BIOCHAM Extracting Qualitative and Quantitative Information from the Structure

Sylvain Soliman, S. Soliman, 2009, Simul. Notes Eur..

Invariants and Other Structural Properties of Biochemical Models as a Constraint Satisfaction Problem

Sylvain Soliman, S. Soliman, 2012, Algorithms for Molecular Biology.

Model-based investigation of the circadian clock and cell cycle coupling in mouse embryonic fibroblasts: Prediction of RevErb-α up-regulation during mitosis

François Fages, Pauline Traynard, Sylvain Soliman, 2016, Biosyst..

Un mod\`ele bool\'een pour l'\'enum\'eration des siphons et des pi\`eges minimaux dans les r\'eseaux de Petri

Sylvain Soliman, Franccois Fages, Thierry Martinez, 2013, 1304.2948.

Type Inference in Systems Biology

François Fages, Sylvain Soliman, S. Soliman, 2006, CMSB.

Influence Networks Compared with Reaction Networks: Semantics, Expressivity and Attractors

Sylvain Soliman, David A. Rosenblueth, Thierry Martinez, 2018, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Graphical Conditions for Rate Independence in Chemical Reaction Networks pdf

Sylvain Soliman, Franccois Fages, Elisabeth Degrand, 2020, CMSB.

Hybrid Simulations of Heterogeneous Biochemical Models in SBML

Jie-Hong Roland Jiang, François Fages, Sylvain Soliman, 2015, ACM Trans. Model. Comput. Simul..

Requirements and specification of use cases

Werner Nutt, Rolf Backofen, Sebastian Will, 2005 .

New Results - Railway Time Tabling Optimization with CMA-ES and Greedy Heuristics

François Fages, Sylvain Soliman, Thierry Martinez, 2013 .

A Boolean Model for Enumerating Minimal Siphons and Traps in Petri Nets

François Fages, Sylvain Soliman, Faten Nabli, 2012, CP.

Modelling molecular networks: relationships between different formalisms and levels of details

Claudine Chaouiya, Laurence Calzone, Franck Pommereau, 2010 .

Special Section on Computational Methods in Systems Biology, second part

Sylvain Soliman, Franccois Fages, 2013 .

Towards a general computational method for robustness analysis (poster)

Sylvain Soliman, Franccois Fages, Grégory Batt, 2008 .

A general computational method for robustness analysis with applications to synthetic gene networks

François Fages, Sylvain Soliman, Grégory Batt, 2009, Bioinform..

Computational Systems Biology in BIOCHAM

Elisabetta De Maria, François Fages, Sylvain Soliman, 2010, ERCIM News.

Guest Editors' Introduction to the Special Section on Computational Methods in Systems Biology

François Fages, Sylvain Soliman, 2012, TCBB.

New Results - Petri Net Analyses of Biochemical Reaction Networks using Constraint Logic Programming

François Fages, Sylvain Soliman, Thierry Martinez, 2013 .

Requirements and specification of bioinformatics use cases

Werner Nutt, Rolf Backofen, Sebastian Will, 2005 .

Proceedings of the Third international conference on Principles and Practice of Semantic Web Reasoning

François Fages, Sylvain Soliman, 2005 .

Steady-state solution of biochemical systems, beyond S-systems via T-invariants

Sylvain Soliman, Faten Nabli, S. Soliman, 2010, CMSB '10.

Modelling molecular networks with the Biocham Graphical User Interface (poster)

Sylvain Soliman, Franccois Fages, Dragana Jovanovska, 2010 .

Modelling and querying interaction networks in the biochemical abstract machine BIOCHAM

François Fages, Sylvain Soliman, Nathalie Chabrier-Rivier, 2002 .

From Reaction Models to Influence Graphs and Back: A Theorem

François Fages, Sylvain Soliman, S. Soliman, 2008, FMSB.

The Biochemical Abstract Machine BIOCHAM (poster)

Sylvain Soliman, Nathalie Chabrier-Rivier, Franccois Fages, 2004 .

Proceedings of PPSWR'05, Third International Workshop on Principles and Practice of Sematic Web

Sylvain Soliman, Franccois Fages, 2005 .

Machine Learning Bio-molecular Interactions from Temporal Logic Properties

François Fages, Laurence Calzone, Sylvain Soliman, 2005 .

Un modèle booléen pour l'énumération des siphons et des pièges minimaux dans les réseaux de Petri pdf

François Fages, Sylvain Soliman, Thierry Martinez, 2012, ArXiv.

A Machine Learning approach to Biochemical Reaction Rules Discovery

François Fages, Laurence Calzone, Sylvain Soliman, 2005 .

New Computational Methods for Systems Biology (tutorial)

Sylvain Soliman, Franccois Fages, 2010 .

On Inferring Reactions from Data Time Series by a Statistical Learning Greedy Heuristics

Sylvain Soliman, François Fages, Julien Martinelli, 2019, CMSB.

