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 …
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 …
High-resolution single-cell models of ensemble chromatin structures during Drosophila embryogenesis from population Hi-C
Q Sun - Biophysical Journal, 2020 - cell.com
We describe a computational method for reconstruction of large 3D ensemble of single-cell
chromatin conformations from population Hi-C. Our method identifies specific interactions …
chromatin conformations from population Hi-C. Our method identifies specific interactions …
[HTML][HTML] High-resolution single-cell 3D-models of chromatin ensembles during Drosophila embryogenesis
Single-cell chromatin studies provide insights into how chromatin structure relates to
functions of individual cells. However, balancing high-resolution and genome wide …
functions of individual cells. However, balancing high-resolution and genome wide …
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 …
Multiscale Modeling of Chromatin Considering the State and Shape of Molecules
Y Togashi - Advances in Computational Modeling and Simulation, 2022 - Springer
Chromatin is a complex of DNA and proteins in the eukaryotic cell nucleus. This highly
complex structure helps not only to fold long DNA and compactly store it into the nucleus but …
complex structure helps not only to fold long DNA and compactly store it into the nucleus but …
[HTML][HTML] 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 …
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 …
[HTML][HTML] How epigenome drives chromatin folding and dynamics, insights from efficient coarse-grained models of chromosomes
The 3D organization of chromosomes is crucial for regulating gene expression and cell
function. Many experimental and polymer modeling efforts are dedicated to deciphering the …
function. Many experimental and polymer modeling efforts are dedicated to deciphering the …
[HTML][HTML] Reconstructing diploid 3D chromatin structures from single cell Hi-C data with a polymer-based approach
J Rothörl, MA Brems, TJ Stevens… - Frontiers in …, 2023 - frontiersin.org
Detailed understanding of the 3D structure of chromatin is a key ingredient to investigate a
variety of processes inside the cell. Since direct methods to experimentally ascertain these …
variety of processes inside the cell. Since direct methods to experimentally ascertain these …