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BioSimulators: a central registry of simulation engines and services for recommending specific tools

 Bilal Shaikh , Lucian Smith , Dan Vasilescu , Gnaneswara Marupilla , Michael Wilson , et al.
Nucleic Acids Research, 2022, pp.1-7. ⟨10.1093/nar/gkac331⟩
Article dans une revue hal-03666382v1

Model-based Investigation of the Circadian Clock and Cell Cycle Coupling in Mouse Embryonic Fibroblasts: Prediction of RevErb-α Up-regulation During Mitosis

 Pauline Traynard , Celine Feillet , Sylvain Soliman , Franck Delaunay , François Fages
Dynamics Days 2017 - XXXVII Dynamics Days Europe International Conference, Jun 2017, Szeged, Hungary
Communication dans un congrès hal-01651833v1
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Computational modeling predicts impaired barrier function and higher sensitivity to skin inflammation following pH elevation

 Eléa Thibault Greugny , Jalil Bensaci , François Fages , Georgios Stamatas
Experimental Dermatology, 2022, ⟨10.1111/exd.14698⟩
Article dans une revue hal-03909897v1
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Metro Energy Optimization through Rescheduling: Mathematical Models and Heuristic Algorithm Compared to MILP and CMA-ES

 David Fournier , Thierry Martinez , François Fages , Denis Mulard
[Research Report] Inria Saclay Ile de France. 2016
Rapport hal-01420311v1

Qualitative Reasoning: A Survey of Techniques Applications

 Jacky Montmaint , Philippe Dague
AI Communications, 1995
Article dans une revue hal-01931753v1
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A large-scale Boolean model of the rheumatoid arthritis fibroblast-like synoviocytes predicts drug synergies in the arthritic joint

 Vidisha Singh , Aurélien Naldi , Sylvain Soliman , Anna Niarakis
npj Systems Biology and Applications, 2023, 9 (33), ⟨10.1038/s41540-023-00294-5⟩
Article dans une revue hal-04187223v1

AI-assisted human biocuration of molecular mechanisms in the COVID-19 Disease Map project

 A. Niarakis
AI BioSS, 2020, Virtual conference, France
Communication dans un congrès hal-04482181v1

Fibroblasts as Therapeutic Targets in Rheumatoid Arthritis and Cancer: Computational Modeling of The Metabolic Reprogramming in Rheumatoid Arthritis Synovial Fibroblasts and Cancer Associated Fibroblasts.

 S Aghakhani , A. Niarakis
Computational Systems Biology of Cancer: Promises of Artificial Intelligence – EMBO, 2020, Virtual conference, France
Poster de conférence hal-04482594v1

Inference of a modular, large-scale Boolean network for modelling the Rheumatoid Arthritis fibroblast-like synoviocytes

 Vidisha Singh , Soliman S , Anna Niarakis
5th Disease Map Community Meeting, 2020, Virtual conference, France
Communication dans un congrès hal-04482346v1
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Building Reconfigurable Circuitry in a Biochemical World

 Hui-Ju Chiang , Jie-Hong Jiang , François Fages
IEEE Proceedings BioCAS 2014 - Biomedical Circuits and Systems Conference, Oct 2014, Lausanne, Switzerland. pp.560 - 563, ⟨10.1109/BioCAS.2014.6981787⟩
Communication dans un congrès hal-01103266v1
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Configurable Linear Control of Biochemical Systems

 Tai-Yin Chiu , Ruei-Yang Huang , Hui-Ju Chiang , Jie-Hong Jiang , François Fages
IWBDA 2014 - 6th international workshop on bio-design automation, Jun 2014, Boston, United States
Communication dans un congrès hal-01103286v1
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Graphical Requirements for Multistationarity in Reaction Networks and their Verification in BioModels

 Adrien Baudier , François Fages , Sylvain Soliman
Journal of Theoretical Biology, 2018, 459, pp.79--89. ⟨10.1016/j.jtbi.2018.09.024⟩
Article dans une revue hal-01879735v1
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Influence Systems vs Reaction Systems

 François Fages , Thierry Martinez , David Rosenblueth , Sylvain Soliman
CMSB'16: Proceedings of the fourteenth international conference on Computational Methods in Systems Biology, Sep 2016, Cambridge, UK, United Kingdom. pp.98-115, ⟨10.1007/978-3-319-45177-0_7⟩
Communication dans un congrès hal-01378470v1
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Abstraction-Based Parameter Synthesis for Multiaffine Systems

 Sergiy Bogomolov , Christian Schilling , Ezio Bartocci , Gregory Batt , Hui Kong , et al.
11th International Haifa Verification Conference, HVC 2015, Haifa, Israel, November 17-19, 2015, Proceedings, Nov 2015, Haifa, Israel. pp.19-35, ⟨10.1007/978-3-319-26287-1_2⟩
Communication dans un congrès hal-01242371v1

