A mathematical model for lymphangiogenesis in normal and diabetic wounds, Journal of theoretical biology, vol.383, pp.61-86, 2015. ,
Mathematical modelling of cancer invasion: the multiple roles of tgf-? pathway on tumour proliferation and cell adhesion, Mathematical Models and Methods in Applied Sciences, vol.27, issue.10, pp.1929-1962, 2017. ,
Kasa: A static analyzer for kappa, Computational Methods in Systems Biology -16th International Conference, vol.11095, pp.285-291, 2018. ,
URL : https://hal.archives-ouvertes.fr/hal-01888951
Incremental update for graph rewriting, editor, Programming Languages and Systems -26th European Symposium on Programming, vol.10201, pp.201-228, 2017. ,
URL : https://hal.archives-ouvertes.fr/hal-02357978
The kappa platform for rule-based modeling, Bioinformatics, vol.34, issue.13, pp.583-592, 2018. ,
URL : https://hal.archives-ouvertes.fr/hal-01962663
Integrinmediated tgf? activation modulates the tumour microenvironment, Cancers, vol.11, issue.9, p.1221, 2019. ,
Context-sensitive flow analyses: A hierarchy of model reductions, Computational Methods in Systems Biology -11th International Conference, CMSB 2013, vol.8130, pp.220-233, 2013. ,
URL : https://hal.archives-ouvertes.fr/hal-00846893
Kade: A tool to compile kappa rules into (reduced) ODE models, Computational Methods in Systems Biology -15th International Conference, vol.10545, pp.291-299, 2017. ,
URL : https://hal.archives-ouvertes.fr/hal-01613600
The plasticity of tgf-? signaling, BMC systems biology, vol.5, issue.1, p.184, 2011. ,
Inducing chondrogenesis in msc/chondrocyte co-cultures using exogenous tgf-?: a mathematical model, Journal of theoretical biology, vol.439, pp.1-13, 2018. ,
Quantitative modeling and analysis of the transforming growth factor beta signaling pathway, Biophys. J, vol.96, issue.5, pp.1733-1750, 2009. ,
Systems theory of smad signalling, IEE Proceedings-Systems Biology, vol.153, issue.6, pp.412-424, 2006. ,
Systems theory of Smad signalling, Syst Biol, vol.153, issue.6, pp.412-424, 2006. ,
Mechanosensitivity of the 2nd kind: Tgf-? mechanism of cell sensing the substrate stiffness, PloS one, vol.10, issue.10, p.139959, 2015. ,
Abstract interpretation: A unified lattice model for static analysis of programs by construction or approximation of fixpoints, Conference Record of the Fourth ACM Symposium on Principles of Programming Languages, pp.238-252, 1977. ,
A mathematical model of wound healing and subsequent scarring, Journal of The Royal Society Interface, vol.7, issue.42, pp.19-34, 2009. ,
Modeling the effects of transforming growth factor-beta on extracellular matrix alignment in dermal wound repair, Wound Repair Regen, vol.9, issue.4, pp.278-286, 2001. ,
Graphs, rewriting and pathway reconstruction for rule-based models, IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science, FSTTCS 2012, vol.18, pp.276-288, 2012. ,
URL : https://hal.archives-ouvertes.fr/hal-00809065
Rule-based modelling of cellular signalling, CONCUR 2007 -Concurrency Theory, 18th International Conference, vol.4703, pp.17-41, 2007. ,
URL : https://hal.archives-ouvertes.fr/hal-00164297
Abstracting the differential semantics of rule-based models: Exact and automated model reduction, Proceedings of the 25th Annual IEEE Symposium on Logic in Computer Science, LICS 2010, pp.362-381, 2010. ,
URL : https://hal.archives-ouvertes.fr/hal-00520112
Scalable simulation of cellular signaling networks, Programming Languages and Systems, 5th Asian Symposium, vol.4807, pp.139-157, 2007. ,
URL : https://hal.archives-ouvertes.fr/inria-00528409
Abstract interpretation of cellular signalling networks, Verification, Model Checking, and Abstract Interpretation, 9th International Conference, vol.4905, pp.83-97, 2008. ,
URL : https://hal.archives-ouvertes.fr/inria-00528352
Formal molecular biology, Theor. Comput. Sci, vol.325, issue.1, pp.69-110, 2004. ,
URL : https://hal.archives-ouvertes.fr/hal-00164591
Specificity and versatility in tgf-beta signaling through Smads, Annu. Rev. Cell Dev. Biol, vol.21, pp.659-693, 2005. ,
Internal coarse-graining of molecular systems, 2009. ,
URL : https://hal.archives-ouvertes.fr/inria-00528330
Reachability analysis via orthogonal sets of patterns, Electr. Notes Theor. Comput. Sci, vol.335, pp.27-48, 2018. ,
URL : https://hal.archives-ouvertes.fr/hal-01379902
Mathematical modeling of liver fibrosis, Mathematical Biosciences & Engineering, vol.14, issue.1, pp.143-164, 2017. ,
In silico investigation of ADAM12 effect on TGF-beta receptors trafficking, BMC Res Notes, vol.2, p.193, 2009. ,
