Data underlying the publication: YAP/TAZ drives Notch and angiogenesis mechanoregulation in silico

Data belonging to the article "YAP/TAZ drives Notch and angiogenesis mechanoregulation in silico"It contains the MATLAB code used to run all simulations, the fitting algorithms and the code used to obtain all Figures.The study focused on the mechanoresponse of Notch and in turn, that of angiogenesis. We hypothesized that this response could be explained through Notch interactions with mechano-sensitive YAP/TAZ. The modeled implementation was used to also investigate and suggest avenues through which to steer angiogenesis; by cytoskeletal manipulations and heterogeneous stiffness patterns.DOI: https://doi.org/10.1038/s41540-024-00444-

Data underlying the publication: "A computational analysis of the role of integrins and Rho-GTPases in the emergence and disruption of apical-basal polarisation in renal epithelial cells"

The data and resulting publication show the role of integrins and Rho-GTPases in the establishment of apical-basal polarization in renal epithelial cells. The dataset contains the code for the 1D computational framework

Data underlying the publication "Notch signaling regulates strain-mediated phenotypic switching of vascular smooth muscle cells"

The data and resulting publication show the role of Notch signaling in regulating strain-mediated phenotypic switching of vascular smooth muscle cells. The dataset consists of custom-built scripts for strain analysis, stretch quantification data, immunofluorescence staining and real-time polymerase chain reaction data

Data belonging to the publication: "Computational analysis of the role of mechanosensitive Notch signaling in arterial adaptation to hypertension"

This study couples a Finite Element model for arterial mechanics to an Agent-Based model for mechanosensitive Notch signaling among vascular smooth muscle cells to predict the phenotype of these cells under hypertension, a loss of residual stresses in the artery, and manipulations of the Notch signaling pathway. This dataset contains the codes for the Finite Element model, the Agent-Based model and the coupling between them, as well as the raw data generated by these models

Data underlying the publication: Computational analysis of heart valve growth and remodeling after the Ross procedure

Simulation and analysis codes that describe and predict the adaptation of a ross autograph after being exposed to increased pressure. This contains abaqus input files (.inp), material models (fortran free form .f), abaqus output (.odb), and analysis and postprocessing codes (.py and .m

Data belonging to the publication "A multiscale computational model of arterial growth and remodeling including Notch signaling"

This study presents a multiscale computational framework coupling a constrained mixture model, capturing the mechanics and turnover of arterial constituents, to a cell-cell signaling model, describing Notch signaling dynamics among vascular smooth muscle cells. Tissue turnover was regulated by both Notch activity, informed by in vitro data obtained from human coronary artery smooth muscle cells, and a phenomenological contribution, accounting for mechanisms other than Notch. The framework was used to predict changes in wall thickness and arterial composition in response to hypertension and thereby demonstrated the effects of Notch signaling and Notch interventions on this process. This dataset contains the computational codes for the multiscale framework (i.e. the constrained mixture model and the Notch signaling model), the codes for the data fitting and optimization, and the raw data from the simulations and the in vitro experiments used to inform the model