148 citations · 747 across the 25 of their papers we have counts for
5 papers · 1 filter
Non-equilibrium chromosome looping via molecular slip-links
C. A. Brackley, J. Johnson, D. Michieletto +4
We propose a model for the formation of chromatin loops based on the diffusive sliding of a DNA-bound factor which can dimerise to form a molecular slip-link. Our slip-links mimic…
A Single Nucleotide Resolution Model for Large-Scale Simulations of Double Stranded DNA
Y. A. G. Fosado, D. Michieletto, J. Allan +3
The computational modelling of DNA is becoming crucial in light of new advances in DNA nanotechnology, single-molecule experiments and in vivo DNA tampering. Here we present a meso…
Ephemeral protein binding to DNA shapes stable nuclear bodies and chromatin domains
C. A. Brackley, B. Liebchen, D. Michieletto +3
Fluorescence microscopy reveals that the contents of many (membrane-free) nuclear "bodies" exchange rapidly with the soluble pool whilst the underlying structure persists; such obs…
A stochastic model of supercoiling-dependent transcription
C. A. Brackley, J. Johnson, A. Bentivoglio +4
We propose a stochastic model for gene transcription coupled to DNA supercoiling, where we incorporate the experimental observation that polymerases create supercoiling as they unw…
Predicting the three-dimensional folding of cis-regulatory regions in mammalian genomes using bioinformatic data and polymer models
Chris A Brackley, Jill M Brown, Dominic Waithe +5
The three-dimensional organisation of chromosomes can be probed using methods such as Capture-C. However it is unclear how such population level data relates to the organisation wi…