On time: developmental timing within and across species

J Garcia-Ojalvo, A Bulut-Karslioglu - Development, 2023 - journals.biologists.com
Organisms across species differ in the relative size and complexity of their tissues to serve
the specific purposes of the host. Correct timing is a crucial ingredient in the development of …

Concentration fluctuations in growing and dividing cells: Insights into the emergence of concentration homeostasis

C Jia, A Singh, R Grima - PLoS computational biology, 2022 - journals.plos.org
Intracellular reaction rates depend on concentrations and hence their levels are often
regulated. However classical models of stochastic gene expression lack a cell size …

Coupling gene expression dynamics to cell size dynamics and cell cycle events: Exact and approximate solutions of the extended telegraph model

C Jia, R Grima - Iscience, 2023 - cell.com
The standard model describing the fluctuations of mRNA numbers in single cells is the
telegraph model which includes synthesis and degradation of mRNA, and switching of the …

[HTML][HTML] Modulation of nuclear and cytoplasmic mRNA fluctuations by time-dependent stimuli: Analytical distributions

T Filatova, N Popović, R Grima - Mathematical biosciences, 2022 - Elsevier
Temporal variation of environmental stimuli leads to changes in gene expression. Since the
latter is noisy and since many reaction events occur between the birth and death of an …

Nonlinear dynamics of tumor cell cycles: From mathematical models to therapeutic insights

WZ Liao, HB Zhou, ZY Zhou, BA Guo, RQ Zeng - Nonlinear Science, 2024 - Elsevier
Cellular proliferation, regulated by the cell cycle, assumes a malignant pattern in cancer. We
summarize how nonlinear dynamics and chaos theory shed light on the irregular rhythm of …

Quantification of transcription noise's impact on cell fate commitment with digital resolutions

F Jiao, M Tang - Bioinformatics, 2022 - academic.oup.com
Motivation Gene transcription is a random and noisy process. Tremendous efforts in single-
cell studies have been mapping transcription noises to phenotypic variabilities between …

Mean trapping time for an arbitrary trap site on a class of fractal scale-free trees

L Gao, J Peng, C Tang - Physical Review E, 2022 - APS
Fractals are ubiquitous in nature and random walks on fractals have attracted lots of
scientific attention in the past several years. In this work, we consider discrete random walks …

The dynamics of gene transcription with a periodic synthesis rate

Q Sun, F Jiao, J Yu - Nonlinear Dynamics, 2021 - Springer
The periodic transcription output is ubiquitously observed in an isogenic cell population. To
understand mechanisms of cyclic behavior in transcription, we extend the gene activation …

A novel dynamical regulation of mRNA distribution by cross-talking pathways

Q Sun, Z Cai, C Zhu - Mathematics, 2022 - mdpi.com
In this paper, we use a similar approach to the one proposed by Chen and Jiao to calculate
the mathematical formulas of the generating function V (z, t) and the mass function P m (t) of …

[PDF][PDF] Accuracy and limitations of extrinsic noise models to describe gene expression in growing cells

C Jia, R Grima - bioRxiv, 2022 - researchgate.net
The standard model describing the fluctuations of mRNA numbers in single cells is the
telegraph model which includes synthesis and degradation of mRNA, and switching of the …