From cells to chromatin: capturing snapshots of genome organization with 5C technology
In eukaryotes, genome organization can be observed on many levels and at different scales.
This organization is important not only to reduce chromosome length but also for the proper …
This organization is important not only to reduce chromosome length but also for the proper …
[HTML][HTML] Spatial organization of the budding yeast genome in the cell nucleus and identification of specific chromatin interactions from multi-chromosome constrained …
Nuclear landmarks and biochemical factors play important roles in the organization of the
yeast genome. The interaction pattern of budding yeast as measured from genome-wide 3C …
yeast genome. The interaction pattern of budding yeast as measured from genome-wide 3C …
Handling realistic assumptions in hypothesis testing of 3D co-localization of genomic elements
The study of chromatin 3D structure has recently gained much focus owing to novel
techniques for detecting genome-wide chromatin contacts using next-generation …
techniques for detecting genome-wide chromatin contacts using next-generation …
[HTML][HTML] Super-resolution visualization and modeling of human chromosomal regions reveals cohesin-dependent loop structures
Background The 3D organization of the chromatin fiber in cell nuclei plays a key role in the
regulation of gene expression. Genome-wide techniques to score DNA-DNA contacts, such …
regulation of gene expression. Genome-wide techniques to score DNA-DNA contacts, such …
[HTML][HTML] Inferential structure determination of chromosomes from single-cell Hi-C data
Chromosome conformation capture (3C) techniques have revealed many fascinating
insights into the spatial organization of genomes. 3C methods typically provide information …
insights into the spatial organization of genomes. 3C methods typically provide information …
[HTML][HTML] Genome3D: a viewer-model framework for integrating and visualizing multi-scale epigenomic information within a three-dimensional genome
TM Asbury, M Mitman, J Tang, WJ Zheng - BMC bioinformatics, 2010 - Springer
Background New technologies are enabling the measurement of many types of genomic
and epigenomic information at scales ranging from the atomic to nuclear. Much of this new …
and epigenomic information at scales ranging from the atomic to nuclear. Much of this new …
[HTML][HTML] Manifold based optimization for single-cell 3D genome reconstruction
The three-dimensional (3D) structure of the genome is important for orchestration of gene
expression and cell differentiation. While mapping genomes in 3D has for a long time been …
expression and cell differentiation. While mapping genomes in 3D has for a long time been …
[HTML][HTML] Connecting high-resolution 3D chromatin organization with epigenomics
The resolution of chromatin conformation capture technologies keeps increasing, and the
recent nucleosome resolution chromatin contact maps allow us to explore how fine-scale 3D …
recent nucleosome resolution chromatin contact maps allow us to explore how fine-scale 3D …
The Nucleome Data Bank: web-based resources to simulate and analyze the three-dimensional genome
VG Contessoto, RR Cheng, A Hajitaheri… - Nucleic Acids …, 2021 - academic.oup.com
Abstract We introduce the Nucleome Data Bank (NDB), a web-based platform to simulate
and analyze the three-dimensional (3D) organization of genomes. The NDB enables …
and analyze the three-dimensional (3D) organization of genomes. The NDB enables …
[HTML][HTML] SPIN reveals genome-wide landscape of nuclear compartmentalization
We report SPIN, an integrative computational method to reveal genome-wide intranuclear
chromosome positioning and nuclear compartmentalization relative to multiple nuclear …
chromosome positioning and nuclear compartmentalization relative to multiple nuclear …