Joint distribution of protein concentration and cell volume coupled by feedback in dilution

I Zabaikina, P Bokes, A Singh - International Conference on Computational …, 2023 - Springer
We consider a protein that negatively regulates the rate with which a cell grows. Since less
growth means less protein dilution, this mechanism forms a positive feedback loop on the …

Modeling bursty transcription and splicing with the chemical master equation

G Gorin, L Pachter - Biophysical Journal, 2022 - cell.com
Splicing cascades that alter gene products posttranscriptionally also affect expression
dynamics. We study a class of processes and associated distributions that emerge from …

Artificial neural network modeling of systems biology datasets fit based on Mittag-Leffler functions with heavy-tailed distributions for diagnostic and predictive precision …

Y Karaca, D Baleanu - Multi-Chaos, Fractal and Multi-Fractional Artificial …, 2022 - Elsevier
Being the most complex physical system in the universe, life, at all scales requires the
understanding of the massive complexity including its origin, structure, dynamic, adaptation …

Optimisation of gene expression noise for cellular persistence against lethal events

P Bokes, A Singh - Journal of Theoretical Biology, 2025 - Elsevier
Bacterial cell persistence, crucial for survival under adverse conditions like antibiotic
exposure, is intrinsically linked to stochastic fluctuations in gene expression. Certain genes …

The impossible challenge of estimating non-existent moments of the Chemical Master Equation

V Wagner, N Radde - Bioinformatics, 2023 - academic.oup.com
Abstract Motivation The Chemical Master Equation (CME) is a set of linear differential
equations that describes the evolution of the probability distribution on all possible …

Reversible transitions in a fluctuation assay modify the tail of luria–delbrück distribution

P Bokes, A Hlubinová, A Singh - Axioms, 2023 - mdpi.com
We consider a fluctuation test experiment in which cell colonies were grown from a single
cell until they reach a given population size and were then exposed to treatment. While they …

On the Solution to the Kolmogorov-Feller Equation Arising in a Biological Evolution Model

OS Rozanova - Moscow University Mathematics Bulletin, 2023 - Springer
Abstract The paper considers Kolmogorov–Feller equation for the probability density of a
Markov process on a half-axis, which arises in important problems of biology. This process …

Hysteresis and noise floor in gene expression optimised for persistence against lethal events

P Bokes, A Singh - bioRxiv, 2024 - biorxiv.org
Bacterial cell persistence, crucial for survival under adverse conditions like antibiotic
exposure, is intrinsically linked to stochastic fluctuations in gene expression. Certain genes …

Exact and WKB-approximate distributions in a gene expression model with feedback in burst frequency, burst size, and protein stability

P Bokes - bioRxiv, 2020 - biorxiv.org
The expression of individual genes into functional protein molecules is a noisy dynamical
process. Here we model the protein concentration as a jump-drift process which combines …

[HTML][HTML] О решении уравнения Колмогорова–Феллера, возникающего в модели биологической эволюции

ОС Розанова - Вестник Московского университета. Серия 1 …, 2023 - cyberleninka.ru
Рассмотрено уравнение Колмогорова–Феллера, описывающее плотность марковского
процесса на полуоси, возникающего в важных задачах биологии. Этот процесс состоит …