Related papers: Theory for stability and regulation of epigenetic …
Stem cell heterogeneity is essential for the homeostasis in tissue development. This paper established a general formulation for understanding the dynamics of stem cell regeneration with cell heterogeneity and random transitions of…
In evolution, the effects of a single deleterious mutation can sometimes be compensated for by a second mutation which recovers the original phenotype. Such epistatic interactions have implications for the structure of genome space -…
We investigate the dynamics of cellular solidification patterns using three-dimensional phase-field simulations. The cells can organize into stable hexagonal patterns or exhibit unsteady evolutions. We identify the relevant secondary…
Boolean networks have been proposed as potentially useful models for genetic control. An important aspect of these networks is the stability of their dynamics in response to small perturbations. Previous approaches to stability have assumed…
Epistasis describes the phenomenon that mutations at different loci do not have independent effects with regard to certain phenotypes. Understanding the global epistatic landscape is vital for many genetic and evolutionary theories. Current…
Reversibility of state transitions is intensively studied topic in many scientific disciplines over many years. In cell biology, it plays an important role in epigenetic variation of phenotypes, known as phenotypic plasticity. More…
Quantifying stochastic processes is essential to understand many natural phenomena, particularly in biology, including cell-fate decision in developmental processes as well as genesis and progression of cancers. While various attempts have…
In this paper, we consider a system of partial differential equations modeling the evolution of a landscape. A ground surface is eroded by the flow of water over it, either by sedimentation or dilution. The system is composed by three…
The cell cycle duration is a variable cellular phenotype that underlies long-term population growth and age structures. By analyzing the stationary solutions of a branching process with heritable cell division times, we demonstrate…
The theory of complex networks and of disordered systems is used to study the stability and dynamical properties of a simple model of material flow networks defined on random graphs. In particular we address instabilities that are…
Genetically identical cells in the same population can take on phenotypically variable states, leading to differentiated responses to external signals, such as nutrients and drug-induced stress. Many models and experiments have focused on a…
There has been a long-standing and at times fractious debate whether complex and large systems can be stable. In ecology, the so-called `diversity-stability debate' arose because mathematical analyses of ecosystem stability were either…
Statistical physics provides a useful perspective for the analysis of many complex systems; it allows us to relate microscopic fluctuations to macroscopic observations. Developmental biology, but also cell biology more generally, are…
Understanding how gene regulatory networks (GRNs) give rise to stable and dynamic cellular states remains a central challenge in theoretical biology, particularly when slow epigenetic feedback reshapes the underlying regulatory landscape.…
We propose a new procedure to monitor and forecast the onset of transitions in high dimensional complex systems. We describe our procedure by an application to the Tangled Nature model of evolutionary ecology. The quasi-stable…
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-transitions are impacted by noisy gene expression. However,…
We propose a class of evolutionary models that involves an arbitrary exchangeable process as the breeding process and different selection schemes. In those models, a new genome is born according to the breeding process, and then a genome is…
Molecular phenotypes are important links between genomic information and organismic functions, fitness, and evolution. Complex phenotypes, which are also called quantitative traits, often depend on multiple genomic loci. Their evolution…
Robustness to mutations and noise has been shown to evolve through stabilizing selection for optimal phenotypes in model gene regulatory networks. The ability to evolve robust mutants is known to depend on the network architecture. How do…
We study a stochastic model proposed recently in the genetic literature to explain the heterogeneity of cell populations or of gene products. Cells are located in two colonies, whose sizes fluctuate as birth and migration processes in…