URL : https://hal.archives-ouvertes.fr/inria-00337265
The extracellular matrix and transforming growth factor-?1: Tale of a strained relationship, Matrix Biol, vol.47, pp.54-65, 2015. ,
Spatio-genetic and phenotypic modelling elucidates resistance and re-sensitisation to treatment in heterogeneous melanoma, Journal of theoretical biology, vol.466, pp.84-105, 2019. ,
Signal propagation in sensing and reciprocating cellular systems with spatial and structural heterogeneity, Bulletin of mathematical biology, vol.80, issue.7, pp.1900-1936, 2018. ,
URL : https://hal.archives-ouvertes.fr/hal-02322020
Modeling pancreatic cancer dynamics with immunotherapy, Bulletin of mathematical biology, vol.81, issue.6, pp.1885-1915, 2019. ,
Overview of the matrisome-an inventory of extracellular matrix constituents and functions. Cold Spring Harbor perspectives in biology, vol.4, p.4903, 2012. ,
Mathematical model of tgf-? signalling: feedback coupling is consistent with signal switching, BMC systems biology, vol.11, issue.1, p.48, 2017. ,
A hybrid model of tumor-stromal interactions in breast cancer, Bulletin of mathematical biology, vol.75, issue.8, pp.1304-1350, 2013. ,
Constitutive equations for polymer melts and solutions: Butterworths series in chemical engineering, 2013. ,
Computational analysis reveals the coupling between bistability and the sign of a feedback loop in a TGF-?1 activation model, BMC Syst Biol, vol.11, issue.7, p.136, 2017. ,
Tgf-?1-a truly transforming growth factor in fibrosis and immunity, Seminars in Cell & Developmental Biology, 2019. ,
Resolving the Combinatorial Complexity of Smad Protein Complex Formation and Its Link to Gene Expression, Cell Syst, vol.6, issue.1, pp.75-89, 2018. ,
Signaling cross talk between tgf-?/smad and other signaling pathways. Cold Spring Harbor perspectives in biology, vol.9, p.22137, 2017. ,
Dynamic filopodial forces induce accumulation, damage, and plastic remodeling of 3d extracellular matrices, PLoS computational biology, vol.15, issue.4, p.1006684, 2019. ,
, , 2019.
, BioModels-15 years of sharing computational models in life science, Nucleic Acids Research, 1055.
A rate equation approach to elucidate the kinetics and robustness of the tgf-? pathway, Biophysical journal, vol.91, issue.12, pp.4368-4380, 2006. ,
A rate equation approach to elucidate the kinetics and robustness of the TGF-beta pathway, Biophys. J, vol.91, issue.12, pp.4368-4380, 2006. ,
Mathematical modeling and numerical simulation of the tgf-?/smad signaling pathway in tumor microenvironments, Applied Numerical Mathematics, vol.133, pp.41-51, 2018. ,
, , 2018.
, Thrombospondin-1 regulation of latent tgf-? activation: a therapeutic target for fibrotic disease, Matrix Biology, vol.68, pp.28-43
Analysis of the transforming growth factor-beta/sub 1/ pathway and extracellular matrix formation as a hybrid system, Conf Proc IEEE Eng Med Biol Soc, vol.4, pp.2901-2904, 2004. ,
A mathematical model of the stoichiometric control of Smad complex formation in TGF-beta signal transduction pathway, J. Theor. Biol, vol.259, issue.2, pp.389-403, 2009. ,
A mathematical model of the stoichiometric control of smad complex formation in tgf-? signal transduction pathway, Journal of theoretical biology, vol.259, issue.2, pp.389-403, 2009. ,
Computational modelling of smad-mediated negative feedback and crosstalk in the tgf-? superfamily network, Journal of The Royal Society Interface, vol.10, issue.86, p.20130363, 2013. ,
Signaling in Fibrosis: TGF-?, WNT, and YAP/TAZ Converge, vol.2, p.59, 2015. ,
Simulated interventions to ameliorate age-related bone loss indicate the importance of timing, Frontiers in endocrinology, vol.7, p.61, 2016. ,
Active gel physics, Nature Physics, vol.11, issue.2, p.111, 2015. ,
Reduction of dynamical biochemical reactions networks in computational biology, Frontiers in genetics, vol.3, p.131, 2012. ,
Fragments generated upon extracellular matrix remodeling: biological regulators and potential drugs, Matrix Biology, vol.75, pp.170-189, 2019. ,
URL : https://hal.archives-ouvertes.fr/hal-02109885
Type beta transforming growth factor: a bifunctional regulator of cellular growth, Proceedings of the National Academy of Sciences, vol.82, issue.1, pp.119-123, 1985. ,
Regulation of the bioavailability of tgf-? and tgf-?-related proteins. Cold Spring Harbor perspectives in biology, vol.8, p.21907, 2016. ,
Geometric analysis of pathways dynamics: Application to versatility of tgf-? receptors, Biosystems, vol.149, pp.3-14, 2016. ,
