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Showing 1–6 of 6 results
Advanced filters: Author: Guanao Yan Clear advanced filters

  • Li and colleagues present CellScope, a tree-structured framework that reveals multi-level cellular hierarchies and gene functions in single-cell data. This approach provides clear clustering, intuitive visualization, and deep biological views into cell types and functions.

    • Bingjie Li
    • Runyu Lin
    • Zhigang Yao
    ResearchOpen Access
    Nature Communications
    Volume: 17, P: 1-18

  • Methods for profiling differences between individual cells are constantly expanding. Here, the authors present a computational framework for the analysis of chromatin accessibility data at the single-cell level that takes into account previous knowledge and data-specific characteristics.

    • Shengquan Chen
    • Guanao Yan
    • Zhixiang Lin
    ResearchOpen Access
    Nature Communications
    Volume: 12, P: 1-13

  • RNAtracker is a computational pipeline that distinguishes variants associated with allele-specific RNA stability from those associated with allele-specific RNA transcription. Variants affecting RNA stability are enriched in immune-related genes and contribute to disease risk.

    • Elaine Huang
    • Ting Fu
    • Xinshu Xiao
    Research
    Nature Genetics
    Volume: 57, P: 2578-2588

  • Benchmarking computational tools for analysis of single-cell sequencing data demands simulation of realistic sequencing reads. However, none of the few existing read simulators aim to mimic real data. Here, the authors introduce scReadSim, a single-cell RNA-seq and ATAC-seq read simulator that works by mimicking real data.

    • Guanao Yan
    • Dongyuan Song
    • Jingyi Jessica Li
    ResearchOpen Access
    Nature Communications
    Volume: 14, P: 1-14

  • In spatial transcriptomics data analysis, identifying spatially variable genes (SVGs) is crucial for understanding tissue organization and function. The authors categorize 34 computational methods for SVG detection, exploring their definitions, methodologies—including statistical approaches—and applications, while proposing future research directions.

    • Guanao Yan
    • Shuo Harper Hua
    • Jingyi Jessica Li
    ReviewsOpen Access
    Nature Communications
    Volume: 16, P: 1-21