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...
Chenxi Zhou,Max Brown,Mark Blaxter;Darwin Tree of Life Project Consortium;Shane A McCarthy et al.
Chenxi Zhou et al.
Plant organelle genomes, particularly large mitochondrial genomes with complex repeats, present significant challenges for assembly. The advent of long-read sequencing enables the assembly of complete genomes, but problems of resolving alte...
scplainer: using linear models to understand mass spectrometry-based single-cell proteomics data [0.03%]
基于质谱的单细胞蛋白质组学数据的理解：线性模型的应用（SCPlainer）
Christophe Vanderaa,Laurent Gatto
Christophe Vanderaa
Analyzing mass spectrometry (MS)-based single-cell proteomics (SCP) data faces important challenges inherent to MS-based technologies and single-cell experiments. We present scplainer, a principled and standardized approach for extracting m...
scTail: precise polyadenylation site detection and its alternative usage analysis from reads 1 preserved 3' scRNA-seq data [0.03%]
基于reads1保留的单细胞3′端测序数据的精确多聚腺苷酸位点检测及其可选使用分析方法(scTail)
Ruiyan Hou,Yuanhua Huang
Ruiyan Hou
The first-strand reads (often reads 1) of three-prime single-cell RNA-seq (3' scRNA-seq) can contain informative cDNA for analysis of polyadenylation sites (PAS), but are often overlooked or trimmed. Here, we describe a computational method...
Identification of replicative aging and inflammatory aging signatures via whole-genome CRISPRi screens [0.03%]
通过全基因组CRISPRi筛选鉴定复制衰老和炎症衰老标志物
Lingling Wu,Xiang Zhu,Yanxia Liu et al.
Lingling Wu et al.
Background: Aging is a major risk factor for chronic diseases and cancer. Cellular aging, particularly in adult stem cells, offers a high-throughput framework for dissecting the molecular mechanisms of aging. ...