Transcriptional bursting: stochasticity in deterministic development
EA Leyes Porello, RT Trudeau, B Lim - Development, 2023 - journals.biologists.com
The transcription of DNA by RNA polymerase occurs as a discontinuous process described
as transcriptional bursting. This bursting behavior is observed across species and has been …
as transcriptional bursting. This bursting behavior is observed across species and has been …
Solving stochastic gene expression models using queueing theory: a tutorial review
J Szavits-Nossan, R Grima - arXiv preprint arXiv:2307.03253, 2023 - arxiv.org
Stochastic models of gene expression are typically formulated using the chemical master
equation, which can be solved exactly or approximately using a repertoire of analytical …
equation, which can be solved exactly or approximately using a repertoire of analytical …
Stochastic modeling of the mRNA life process: A generalized master equation
C Shi, X Yang, J Zhang, T Zhou - Biophysical Journal, 2023 - cell.com
The mRNA life cycle is a complex biochemical process, involving transcription initiation,
elongation, termination, splicing, and degradation. Each of these molecular events is …
elongation, termination, splicing, and degradation. Each of these molecular events is …
[HTML][HTML] Analysis of a detailed multi-stage model of stochastic gene expression using queueing theory and model reduction
We introduce a biologically detailed, stochastic model of gene expression describing the
multiple rate-limiting steps of transcription, nuclear pre-mRNA processing, nuclear mRNA …
multiple rate-limiting steps of transcription, nuclear pre-mRNA processing, nuclear mRNA …
Phase separation provides a mechanism to drive phenotype switching
L Hong, Z Zhang, Z Wang, X Yu, J Zhang - Physical Review E, 2024 - APS
Phenotypic switching plays a crucial role in cell fate determination across various
organisms. Recent experimental findings highlight the significance of protein …
organisms. Recent experimental findings highlight the significance of protein …
The asynchrony in the exit from naive pluripotency cannot be explained by differences in the cell cycle phase
Development is characterized by consecutive cell state transitions that build on each other
and ultimately lead to the generation of the numerous different cell types found in the …
and ultimately lead to the generation of the numerous different cell types found in the …
Solving stochastic gene expression models using queueing theory: a tutorial review
J Szavits-Nossan, R Grima - Biophysical Journal, 2024 - cell.com
Stochastic models of gene expression are typically formulated using the chemical master
equation, which can be solved exactly or approximately using a repertoire of analytical …
equation, which can be solved exactly or approximately using a repertoire of analytical …
Molecular-Memory-Induced Counter-Intuitive Noise Attenuator in Protein Polymerization
X Bai, S Wang, X Zhang, H Wang - Symmetry, 2024 - mdpi.com
Gene expression comprises many asymmetric and complex processes. Transcriptional
details revealed by the whole genome indicate that genes resort to transcriptional bursting …
details revealed by the whole genome indicate that genes resort to transcriptional bursting …
Neuronal phenotype defined by transcriptome-wide bursting kinetics in pyramidal and fast-spiking cells
Single-cell sequencing revealed the transcriptional heterogeneity of neurons and introduced
transcriptome-defined neuron types and subtypes. Temporal recordings of gene …
transcriptome-defined neuron types and subtypes. Temporal recordings of gene …
Nascent RNA kinetics with complex promoter architecture: Analytic results and parameter inference
C Shi, X Yang, T Zhou, J Zhang - bioRxiv, 2023 - biorxiv.org
The stochastic kinetics of transcription can be accurately inferred from the distribution of
nascent RNA. However, the inferences using conventional gene-expression models with …
nascent RNA. However, the inferences using conventional gene-expression models with …