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2 months ago | 
nature.com | Yuyao Liu |Zhen Li |Xiaoyang Chen |Xuejian Cui |Zijing Gao
AbstractRecent advances in spatial epigenomic techniques have given rise to spatial assay for transposase-accessible chromatin using sequencing (spATAC-seq) data, enabling the characterization of epigenomic heterogeneity and spatial information simultaneously.
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Jan 17, 2025 | 
biorxiv.org | Zhen Li |Xuejian Cui |Xiaoyang Chen |Zijing Gao
AbstractSpatially resolved sequencing technologies have revolutionized our understanding of biological regulatory processes within the microenvironment by accessing the states of genomic regions, genes and proteins as well as spatial coordinates of cells. However, discrepancies between different modalities and samples hinder the analysis of spatial omics data, necessitating the development of advanced computational methods.
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Dec 30, 2024 | 
genomebiology.biomedcentral.com | Xiaoyang Chen |Keyi LI |Xiaoqing Wu |Zhen Li |Qun Jiang |Xuejian Cui | +3 more
To capture spatial accessibility pattern of each peak, Descart construct a spatial graph based on spatial locations of spots (can also be replaced by cells).
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Oct 3, 2024 | 
biorxiv.org | Xuejian Cui |Qijin Yin |Zijing Gao |Zhen Li
AbstractIdentifying cis-regulatory elements (CREs) within non-coding genomic regions-such as enhancers, silencers, promoters, and insulators-is pivotal for elucidating the intricate gene regulatory mechanisms underlying complex biological traits. The current prevalent sequence-based methods often focus on singular CRE types, limiting insights into cell-type-specific biological implications.
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Sep 30, 2024 | 
biorxiv.org | Yuyao Liu |Zhen Li |Xiaoyang Chen |Xuejian Cui
AbstractRecent advances in spatial epigenomic techniques have given rise to spatial assay for transposase-accessible chromatin using sequencing (spATAC-seq) data, enabling the characterization of epigenomic heterogeneity and spatial information simultaneously.
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Jun 11, 2024 | 
biorxiv.org | Zhen Li |Xuejian Cui |Xiaoyang Chen |Zijing Gao
AbstractSpatially resolved sequencing technologies have revolutionized the characterization of biological regulatory processes within microenvironment by simultaneously accessing the states of genomic regions, genes and proteins, along with the spatial coordinates of cells, necessitating advanced computational methods for the cross-modality and multi-sample integrated analysis of spatial omics datasets.
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May 31, 2024 | 
biorxiv.org | Yuyao Liu |Zhen Li |Xiaoyang Chen |Xuejian Cui
AbstractRecent advances in spatial epigenomic techniques have given rise to spatial assay for transposase-accessible chromatin using sequencing (spATAC-seq) data, enabling the characterization of epigenomic heterogeneity and spatial information simultaneously.
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Mar 12, 2024 | 
nature.com | Xuejian Cui
Correction to: Nature Communications https://doi.org/10.1038/s41467-024-46045-w, published online 22 February 2024In this article the legend for Fig. 6, had the text “PLEASEKEYTHETEXTHERE” inadvertently inserted into it. The original article has been corrected.
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Feb 21, 2024 | 
nature.com | Xuejian Cui
AbstractSingle-cell chromatin accessibility sequencing (scCAS) has emerged as a valuable tool for interrogating and elucidating epigenomic heterogeneity and gene regulation. However, scCAS data inherently suffers from limitations such as high sparsity and dimensionality, which pose significant challenges for downstream analyses. Although several methods are proposed to enhance scCAS data, there are still challenges and limitations that hinder the effectiveness of these methods.
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Apr 29, 2023 | 
biorxiv.org | Xiaoyang Chen |Zhen Li |Zijing Gao |Xuejian Cui
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