Results 71 to 80 of about 5,043,774 (177)

Computational methods for analysing multiscale 3D genome organization. [PDF]

Nat Rev Genet, 2023
Recent progress in whole-genome mapping and imaging technologies has enabled the characterization of the spatial organization and folding of the genome in the nucleus. In parallel, advanced computational methods have been developed to leverage these mapping data to reveal multiscale three-dimensional (3D) genome features and to provide a more complete ...
Zhang Y, Boninsegna L, Yang M, Misteli T, Alber F, Ma J.   +5 more
europepmc   +3 more sources

The 3D Genome Browser: a web-based browser for visualizing 3D genome organization and long-range chromatin interactions

Genome Biology, 2018
Here, we introduce the 3D Genome Browser, http://3dgenome.org, which allows users to conveniently explore both their own and over 300 publicly available chromatin interaction data of different types.
Yanli Wang, Fan Song, Bo Zhang, Lijun Zhang, Jie Xu, Da Kuang, Daofeng Li, Mayank N. K. Choudhary, Yun Li, Ming Hu, Ross Hardison, Ting Wang, Feng Yue   +12 more
doaj   +1 more source

HiC-DC+ enables systematic 3D interaction calls and differential analysis for Hi-C and HiChIP

Nature Communications, 2021
The genome-wide investigation of chromatin organization enables insights into global gene expression control. Here, the authors present a computationally efficient method for the analysis of chromatin organization data and use it to recover principles of
Merve Sahin, Wilfred Wong, Yingqian Zhan, Kinsey Van Deynze, Richard Koche, Christina S. Leslie   +5 more
doaj   +1 more source

3D or Not 3D: Shaping the Genome during Development

, 2021
One of the most fundamental questions in developmental biology is how one fertilized cell can give rise to a fully mature organism and how gene regulation governs this process.
Mundlos, S., Glaser, J., Stefan Mundlos, Glaser, Juliane, Glaser, J. ; https://orcid.org/, Mundlos, S. ; https://orcid.org/, Juliane Glaser, Mundlos, Stefan   +7 more
core   +1 more source

Methyl-donor inhibitors relax 3D genome structures to promote totipotent reprogramming

Cell Reports
Summary: The 3D genome safeguards cell identity while shaping developmental plasticity, yet its coordination with metabolism during cell fate transitions remains unclear.
Tianchang Yang, Lincheng Li, Jingru Zhao, Ruoqi Cheng, Yueyao Qi, Yifan Bu, Hebing Chen, Minglei Shi, Jun Xu, Hongkui Deng, Cheng Li   +10 more
doaj   +1 more source

Gene regulation in the 3D genome [PDF]

, 2018
The spatial organization of the genome is essential for the precise control of gene expression. Recent advances in sequencing and imaging technologies allow us to explore the 3D genome and its relationship to gene regulation at an unprecedented scale. In
Hu, M., Ming Hu, Shen, Y., Yin Shen, Yun Li, Li, Y.   +5 more
core   +1 more source

An integrated multi-omics and network analysis of neutrophil differentiation from initial- to late-stage

Genome Biology
Background Neutrophil differentiation is a well-orchestrated process that involves coordinated changes in the chromatin accessibility, transcription factor (TF) binding, 3D genome-structure and transcription.
Qing Chen, Tianchang Yang, Yingping Hou, Kai Wang, Tingting Li, Longteng Wang, Cuiyun Dou, Panpan Cheng, Minglei Shi, Wei Li   +9 more
doaj   +1 more source

NanoLoop: A Deep Learning Framework Leveraging Nanopore Sequencing for Chromatin Loop Prediction

Advanced Science
Chromatin loops play a crucial role in gene regulation and cellular function, providing key insights into understanding the 3D structure of the genome and its impact on cellular homeostasis.
Wenjie Huang, Li Tang, Matthew C. Hill, Yonghao Zhang, Jun Xie, Min Li   +5 more
doaj   +1 more source

Structural Modeling of Chromatin Integrates Genome Features and Reveals Chromosome Folding Principle

Scientific Reports, 2017
How chromosomes fold into 3D structures and how genome functions are affected or even controlled by their spatial organization remain challenging questions. Hi-C experiment has provided important structural insights for chromosome, and Hi-C data are used
Wen Jun Xie, Luming Meng, Sirui Liu, Ling Zhang, Xiaoxia Cai, Yi Qin Gao   +5 more
doaj   +1 more source

A scientific network serving the uses of 3D humanities

, 2020
" The 3D Consortium of the TGIR Huma-Num has been created based on the observation that there are many initiatives around 3D for the Digital Humanities without real coordination between them.
Consortium 3D SHS Team
core