Melody: meta-analysis of microbiome association studies for discovering generalizable microbial signatures [0.03%]
旋律：元分析微生物关联研究以发现具普适性的微生物标志物
Zhoujingpeng Wei,Guanhua Chen,Zheng-Zheng Tang
Zhoujingpeng Wei
Standard protocols for meta-analysis of association studies are inadequate for microbiome data due to their complex compositional structure, leading to inaccurate and unstable microbial signature selection. To address this issue, we introdu...
Beware of counter-intuitive levels of false discoveries in datasets with strong intra-correlations [0.03%]
谨防强相关数据集中反直觉的假阳性水平
Chakravarthi Kanduri,Maria Mamica,Emilie Willoch Olstad et al.
Chakravarthi Kanduri et al.
The false discovery rate (FDR) controlling method by Benjamini and Hochberg (BH) is a popular choice in the omics fields. Here, we demonstrate that in datasets with a large degree of dependencies between features, FDR correction methods lik...
Direct and bisulfite-free 5-methylcytosine and 5-hydroxymethylcytosine sequencing at single-cell resolution with scTAPS and scCAPS + [0.03%]
基于scTAPS和scCAPS +的单细胞直接非硫酸盐测序分辨5-甲基胞嘧啶和5-羟甲基胞嘧啶
Xiufei Chen,Jingfei Cheng,Linzhen Kong et al.
Xiufei Chen et al.
We present direct sequencing methodologies, scTAPS for 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) and scCAPS + specifically for 5hmC, enabling quantitative detection of 5mC and 5hmC at single-base resolution and single-cell l...
The epigenetics effects of transposable elements are genomic context dependent and not restricted to gene silencing in Drosophila [0.03%]
果蝇转座子的表观遗传效应依赖于基因组背景且不局限于基因沉默作用
Marta Coronado-Zamora,Josefa González
Marta Coronado-Zamora
Background: Transposable elements (TEs) represent a threat to genome integrity due to their proliferative capacity. Eukaryotic cells silence TEs through different molecular mechanisms, including the deposition of repressi...
Y-mer: a k-mer based method for determining human Y chromosome haplogroups from ultra-low sequencing depth data [0.03%]
基于k-mer的Y-mer方法用于从超低深度测序数据中确定人类Y染色体单倍群
Tarmo Puurand,Märt Möls,Lauris Kaplinski et al.
Tarmo Puurand et al.
Determining genetic ancestry of an individual is challenging from poorly preserved or mixed samples that permit only ultra-low coverage sequence at depths less than 0.1 × at target loci. Leveraging recent advances in telomere-to-telomere s...
Mutations of short tandem repeats explain abundant trait heritability in Arabidopsis [0.03%]
短串联重复序列的变异解释了拟南芥丰富的性状遗传率
Zhi-Qin Zhang,Juan Jiang,Yong-Chao Xu et al.
Zhi-Qin Zhang et al.
Background: Short tandem repeat (STR) mutations are major drivers of genetic variation and deeply influence phenotypic diversity and evolution, they are often overlooked despite their significant effects. ...
spVelo: RNA velocity inference for multi-batch spatial transcriptomics data [0.03%]
spVelo：多批次空间转录组学数据的RNA速度推断
Wenxin Long,Tianyu Liu,Lingzhou Xue et al.
Wenxin Long et al.
RNA velocity has emerged as a powerful tool to interpret transcriptional dynamics and infer trajectory from snapshot datasets. However, current methods fail to utilize the spatial information inherent in spatial transcriptomics and lack sca...
Common cell lysis procedures distort ribosome profiling analyses of gene expression [0.03%]
常见的细胞裂解程序会扭曲核糖体图谱分析中的基因表达结果
Aoife O&#x;Connell,Alla D Fedorova,Patrick B F O&#x;Connor et al.
Aoife O&#x;Connell et al.
Ribosome profiling is a powerful technique used to study gene expression on a transcriptome-wide scale. It involves sequencing of mRNA fragments protected by ribosomes from ribonuclease digestion. The initial steps commonly involve cell lys...
The evolutionary dynamics of organellar pan-genomes in Arabidopsis thaliana [0.03%]
拟南芥细胞器开放基因组的进化动态分析
Yi Zou,Weidong Zhu,Yingke Hou et al.
Yi Zou et al.
Background: In plants, comparative analyses of organellar genomes are often based on draft assemblies. Large-scale investigations into the complex structural rearrangements of mitochondrial genomes remain scarce. ...
LSGI: interpretable spatial gradient analysis for spatial transcriptomics data [0.03%]
基于空间转录组数据的可解释的空间梯度分析(LSGI)
Qingnan Liang,Luisa Solis Soto,Cara Haymaker et al.
Qingnan Liang et al.
Cellular anatomy and signaling vary across niches, which can induce gradated gene expressions in subpopulations of cells. Such spatial transcriptomic gradient (STG) makes a significant source of intra-tumor heterogeneity. We present Local S...