Disparities in spatially variable gene calling highlight the need for benchmarking spatial transcriptomics methods [0.03%]
空间可变基因呼叫的差异突显了对空间转录组学方法进行基准测试的需求
Natalie Charitakis,Agus Salim,Adam T Piers et al.
Natalie Charitakis et al.
Identifying spatially variable genes (SVGs) is a key step in the analysis of spatially resolved transcriptomics data. SVGs provide biological insights by defining transcriptomic differences within tissues, which was previously unachievable ...
Structural variation and introgression from wild populations in East Asian cattle genomes confer adaptation to local environment [0.03%]
东亚家牛基因组中的结构变异和来自野生群体的基因渗入使其适应当地环境
Xiaoting Xia,Fengwei Zhang,Shuang Li et al.
Xiaoting Xia et al.
Background: Structural variations (SVs) in individual genomes are major determinants of complex traits, including adaptability to environmental variables. The Mongolian and Hainan cattle breeds in East Asia are of taurine...
COLLAGENE enables privacy-aware federated and collaborative genomic data analysis [0.03%]
COLLAGENE实现隐私保护的联邦和协作基因组数据分析
Wentao Li,Miran Kim,Kai Zhang et al.
Wentao Li et al.
Growing regulatory requirements set barriers around genetic data sharing and collaborations. Moreover, existing privacy-aware paradigms are challenging to deploy in collaborative settings. We present COLLAGENE, a tool base for building secu...
Coupling of co-transcriptional splicing and 3' end Pol II pausing during termination in Arabidopsis [0.03%]
拟南芥中转录终止期间的协同转录剪接和Pol II在3'端的暂停耦合现象
Sixian Zhou,Fengli Zhao,Danling Zhu et al.
Sixian Zhou et al.
Background: In Arabidopsis, RNA Polymerase II (Pol II) often pauses within a few hundred base pairs downstream of the polyadenylation site, reflecting efficient transcriptional termination, but how such pausing is regulat...
PhaseDancer: a novel targeted assembler of segmental duplications unravels the complexity of the human chromosome 2 fusion going from 48 to 46 chromosomes in hominin evolution [0.03%]
相位舞者：一种新颖的靶向重复序列组装程序揭示了从四十八到四十六染色体的人类二号染色体融合复杂性
Barbara Poszewiecka,Krzysztof Gogolewski,Justyna A Karolak et al.
Barbara Poszewiecka et al.
Resolving complex genomic regions rich in segmental duplications (SDs) is challenging due to the high error rate of long-read sequencing. Here, we describe a targeted approach with a novel genome assembler PhaseDancer that extends SD-rich r...
The relationship between regulatory changes in cis and trans and the evolution of gene expression in humans and chimpanzees [0.03%]
人类和黑猩猩顺式和反式调控变化与基因表达进化的关系研究
Kenneth A Barr,Katherine L Rhodes,Yoav Gilad
Kenneth A Barr
Background: Comparative gene expression studies in apes are fundamentally limited by the challenges associated with sampling across different tissues. Here, we used single-cell RNA sequencing of embryoid bodies to collect...
ZINBMM: a general mixture model for simultaneous clustering and gene selection using single-cell transcriptomic data [0.03%]
基于单细胞转录组数据的同时聚类和基因选择的通用混合模型(ZINBMM)
Yang Li,Mingcong Wu,Shuangge Ma et al.
Yang Li et al.
Clustering is a critical component of single-cell RNA sequencing (scRNA-seq) data analysis and can help reveal cell types and infer cell lineages. Despite considerable successes, there are few methods tailored to investigating cluster-speci...
Artur Jaroszewicz,Jason Ernst
Artur Jaroszewicz
Various computational approaches have been developed to annotate epigenomes on a per-position basis by modeling combinatorial and spatial patterns within epigenomic data. However, such annotations are less suitable for gene-based analyses. ...
Quartet protein reference materials and datasets for multi-platform assessment of label-free proteomics [0.03%]
基于无标记蛋白质组学多平台评估的四重奏蛋白参考材料和数据集
Sha Tian,Dongdong Zhan,Ying Yu et al.
Sha Tian et al.
Background: Quantitative proteomics is an indispensable tool in life science research. However, there is a lack of reference materials for evaluating the reproducibility of label-free liquid chromatography-tandem mass spe...
Correcting batch effects in large-scale multiomics studies using a reference-material-based ratio method [0.03%]
利用参考材料的比率法校正大规模多组学研究中的批次效应
Ying Yu,Naixin Zhang,Yuanbang Mai et al.
Ying Yu et al.
Background: Batch effects are notoriously common technical variations in multiomics data and may result in misleading outcomes if uncorrected or over-corrected. A plethora of batch-effect correction algorithms are propose...