Related papers: Discrete gene replication events drive coupling be…
Biochemical oscillation systems often consist of negative feedback loops with repressive transcription regulation. Such systems have distinctive characteristics in comparison with ordinary chemical systems: i) the numbers of molecules…
Cellular populations are typically heterogenous collections of cells at different points in their respective cell cycles, each with a cell cycle time that varies from individual to individual. As a result, true single-cell behavior,…
The time taken for gene expression varies not least because proteins vary in length considerably. This paper uses an abstract, tuneable Boolean regulatory network model to explore gene expression time variation. In particular, it is shown…
Molecular clock (MC) is a central concept of molecular evolution according to which each gene evolves at a characteristic, near constant rate. Numerous evolutionary studies have demonstrated the validity of MC but also have shown that MC is…
Motivation: Alternative splicing is an important mechanism in which the regions of pre-mRNAs are differentially joined in order to form different transcript isoforms. Alternative splicing is involved in the regulation of normal…
The cosinor model is frequently used to represent the oscillatory behavior of different genes over time. When data are collected from multiple individuals, the cosinor model is estimated with recorded gene expression levels and the 24 hour…
The epigenetic pathway of a cell as it differentiates from a stem cell state to a mature lineage-committed one has been historically understood in terms of Waddington's landscape, consisting of hills and valleys. The smooth top and…
A dynamical mean-field theory is developed to analyze stochastic single-cell dynamics of gene expression. By explicitly taking account of nonequilibrium and nonadiabatic features of the DNA state fluctuation, two-time correlation functions…
Cells receive a wide variety of cellular and environmental signals, which must be processed combinatorially to generate specific and timely genetic responses. We present here a theoretical study on the combinatorial control and integration…
DNA amplification is the process of replication of a specified DNA sequence \emph{in vitro} through time-dependent manipulation of its external environment. A theoretical framework for determination of the optimal dynamic operating…
The number of fixed mutations accumulated in an evolving population often displays a variance that is significantly larger than the mean (the overdispersed molecular clock). By examining a generic evolutionary process on a neutral network…
Almost all organisms show some kind of time periodicity in their behavior. Especially in mammals the neurons of the suprachiasmatic nucleus form a biological clock regulating the activity-inactivity cycle of the animal. This clock is…
This paper presents an intracellular feedback control strategy, to regulate the gene expression process dynamics. For this purpose, two types of genetic circuits are designed in order to compare concentrations of the input transcription…
Collective oscillation of cells in a population has been reported under diverse biological contexts and with vastly different molecular constructs. Could there be common principles similar to those that govern spontaneous oscillation in…
Cytoskeletal crowding plays a key role in the diffusion of DNA molecules through the cell, acting as a barrier to effective intracellular transport and conformational stability required for such processes as transfection, viral infection,…
During organismal development, biochemical reaction networks sense and respond to mechanical forces to coordinate embryonic patterning with embryo morphogenesis. Factors such as cortical tension, cell density, and matrix mechanical…
Conformational change of a DNA molecule is frequently observed in multiple biological processes and has been modelled using a chain of strongly coupled oscillators with a nonlinear bistable potential. While the mechanism and properties of…
Using an analytically solvable stochastic model, we study the properties of a simple genetic circuit consisting of multiple copies of an self-regulating gene. We analyse how the variation in gene copy number and the mutations changing the…
In cellular reprogramming, almost all epigenetic memories of differentiated cells are erased by the overexpression of few genes, regaining pluripotency, potentiality for differentiation. Considering the interplay between oscillatory gene…
We present a model of the evolution of control systems in a genome under environmental constraints. The model conceptually follows the Jacob and Monod model of gene control. Genes contain control elements which respond to the internal state…