Effective modeling of the chromatin structure by coarse-grained methods
I Tuszynska, P Bednarz, B Wilczynski - Journal of Biomolecular …, 2023 - Taylor & Francis
The interphase chromatin structure is extremely complex, precise and dynamic.
Experimental methods can only show the frequency of interaction of the various parts of the …
Experimental methods can only show the frequency of interaction of the various parts of the …
Black chromatin is indispensable for accurate simulations of Drosophila melanogaster chromatin structure
I Tuszynska, P Bednarz, B Wilczynski - bioRxiv, 2021 - biorxiv.org
The interphase chromatin structure is extremely complex, precise and dynamic.
Experimental methods can only show the frequency of interaction of the various parts of the …
Experimental methods can only show the frequency of interaction of the various parts of the …
The chromatin fiber: multiscale problems and approaches
The structure of chromatin, affected by many factors from DNA linker lengths to
posttranslational modifications, is crucial to the regulation of eukaryotic cells. Combined …
posttranslational modifications, is crucial to the regulation of eukaryotic cells. Combined …
Predicting three-dimensional genome organization with chromatin states
Y Qi, B Zhang - PLoS computational biology, 2019 - journals.plos.org
We introduce a computational model to simulate chromatin structure and dynamics. Starting
from one-dimensional genomics and epigenomics data that are available for hundreds of …
from one-dimensional genomics and epigenomics data that are available for hundreds of …
Three-dimensional modeling of chromatin structure from interaction frequency data using Markov chain Monte Carlo sampling
Background Long-range interactions between regulatory DNA elements such as enhancers,
insulators and promoters play an important role in regulating transcription. As chromatin …
insulators and promoters play an important role in regulating transcription. As chromatin …
Mechanistic modeling of chromatin folding to understand function
Experimental approaches have been applied to address questions in understanding three-
dimensional chromatin organization and function. As datasets increase in size and …
dimensional chromatin organization and function. As datasets increase in size and …
Bottom-up data integration in polymer models of chromatin organization
Cellular functions crucially depend on the precise execution of complex biochemical
reactions taking place on the chromatin fiber in the tightly packed environment of the cell …
reactions taking place on the chromatin fiber in the tightly packed environment of the cell …
Bottom-up meets top-down: the crossroads of multiscale chromatin modeling
J Moller, JJ de Pablo - Biophysical Journal, 2020 - cell.com
Chromatin can be viewed as a hierarchically structured fiber that regulates gene expression.
It consists of a complex network of DNA and proteins whose characteristic dynamical modes …
It consists of a complex network of DNA and proteins whose characteristic dynamical modes …
Role of protein-protein interactions on model chromatin organization
The three-dimensional organization of chromatin is influenced by DNA-binding proteins,
through specific and non-specific interactions. However, the role of DNA sequence and …
through specific and non-specific interactions. However, the role of DNA sequence and …
Inference of the three-dimensional chromatin structure and its temporal behavior
Understanding the three-dimensional (3D) structure of the genome is essential for
elucidating vital biological processes and their links to human disease. To determine how …
elucidating vital biological processes and their links to human disease. To determine how …