Regulatory analysis of single cell multiome gene expression and chromatin accessibility data with scREG [0.03%]
基于scREG的单细胞多组学基因表达和染色质可及性数据的调控分析方法
Zhana Duren,Fengge Chang,Fnu Naqing et al.
Zhana Duren et al.
Technological development has enabled the profiling of gene expression and chromatin accessibility from the same cell. We develop scREG, a dimension reduction methodology, based on the concept of cis-regulatory potential, for single cell mu...
Michael Piechotta,Isabel S Naarmann-de Vries,Qi Wang et al.
Michael Piechotta et al.
Several high-throughput antibody-free methods for RNA modification detection from sequencing data have been developed. We present JACUSA2 as a versatile software solution and comprehensive analysis framework for RNA modification detection a...
Refining colorectal cancer classification and clinical stratification through a single-cell atlas [0.03%]
通过单细胞图谱 refining 结直肠癌分类和临床分层
Ateeq M Khaliq,Cihat Erdogan,Zeyneb Kurt et al.
Ateeq M Khaliq et al.
Background: Colorectal cancer (CRC) consensus molecular subtypes (CMS) have different immunological, stromal cell, and clinicopathological characteristics. Single-cell characterization of CMS subtype tumor microenvironmen...
Dmitry E Andreev,Gary Loughran,Alla D Fedorova et al.
Dmitry E Andreev et al.
Recent proteogenomic studies revealed extensive translation outside of annotated protein coding regions, such as non-coding RNAs and untranslated regions of mRNAs. This non-canonical translation is largely due to start codon plurality withi...
Jinzhuang Dou,Shaoheng Liang,Vakul Mohanty et al.
Jinzhuang Dou et al.
Integration of single-cell multiomics profiles generated by different single-cell technologies from the same biological sample is still challenging. Previous approaches based on shared features have only provided approximate solutions. Here...
TT-Mars: structural variants assessment based on haplotype-resolved assemblies [0.03%]
TT-Mars：基于单倍体型解析装配的结构变异评估方法
Jianzhi Yang,Mark J P Chaisson
Jianzhi Yang
Variant benchmarking is often performed by comparing a test callset to a gold standard set of variants. In repetitive regions of the genome, it may be difficult to establish what is the truth for a call, for example, when different alignmen...
Enhancer transcription detected in the nascent transcriptomic landscape of bread wheat [0.03%]
从面包小麦的新生转录组景观中检测到增强子转录
Yilin Xie,Yan Chen,Zijuan Li et al.
Yilin Xie et al.
The precise spatiotemporal gene expression is orchestrated by enhancers that lack general sequence features and thus are difficult to be computationally identified. By nascent RNA sequencing combined with epigenome profiling, we detect acti...
DeepRepeat: direct quantification of short tandem repeats on signal data from nanopore sequencing [0.03%]
深度重复：直接量化纳米孔测序信号数据中的短串联重复序列
Li Fang,Qian Liu,Alex Mas Monteys et al.
Li Fang et al.
Despite recent improvements in basecalling accuracy, nanopore sequencing still has higher error rates on short-tandem repeats (STRs). Instead of using basecalled reads, we developed DeepRepeat which converts ionic current signals into red-g...
Systematic evaluation of colorectal cancer organoid system by single-cell RNA-Seq analysis [0.03%]
单细胞RNA测序分析结直肠癌肿瘤类器官的系统性评价研究
Rui Wang,Yunuo Mao,Wendong Wang et al.
Rui Wang et al.
Background: Patient-derived organoid culture is a powerful system for studying the molecular mechanisms of cancers, especially colorectal cancer (CRC), one of the most prevalent cancers worldwide. There are two main types...
Author Correction: Mutational signatures reveal the role of RAD52 in p53-independent p21-driven genomic instability [0.03%]
作者更正：突变特征揭示了RAD52在p53独立的p21驱动的基因组不稳定性中的作用
Panagiotis Galanos,George Pappas,Alexander Polyzos et al.
Panagiotis Galanos et al.
Published Erratum
Genome biology. 2022 Apr 28;23(1):107. DOI:10.1186/s13059-022-02678-y 2022