Pyecolib: a python library for simulating stochastic cell size dynamics

C Nieto, SC Blanco, C Vargas-García, A Singh… - Physical …, 2023 - iopscience.iop.org
Recently, there has been an increasing need for tools to simulate cell size regulation due to
important applications in cell proliferation and gene expression. However, implementing the …

Efficient computation of stochastic cell-size transient dynamics

CA Nieto-Acuna, CA Vargas-Garcia, A Singh… - BMC …, 2019 - Springer
Background How small, fast-growing bacteria ensure tight cell-size distributions remains
elusive. High-throughput measurement techniques have propelled efforts to build modeling …

PyEcoLib: a python library for simulating E. coli stochastic size dynamics

C Blanco, C Nieto, C Vargas, J Pedraza - bioRxiv, 2020 - biorxiv.org
Recent studies describe bacterial division as a jump process triggered when it reaches a
fixed number of stochastic discrete events at a rate depending on the cell-size. This …

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 …

Predicting stochastic gene expression dynamics in single cells

JT Mettetal, D Muzzey, JM Pedraza… - Proceedings of the …, 2006 - National Acad Sciences
Fluctuations in protein numbers (noise) due to inherent stochastic effects in single cells can
have large effects on the dynamic behavior of gene regulatory networks. Although …

Relevant parameters in models of cell division control

J Grilli, M Osella, AS Kennard, MC Lagomarsino - Physical Review E, 2017 - APS
A recent burst of dynamic single-cell data makes it possible to characterize the stochastic
dynamics of cell division control in bacteria. Different models were used to propose specific …

Intrinsic and extrinsic noise of gene expression in lineage trees

P Thomas - Scientific reports, 2019 - nature.com
Cell-to-cell heterogeneity is driven by stochasticity in intracellular reactions and the
population dynamics. While these sources are usually studied separately, we develop an …

A mechanistic stochastic framework for regulating bacterial cell division

KR Ghusinga, CA Vargas-Garcia, A Singh - Scientific reports, 2016 - nature.com
How exponentially growing cells maintain size homeostasis is an important fundamental
problem. Recent single-cell studies in prokaryotes have uncovered the adder principle …

Concentration fluctuations due to size-dependent gene expression and cell-size control mechanisms

C Jia, A Singh, R Grima - BioRxiv, 2021 - biorxiv.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 …

Stochastic Models for Population Dynamics

SX Sun - bioRxiv, 2015 - biorxiv.org
Cell growth and division are stochastic processes that exhibit significant amount of cell-to-
cell variation and randomness. In order to connect single cell division dynamics with overall …