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- W4382631698 abstract "Accurately assessing contacts between DNA fragments inside the nucleus with Hi-C experiment is crucial for understanding the role of 3D genome organization in gene regulation. This challenging task is due in part to the high sequencing depth of Hi-C libraries required to support high-resolution analyses. Most existing Hi-C data are collected with limited sequencing coverage, leading to poor chromatin interaction frequency estimation. Current computational approaches to enhance Hi-C signals focus on the analysis of individual Hi-C datasets of interest, without taking advantage of the facts that (i) several hundred Hi-C contact maps are publicly available and (ii) the vast majority of local spatial organizations are conserved across multiple cell types.Here, we present RefHiC-SR, an attention-based deep learning framework that uses a reference panel of Hi-C datasets to facilitate the enhancement of Hi-C data resolution of a given study sample. We compare RefHiC-SR against tools that do not use reference samples and find that RefHiC-SR outperforms other programs across different cell types, and sequencing depths. It also enables high-accuracy mapping of structures such as loops and topologically associating domains.https://github.com/BlanchetteLab/RefHiC." @default.
- W4382631698 created "2023-07-01" @default.
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- W4382631698 date "2023-06-01" @default.
- W4382631698 modified "2023-09-26" @default.
- W4382631698 title "Reference panel-guided super-resolution inference of Hi-C data" @default.
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- W4382631698 doi "https://doi.org/10.1093/bioinformatics/btad266" @default.
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