Clustering Deviation Index (CDI): a robust and accurate internal measure for evaluating scRNA-seq data clustering [0.03%]
聚类偏移指数（CDI）：一种用于评估单细胞RNA测序数据聚类的稳健且准确的内部测量方法
Jiyuan Fang,Cliburn Chan,Kouros Owzar et al.
Jiyuan Fang et al.
Most single-cell RNA sequencing (scRNA-seq) analyses begin with cell clustering; thus, the clustering accuracy considerably impacts the validity of downstream analyses. In contrast with the abundance of clustering methods, the tools to asse...
Truvari: refined structural variant comparison preserves allelic diversity [0.03%]
Truvari：精细的结构变异比较保留了等位基因多样性
Adam C English,Vipin K Menon,Richard A Gibbs et al.
Adam C English et al.
The fundamental challenge of multi-sample structural variant (SV) analysis such as merging and benchmarking is identifying when two SVs are the same. Common approaches for comparing SVs were developed alongside technologies which produce il...
Implicating genes, pleiotropy, and sexual dimorphism at blood lipid loci through multi-ancestry meta-analysis [0.03%]
通过多祖先的荟萃分析，在血液脂质位点牵涉基因，多重性以及性别二型性
Stavroula Kanoni,Sarah E Graham,Yuxuan Wang et al.
Stavroula Kanoni et al.
Background: Genetic variants within nearly 1000 loci are known to contribute to modulation of blood lipid levels. However, the biological pathways underlying these associations are frequently unknown, limiting understandi...
Meta-Analysis
Genome biology. 2022 Dec 27;23(1):268. DOI:10.1186/s13059-022-02837-1 2022
NetAct: a computational platform to construct core transcription factor regulatory networks using gene activity [0.03%]
NetAct：一个使用基因活性构建核心转录因子调控网络的计算平台
Kenong Su,Ataur Katebi,Vivek Kohar et al.
Kenong Su et al.
A major question in systems biology is how to identify the core gene regulatory circuit that governs the decision-making of a biological process. Here, we develop a computational platform, named NetAct, for constructing core transcription f...
Saturation-scale functional evidence supports clinical variant interpretation in Lynch syndrome [0.03%]
支持Lynch综合征临床变异解释的饱和尺度功能证据
Anthony Scott,Felicia Hernandez,Adam Chamberlin et al.
Anthony Scott et al.
Background: Lynch syndrome (LS) is a cancer predisposition syndrome affecting more than 1 in every 300 individuals worldwide. Clinical genetic testing for LS can be life-saving but is complicated by the heavy burden of va...
Large-scale genomic and transcriptomic profiles of rice hybrids reveal a core mechanism underlying heterosis [0.03%]
水稻杂交品种的大型基因组及转录组谱揭示了异质性的内在核心机制
Jianyin Xie,Weiping Wang,Tao Yang et al.
Jianyin Xie et al.
Background: Heterosis is widely used in agriculture. However, its molecular mechanisms are still unclear in plants. Here, we develop, sequence, and record the phenotypes of 418 hybrids from crosses between two testers and...
Parallel single-cell and bulk transcriptome analyses reveal key features of the gastric tumor microenvironment [0.03%]
平行的单细胞和批量转录组分析揭示了胃肿瘤微环境的关键特征
Boxi Kang,Jordi Camps,Biao Fan et al.
Boxi Kang et al.
Background: The tumor microenvironment (TME) has been shown to strongly influence treatment outcome for cancer patients in various indications and to influence the overall survival. However, the cells forming the TME in g...
Canalization of genome-wide transcriptional activity in Arabidopsis thaliana accessions by MET1-dependent CG methylation [0.03%]
拟南芥种质中由MET1依赖的CG甲基化对全基因组转录活性的调控作用
Thanvi Srikant,Wei Yuan,Kenneth Wayne Berendzen et al.
Thanvi Srikant et al.
Background: Despite its conserved role on gene expression and transposable element (TE) silencing, genome-wide CG methylation differs substantially between wild Arabidopsis thaliana accessions. ...
Single-cell transcriptome reveals dominant subgenome expression and transcriptional response to heat stress in Chinese cabbage [0.03%]
单细胞转录组揭示了中国白菜主要亚基因组表达和热应激的转录反应
Xiaoxue Sun,Daling Feng,Mengyang Liu et al.
Xiaoxue Sun et al.
Background: Chinese cabbage (Brassica rapa ssp. pekinensis) experienced a whole-genome triplication event and thus has three subgenomes: least fractioned, medium fractioned, and most fractioned subgenome. Environmental ch...
Exploring functional protein covariation across single cells using nPOP [0.03%]
使用nPOP探索单细胞之间的功能性蛋白质共变关系
Andrew Leduc,R Gray Huffman,Joshua Cantlon et al.
Andrew Leduc et al.
Background: Many biological processes, such as cell division cycle and drug resistance, are reflected in protein covariation across single cells. This covariation can be quantified and interpreted by single-cell mass spec...