Stochastic timing in gene expression for simple regulatory strategies

AD Co, MC Lagomarsino, M Caselle… - Nucleic acids …, 2017 - academic.oup.com
Timing is essential for many cellular processes, from cellular responses to external stimuli to
the cell cycle and circadian clocks. Many of these processes are based on gene expression …

First-passage time approach to controlling noise in the timing of intracellular events

KR Ghusinga, JJ Dennehy… - Proceedings of the …, 2017 - National Acad Sciences
In the noisy cellular environment, gene products are subject to inherent random fluctuations
in copy numbers over time. How cells ensure precision in the timing of key intracellular …

Delay-induced stochastic oscillations in gene regulation

D Bratsun, D Volfson, LS Tsimring… - Proceedings of the …, 2005 - National Acad Sciences
The small number of reactant molecules involved in gene regulation can lead to significant
fluctuations in intracellular mRNA and protein concentrations, and there have been …

[HTML][HTML] Stochasticity in transcriptional regulation: origins, consequences, and mathematical representations

TB Kepler, TC Elston - Biophysical journal, 2001 - cell.com
Transcriptional regulation is an inherently noisy process. The origins of this stochastic
behavior can be traced to the random transitions among the discrete chemical states of …

The ups and downs of biological timers

N Rappaport, S Winter, N Barkai - Theoretical Biology and Medical …, 2005 - Springer
Background The need to execute a sequence of events in an orderly and timely manner is
central to many biological processes, including cell cycle progression and cell …

A stochastic vs deterministic perspective on the timing of cellular events

L Ham, MA Coomer, K Öcal, R Grima… - Nature …, 2024 - nature.com
Cells are the fundamental units of life, and like all life forms, they change over time. Changes
in cell state are driven by molecular processes; of these many are initiated when molecule …

First-passage time calculations for a gene expression model

KR Ghusinga, A Singh - 53rd IEEE Conference on Decision …, 2014 - ieeexplore.ieee.org
The stochastic nature of gene expression can lead to significant cell-to-cell variability in the
time at which a certain protein level is attained. This is reflected in the timing of cellular …

Stochastic delay accelerates signaling in gene networks

K Josić, JM López, W Ott, LJ Shiau… - PLoS computational …, 2011 - journals.plos.org
The creation of protein from DNA is a dynamic process consisting of numerous reactions,
such as transcription, translation and protein folding. Each of these reactions is further …

Delays induce novel stochastic effects in negative feedback gene circuits

E Zavala, TT Marquez-Lago - Biophysical journal, 2014 - cell.com
Stochastic models of reaction networks are widely used to depict gene expression
dynamics. However, stochastic does not necessarily imply accurate, as subtle assumptions …

Reliability of frequency and amplitude decoding in gene regulation

F Tostevin, W de Ronde, PR Ten Wolde - Physical Review Letters, 2012 - APS
In biochemical signaling, information is often encoded in oscillatory signals. However, the
advantages of such a coding strategy over an amplitude-encoding scheme of constant …