Robust differential expression testing for single-cell CRISPR screens at low multiplicity of infection [0.03%]
低感染复数下单细胞CRISPR筛选的稳健差异表达分析方法
Timothy Barry,Kaishu Mason,Kathryn Roeder et al.
Timothy Barry et al.
Single-cell CRISPR screens (perturb-seq) link genetic perturbations to phenotypic changes in individual cells. The most fundamental task in perturb-seq analysis is to test for association between a perturbation and a count outcome, such as ...
Breaking down causes, consequences, and mediating effects of telomere length variation on human health [0.03%]
端粒长度变化对人体健康影响的因果关系、后果及中介作用分析
Samuel Moix,Marie C Sadler,Zoltán Kutalik et al.
Samuel Moix et al.
Background: Telomeres form repeated DNA sequences at the ends of chromosomes, which shorten with each cell division. Yet, factors modulating telomere attrition and the health consequences thereof are not fully understood....
Comparative 3D genome analysis between neural retina and retinal pigment epithelium reveals differential cis-regulatory interactions at retinal disease loci [0.03%]
比较神经视网膜和视网膜色素上皮的三维基因组分析可揭示视网膜疾病位点差异性顺式调控相互作用
Eva D&#x;haene,Víctor López-Soriano,Pedro Manuel Martínez-García et al.
Eva D&#x;haene et al.
Background: Vision depends on the interplay between photoreceptor cells of the neural retina and the underlying retinal pigment epithelium (RPE). Most genes involved in inherited retinal diseases display specific spatiote...
Comparative Study
Genome biology. 2024 May 17;25(1):123. DOI:10.1186/s13059-024-03250-6 2024
Single-cell 3D genome structure reveals distinct human pluripotent states [0.03%]
单细胞三维基因组结构揭示了人类多能状态的区别
Niannian Li,Kairang Jin,Bin Liu et al.
Niannian Li et al.
Background: Pluripotent states of embryonic stem cells (ESCs) with distinct transcriptional profiles affect ESC differentiative capacity and therapeutic potential. Although single-cell RNA sequencing has revealed addition...
EmptyDropsMultiome discriminates real cells from background in single-cell multiomics assays [0.03%]
空滴多组学辨别单细胞多组学分析中的真实细胞和背景噪音
Stathis Megas,Valentina Lorenzi,John C Marioni
Stathis Megas
Multiomic droplet-based technologies allow different molecular modalities, such as chromatin accessibility and gene expression (scATAC-seq and scRNA-seq), to be probed in the same nucleus. We develop EmptyDropsMultiome, an approach that dis...
Commonly used software tools produce conflicting and overly-optimistic AUPRC values [0.03%]
常用的软件工具会产生矛盾且过于乐观的AUPRC值
Wenyu Chen,Chen Miao,Zhenghao Zhang et al.
Wenyu Chen et al.
The precision-recall curve (PRC) and the area under the precision-recall curve (AUPRC) are useful for quantifying classification performance. They are commonly used in situations with imbalanced classes, such as cancer diagnosis and cell ty...
Dailin Gan,Yini Zhu,Xin Lu et al.
Dailin Gan et al.
Numerous algorithms have been proposed to identify cell types in single-cell RNA sequencing data, yet a fundamental problem remains: determining associations between cells and phenotypes such as cancer. We develop SCIPAC, the first algorith...
A novel approach to exploring the dark genome and its application to mapping of the vertebrate virus fossil record [0.03%]
探索暗基因组的新方法及其在映射脊椎动物病毒化石记录方面的应用
Daniel Blanco-Melo,Matthew A Campbell,Henan Zhu et al.
Daniel Blanco-Melo et al.
Background: Genomic regions that remain poorly understood, often referred to as the dark genome, contain a variety of functionally relevant and biologically informative features. These include endogenous viral elements (E...
Disruption of maternal vascular remodeling by a fetal endoretrovirus-derived gene in preeclampsia [0.03%]
子粒层病毒衍生基因干扰子痫前期血管重塑作用机制研究
Xiaoli Gong,Wei He,Wan Jin et al.
Xiaoli Gong et al.
Background: Preeclampsia, one of the most lethal pregnancy-related diseases, is associated with the disruption of uterine spiral artery remodeling during placentation. However, the early molecular events leading to preecl...
Mapping and functional characterization of structural variation in 1060 pig genomes [0.03%]
1060个猪基因组结构变异的图谱构建与功能分析
Liu Yang,Hongwei Yin,Lijing Bai et al.
Liu Yang et al.
Background: Structural variations (SVs) have significant impacts on complex phenotypes by rearranging large amounts of DNA sequence. Results: ...