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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   +5 more sources

Mapping the semi-nested community structure of 3D chromosome contact networks.

PLoS Computational Biology, 2023
Mammalian DNA folds into 3D structures that facilitate and regulate genetic processes such as transcription, DNA repair, and epigenetics. Several insights derive from chromosome capture methods, such as Hi-C, which allow researchers to construct contact ...
Dolores Bernenko, Sang Hoon Lee, Per Stenberg, Ludvig Lizana   +3 more
doaj   +4 more sources

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
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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

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
doaj   +1 more source

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
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
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Application of Hi-C and other omics data analysis in human cancer and cell differentiation research

Computational and Structural Biotechnology Journal, 2021
With the development of 3C (chromosome conformation capture) and its derivative technology Hi-C (High-throughput chromosome conformation capture) research, the study of the spatial structure of the genomic sequence in the nucleus helps researchers ...
Haiyan Gong, Yi Yang, Sichen Zhang, Minghong Li, Xiaotong Zhang   +4 more
doaj   +1 more source