Related papers: Dynamics of gene expression under feedback
Extrinsic noise-induced transitions to bimodal dynamics have been largely investigated in a variety of chemical, physical, and biological systems. In the standard approach in physical and chemical systems, the key properties that make these…
A key goal of systems biology is the predictive mathematical description of gene regulatory circuits. Different approaches are used such as deterministic and stochastic models, models that describe cell growth and division explicitly or…
Observation of phenotypic diversity in a population of genetically identical cells is often linked to the stochastic nature of chemical reactions involved in gene regulatory networks. We investigate the distribution of population averaged…
Some genes can promote or repress their own expressions, which is called autoregulation. Although gene regulation is a central topic in biology, autoregulation is much less studied. In general, it is extremely difficult to determine the…
A natural phenomenon occurring in a living system is an outcome of the dynamics of the specific biological network underlying the phenomenon. The collective dynamics have both deterministic and stochastic components. The stochastic nature…
The structure of a stochastic nonlinear gene regulatory network is uncovered by studying its response to input signal generators. Four applications are studied in detail: a nonlinear connection of two linear systems, the design of a logic…
In this work, the dynamics of fluctuations in gene expression time series is investigated. By using collected data of gene expression from yeast and human organisms, we found that the fluctuations of gene expression level and its average…
The different cell types in a living organism acquire their identity through the process of cell differentiation in which the multipotent progenitor cells differentiate into distinct cell types. Experimental evidence and analysis of…
Stochasticity in gene expression gives rise to fluctuations in protein levels across a population of genetically identical cells. Such fluctuations can lead to phenotypic variation in clonal populations, hence there is considerable interest…
Stochastic reaction network models are widely utilized in biology and chemistry to describe the probabilistic dynamics of biochemical systems in general, and gene interaction networks in particular. Most often, statistical analysis and…
In biophysics, the search for analytical solutions of stochastic models of cellular processes is often a challenging task. In recent work on models of gene expression, it was shown that a mapping based on partitioning of Poisson arrivals…
During tissue development, patterns of gene expression determine the spatial arrangement of cell types. In many cases, gradients of secreted signaling molecules - morphogens - guide this process. The continuous positional information…
Auto-regulation, a process wherein a protein negatively regulates its own production, is a common motif in gene expression networks. Negative feedback in gene expression plays a critical role in buffering intracellular fluctuations in…
Genetic circuits need a cellular environment to operate in, which naturally couples the circuit function with the overall functionality of gene regulatory network. To execute their functions all gene circuits draw resources in the form of…
This paper investigates the stochastic fluctuations of the number of copies of a given protein in a cell. This problem has already been addressed in the past and closed-form expressions of the mean and variance have been obtained for a…
In this paper we motivate and develop a model of gene expression for the purpose of studying the interaction between synthetic gene circuits and the chassis cell within which they are in- serted. This model focuses on the translational…
Gene transcription is a stochastic process that involves thousands of reactions. The first set of these reactions, which happen near a gene promoter, are considered to be the most important in the context of stochastic noise. The most…
Elucidating the architecture and dynamics of large scale genetic regulatory networks of cells is an important goal in systems biology. We study the system level dynamical properties of the genetic network of Escherichia coli that regulates…
Stochastic simulation can make the molecular processes of cellular control more vivid than the traditional differential-equation approach by generating typical system histories instead of just statistical measures such as the mean and…
Stochastic dynamics of chemical reactions in a mutually repressing two-gene circuit is numerically simulated. The circuit has a rich variety of different states when the kinetic change of DNA status is slow. The stochastic switching…