混合：概率细胞反卷积与个体化单细胞参考积分

IF 10.1 1区生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Genome Biology Pub Date : 2025-10-02 DOI:10.1186/s13059-025-03765-6

Penghui Huang, Manqi Cai, Chris McKennan, Jiebiao Wang

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引用次数: 0

摘要

细胞反褶积从大量转录组学数据中估计细胞类型分数，但目前的方法往往忽略了不同样本中细胞类型特异性表达的变化，大量和单细胞数据之间的差异，或者缺乏对参考数据选择和整合的指导。因此，我们提出了BLEND，这是一种分层贝叶斯方法，利用多个单细胞参考数据集来执行细胞反褶积。BLEND通过学习每个大样本最合适的参考来准确地估计细胞分数，考虑到上述问题。BLEND在使用人类大脑皮层数据的综合基准研究中优于最先进的方法，并为阿尔茨海默病的进展提供可靠的见解。

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BLEND: probabilistic cellular deconvolution with individualized single-cell reference integration

Cellular deconvolution estimates cell-type fractions from bulk transcriptomic data, but current methods often overlook cell type-specific expression varying across samples, discrepancies between bulk and single-cell data, or lack guidance on reference data selection and integration. Therefore, we present BLEND, a hierarchical Bayesian method that leverages multiple single-cell reference datasets to perform cellular deconvolution. BLEND estimates cellular fractions accurately by learning the most suitable reference for each bulk sample, accounting for the aforementioned issues. BLEND outperforms state-of-the-art methods in comprehensive benchmarking studies using human brain cortex data and provides reliable insights into Alzheimer’s disease progression.

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来源期刊

Genome Biology Biochemistry, Genetics and Molecular Biology-Genetics

CiteScore

21.00

自引率

3.30%

发文量

241

审稿时长

2 months

期刊介绍： Genome Biology stands as a premier platform for exceptional research across all domains of biology and biomedicine, explored through a genomic and post-genomic lens. With an impressive impact factor of 12.3 (2022),* the journal secures its position as the 3rd-ranked research journal in the Genetics and Heredity category and the 2nd-ranked research journal in the Biotechnology and Applied Microbiology category by Thomson Reuters. Notably, Genome Biology holds the distinction of being the highest-ranked open-access journal in this category. Our dedicated team of highly trained in-house Editors collaborates closely with our esteemed Editorial Board of international experts, ensuring the journal remains on the forefront of scientific advances and community standards. Regular engagement with researchers at conferences and institute visits underscores our commitment to staying abreast of the latest developments in the field.