Related papers: Stochastic modeling of gene expression, protein mo…
For cellular biochemical reaction systems where the numbers of molecules is small, significant noise is associated with chemical reaction events. This molecular noise can give rise to behavior that is very different from the predictions of…
The bulk of stochastic gene expression models in the literature do not have an explicit description of the age of a cell within a generation and hence they cannot capture events such as cell division and DNA replication. Instead, many…
How to induce differentiated cells into pluripotent cells has elicited researchers' interests for a long time since pluripotent stem cells are able to offer remarkable potential in numerous subfields of biological research. However, the…
Intrinsic transcriptional noise induced by operator fluctuations is investigated with a simple spin like stochastic model. The effects of transcriptional fluctuations in protein synthesis is probed by coupling transcription and translation…
In a multicellular organism different cell types express a gene in different amounts. Samples from which gene expression levels can be measured typically contain a mixture of different cell types, the resulting measurements thus give only…
A general theoretical framework is put forth to organize and understand various observed phenomena and mathematical relationships in the field of molecular biology. By modeling each cell in eukaryotic organisms as a processor having a…
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…
Stochastic modeling of gene expression is a classic problem in theoretical biophysics, and the burst approximation is widely used to simplify gene expression models formulated via the chemical master equation. However, the approximation…
Telomeres are repetitive sequences of nucleotides at the end of chromosomes, whose evolution over time is intrinsically related to biological ageing. In most cells, with each cell division, telomeres shorten due to the so-called end…
Replication of genetic material is an important process for all living organisms. Origins of replication initiate the copying of DNA at many points on a chromosome, and it is the distribution of these points that is relevant here, as it…
We show how one may analytically compute the stationary density of the distribution of molecular constituents in populations of cells in the presence of noise arising from either bursting transcription or translation, or noise in…
This chapter provides a brief introduction to the theory and practice of spatial stochastic simulations. It begins with an overview of different methods available for biochemical simulations highlighting their strengths and limitations.…
We illustrate the use of tools (asymptotic theories of standard error quantification using appropriate statistical models, bootstrapping, model comparison techniques) in addition to sensitivity that may be employed to determine the…
Cells exhibit a wide variety of different shapes. This diversity poses a challenge for computational approaches that attempt to shed light on the role cell geometry plays in regulating cell physiology and behavior. The simulation platform…
The genetic blueprint for the essential functions of life is encoded in DNA, which is translated into proteins -- the engines driving most of our metabolic processes. Recent advancements in genome sequencing have unveiled a vast diversity…
In this paper we introduce a general stochastic representation for an important class of processes with resetting. It allows to describe any stochastic process intermittently terminated and restarted from a predefined random or non-random…
An important occurrence in many cellular contexts is the crossing of a prescribed threshold by a regulatory protein. The timing of such events is stochastic as a consequence of the innate randomness in gene expression. A question of…
Cell polarity refers to the spatial asymmetry of molecules on the cell membrane. Altschuler, Angenent, Wang and Wu have proposed a stochastic model for studying the emergence of polarity in the presence of feedback between molecules. We…
A practical introduction to stochastic modelling of reaction-diffusion processes is presented. No prior knowledge of stochastic simulations is assumed. The methods are explained using illustrative examples. The article starts with the…
We seek models for the genotype evolution of agricultural animals, animals involved in primary production processes. Classical models for genotype evolution have tended to be very simple in order that analytic methods may be employed in…