Non-genetic heterogeneity of cells in development: more than just noise

S Huang - Development, 2009 - journals.biologists.com
Cell-to-cell variability of gene expression in clonal populations of mammalian cells is
ubiquitous. However, because molecular biologists habitually assume uniformity of the cell …

[HTML][HTML] Noise distorts the epigenetic landscape and shapes cell-fate decisions

MA Coomer, L Ham, MPH Stumpf - Cell Systems, 2022 - cell.com
The Waddington epigenetic landscape has become an iconic representation of the cellular
differentiation process. Recent single-cell transcriptomic data provide new opportunities for …

Kinetic models of gene expression including non-coding RNAs

VP Zhdanov - Physics Reports, 2011 - Elsevier
In cells, genes are transcribed into mRNAs, and the latter are translated into proteins. Due to
the feedbacks between these processes, the kinetics of gene expression may be complex …

[HTML][HTML] Cell-to-cell variability in the propensity to transcribe explains correlated fluctuations in gene expression

MS Sherman, K Lorenz, MH Lanier, BA Cohen - Cell systems, 2015 - cell.com
Random fluctuations in gene expression lead to wide cell-to-cell differences in RNA and
protein counts. Most efforts to understand stochastic gene expression focus on local …

Lévy noise induced switch in the gene transcriptional regulatory system

Y Xu, J Feng, JJ Li, H Zhang - Chaos: An Interdisciplinary Journal of …, 2013 - pubs.aip.org
The study of random fluctuations in a gene transcriptional regulatory system is extended to
the case of non-Gaussian Lévy noise, which can describe unpredictable jump changes of …

Stochastic dynamics driven by combined Lévy–Gaussian noise: fractional Fokker–Planck–Kolmogorov equation and solution

W Zan, Y Xu, J Kurths, AV Chechkin… - Journal of Physics A …, 2020 - iopscience.iop.org
Starting with a stochastic differential equation driven by combined Gaussian and Lévy noise
terms we determine the associated fractional Fokker–Planck–Kolmogorov equation …

[图书][B] Simple mathematical models of gene regulatory dynamics

We survey work that has been carried out in the attempts of biomathematicians to
understand the dynamic behavior of simple bacterial operons starting with the initial work of …

A computational framework for analyzing stochasticity in gene expression

MS Sherman, BA Cohen - PLoS computational biology, 2014 - journals.plos.org
Stochastic fluctuations in gene expression give rise to distributions of protein levels across
cell populations. Despite a mounting number of theoretical models explaining stochasticity …

Strand-Specific RNA-Seq Reveals Ordered Patterns of Sense and Antisense Transcription in Bacillus anthracis

KD Passalacqua, A Varadarajan, C Weist, BD Ondov… - 2012 - journals.plos.org
Background Although genome-wide transcriptional analysis has been used for many years
to study bacterial gene expression, many aspects of the bacterial transcriptome remain …

Adiabatic reduction of a model of stochastic gene expression with jump Markov process

R Yvinec, C Zhuge, J Lei, MC Mackey - Journal of mathematical biology, 2014 - Springer
This paper considers adiabatic reduction in a model of stochastic gene expression with
bursting transcription considered as a jump Markov process. In this model, the process of …