Cell size distribution of lineage data: analytic results and parameter inference
Recent advances in single-cell technologies have enabled time-resolved measurements of
the cell size over several cell cycles. These data encode information on how cells correct …
the cell size over several cell cycles. These data encode information on how cells correct …
Single-cell stochastic gene expression kinetics with coupled positive-plus-negative feedback
Here we investigate single-cell stochastic gene expression kinetics in a minimal coupled
gene circuit with positive-plus-negative feedback. A triphasic stochastic bifurcation is …
gene circuit with positive-plus-negative feedback. A triphasic stochastic bifurcation is …
A stochastic and dynamical view of pluripotency in mouse embryonic stem cells
Pluripotent embryonic stem cells are of paramount importance for biomedical sciences
because of their innate ability for self-renewal and differentiation into all major cell lines. The …
because of their innate ability for self-renewal and differentiation into all major cell lines. The …
A review of complex systems approaches to cancer networks
A Uthamacumaran - arXiv preprint arXiv:2009.12693, 2020 - arxiv.org
Cancers remain the lead cause of disease-related, pediatric death in North America. The
emerging field of complex systems has redefined cancer networks as a computational …
emerging field of complex systems has redefined cancer networks as a computational …
Squared Wasserstein-2 distance for efficient reconstruction of stochastic differential equations
We provide an analysis of the squared Wasserstein-2 ($ W_2 $) distance between two
probability distributions associated with two stochastic differential equations (SDEs). Based …
probability distributions associated with two stochastic differential equations (SDEs). Based …
Absolutely robust controllers for chemical reaction networks
In this work, we design a type of controller that consists of adding a specific set of reactions
to an existing mass-action chemical reaction network in order to control a target species …
to an existing mass-action chemical reaction network in order to control a target species …
Rare-event sampling of epigenetic landscapes and phenotype transitions
MJ Tse, BK Chu, CP Gallivan… - PLoS computational …, 2018 - journals.plos.org
Stochastic simulation has been a powerful tool for studying the dynamics of gene regulatory
networks, particularly in terms of understanding how cell-phenotype stability and fate …
networks, particularly in terms of understanding how cell-phenotype stability and fate …
[HTML][HTML] Stochastic hybrid models of gene regulatory networks–a pde approach
A widely used approach to describe the dynamics of gene regulatory networks is based on
the chemical master equation, which considers probability distributions over all possible …
the chemical master equation, which considers probability distributions over all possible …
Model reduction methods for population dynamics with fast-switching environments: Reduced master equations, stochastic differential equations, and applications
We study stochastic population dynamics coupled to fast external environments and
combine expansions in the inverse switching rate of the environment and a Kramers–Moyal …
combine expansions in the inverse switching rate of the environment and a Kramers–Moyal …
Generalizing Gillespie's direct method to enable network-free simulations
Gillespie's direct method for stochastic simulation of chemical kinetics is a staple of
computational systems biology research. However, the algorithm requires explicit …
computational systems biology research. However, the algorithm requires explicit …