URL : https://hal.archives-ouvertes.fr/hal-01379033
Mathematical modeling identifies Smad nucleocytoplasmic shuttling as a dynamic signal-interpreting system, Proc. Natl. Acad. Sci. U.S.A, vol.105, issue.18, pp.6608-6613, 2008. ,
Mathematical modeling identifies smad nucleocytoplasmic shuttling as a dynamic signal-interpreting system, Proceedings of the National Academy of Sciences, vol.105, pp.6608-6613, 2008. ,
Smad signaling dynamics: insights from a parsimonious model, Sci Signal, vol.1, issue.36, p.41, 2008. ,
Encoding of temporal signals by the tgf-? pathway and implications for embryonic patterning, Developmental cell, vol.30, issue.3, pp.334-342, 2014. ,
URL : https://hal.archives-ouvertes.fr/hal-02409076
Combinatorial interventions inhibit tgf?-driven epithelial-to-mesenchymal transition and support hybrid cellular phenotypes, NPJ systems biology and applications, vol.1, p.15014, 2015. ,
Network modeling of TGF? signaling in hepatocellular carcinoma epithelial-to-mesenchymal transition reveals joint sonic hedgehog and Wnt pathway activation, Cancer Res, vol.74, issue.21, pp.5963-5977, 2014. ,
Integration of tgf-?-and egfr-based signaling pathways using an agent-based model of epithelial restitution. Wound Repair and Regeneration, vol.20, pp.862-863, 2012. ,
Cell-specific responses to the cytokine TGF? are determined by variability in protein levels, Mol. Syst. Biol, vol.14, issue.1, p.7733, 2018. ,
Exploring hypotheses of the actions of tgf-?1 in epidermal wound healing using a 3d computational multiscale model of the human epidermis, PloS one, vol.4, issue.12, p.8515, 2009. ,
Selected parts of the kappa model for the tgf-beta extracellular matrix, 2020. ,
, , 2020.
Transforming growth factor-? and the hallmarks of cancer, Cellular signalling, vol.23, issue.6, pp.951-962, 2011. ,
Advances in dynamic modeling of colorectal cancer signaling-network regions, a path toward targeted therapies, Oncotarget, vol.6, issue.7, p.5041, 2015. ,
Plasmin triggers a switch-like decrease in thrombospondin-dependent activation of tgf-?1, Biophysical journal, vol.103, issue.5, pp.1060-1068, 2012. ,
Signal processing in the tgf-? superfamily ligand-receptor network, PLoS computational biology, vol.2, issue.1, p.3, 2006. ,
Trafficking coordinate description of intracellular transport control of signaling networks, Biophysical journal, vol.101, issue.10, pp.2315-2323, 2011. ,
Signal processing in the TGF-beta superfamily ligand-receptor network, PLoS Comput. Biol, vol.2, issue.1, p.3, 2006. ,
Controlling long-term signaling: receptor dynamics determine attenuation and refractory behavior of the TGF-? pathway, Sci Signal, vol.6, issue.305, p.106, 2013. ,
The self-limiting dynamics of tgf-? signaling in silico and in vitro, with negative feedback through ppm1a upregulation, PLoS computational biology, vol.10, issue.6, p.1003573, 2014. ,
A multiscale hybrid mathematical model of epidermal-dermal interactions during skin wound healing, Experimental dermatology, vol.28, issue.4, pp.493-502, 2019. ,
Cross-scale, cross-pathway evaluation using an agent-based nonsmall cell lung cancer model, Bioinformatics, vol.25, issue.18, pp.2389-2396, 2009. ,
Identifying mechanisms of homeostatic signaling in fibroblast differentiation, Bulletin of mathematical biology, vol.77, issue.8, pp.1556-1582, 2015. ,
, , 2006.
, Macrophage dynamics in diabetic wound dealing, Bulletin of mathematical biology, vol.68, issue.1, pp.197-207
Dynamics and feedback loops in the transforming growth factor ? signaling pathway, Biophysical chemistry, vol.162, pp.22-34, 2012. ,
A mathematical model of the enhancement of tumor vaccine efficacy by immunotherapy, Bulletin of mathematical biology, vol.74, issue.7, pp.1485-1500, 2012. ,
Pathway crosstalk enables cells to interpret tgf-? duration, NPJ systems biology and applications, vol.4, issue.1, p.18, 2018. ,
Non-Smad Signaling Pathways of the TGF? Family, Cold Spring Harb Perspect Biol, vol.9, issue.2, 2017. ,
Dynamics of TGF?/Smad signaling, FEBS Lett, vol.586, issue.14, pp.1921-1928, 2012. ,
Quantitative analysis of transient and sustained transforming growth factor-? signaling dynamics, Mol. Syst. Biol, vol.7, p.492, 2011. ,
Quantitative analysis of transient and sustained transforming growth factor-? signaling dynamics, Molecular systems biology, vol.7, issue.1, 2011. ,
Constraint-based modeling and kinetic analysis of the smad dependent tgf-? signaling pathway, PloS one, vol.2, issue.9, p.936, 2007. ,