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GINsim: A software suite for the qualitative modelling, simulation and analysis of regulatory networks

 A.G. Gonzalez , Aurélien Naldi , L. Sanchez , D. Thieffry , C. Chaouiya
BioSystems, 2006, 84, pp.91-100
Article dans une revue hal-00088152v1
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SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools

 Claudine Chaouiya , Duncan Bérenguier , Sarah Keating , Aurélien Naldi , Martijn van Iersel , et al.
BMC Systems Biology, 2013, 7 (1), pp.135. ⟨10.1186/1752-0509-7-135⟩
Article dans une revue hal-00926033v1
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The combination of the functionalities of feedback circuits is determinant for the attractors' number and size in pathway-like Boolean networks

 Eugenio Azpeitia , Stalin Munoz , Daniel Gonzalez-Tokman , Mariana Esther Martinez-Sanchez , Nathan Weinstein , et al.
Scientific Reports, 2017, 7, pp.1-14. ⟨10.1038/srep42023⟩
Article dans une revue hal-01606130v1

Model checking to assess T-helper cell plasticity

 Wassim Abou-Jaoudé , Pedro T. Monteiro , Aurélien Naldi , Maximilien Grandclaudon , Vassili Soumelis , et al.
Frontiers in Bioengineering and Biotechnology, 2014, Computational methods for understanding complexity: the use of formal methods in biology, pp.22. ⟨10.3389/fbioe.2014.00086⟩
Article dans une revue hal-01099490v1
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Drug-target identification in COVID-19 disease mechanisms using computational systems biology approaches

 Anna Niarakis , Marek Ostaszewski , Alexander Mazein , Inna Kuperstein , Martina Kutmon , et al.
Frontiers in Immunology, 2024, 14, ⟨10.3389/fimmu.2023.1282859⟩
Article dans une revue hal-04454379v1
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PTPN13 induces cell junction stabilization and inhibits mammary tumor invasiveness

 Mohamed Hamyeh , Florence F. Bernex , Romain M Larive , Aurélien Naldi , S Urbach , et al.
Theranostics, In press, 10 (3), pp.1016-1032. ⟨10.7150/thno.38537⟩
Article dans une revue hal-02401068v1
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Reconstruction and signal propagation analysis of the Syk signaling network in breast cancer cells

 Aurélien Naldi , Romain Larive , Urszula Czerwinska , Serge Urbach , Philippe Montcourrier , et al.
PLoS Computational Biology, 2017, 13 (3), pp.e1005432. ⟨10.1371/journal.pcbi.1005432⟩
Article dans une revue hal-02073659v1
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Benchmarking joint multi-omics dimensionality reduction approaches for the study of cancer

 Laura Cantini , Pooya Zakeri , Céline Hernandez , Aurelien Naldi , Denis Thieffry , et al.
Nature Communications, 2021, 12, ⟨10.1038/s41467-020-20430-7⟩
Article dans une revue hal-03102088v1
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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
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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
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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

Dynamically consistent reduction of logical regulatory graphs

 Aurélien Naldi , Elisabeth Remy , Denis Thieffry , Claudine Chaouiya
Theoretical Computer Science, 2011, 412 (21), ⟨10.1016/j.tcs.2010.10.021⟩
Article dans une revue hal-01284743v1
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Benchmarking joint multi-omics dimensionality reduction approaches for cancer study

 Laura Cantini , Pooya Zakeri , Céline Hernandez , Aurelien Naldi , Denis Thieffry , et al.
2020
Pré-publication, Document de travail hal-02998156v1

Linear cuts in Boolean networks

 Aurélien Naldi , Adrien Richard , Elisa Tonello
Natural Computing, 2023, 22 (3), pp.431-451. ⟨10.1007/s11047-023-09945-2⟩
Article dans une revue hal-04304408v1

Dynamical analysis of a generic Boolean model for the control of the mammalian cell cycle.

