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 +3 more
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A maximum likelihood algorithm for reconstructing 3D structures of human chromosomes from chromosomal contact data [PDF]
BMC Genomics, 2018 Background The development of chromosomal conformation capture techniques, particularly, the Hi-C technique, has made the analysis and study of the spatial conformation of a genome an important topic in bioinformatics and computational biology.
Oluwatosin Oluwadare +2 more
doaj +3 more sources
Recovery and Visualization of 3D Structure of Chromosomes from Tomographic Reconstruction Images [PDF]
EURASIP Journal on Advances in Signal Processing, 2006 The objectives of this work include automatic recovery and visualization of a 3D chromosome structure from a sequence of 2D tomographic reconstruction images taken through the nucleus of a cell.
Tsap Leonid V +3 more
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GSDB: a database of 3D chromosome and genome structures reconstructed from Hi-C data [PDF]
BMC Molecular and Cell Biology, 2020 Advances in the study of chromosome conformation capture technologies, such as Hi-C technique - capable of capturing chromosomal interactions in a genome-wide scale - have led to the development of three-dimensional chromosome and genome structure ...
Oluwatosin Oluwadare +4 more
doaj +4 more sources
EVR: reconstruction of bacterial chromosome 3D structure models using error-vector resultant algorithm [PDF]
BMC Genomics, 2019 Background More and more 3C/Hi-C experiments on prokaryotes have been published. However, most of the published modeling tools for chromosome 3D structures are targeting at eukaryotes. How to transform prokaryotic experimental chromosome interaction data
Kang-Jian Hua, Bin-Guang Ma
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Orientation-dependent Dxz4 contacts shape the 3D structure of the inactive X chromosome [PDF]
Nature Communications, 2018 The inactive X chromosome condenses into a bipartite structure. Here the authors use cells with allelic deletions or inversions to show that the Dxz4 locus is necessary to maintain the bipartite structure and that Dxz4 orientation controls the ...
G. Bonora +10 more
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MaxComp: Predicting single-cell chromatin compartments from 3D chromosome structures.
PLoS Computational BiologyThe genome is organized into distinct chromatin compartments with at least two main classes, a transcriptionally active A and an inactive B compartment, broadly corresponding to euchromatin and heterochromatin.
Yuxiang Zhan +2 more
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Inferring Single-Cell 3D Chromosomal Structures Based on the Lennard-Jones Potential [PDF]
International Journal of Molecular Sciences, 2021 Reconstructing three-dimensional (3D) chromosomal structures based on single-cell Hi-C data is a challenging scientific problem due to the extreme sparseness of the single-cell Hi-C data. In this research, we used the Lennard-Jones potential to reconstruct both 500 kb and high-resolution 50 kb chromosomal structures based on single-cell Hi-C data.
Zha, Mengsheng +3 more
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The “lnc” between 3D chromatin structure and X chromosome inactivation [PDF]
Seminars in Cell & Developmental Biology, 2016 The long non-coding RNA Xist directs a remarkable instance of developmentally regulated, epigenetic change known as X Chromosome Inactivation (XCI). By spreading in cis across the X chromosome from which it is expressed, Xist RNA facilitates the creation of a heritably silent, heterochromatic nuclear territory that displays a three-dimensional ...
Pandya-Jones, Amy, Plath, Kathrin
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Ultra-Structural Imaging Provides 3D Organization of 46 Chromosomes of a Human Lymphocyte Prophase Nucleus [PDF]
International Journal of Molecular Sciences, 2021 Three dimensional (3D) ultra-structural imaging is an important tool for unraveling the organizational structure of individual chromosomes at various stages of the cell cycle. Performing hitherto uninvestigated ultra-structural analysis of the human genome at prophase, we used serial block-face scanning electron microscopy (SBFSEM) to understand ...
Sajid, Atiqa +8 more
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