Publications

Van-Giang Trinh, Sylvain Soliman, François Fages, Belaid Benhamou (2025). On the Trap Space Semantics of Normal Logic Programs. In Daniela Inclezan Martin Gebser, Francesco Ricca, editor, ICLP 2025 - 41st International Conference on Logic Programming, pages 294–319.

Ouissem Saidi, Nicolas Gaudenzio, Sylvain Soliman, Fabien Crauste, Anna Niarakis (2025). DigiDermA: Modeling Cellular and Molecular Interactions in Atopic Dermatitis. In JOBIM 2025 - Journées Ouvertes en Biologie, Informatique et Mathématiques.

François Fages, Mathieu Hemery, Sylvain Soliman (2025). On BIOCHAM Symbolic Computation Pipeline for Compiling Mathematical Functions into Biochemistry. ACM Communications in Computer Algebra, 58 (2):15-22.

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.

Anna Niarakis et al (2024). Drug-target identification in COVID-19 disease mechanisms using computational systems biology approaches. Frontiers in Immunology, 14.

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.

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.

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.

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.

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.

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).

Sahar Aghakhani, Sylvain Soliman, Anna Niarakis (2022). Metabolic Reprogramming in Rheumatoid Arthritis Synovial Fibroblasts: a Hybrid Modeling Approach. PLoS Computational Biology, 18 (12):e1010408.

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.

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.

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.

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.

Marek Ostaszewski et al (2021). COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms. Molecular Systems Biology, 17 (10):e10387.

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..

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.

Julien Martinelli et al (2021). Model learning to identify systemic regulators of the peripheral circadian clock. Bioinformatics, 37 (Supplement_1):9.