Related papers: Phenotypic Heterogeneity in Mycobacterial Stringen…
We develop a model for speciation due to postzygotic incompatibility generated by autoimmune reactions. The model is based on predator-prey interactions between a host plants and their pathogens. Such interactions are often…
We study a stochastic model of biosynthesis of proteins in generic bacterial operons. The stochasticity arises from two different processes, namely from `bursting' production of either mRNA and/or protein (in the transcription/translation…
Phenotype-switching with and without sensing environment is a ubiquitous strategy of organisms to survive in fluctuating environment. Fitness of a population of organisms with phenotype-switching may be constrained and restricted by hidden…
In the context of multistability driven diseases, like cancer, spatiotemporal plasticity plays a significant role to achieve a spectrum of phenotypic variations. The interplay between gene regulatory networks and environmental factors, such…
We introduce a biologically detailed, stochastic model of gene expression describing the multiple rate-limiting steps of transcription, nuclear pre-mRNA processing, nuclear mRNA export, cytoplasmic mRNA degradation and translation of mRNA…
Recent experiments at the level of a single cell have shown that gene expression occurs in abrupt stochastic bursts. Further, in an ensemble of cells, the levels of proteins produced have a bimodal distribution. In a large fraction of…
Quantitative genetic studies that model complex, multivariate phenotypes are important for both evolutionary prediction and artificial selection. For example, changes in gene expression can provide insight into developmental and…
Many types of bacteria can survive under stress by switching stochastically between two different phenotypes: the "normals" who multiply fast, but are vulnerable to stress, and the "persisters" who hardly multiply, but are resilient to…
Cellular responses often require the fast activation or repression of specific genes, which depends on Transcription Factors (TFs) that have to quickly find the promoters of these genes within a large genome. Transcription Factors (TFs)…
We present an algorithm for the stochastic simulation of gene expression and heterogeneous population dynamics. The algorithm combines an exact method to simulate molecular-level fluctuations in single cells and a constant-number Monte…
Organisms adapt to fluctuating environments by regulating their dynamics, and by adjusting their phenotypes to environmental changes. We model population growth using multitype branching processes in random environments, where the offspring…
Living species, ranging from bacteria to animals, exist in environmental conditions that exhibit spatial and temporal heterogeneity which requires them to adapt. Risk-spreading through spontaneous phenotypic variations is a known concept in…
Transcription is regulated through binding factors to gene promoters to activate or repress expression, however, the mechanisms by which factors find targets remain unclear. Using single-molecule fluorescence microscopy, we determined in…
Motivation: The discovery of relationships between gene expression measurements and phenotypic responses is hampered by both computational and statistical impediments. Conventional statistical methods are less than ideal because they either…
This paper addresses the question of optimal phenotypic plasticity as a response to environmental fluctuations while optimizing the cost/benefit ratio, where the cost is energetic expense of plasticity, and benefit is fitness. The…
Gene products (RNAs, proteins) often occur at low molecular counts inside individual cells, and hence are subject to considerable random fluctuations (noise) in copy number over time. Not surprisingly, cells encode diverse regulatory…
We consider a reaction-diffusion system with discontinuous reaction terms modeled by non-ideal relays. The system is motivated by an epigenetic population model of evolution of two-phenotype bacteria which switch phenotype in response to…
Background: Continuous traits evolution of a group of taxa that are correlated through a phylogenetic tree is commonly modelled using parametric stochastic differential equations to represent deterministic change of trait through time,…
Statistical fluctuations in population sizes of microbes may be quite large depending on the nature of their underlying stochastic dynamics. For example, the variance of the population size of a microbe undergoing a pure birth process with…
The dynamics of gene regulatory networks are often modeled with the assumption of cellular homogeneity. However, this assumption contradicts the plethora of experimental results in a variety of systems, which designates that cell…