Gestion de l'évolutif et de l'incertain dans une base de connaissances

 Nicole Bidoit , Serenella Cerrito , Laurence Cholvy , Marie-Odile Cordier , Philippe Dague , et al.
5èmes Journées Nationales du PRC-GDR : Intelligence Artificielle (1995), Groupe de Recherche IA du CNRS, Feb 1995, Nancy, France. pp.77--121
Communication dans un congrès hal-04050876v1
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A Greedy Heuristic for Optimizing Metro Regenerative Energy Usage

 David Fournier , François Fages , Denis Mulard
Railways 2014, Apr 2014, Ajaccio, France. ⟨10.4203/ccp.104.240⟩
Communication dans un congrès hal-01103710v1
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A Polynomialization Algorithm for Elementary Functions and ODEs, and their Compilation into Chemical Reaction Networks

 Mathieu Hemery , François Fages , Sylvain Soliman
CASC'21 - Computer Algebra in Scientific Computing., Sep 2021, Sochi, Russia
Communication dans un congrès hal-03271828v1

Simulations of pH-effects on kallikrein activity predict compromised skin barrier and predisposition to irritations and dryness characteristic of atopic dermatitis (poster abstract)

 Elea Greugny , Jalil Bensaci , François Fages , Georgios Stamatas
Journal of Investigative Dermatology, 2021, 141 (10), pp.S171. ⟨10.1016/j.jid.2021.08.136⟩
Article dans une revue hal-03504443v1
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Symbolic Methods for Biological Networks D2.1 Report on Scalable Methods for Tropical Solutions (T1.2)

 Christoph Lüders , Eléonore Bellot , François Fages , Ovidiu Radulescu , Sylvain Soliman
[Research Report] Inria Saclay. 2022
Rapport hal-03648027v1
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On a model of online analog computation in the cell with absolute functional robustness: algebraic characterization, function compiler and error control

 Mathieu Hemery , François Fages
Theoretical Computer Science, In press
Article dans une revue hal-04252933v2
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Developing new tools and platforms for mammalian synthetic biology: From the assembly and chromosomal integration of complex DNA circuits to the engineering of artificial intercellular communication systems

 Xavier Duportet
Biotechnology. Université Paris Diderot (Paris 7), 2014. English. ⟨NNT : ⟩
Thèse tel-01108520v1
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Can optimal experimental design serve as a tool to characterize highly non-linear synthetic circuits?

 Maxim Kryukov , Arthur Carcano , Grégory Batt , Jakob Ruess
ECC 2019 - European Control Conference, Jun 2019, Naples, Italy
Communication dans un congrès hal-02304425v1
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Estimating information in time-varying signals

 Sarah Anhala Cepeda-Humerez , Jakob Ruess , Gašper Tkačik
PLoS Computational Biology, 2019, 15 (9:e1007290), pp.1--33. ⟨10.1371/journal.pcbi.1007290⟩
Article dans une revue hal-02304413v1
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Comparison of SYK Signaling Networks Reveals the Potential Molecular Determinants of Its Tumor-Promoting and Suppressing Functions

 Marion Buffard , Aurélien Naldi , Gilles Gf Freiss , Marcel Deckert , Ovidiu Radulescu , et al.
Biomolecules, 2021, 11 (2), pp.308. ⟨10.3390/biom11020308⟩
Article dans une revue hal-03160560v1
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Biochemical Threshold Function Implementation with Zero-Order Ultrasensitivity

 Wei-Chih Huang , Jie-Hong Jiang , François Fages , Franck Molina
BioCAS 2019 - IEEE Biomedical Circuits and Systems Conference, Oct 2019, Nara, Japan. pp.1-4, ⟨10.1109/BIOCAS.2019.8919176⟩
Communication dans un congrès hal-02425761v1
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Convergent evolution in silico of biochemical log-response

 Mathieu Hemery , Paul François
Journal of Chemical Physics, 2019
Article dans une revue hal-02389284v1
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Efficient Enumeration of Fixed Points in Complex Boolean Networks Using Answer Set Programming

 Van-Giang Trinh , Belaid Benhamou , Sylvain Soliman
29th International Conference on Principles and Practice of Constraint Programming (CP 2023), Aug 2023, Toronto, Canada. pp.35:1--35:19, ⟨10.4230/LIPIcs.CP.2023.35⟩
Communication dans un congrès hal-04209296v1

Computing EFMs consistent with equilibrium constants

 Sabine Pérès , Philippe Dague , Mario Jolicœur , Stefan Schuster
Metabolic Pathway Analysis MPA 2017, Jul 2017, Bozeman, United States
Communication dans un congrès hal-01676892v1

Building digital twins of the human immune system: toward a roadmap

 Reinhard Laubenbacher , A. Niarakis , Tomáš Helikar , Gary An , Bruce Shapiro , et al.
npj Digital Medicine, 2022, 5 (64), ⟨10.1038/s41746-022-00610-z⟩
Article dans une revue hal-03699607v1
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Reactmine: a statistical search algorithm for inferring chemical reactions from time series data

 Julien Martinelli , Jeremy Grignard , Sylvain Soliman , Annabelle Ballesta , François Fages
2023
Pré-publication, Document de travail hal-03769872v2
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