BIOCHAM user's manual

Nathalie Chabrier, Sylvain Soliman, Franccois Fages, 2004 .

On Coupling Models Using Model-Checking: Effects of Irinotecan Injections on the Mammalian Cell Cycle

Elisabetta De Maria, François Fages, Sylvain Soliman, 2009, CMSB.

Concurrent constraint programming and linear logic

Sylvain Soliman, 2001 .

Model-Based Investigation of the Effect of the Cell Cycle on the Circadian Clock Through Transcription Inhibition During Mitosis

François Fages, Pauline Traynard, Sylvain Soliman, 2015, CMSB.

Linear Concurrent Constraint Programming: Operational and Phase Semantics

François Fages, Paul Ruet, Sylvain Soliman, 2001, Inf. Comput..

New Software and Platforms - ClpZinc

François Fages, Sylvain Soliman, Thierry Martinez, 2014 .

On the subgraph epimorphism problem

Christine Solnon, François Fages, Sylvain Soliman, 2014, Discret. Appl. Math..

Design, Optimization, and Predictions of a Coupled Model of the Cell Cycle, Circadian Clock, DNA

Elisabetta De Maria, Sylvain Soliman, Franccois Fages, 2010 .

Design, optimization and predictions of a coupled model of the cell cycle, circadian clock, DNA repair system, irinotecan metabolism and exposure control under temporal logic constraints

Elisabetta De Maria, François Fages, Sylvain Soliman, 2011, Theor. Comput. Sci..

Model Revision from Temporal Logic Properties in Systems Biology

Sylvain Soliman, Franccois Fages, 2008 .

New Results - « Model checking » symbolique en biologie des réseaux moléculaires

François Fages, Nathalie Chabrier, Sylvain Soliman, 2002 .

Automatic Curation of SBML Models based on their ODE Semantics

François Fages, Sylvain Soliman, S. Soliman, 2012 .

Langages formels dans la machine abstraite biochimique BIOCHAM

François Fages, Laurence Calzone, Sylvain Soliman, 2007, Tech. Sci. Informatiques.

CLP Implementation of a Phase Model Checker

Sylvain Soliman, 2002 .

New Results - Reconfigurable Circuitry in Biochemical Systems

Sylvain Soliman, François Fages, Hui-Ju Chiang, 2014 .

Search by constraint propagation

François Fages, Sylvain Soliman, Thierry Martinez, 2015, PPDP.

Constraint Programming for the Dynamical Analysis of Biochemical Systems – A Survey

Sylvain Soliman, S. Soliman, 2011 .

A graphical method for reducing and relating models in systems biology

François Fages, Sylvain Soliman, Steven Gay, 2010, Bioinform..

Inferring reaction systems from ordinary differential equations

François Fages, Sylvain Soliman, Steven Gay, 2015, Theor. Comput. Sci..

Trace Simplifications Preserving Temporal Logic Formulae with Case Study in a Coupled Model of the Cell Cycle and the Circadian Clock

François Fages, Pauline Traynard, Sylvain Soliman, 2014, CMSB.

BIOCHAM v2.8 user's manual

Sylvain Soliman, Franccois Fages, Aurélien Rizk, 2009 .

Principles and Practice of Semantic Web Reasoning, Third International Workshop, PPSWR 2005, Dagstuhl Castle, Germany, September 11-16, 2005, Proceedings

François Fages, Sylvain Soliman, Ppswr, 2005, PPSWR.

Graphical Requirements for Multistationarity in Reaction Networks and their Verification in BioModels

François Fages, Sylvain Soliman, Adrien Baudier, 2018, Journal of theoretical biology.

SBGN support in BIOCHAM

François Fages, Sylvain Soliman, Dragana Jovanovska, 2010 .

New Software and Platforms - The Biochemical Abstract Machine

François Fages, Pauline Traynard, Sylvain Soliman, 2014 .

On enumerating minimal siphons in Petri nets using CLP and SAT solvers: theoretical and practical complexity

François Fages, Sylvain Soliman, Thierry Martinez, 2016, Constraints.

BIOCHAM v3.4 Reference Manual

Sylvain Soliman, Franccois Fages, Aurélien Rizk, 2012 .

On Robustness Computation and Optimization in BIOCHAM-4

François Fages, Sylvain Soliman, S. Soliman, 2018, CMSB.

A Stronger Necessary Condition for the Multistationarity of Chemical Reaction Networks

Sylvain Soliman, S. Soliman, 2013, Bulletin of mathematical biology.

Recent Advances in Constraints, 12th Annual ERCIM International Workshop on Constraint Solving and Constraint Logic Programming, CSCLP 2007, Rocquencourt, France, June 7-8, 2007, Revised Selected Papers

Francesca Rossi, François Fages, Sylvain Soliman, 2008, CSCLP.

Qualitative Modelling of the RB/E2F network

Claudine Chaouiya, Laurence Calzone, Elisabeth Remy, 2011 .

