Related papers: A stochastic model of supercoiling-dependent trans…
Transcription factors (TFs) are key regulators of gene expression. Based on the classical scenario in which the TF search process switches between one-dimensional motion along the DNA molecule and free Brownian motion in the nucleus, we…
Proteins are polymerized by cyclic machines called ribosome which use their messenger RNA (mRNA) track also as the corresponding template and the process is called translation. We explore, in depth and detail, the stochastic nature of the…
The well-known issue of reconstructing regulatory networks from gene expression measurements has been somewhat disrupted by the emergence and rapid development of single-cell data. Indeed, the traditional way of seeing a gene regulatory…
The recent advancement of spatial transcriptomics (ST) allows to characterize spatial gene expression within tissue for discovery research. However, current ST platforms suffer from low resolution, hindering in-depth understanding of…
We present computer-assisted methods for analyzing stochastic models of gene regulatory networks. The main idea that underlies this equation-free analysis is the design and execution of appropriately-initialized short bursts of stochastic…
Spatial transcriptomics data analysis integrates cellular transcriptional activity with spatial coordinates to identify spatial domains, infer cell-type dynamics, and characterize gene expression patterns within tissues. Despite recent…
The regulation of a gene depends on the binding of transcription factors to specific sites located in the regulatory region of the gene. The generation of these binding sites and of cooperativity between them are essential building blocks…
A unified model is constructed to study the recently observed DNA entropic elasticity, cooperative extensibility, and supercoiling property. With the introduction of a new structural parameter (the folding angle $\phi$), bending…
We examine immunostaining experimental data for the formation of the strip 2 of $even-skipped$ ($eve$) transcripts on $D.$ $melanogaster$ embryos. An estimate of the factor converting immunofluorescence intensity units into molecular…
In mechanical manipulation experiments, a single DNA molecule overwound at constant force undergoes a discontinuous drop in extension as it buckles and forms a superhelical loop (a plectoneme). Further overwinding the DNA, we observe an…
DNA and other biopolymers differ from classical polymers due to their torsional stiffness. This property changes the statistical character of their conformations under tension from a classical random walk to a problem we call the `torsional…
We study several Fokker-Planck equations arising from a stochastic chemical kinetic system modeling a gene regulatory network in biology. The densities solving the Fokker-Planck equations describe the joint distribution of the messenger RNA…
We study the most probable trajectories of the concentration evolution for the transcription factor activator in a genetic regulation system, with non-Gaussian stable L\'evy noise in the synthesis reaction rate taking into account. We…
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…
We propose a stochastic method to generate exactly the overdamped Langevin dynamics of semi-flexible Gaussian chains, conditioned to evolve between given initial and final conformations in a preassigned time. The initial and final…
Gene regulation is a complex process involving the role of several genomic elements which work in concert to drive spatio-temporal expression. The experimental characterization of gene regulatory elements is a very complex and…
We study a stochastic model of gene expression, in which protein production has a form of random bursts whose size distribution is arbitrary, whereas protein decay is a first-order reaction. We find exact analytical expressions for the time…
DNA torsion dynamics is essential in the transcription process; a simple model for it, in reasonable agreement with experimental observations, has been proposed by Yakushevich (Y) and developed by several authors; in this, the DNA subunits…
This study introduces a novel theoretical framework, the Stacked Autoencoder Evolution Hypothesis, which proposes that biological evolutionary systems operate through multi-layered self-encoding and decoding processes, analogous to stacked…
We analyst in detail a new approach to the monitoring and forecasting of the onset of transitions in high dimensional complex systems (see Phys. Rev. Lett . vol. 113, 264102 (2014)) by application to the Tangled Nature Model of evolutionary…