 A. Fauré , Aurélien Naldi , C. Chaouiya , D. Thieffry
Bioinformatics, 2006, pp.22: e124-31
Article dans une revue hal-00310984v1

On circuit functionality in Boolean networks

 Jean-Paul Comet , Mathilde Noual , Adrien Richard , J. Aracena , Laurence Calzone , et al.
Bulletin of Mathematical Biology, 2013, 75 (6), pp.906-919. ⟨10.1007/s11538-013-9829-2⟩
Article dans une revue istex hal-01242396v1
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Logical modelling of in vitro differentiation of human monocytes into dendritic cells unravels novel transcriptional regulatory interactions

 Karen J Nuñez-Reza , Aurélien Naldi , Arantza Sánchez-Jiménez , Ana V Leon-Apodaca , M. Angélica Angélica Santana , et al.
Interface Focus, 2021, 11 (4), pp.20200061. ⟨10.1098/rsfs.2020.0061⟩
Article dans une revue hal-03352078v1
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Computational Verification of Large Logical Models—Application to the Prediction of T Cell Response to Checkpoint Inhibitors

 Céline Hernandez , Morgane Thomas-Chollier , Aurélien Naldi , Denis Thieffry
Frontiers in Physiology, 2020, 11, ⟨10.3389/fphys.2020.558606⟩
Article dans une revue hal-03352080v1
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LNetReduce: tool for reducing linear dynamic networks with separated time scales

 Marion Buffard , Aurélien Desoeuvres , Aurélien Naldi , Clément Requilé , Andrei Zinovyev , et al.
Computational Methods in Systems Biology, Sep 2021, Bordeaux, France. ⟨10.1007/978-3-030-85633-5_15⟩
Communication dans un congrès hal-03226633v1
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Diversity and Plasticity of Th Cell Types Predicted from Regulatory Network Modelling.

 Aurélien Naldi , Jorge Carneiro , Claudine Chaouiya , Denis Thieffry
PLoS Computational Biology, 2010, 6 (9), pp.e1000912. ⟨10.1371/journal.pcbi.1000912⟩
Article dans une revue inserm-00704876v1
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The CoLoMoTo Interactive Notebook: Accessible and Reproducible Computational Analyses for Qualitative Biological Networks

 Aurélien Naldi , Céline Hernandez , Nicolas Levy , Gautier Stoll , Pedro Monteiro , et al.
Frontiers in Physiology, 2018, 9, pp.n°680:1-13. ⟨10.3389/fphys.2018.00680⟩
Article dans une revue hal-01794294v2
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SBML Level 3: an extensible format for the exchange and reuse of biological models

 Sarah Keating , Frank Bergmann , Tomáš Helikar , Rahuman Malik‐sheriff , Ion Moraru , et al.
Molecular Systems Biology, 2020, 16 (8), pp.1-21. ⟨10.15252/msb.20199110⟩
Article dans une revue hal-02924909v1
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UPMaBoSS: A Novel Framework for Dynamic Cell Population Modeling

 Gautier Stoll , Aurélien Naldi , Vincent Noël , Eric Viara , Emmanuel Barillot , et al.
Frontiers in Molecular Biosciences, 2022, 9, ⟨10.3389/fmolb.2022.800152⟩
Article dans une revue hal-03696031v1
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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.
2022
Pré-publication, Document de travail hal-03613651v1
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Linear cuts in Boolean networks

 Aurélien Naldi , Adrien Richard , Elisa Tonello
2022
Pré-publication, Document de travail hal-03696050v1
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Geometric analysis of pathways dynamics: application to versatility of TGF-β receptors

 Satya Swarup Samal , Aurélien Naldi , Dima Grigoriev , Andreas Weber , Nathalie Théret , et al.
BioSystems, 2016, 149, pp.3-14. ⟨10.1016/j.biosystems.2016.07.004⟩
Article dans une revue hal-01379033v1
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Network Reconstruction and Significant Pathway Extraction Using Phosphoproteomic Data from Cancer Cells

 Marion Buffard , Aurélien Naldi , Ovidiu Radulescu , Peter Coopman , Romain Larive , et al.
Proteomics, 2019, 19 (21-22), pp.1800450. ⟨10.1002/pmic.201800450⟩
Article dans une revue hal-03049205v1
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Logical modelling of cellular decision processes with GINsim

 Claudine Chaouiya , Aurélien Naldi , Lionel Spinelli , Pedro Monteiro , Duncan Berenguier , et al.
JOBIM 2012, Jul 2012, Rennes, France
Communication dans un congrès hal-01261855v1
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A versatile and interoperable computational framework for the analysis and modeling of COVID-19 disease mechanisms

 Anna Niarakis , Marek Ostaszewski , Alexander Mazein , Inna Kuperstein , Martina Kutmon , et al.
2022
Pré-publication, Document de travail hal-03907738v1
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COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms

 Marek Ostaszewski , Anna Niarakis , Alexander Mazein , Inna Kuperstein , Robert Phair , et al.
Molecular Systems Biology, 2021, 17 (10), pp.e10387. ⟨10.15252/msb.202110387⟩
Article dans une revue hal-03385317v2
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