Human papillomavirus integration transforms chromatin to drive oncogenesis [0.03%]
人乳头瘤病毒的整合会转化染色体以驱动肿瘤发生
Mehran Karimzadeh,Christopher Arlidge,Ariana Rostami et al.
Mehran Karimzadeh et al.
Background: Human papillomavirus (HPV) drives almost all cervical cancers and up to 70% of head and neck cancers. Frequent integration into the host genome occurs predominantly in tumorigenic types of HPV. We hypothesize ...
DCATS: differential composition analysis for flexible single-cell experimental designs [0.03%]
DCATS：灵活的单细胞实验设计的差异组成分析
Xinyi Lin,Chuen Chau,Kun Ma et al.
Xinyi Lin et al.
Differential composition analysis - the identification of cell types that have statistically significant changes in abundance between multiple experimental conditions - is one of the most common tasks in single cell omic data analysis. Howe...
Transcriptome- and proteome-wide association studies nominate determinants of kidney function and damage [0.03%]
转录组和蛋白质组的全尺度关联研究确定了肾功能和损伤的决定因素
Pascal Schlosser,Jingning Zhang,Hongbo Liu et al.
Pascal Schlosser et al.
Background: The pathophysiological causes of kidney disease are not fully understood. Here we show that the integration of genome-wide genetic, transcriptomic, and proteomic association studies can nominate causal determi...
scTour: a deep learning architecture for robust inference and accurate prediction of cellular dynamics [0.03%]
基于深度学习的稳健推理和准确预测细胞动力学模型
Qian Li
Qian Li
Despite the continued efforts, a batch-insensitive tool that can both infer and predict the developmental dynamics using single-cell genomics is lacking. Here, I present scTour, a novel deep learning architecture to perform robust inference...
Engineered circular guide RNAs boost CRISPR/Cas12a- and CRISPR/Cas13d-based DNA and RNA editing [0.03%]
工程化的环状向导RNA能够增强CRISPR/Cas12a和CRISPR/Cas13d介导的DNA与RNA编辑功能
Xin Zhang,Xinlong Wang,Jie Lv et al.
Xin Zhang et al.
Background: The CRISPR/Cas12a and CRISPR/Cas13d systems are widely used for fundamental research and hold great potential for future clinical applications. However, the short half-life of guide RNAs (gRNAs), particularly ...
CATI: an efficient gene integration method for rodent and primate embryos by MMEJ suppression [0.03%]
通过抑制MMEJ有效整合外源基因的啮齿类和灵长类胚胎的方法CATI
Hongyu Chen,Xingchen Liu,Lanxin Li et al.
Hongyu Chen et al.
The efficiency of homology-directed repair (HDR) plays a crucial role in the development of animal models and gene therapy. We demonstrate that microhomology-mediated end-joining (MMEJ) constitutes a substantial proportion of DNA repair dur...
VarID2 quantifies gene expression noise dynamics and unveils functional heterogeneity of ageing hematopoietic stem cells [0.03%]
VarID2 量化基因表达噪声动力学并揭示衰老造血干细胞的功能异质性
Reyna Edith Rosales-Alvarez,Jasmin Rettkowski,Josip Stefan Herman et al.
Reyna Edith Rosales-Alvarez et al.
Variability of gene expression due to stochasticity of transcription or variation of extrinsic signals, termed biological noise, is a potential driving force of cellular differentiation. Utilizing single-cell RNA-sequencing, we develop VarI...
CNETML: maximum likelihood inference of phylogeny from copy number profiles of multiple samples [0.03%]
利用多例样本拷贝数谱型进行系谱推断的极大似然法研究(CNETML)
Bingxin Lu,Kit Curtius,Trevor A Graham et al.
Bingxin Lu et al.
Phylogenetic trees based on copy number profiles from multiple samples of a patient are helpful to understand cancer evolution. Here, we develop a new maximum likelihood method, CNETML, to infer phylogenies from such data. CNETML is the fir...
A benchmark of computational pipelines for single-cell histone modification data [0.03%]
单细胞组蛋白修饰数据计算流程的基准测试
Félix Raimundo,Pacôme Prompsy,Jean-Philippe Vert et al.
Félix Raimundo et al.
Background: Single-cell histone post translational modification (scHPTM) assays such as scCUT&Tag or scChIP-seq allow single-cell mapping of diverse epigenomic landscapes within complex tissues and are likely to unlock ou...
The effect of background noise and its removal on the analysis of single-cell expression data [0.03%]
背景噪声及其消除对单细胞表达数据的影响分析
Philipp Janssen,Zane Kliesmete,Beate Vieth et al.
Philipp Janssen et al.
Background: In droplet-based single-cell and single-nucleus RNA-seq experiments, not all reads associated with one cell barcode originate from the encapsulated cell. Such background noise is attributed to spillage from ce...