Predicting genome architecture: challenges and solutions
P Belokopytova, V Fishman - Frontiers in genetics, 2021 - frontiersin.org
Genome architecture plays a pivotal role in gene regulation. The use of high-throughput
methods for chromatin profiling and 3-D interaction map** provide rich experimental data …
methods for chromatin profiling and 3-D interaction map** provide rich experimental data …
Higher-order chromosome structures investigated by polymer physics in cellular morphogenesis and differentiation
Abstract Experimental advances in Molecular Biology demonstrated that chromatin
architecture and gene regulation are deeply related. Hi-C data, for instance, returned a …
architecture and gene regulation are deeply related. Hi-C data, for instance, returned a …
Molecular dynamics simulations of the strings and binders switch model of chromatin
In recent years interest has grown on the applications of polymer physics to model chromatin
folding in order to try to make sense of the complexity of experimental data emerging from …
folding in order to try to make sense of the complexity of experimental data emerging from …
Models of polymer physics for the architecture of the cell nucleus
The depth and complexity of data now available on chromosome 3D architecture, derived by
new technologies such as Hi‐C, have triggered the development of models based on …
new technologies such as Hi‐C, have triggered the development of models based on …
Inference of chromosome 3D structures from GAM data by a physics computational approach
The combination of modelling and experimental advances can provide deep insights for
understanding chromatin 3D organization and ultimately its underlying mechanisms. In …
understanding chromatin 3D organization and ultimately its underlying mechanisms. In …
Further Delineation of Duplications of ARX Locus Detected in Male Patients with Varying Degrees of Intellectual Disability
L Poeta, M Malacarne, A Padula, D Drongitis… - International journal of …, 2022 - mdpi.com
The X-linked gene encoding aristaless-related homeobox (ARX) is a bi-functional
transcription factor capable of activating or repressing gene transcription, whose mutations …
transcription factor capable of activating or repressing gene transcription, whose mutations …
Efficient computational implementation of polymer physics models to explore chromatin structure
The development of novel experimental technologies able to map genome-wide chromatin
contacts, as Hi-C, GAM or SPRITE, allowed to derive detailed information about the spatial …
contacts, as Hi-C, GAM or SPRITE, allowed to derive detailed information about the spatial …
A polymer physics model to dissect genome organization in healthy and pathological phenotypes
Novel technologies revealed a nontrivial spatial organization of the chromosomes within the
cell nucleus, which includes different levels of compartmentalization and architectural …
cell nucleus, which includes different levels of compartmentalization and architectural …
The scaling features of the 3D organization of chromosomes are highlighted by a transformation à la Kadanoff of Hi-C data
Technologies such as Hi-C and GAM have revealed that chromosomes are not randomly
folded into the nucleus of cells, but are composed by a sequence of contact domains (TADs) …
folded into the nucleus of cells, but are composed by a sequence of contact domains (TADs) …
Hybrid Machine Learning and Polymer Physics Approach to Investigate 3D Chromatin Structure
Innovative experimental protocols from Molecular Biology provided in recent years
quantitative data about the structure of the cell nucleus. These technologies, such as Hi-C …
quantitative data about the structure of the cell nucleus. These technologies, such as Hi-C …