siVAE: interpretable deep generative models for single-cell transcriptomes [0.03%]
可解释的深度生成模型在单细胞转录组学中的应用
Yongin Choi,Ruoxin Li,Gerald Quon
Yongin Choi
Neural networks such as variational autoencoders (VAE) perform dimensionality reduction for the visualization and analysis of genomic data, but are limited in their interpretability: it is unknown which data features are represented by each...
DNA methylation entropy as a measure of stem cell replication and aging [0.03%]
表观遗传学熵作为干细胞复制和衰老的衡量指标
Himani Vaidya,Hye Seon Jeong,Kelsey Keith et al.
Himani Vaidya et al.
Background: Epigenetic marks are encoded by DNA methylation and accumulate errors as organisms age. This drift correlates with lifespan, but the biology of how this occurs is still unexplained. We analyze DNA methylation ...
An overview of DNA methylation-derived trait score methods and applications [0.03%]
DNA甲基化衍生的性状评分方法及应用研究进展
Marta F Nabais,Danni A Gadd,Eilis Hannon et al.
Marta F Nabais et al.
Microarray technology has been used to measure genome-wide DNA methylation in thousands of individuals. These studies typically test the associations between individual DNA methylation sites ("probes") and complex traits or diseases. The re...
Leveraging massively parallel reporter assays for evolutionary questions [0.03%]
利用大规模并行报告基因检测方法解决进化问题
Irene Gallego Romero,Amanda J Lea
Irene Gallego Romero
A long-standing goal of evolutionary biology is to decode how gene regulation contributes to organismal diversity. Doing so is challenging because it is hard to predict function from non-coding sequence and to perform molecular research wit...
BIGKnock: fine-mapping gene-based associations via knockoff analysis of biobank-scale data [0.03%]
通过大规模生物银行数据的knockoff分析进行精细定位基因水平关联研究 BIGKNOCK方法论文
Shiyang Ma,Chen Wang,Atlas Khan et al.
Shiyang Ma et al.
We propose BIGKnock (BIobank-scale Gene-based association test via Knockoffs), a computationally efficient gene-based testing approach for biobank-scale data, that leverages long-range chromatin interaction data, and performs conditional ge...
H3.3 contributes to chromatin accessibility and transcription factor binding at promoter-proximal regulatory elements in embryonic stem cells [0.03%]
H3.3通过胚胎干细胞中启动子附近的调节元件促进染色质的可接近性和转录因子结合
Amanuel Tafessu,Ryan O&#x;Hara,Sara Martire et al.
Amanuel Tafessu et al.
Background: The histone variant H3.3 is enriched at active regulatory elements such as promoters and enhancers in mammalian genomes. These regions are highly accessible, creating an environment that is permissive to trans...
SampleQC: robust multivariate, multi-cell type, multi-sample quality control for single-cell data [0.03%]
示例数据质量控制：单细胞数据的稳健多变量、多细胞类型、多样本质量控制
Will Macnair,Mark Robinson
Will Macnair
Quality control (QC) is a critical component of single-cell RNA-seq (scRNA-seq) processing pipelines. Current approaches to QC implicitly assume that datasets are comprised of one cell type, potentially resulting in biased exclusion of rare...
REPAC: analysis of alternative polyadenylation from RNA-sequencing data [0.03%]
REPAC：通过RNA测序数据对选择性多聚腺苷酸化进行分析
Eddie L Imada,Christopher Wilks,Ben Langmead et al.
Eddie L Imada et al.
Alternative polyadenylation (APA) is an important post-transcriptional mechanism that has major implications in biological processes and diseases. Although specialized sequencing methods for polyadenylation exist, availability of these data...
Leveraging explainable AI for gut microbiome-based colorectal cancer classification [0.03%]
利用可解释的人工智能进行基于肠道微生物组的结直肠癌分类
Ryza Rynazal,Kota Fujisawa,Hirotsugu Shiroma et al.
Ryza Rynazal et al.
Studies have shown a link between colorectal cancer (CRC) and gut microbiome compositions. In these studies, machine learning is used to infer CRC biomarkers using global explanation methods. While these methods allow the identification of ...
The collateral activity of RfxCas13d can induce lethality in a RfxCas13d knock-in mouse model [0.03%]
一种RfxCas13d敲入小鼠模型中的脱靶活动可诱导致死性
Yunfei Li,Junjie Xu,Xuefei Guo et al.
Yunfei Li et al.
Background: The CRISPR-Cas13 system is an RNA-guided RNA-targeting system and has been widely used in transcriptome engineering with potentially important clinical applications. However, it is still controversial whether ...