65 citations · 65 across the 2 of their papers we have counts for
6 papers · 1 filter
Polymer Modelling Predicts Chromosome Reorganisation in Senescence
Michael Chiang, Davide Michieletto, Chris A. Brackley +4
Lamina-associated domains (LADs) cover a large part of the human genome and are thought to play a major role in shaping the nuclear architectural landscape. Here, we perform polyme…
Simulating topological domains in human chromosomes with a fitting-free model
C. A. Brackley, D. Michieletto, F. Mouvet +4
We discuss a polymer model for the 3D organization of human chromosomes. A chromosome is represented by a string of beads, with each bead being "colored" according to 1D bioinforma…
Mechanistic Modelling of Chromatin Folding to Understand Function
Chris A. Brackley, Davide Marenduzzo, Nick Gilbert
Experimental approaches have been applied to address questions in understanding three-dimensional chromatin organisation and function. As datasets increase in size and complexity,…
Extrusion without a motor: a new take on the loop extrusion model of genome organization
C. A. Brackley, J. Johnson, D. Michieletto +4
Chromatin loop extrusion is a popular model for the formation of CTCF loops and topological domains. Recent HiC data have revealed a strong bias in favour of a particular arrangeme…
Transcriptional bursts in a non-equilibrium model for gene regulation by supercoiling
Marco Ancona, Alessandro Bentivoglio, Chris A. Brackley +2
We analyse transcriptional bursting within a stochastic non-equilibrium model which accounts for the coupling between the dynamics of DNA supercoiling and gene transcription. We fi…
Facilitated diffusion on mobile DNA: configurational traps and sequence heterogeneity
C. A. Brackley, M. E. Cates, D. Marenduzzo
We present Brownian dynamics simulations of the facilitated diffusion of a protein, modelled as a sphere with a binding site on its surface, along DNA, modelled as a semi-flexible…