187 citations
Counting papers with at most 25 authors, so collaboration author lists do not stand in for the people here.
- University of EdinburghGB14 papers
- Institute of Genetics and CancerGB12 papers
- University of BathGB4 papers
- The Alan Turing InstituteGB2 papers
- Western General HospitalGB2 papers
- Aoyama Gakuin UniversityJP1 paper
- Delft University of TechnologyNL1 paper
- Hausdorff Center for MathematicsDE1 paper
- Institute of Science and Technology AustriaAT1 paper
- Istituto Nazionale di Fisica Nucleare, Sezione di BariIT1 paper
- Karolinska InstitutetSE1 paper
- Laboratoire de Physique Théorique et Modèles StatistiquesFR1 paper
14 papers
Fluidification of Entangled Polymers by Loop Extrusion
Filippo Conforto, Yair Augusto Gutierrez Fosado, Davide Michieletto
Loop extrusion is one of the main processes shaping chromosome organisation across the cell cycle, yet its role in regulating DNA entanglement and nucleoplasm viscoelasticity remai…
Runaway Transition in Irreversible Polymer Condensation with Cyclisation
Maria Panoukidou, Simon Weir, Valerio Sorichetti +3
The process of polymer condensation, i.e. the formation of bonds between reactive end-groups, is ubiquitous in both industry and biology. Here we study generic systems undergoing p…
Higher-order interactions in statistical physics and machine learning: A model-independent solution to the inverse problem at equilibrium
Sjoerd Viktor Beentjes, Ava Khamseh
The problem of inferring pair-wise and higher-order interactions in complex systems involving large numbers of interacting variables, from observational data, is fundamental to man…
Competition between local erasure and long-range spreading of a single biochemical mark leads to epigenetic bistability
Marco Ancona, Davide Michieletto, Davide Marenduzzo
The mechanism through which cells determine their fate is intimately related to the spreading of certain biochemical (so-called epigenetic) marks along their genome. The mechanisms…
A nonequilibrium strategy for fast target search on the genome
F. Cagnetta, D. Michieletto, D. Marenduzzo
Vital biological processes such as genome repair require fast and efficient binding of selected proteins to specific target sites on DNA. Here we propose an active target search me…
Transcription-driven DNA Supercoiling: Non-Equilibrium Dynamics and Action-at-a-distance
Y. A. G. Fosado, D. Michieletto, C. A. Brackley +1
We study the effect of transcription on the kinetics of DNA supercoiling in 3D by means of Brownian dynamics simulations of a single nucleotide resolution coarse-grained model for…
Machine learning determination of dynamical parameters: The Ising model case
Guido Cossu, Luigi Del Debbio, Tommaso Giani +2
We train a set of Restricted Boltzmann Machines (RBMs) on one- and two-dimensional Ising spin configurations at various values of temperature, generated using Monte Carlo simulatio…
Shrinkage estimation of large covariance matrices using multiple shrinkage targets
Harry Gray, Gwenaël G. R. Leday, Catalina A. Vallejos +1
Linear shrinkage estimators of a covariance matrix --- defined by a weighted average of the sample covariance matrix and a pre-specified shrinkage target matrix --- are popular whe…
Magnetic Polymer Models for Epigenomic Organisation and Phase Separation
Davide Coli, Davide Michieletto, Davide Marenduzzo +1
The genetic instructions stored in the genome require an additional layer of information to robustly determine cell fate. This additional regulation is provided by the interplay be…
Probabilistic partial least squares model: Identifiability, estimation and application
Said el Bouhaddani, Hae-Won Uh, Caroline Hayward +2
With a rapid increase in volume and complexity of data sets, there is a need for methods that can extract useful information, for example the relationship between two data sets mea…
A multi-stage representation of cell proliferation as a Markov process
Christian A Yates, Matthew J Ford, Richard L Mort
The stochastic simulation algorithm commonly known as Gillespie's algorithm is now used ubiquitously in the modelling of biological processes in which stochastic effects play an im…
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…
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…
Natural CMT2 variation is associated with genome-wide methylation changes and temperature adaptation
Xia Shen, Simon Forsberg, Mats Pettersson +2
A central problem when studying adaptation to a new environment is the interplay between genetic variation and phenotypic plasticity. Arabidopsis thaliana has colonized a wide rang…