New Results - Parameter Search and Robustness Analysis w.r.t. Temporal Logic Properties

François Fages, Sylvain Soliman, Grégory Batt, 2008 .

Model Revision from Temporal Logic Properties in Computational Systems Biology

François Fages, Sylvain Soliman, S. Soliman, 2008, Probabilistic Inductive Logic Programming.

Formal Cell Biology in Biocham

François Fages, Sylvain Soliman, S. Soliman, 2008, SFM.

COVID-19 Disease Map, a computational knowledge repository of SARS-CoV-2 virus-host interaction mechanisms

Hiroaki Kitano, Xiaoming Hu, Marina Esteban-Medina, 2020, bioRxiv.

Automated inference of Boolean models from molecular interaction maps using CaSQ

Anna Niarakis, Jinbo Xu, Vidisha Singh, 2020, Bioinform..

New Results - Temporal Logic Modeling of Dynamical Behaviors: First-Order Patterns and Solvers

François Fages, Pauline Traynard, Sylvain Soliman, 2014 .

A constraint solving approach to model reduction by tropical equilibration

François Fages, Sylvain Soliman, Ovidiu Radulescu, 2014, Algorithms for Molecular Biology.

State-of-the-art in Bioinformatics

Werner Nutt, Michael Schroeder, Rolf Backofen, 2004 .

Guest Editors' Introduction to the Special Section on Computational Methods in Systems Biology

François Fages, Sylvain Soliman, 2013, TCBB.

On the Complexity of Quadratization for Polynomial Differential Equations

Sylvain Soliman, Franccois Fages, Mathieu Hemery, 2020, CMSB.

Influence Systems vs Reaction Systems

François Fages, Sylvain Soliman, David A. Rosenblueth, 2016, CMSB.

Patient-Tailored Cancer Therapeutics - The Tempo Project

François Fages, Sylvain Soliman, Jean Clairambault, 2007, ERCIM News.

Towards a Semantic Web for Bioinformatics

Werner Nutt, Rolf Backofen, Sebastian Will, 2004 .

Finding minimal P/T-invariants as a CSP

Sylvain Soliman, S. Soliman, 2008 .

Implementation of prototypes

Rolf Backofen, Sebastian Will, François Fages, 2007 .

A Statistical Unsupervised Learning Algorithm for Inferring Reaction Networks from Time Series Data

Sylvain Soliman, François Fages, Julien Martinelli, 2019, ICML 2019.

Pi-calcul et LCC, une odyssée de l'espace

Sylvain Soliman, 2004, JFPLC.

Analyzing various models of Circadian Clock and Cell Cycle coupling

Paola Lecca, Paolo Ballarini, Heike Siebert, 2009, Formal Methods in Molecular Biology.

The Biochemical Abstract Machine BIOCHAM

François Fages, Sylvain Soliman, Nathalie Chabrier-Rivier, 2004, CMSB.

Bipartite Graph Properties and Systems Biology (poster)

Sylvain Soliman, Franccois Fages, Faten Nabli, 2010 .

On the Hybrid Composition and Simulation of Heterogeneous Biochemical Models

Jie-Hong Roland Jiang, François Fages, Sylvain Soliman, 2013, CMSB.

Machine Learning Biochemical Networks from Temporal Logic Properties

François Fages, Laurence Calzone, Sylvain Soliman, 2006, Trans. Comp. Sys. Biology.

A structural perspective on the dynamics of biochemical systems. (Une perspective structurelle sur la dynamique des systèmes biochimiques)

Sylvain Soliman, S. Soliman, 2016 .

Model learning to identify systemic regulators of the peripheral circadian clock

François Fages, Sylvain Soliman, Annabelle Ballesta, 2021, Bioinform..

Compiling Elementary Mathematical Functions into Finite Chemical Reaction Networks via a Polynomialization Algorithm for ODEs

Sylvain Soliman, Franccois Fages, Mathieu Hemery, 2021, CMSB.

Setting the basis of best practices and standards for curation and annotation of logical models in biology - highlights of the [BC]2 2019 CoLoMoTo/SysMod Workshop

Aurélien Naldi, Denis Thieffry, Claudine Chaouiya, 2020, Briefings Bioinform..

A Constraint Solving Approach to Tropical Equilibration and Model Reduction

Sylvain Soliman, Ovidiu Radulescu, S. Soliman, 2014, 1401.6337.

Learning Transition Rules from Temporal Logic Properties

François Fages, Laurence Calzone, Sylvain Soliman, 2005 .

Coupling the Cell cycle and the Circadian Cycle

Laurence Calzone, Sylvain Soliman, S. Soliman, 2006 .

Dynamics of the interlocked positive feedback loops explaining the robust epigenetic switching in Candida albicans.

François Fages, Sylvain Soliman, S. Soliman, 2009, Journal of theoretical biology.