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Publications
Van-Giang Trinh
,
Belaid Benhamou
,
Sylvain Soliman
,
François Fages
(2024).
Graphical conditions for the existence, unicity and number of regular models
. In Pedro Cabalar, Francesco Fabiano, Martin Gebser, Gopal Gupta, Theresa Swift, editor,
ICLP 2024 - 40th International Conference on Logic Programming
, pages 175-187.
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François Fages
,
Mathieu Hemery
,
Sylvain Soliman
(2024).
On BIOCHAM Symbolic Computation Pipeline for Compiling Mathematical Functions into Biochemistry
. In
ISSAC 2024 - 49th International Symposium on Symbolic and Algebraic Computation
.
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Giang Trinh
,
Belaid Benhamou
,
Samuel Pastva
,
Sylvain Soliman
(2024).
Scalable Enumeration of Trap Spaces in Boolean Networks via Answer Set Programming
. In
AAAI 2024 - The 38th Annual Conference on Artificial Intelligence
, pages 10714-10722.
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Sahar Aghakhani
,
Anna Niarakis
,
Sylvain Soliman
(2024).
MetaLo: metabolic analysis of Logical models extracted from molecular interaction maps
.
Journal of Integrative Bioinformatics
, 21 (1):20230048.
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Anna Niarakis Et Al
(2024).
Drug-target identification in COVID-19 disease mechanisms using computational systems biology approaches
.
Frontiers in Immunology
, 14.
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Van-Giang Trinh
,
Belaid Benhamou
,
Sylvain Soliman
(2023).
Trap spaces of Boolean networks are conflict-free siphons of their Petri net encoding
.
Theoretical Computer Science
, 971:114073.
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Sahar Aghakhani
,
Sacha E Silva-Saffar
,
Sylvain Soliman
,
Anna Niarakis
(2023).
Hybrid computational modeling highlights reverse warburg effect in breast cancer-associated fibroblasts
.
Computational and Structural Biotechnology Journal
, 21:4196-4206.
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Van-Giang Trinh
,
Belaid Benhamou
,
Sylvain Soliman
(2023).
Efficient Enumeration of Fixed Points in Complex Boolean Networks Using Answer Set Programming
. In Roland H. C. Yap, editor,
29th International Conference on Principles and Practice of Constraint Programming (CP 2023)
, pages 35:1–35:19, Schloss Dagstuhl - Leibniz-Zentrum für Informatik.
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Vidisha Singh
,
Aurélien Naldi
,
Sylvain Soliman
,
Anna Niarakis
(2023).
A large-scale Boolean model of the rheumatoid arthritis fibroblast-like synoviocytes predicts drug synergies in the arthritic joint
.
npj Systems Biology and Applications
, 9 (33).
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Sahar Aghakhani
,
Sylvain Soliman
,
Anna Niarakis
(2022).
Metabolic Reprogramming in Rheumatoid Arthritis Synovial Fibroblasts: a Hybrid Modeling Approach
.
PLoS Computational Biology
, 18 (12):e1010408.
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Van-Giang Trinh
,
Belaid Benhamou
,
Kunihiko Hiraishi
,
Sylvain Soliman
(2022).
Minimal trap spaces of Logical models are maximal siphons of their Petri net encoding
. In Ion Petre, Andrei Păun, editor,
CMSB 2022 - International Conference on Computational Methods in Systems Biology
, volume 13447 of
Lecture Notes in Computer Science
, pages 158–176, Springer.
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Anna Niarakis Et Al
(2022).
Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology
.
Briefings in Bioinformatics
, 23 (4):1-11.
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Christoph Lüders
,
Eléonore Bellot
,
François Fages
,
Ovidiu Radulescu
,
Sylvain Soliman
(2022).
Symbolic Methods for Biological Networks D2.1 Report on Scalable Methods for Tropical Solutions (T1.2)
. Research Report.
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Anna Niarakis Et Al
(2021).
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
.
Briefings in Bioinformatics
, 22 (2):1848–1859.
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Marek Ostaszewski Et Al
(2021).
COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms
.
Molecular Systems Biology
, 17 (10):e10387.
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Mathieu Hemery
,
François Fages
,
Sylvain Soliman
(2021).
Compiling Elementary Mathematical Functions into Finite Chemical Reaction Networks via a Polynomialization Algorithm for ODEs
. In
CMSB 2021 - 19th International Conference on Computational Methods in Systems Biology
.
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Mathieu Hemery
,
François Fages
,
Sylvain Soliman
(2021).
A Polynomialization Algorithm for Elementary Functions and ODEs, and their Compilation into Chemical Reaction Networks
. In
CASC'21 - Computer Algebra in Scientific Computing.
.
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Julien Martinelli Et Al
(2021).
Model learning to identify systemic regulators of the peripheral circadian clock
.
Bioinformatics
, 37 (Supplement_1):9.
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Mathieu Hemery
,
François Fages
,
Sylvain Soliman
(2020).
On the Complexity of Quadratization for Polynomial Differential Equations
. In
CMSB 2020 - 18th International Conference on Computational Methods in Systems Biology
.
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Elisabeth Degrand
,
François Fages
,
Sylvain Soliman
(2020).
Graphical Conditions for Rate Independence in Chemical Reaction Networks
. In
CMSB 2020 - 18th International Conference on Computational Methods in Systems Biology
.
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