Systematic inference identifies a major source of heterogeneity in cell signaling dynamics: The rate-limiting step number
Identifying the sources of cell-to-cell variability in signaling dynamics is essential to
understand drug response variability and develop effective therapeutics. However, it is …
understand drug response variability and develop effective therapeutics. However, it is …
Quantifying and correcting bias in transcriptional parameter inference from single-cell data
R Grima, PM Esmenjaud - Biophysical Journal, 2024 - cell.com
The snapshot distribution of mRNA counts per cell can be measured using single-molecule
fluorescence in situ hybridization or single-cell RNA sequencing. These distributions are …
fluorescence in situ hybridization or single-cell RNA sequencing. These distributions are …
Inferring delays in partially observed gene regulation processes
Motivation Cell function is regulated by gene regulatory networks (GRNs) defined by protein-
mediated interaction between constituent genes. Despite advances in experimental …
mediated interaction between constituent genes. Despite advances in experimental …
Density physics-informed neural networks reveal sources of cell heterogeneity in signal transduction
The transduction time between signal initiation and final response provides valuable
information on the underlying signaling pathway, including its speed and precision …
information on the underlying signaling pathway, including its speed and precision …
Noisy delay denoises biochemical oscillators
Genetic oscillations are generated by delayed transcriptional negative feedback loops,
wherein repressor proteins inhibit their own synthesis after a temporal production delay. This …
wherein repressor proteins inhibit their own synthesis after a temporal production delay. This …
DelaySSAToolkit. jl: stochastic simulation of reaction systems with time delays in Julia
DelaySSAToolkit. jl is a Julia package for modelling reaction systems with non-Markovian
dynamics, specifically those with time delays. These delays implicitly capture multiple …
dynamics, specifically those with time delays. These delays implicitly capture multiple …
Inferring delays in partially observed gene regulatory networks
Motivation Cell function is regulated by gene regulatory networks (GRNs) defined by protein-
mediated interaction between constituent genes. Despite advances in experimental …
mediated interaction between constituent genes. Despite advances in experimental …
Bayesian Inference and Information Learning for Switching Nonlinear Gene Regulatory Networks
NL Vélez-Cruz - 2023 - search.proquest.com
This dissertation centers on the development of Bayesian methods for learning different
types of variation in switching nonlinear gene regulatory networks (GRNs). A new nonlinear …
types of variation in switching nonlinear gene regulatory networks (GRNs). A new nonlinear …
[PDF][PDF] Density Physics-Informed Neural Network reveals sources of cell heterogeneity in signal
The transduction time between signal initiation and final response provides valuable
information on the underlying signaling pathway, including its speed and precision …
information on the underlying signaling pathway, including its speed and precision …
Bayesian inference and modelling of gene expression dynamics
JM Burton - 2023 - search.proquest.com
The regulation of differentiation is essential for the growth and development of living
organisms. Changes in the dynamic expression of certain genes have been associated with …
organisms. Changes in the dynamic expression of certain genes have been associated with …