cell-signalling

↗️ Influence graph analysis, consistency check, diagnosis, repair and prediction

napari-plugin to analyse collective signalling events

CeCe is a platform for advanced simulation of cells and cell signalling in 2D. It includes a physical engine, stochastic chemical reactions, cell-cell bonding, diffusion, hydrodynamics, and a growth model.

Influence graph analysis, consistency check, diagnosis, repair and prediction

Convolutional Neural Network for Dynamics EXploration (CODEX) is a method for mining time-series dataset by leveraging CNN features.

Design experiments to differentiate interaction graph models

A collection of summaries and reflective notes from foundational biochemistry courses, including energy metabolism, cell signaling, small molecules, and chemical biology, developed to strengthen understanding of molecular mechanisms and support advanced studies in biochemistry and molecular biology

PAR2 Activation and calcium signaling Reaction Model in PySB

Reproducible R/Quarto workflow for the analysis of quantitative phosphoproteomics data from HCT116 cells following TNF stimulation.

Python pipeline to build empirical kinase networks and identify kinase signalling communities from quantitative phosphoproteomics data.

Maximum Entropy (MaxEnt) parameter inference in biological networks.

Source code for "Coupling dynamics of 2D Notch-Delta signalling", by Francisco Berkemeier and Karen M. Page