Benchmarking alignment strategies for Hi-C reads in metagenomic Hi-C data [PDF]
Genome BiologyBackground Metagenomics combined with High-throughput Chromosome Conformation Capture (Hi-C) provides a powerful approach to study microbial communities by linking genomic content with spatial interactions.
Yuqiu Wang +4 more
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ScHiCAtt: Enhancing single-cell Hi-C data resolution using attention-based models [PDF]
Computational and Structural Biotechnology JournalThe spatial organization of chromatin is fundamental to gene regulation and essential for proper cellular function. The Hi-C technique remains one of the leading methods for unraveling 3D genome structures; however, limited resolution, data sparsity, and
Rohit Menon +2 more
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Unveiling Multi‐Scale Architectural Features in Single‐Cell Hi‐C Data Using scCAFE [PDF]
Advanced ScienceSingle‐cell Hi‐C (scHi‐C) has provided unprecedented insights into the heterogeneity of 3D genome organization. However, its sparse and noisy nature poses challenges for computational analyses, such as chromatin architectural feature identification. Here,
Fuzhou Wang +12 more
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SCW: building the whole-genome 3D structures based on extremely sparse single-cell Hi-C data [PDF]
BMC BioinformaticsBackground The study of three-dimensional (3D) genome structures at the single-cell level is crucial for understanding cell-to-cell variability. However, it is challenging to reconstruct the 3D structures of the whole genome based on single-cell Hi-C ...
Hao Zhu +3 more
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Enhancing Single-Cell and Bulk Hi-C Data Using a Generative Transformer Model [PDF]
BiologyThe 3D organization of chromatin in the nucleus plays a critical role in regulating gene expression and maintaining cellular functions in eukaryotic cells.
Ruoying Gao +4 more
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Effectiveness of machine learning at modeling the relationship between Hi‐C data and copy number variation [PDF]
Quantitative BiologyCopy number variation (CNV) refers to the number of copies of a specific sequence in a genome and is a type of chromatin structural variation. The development of the Hi‐C technique has empowered research on the spatial structure of chromatins by ...
Yuyang Wang +13 more
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HiCEnterprise: identifying long range chromosomal contacts in Hi-C data [PDF]
PeerJ, 2021 Motivation Computational analysis of chromosomal contact data is currently gaining popularity with the rapid advance in experimental techniques providing access to a growing body of data.
Hanna Kranas +2 more
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covNorm: An R package for coverage based normalization of Hi-C and capture Hi-C data
Computational and Structural Biotechnology Journal, 2021 Hi-C and capture Hi-C have greatly advanced our understanding of the principles of higher-order chromatin structure. In line with the evolution of the Hi-C protocols, there is a demand for an advanced computational method that can be applied to the ...
Kyukwang Kim, Inkyung Jung
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Scientific Reports, 2021 Chromatin conformation plays an important role in a variety of genomic processes. Hi-C is one of the most popular assays for inspecting chromatin conformation. However, the utility of Hi-C contact maps is bottlenecked by resolution.
Max Highsmith, Jianlin Cheng
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Extracting multi-way chromatin contacts from Hi-C data.
PLoS Computational Biology, 2021 There is a growing realization that multi-way chromatin contacts formed in chromosome structures are fundamental units of gene regulation. However, due to the paucity and complexity of such contacts, it is challenging to detect and identify them using ...
Lei Liu +3 more
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