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Metabolic reprogramming in Rheumatoid Arthritis Synovial Fibroblasts: A hybrid modeling approach

PLoS computational biology, 2022-12, Vol.18 (12), p.e1010408-e1010408

2022

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A unique transformation from ordinary differential equations to reaction networks

PloS one, 2010-12, Vol.5 (12), p.e14284-e14284

2010

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Invariants and other structural properties of biochemical models as a constraint satisfaction problem

Algorithms for molecular biology, 2012-05, Vol.7 (1), p.15-15, Article 15

Soliman, Sylvain

2012

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MetaLo: metabolic analysis of Logical models extracted from molecular interaction maps

Journal of integrative bioinformatics, 2024-02, Vol.21 (1), p.1-13

2024

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A large-scale Boolean model of the rheumatoid arthritis fibroblast-like synoviocytes predicts drug synergies in the arthritic joint

NPJ systems biology and applications, 2023-07, Vol.9 (1), p.33-33, Article 33

2023

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Hybrid computational modeling highlights reverse warburg effect in breast cancer-associated fibroblasts

Computational and structural biotechnology journal, 2023-01, Vol.21, p.4196-4206

2023

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A Stronger Necessary Condition for the Multistationarity of Chemical Reaction Networks

Bulletin of mathematical biology, 2013-11, Vol.75 (11), p.2289-2303

Soliman, Sylvain

2013

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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

Theoretical computer science, 2011-05, Vol.412 (21), p.2108-2127

2011

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Trap spaces of Boolean networks are conflict-free siphons of their Petri net encoding

Theoretical computer science, 2023-09, Vol.971, p.114073, Article 114073

2023

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Automated inference of Boolean models from molecular interaction maps using CaSQ

Bioinformatics, 2020-08, Vol.36 (16), p.4473-4482

2020

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Inferring reaction systems from ordinary differential equations

Theoretical computer science, 2015-09, Vol.599, p.64-78

2015

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Graphical requirements for multistationarity in reaction networks and their verification in BioModels

Journal of theoretical biology, 2018-12, Vol.459, p.79-89

2018

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

Bioinformatics, 2006-07, Vol.22 (14), p.1805-1807

2006

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Model learning to identify systemic regulators of the peripheral circadian clock

Bioinformatics, 2021-07, Vol.37 (Supplement_1), p.i401-i409

2021

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Abstract interpretation and types for systems biology

Theoretical computer science, 2008-08, Vol.403 (1), p.52-70

2008

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Semantic Web Architecture: Stack or Two Towers?

Lecture notes in computer science, 2005, p.37-41

2005

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A graphical method for reducing and relating models in systems biology

Bioinformatics, 2010-09, Vol.26 (18), p.i575-i581

2010

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

Bioinformatics, 2009-06, Vol.25 (12), p.i169-i178

2009

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

2005., 2005

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Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology

Briefings in bioinformatics, 2022-07, Vol.23 (4), p.1-11

2022

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Minimal Trap Spaces of Logical Models are Maximal Siphons of Their Petri Net Encoding

Computational Methods in Systems Biology, p.158-176

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

Computational Methods in Systems Biology, 2021, Vol.12881, p.74-90

2021

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SBGN support in BIOCHAM

Nature precedings, 2010-11

2010

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On Robustness Computation and Optimization in BIOCHAM-4

Computational Methods in Systems Biology, p.292-299

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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

BioSystems, 2016-11, Vol.149, p.59-69

2016

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Metabolic reprogramming in Rheumatoid Arthritis Synovial Fibroblasts: A hybrid modeling approach

A unique transformation from ordinary differential equations to reaction networks

Invariants and other structural properties of biochemical models as a constraint satisfaction problem

MetaLo: metabolic analysis of Logical models extracted from molecular interaction maps

A large-scale Boolean model of the rheumatoid arthritis fibroblast-like synoviocytes predicts drug synergies in the arthritic joint

Hybrid computational modeling highlights reverse warburg effect in breast cancer-associated fibroblasts

A Stronger Necessary Condition for the Multistationarity of Chemical Reaction Networks

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

Trap spaces of Boolean networks are conflict-free siphons of their Petri net encoding

Automated inference of Boolean models from molecular interaction maps using CaSQ

Inferring reaction systems from ordinary differential equations

Graphical requirements for multistationarity in reaction networks and their verification in BioModels

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

Model learning to identify systemic regulators of the peripheral circadian clock

Abstract interpretation and types for systems biology

Semantic Web Architecture: Stack or Two Towers?

A graphical method for reducing and relating models in systems biology

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

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

Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology

Minimal Trap Spaces of Logical Models are Maximal Siphons of Their Petri Net Encoding

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

SBGN support in BIOCHAM

On Robustness Computation and Optimization in BIOCHAM-4

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

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