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ParticleChromo3D+: A Web Server for ParticleChromo3D Algorithm for 3D Chromosome Structure Reconstruction [PDF]

Current Issues in Molecular Biology, 2023
Understanding the three-dimensional (3D) structure of chromatin is invaluable for researching how it functions. One way to gather this information is the chromosome conformation capture (3C) technique and its follow-up technique Hi-C.
David Vadnais, Oluwatosin Oluwadare
doaj   +4 more sources

Chromosome conformation capture technologies as tools to detect structural variations and their repercussion in chromatin 3D configuration

Frontiers in Cell and Developmental Biology, 2023
3D genome organization regulates gene expression in different physiological and pathological contexts. Characterization of chromatin structure at different scales has provided information about how the genome organizes in the nuclear space, from ...
Aura Stephenson-Gussinye, Mayra Furlan-Magaril   +1 more
doaj   +3 more sources

Bayesian inference of spatial organizations of chromosomes. [PDF]

PLoS Computational Biology, 2013
Knowledge of spatial chromosomal organizations is critical for the study of transcriptional regulation and other nuclear processes in the cell. Recently, chromosome conformation capture (3C) based technologies, such as Hi-C and TCC, have been developed ...
Ming Hu, Ke Deng, Zhaohui Qin, Jesse Dixon, Siddarth Selvaraj, Jennifer Fang, Bing Ren, Jun S Liu   +7 more
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From 2D to 4D: a containerized workflow and browser to explore dynamic chromatin architecture [PDF]

BMC Bioinformatics
Background Characterizing the physical organization of the genome is essential for understanding long-range gene regulation, chromatin compartmentalization, and epigenetic accessibility.
David H. Rogers, Cullen Roth, Cameron Tauxe, Jeannie T. Lee, Christina R. Steadman, Karissa Y. Sanbonmatsu, Anna Lappala, Shawn R. Starkenburg   +7 more
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3D genome organization and epigenetic regulation in autoimmune diseases

Frontiers in Immunology, 2023
Three-dimensional (3D) genomics is an emerging field of research that investigates the relationship between gene regulatory function and the spatial structure of chromatin.
Yueqi Qiu, Yueqi Qiu, Delong Feng, Wenjuan Jiang, Wenjuan Jiang, Tingting Zhang, Tingting Zhang, Tingting Zhang, Qianjin Lu, Qianjin Lu, Qianjin Lu, Ming Zhao, Ming Zhao, Ming Zhao   +13 more
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Every gene everywhere all at once: High-precision measurement of 3D chromosome architecture with single-cell Hi-C

Frontiers in Molecular Biosciences, 2022
The three-dimensional (3D) structure of chromosomes influences essential biological processes such as gene expression, genome replication, and DNA damage repair and has been implicated in many developmental and degenerative diseases.
Yi Chi, Yi Chi, Jenny Shi, Jenny Shi, Jenny Shi, Dong Xing, Dong Xing, Longzhi Tan, Longzhi Tan   +8 more
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HiC-GNN: A generalizable model for 3D chromosome reconstruction using graph convolutional neural networks

Computational and Structural Biotechnology Journal, 2023
Chromosome conformation capture (3 C) is a method of measuring chromosome topology in terms of loci interaction. The Hi-C method is a derivative of 3 C that allows for genome-wide quantification of chromosome interaction.
Van Hovenga, Jugal Kalita, Oluwatosin Oluwadare   +2 more
doaj   +1 more source

ParticleChromo3D: a Particle Swarm Optimization algorithm for chromosome 3D structure prediction from Hi-C data

BioData Mining, 2022
Background The three-dimensional (3D) structure of chromatin has a massive effect on its function. Because of this, it is desirable to have an understanding of the 3D structural organization of chromatin.
David Vadnais, Michael Middleton, Oluwatosin Oluwadare   +2 more
doaj   +1 more source

Imputation-free reconstructions of three-dimensional chromosome architectures in human diploid single-cells using allele-specified contacts

Scientific Reports, 2022
Single-cell Hi-C analysis of diploid human cells is difficult because of the lack of dense chromosome contact information and the presence of homologous chromosomes with very similar nucleotide sequences.
Yoshito Hirata, Arisa H. Oda, Chie Motono, Masanori Shiro, Kunihiro Ohta   +4 more
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Three‐dimensional genome structure shapes the recombination landscape of chromatin features during female germline stem cell development

Clinical and Translational Medicine, 2022
Background During meiosis of mammalian cells, chromatin undergoes drastic reorganization. However, the dynamics of the three‐dimensional (3D) chromatin structure during the development of female germline stem cells (FGSCs) are poorly understood.
Geng G. Tian, Changliang Hou, Jing Li, Ji Wu   +3 more
doaj   +1 more source