A benchmark study of deep learning-based multi-omics data fusion methods for cancer [0.03%]
基于深度学习的癌症多组学数据融合方法基准研究
Dongjin Leng,Linyi Zheng,Yuqi Wen et al.
Dongjin Leng et al.
Background: A fused method using a combination of multi-omics data enables a comprehensive study of complex biological processes and highlights the interrelationship of relevant biomolecules and their functions. Driven by...
BASS: multi-scale and multi-sample analysis enables accurate cell type clustering and spatial domain detection in spatial transcriptomic studies [0.03%]
基于多尺度和多样本分析的准确细胞类型聚类和空间转录组研究中的区域检测方法
Zheng Li,Xiang Zhou
Zheng Li
Spatial transcriptomic studies are reaching single-cell spatial resolution, with data often collected from multiple tissue sections. Here, we present a computational method, BASS, that enables multi-scale and multi-sample analysis for singl...
Survey of the binding preferences of RNA-binding proteins to RNA editing events [0.03%]
关于RNA结合蛋白与RNA编辑事件结合偏好的调查研究
Xiaolin Hu,Qin Zou,Li Yao et al.
Xiaolin Hu et al.
Background: Adenosine-to-inosine (A-to-I) editing is an important RNA posttranscriptional process related to a multitude of cellular and molecular activities. However, systematic characterizations of whether and how the e...
Methylome decoding of RdDM-mediated reprogramming effects in the Arabidopsis MSH1 system [0.03%]
MSH1系统中拟南芥RdDM介导的表观重编程效应的甲基化组解析
Hardik Kundariya,Robersy Sanchez,Xiaodong Yang et al.
Hardik Kundariya et al.
Background: Plants undergo programmed chromatin changes in response to environment, influencing heritable phenotypic plasticity. The RNA-directed DNA methylation (RdDM) pathway is an essential component of this reprogramm...
Differential richness inference for 16S rRNA marker gene surveys [0.03%]
基于16S rDNA测序数据的物种丰度差异推断方法研究
M Senthil Kumar,Eric V Slud,Christine Hehnly et al.
M Senthil Kumar et al.
Background: Individual and environmental health outcomes are frequently linked to changes in the diversity of associated microbial communities. Thus, deriving health indicators based on microbiome diversity measures is es...
Target residence of Cas9-sgRNA influences DNA double-strand break repair pathway choices in CRISPR/Cas9 genome editing [0.03%]
CRISPR/Cas9基因编辑中Cas9-sgRNA的作用靶点影响DNA双链断裂的修复路径选择
Si-Cheng Liu,Yi-Li Feng,Xiu-Na Sun et al.
Si-Cheng Liu et al.
Background: Due to post-cleavage residence of the Cas9-sgRNA complex at its target, Cas9-induced DNA double-strand breaks (DSBs) have to be exposed to engage DSB repair pathways. Target interaction of Cas9-sgRNA determine...
Author Correction: High-throughput techniques enable advances in the roles of DNA and RNA secondary structures in transcriptional and post-transcriptional gene regulation [0.03%]
作者更正：高通量技术使人们能够推进对DNA和RNA二级结构在转录和转录后基因调控中的作用的理解
Ilias Georgakopoulos-Soares,Candace S Y Chan,Nadav Ahituv et al.
Ilias Georgakopoulos-Soares et al.
Published Erratum
Genome biology. 2022 Jul 27;23(1):164. DOI:10.1186/s13059-022-02733-8 2022
Large-scale manipulation of promoter DNA methylation reveals context-specific transcriptional responses and stability [0.03%]
大规模操纵启动子DNA甲基化揭示了特定环境的转录反应和稳定性
Alex de Mendoza,Trung Viet Nguyen,Ethan Ford et al.
Alex de Mendoza et al.
Background: Cytosine DNA methylation is widely described as a transcriptional repressive mark with the capacity to silence promoters. Epigenome engineering techniques enable direct testing of the effect of induced DNA met...
Juan Li,Like Chen,Jing Liang et al.
Juan Li et al.
Low efficiency has seriously restricted the application of prime editing (PE) systems in plants. In this study, we develop an enhanced plant prime editor 2 system, enpPE2, by stacking various optimization strategies, including updating the ...
ZetaSuite: computational analysis of two-dimensional high-throughput data from multi-target screens and single-cell transcriptomics [0.03%]
ZetaSuite：来自多靶标筛选和单细胞转录组学的二维高通量数据的计算分析
Yajing Hao,Shuyang Zhang,Changwei Shao et al.
Yajing Hao et al.
Two-dimensional high-throughput data have become increasingly common in functional genomics studies, which raises new challenges in data analysis. Here, we introduce a new statistic called Zeta, initially developed to identify global splici...