DeepEdit: single-molecule detection and phasing of A-to-I RNA editing events using nanopore direct RNA sequencing [0.03%]
基于纳米孔直接RNA测序的A到I RNA编辑事件单分子检测和拆相软件DeepEdit
Longxian Chen,Liang Ou,Xinyun Jing et al.
Longxian Chen et al.
Single-molecule detection and phasing of A-to-I RNA editing events remain an unresolved problem. Long-read and PCR-free nanopore native RNA sequencing offers a great opportunity for direct RNA editing detection. Here, we develop a neural ne...
Improved analysis of (e)CLIP data with RCRUNCH yields a compendium of RNA-binding protein binding sites and motifs [0.03%]
改进的(e)CLIP数据分析方法RCRUNCH获得了一系列RNA结合蛋白的结合位点及基序图谱
Maria Katsantoni,Erik van Nimwegen,Mihaela Zavolan
Maria Katsantoni
We present RCRUNCH, an end-to-end solution to CLIP data analysis for identification of binding sites and sequence specificity of RNA-binding proteins. RCRUNCH can analyze not only reads that map uniquely to the genome but also those that ma...
Large-scale genome sequencing redefines the genetic footprints of high-altitude adaptation in Tibetans [0.03%]
大规模基因组测序重新定义了藏族高原适应性遗传特征
Wangshan Zheng,Yaoxi He,Yongbo Guo et al.
Wangshan Zheng et al.
Background: Tibetans are genetically adapted to high-altitude environments. Though many studies have been conducted, the genetic basis of the adaptation remains elusive due to the poor reproducibility for detecting select...
Comprehensive benchmark and architectural analysis of deep learning models for nanopore sequencing basecalling [0.03%]
纳米孔测序基线调用深度学习模型的全面基准和架构分析
Marc Pagès-Gallego,Jeroen de Ridder
Marc Pagès-Gallego
Background: Nanopore-based DNA sequencing relies on basecalling the electric current signal. Basecalling requires neural networks to achieve competitive accuracies. To improve sequencing accuracy further, new models are c...
PhyloMed: a phylogeny-based test of mediation effect in microbiome [0.03%]
基于系统发育的测试肠菌中介效应的工具_phyloMed
Qilin Hong,Guanhua Chen,Zheng-Zheng Tang
Qilin Hong
Microbiome data from sequencing experiments contain the relative abundance of a large number of microbial taxa with their evolutionary relationships represented by a phylogenetic tree. The compositional and high-dimensional nature of the mi...
Identification of cell barcodes from long-read single-cell RNA-seq with BLAZE [0.03%]
使用BLAZE从长读单细胞RNA测序中识别细胞条形码
Yupei You,Yair D J Prawer,Ricardo De Paoli-Iseppi et al.
Yupei You et al.
Long-read single-cell RNA sequencing (scRNA-seq) enables the quantification of RNA isoforms in individual cells. However, long-read scRNA-seq using the Oxford Nanopore platform has largely relied upon matched short-read data to identify cel...
Large-scale analysis of de novo mutations identifies risk genes for female infertility characterized by oocyte and early embryo defects [0.03%]
大规模的从头突变分析鉴定出卵巢卵母细胞和早期胚胎缺陷导致的女性不孕风险基因
Qun Li,Lin Zhao,Yang Zeng et al.
Qun Li et al.
Background: Oocyte maturation arrest and early embryonic arrest are important reproductive phenotypes resulting in female infertility and cause the recurrent failure of assisted reproductive technology (ART). However, the...
FIPRESCI: droplet microfluidics based combinatorial indexing for massive-scale 5'-end single-cell RNA sequencing [0.03%]
基于微流体的组合索引技术进行大规模单细胞RNA测序
Yun Li,Zheng Huang,Zhaojun Zhang et al.
Yun Li et al.
Single-cell RNA sequencing methods focusing on the 5'-end of transcripts can reveal promoter and enhancer activity and efficiently profile immune receptor repertoire. However, ultra-high-throughput 5'-end single-cell RNA sequencing methods ...
Flexible and efficient handling of nanopore sequencing signal data with slow5tools [0.03%]
使用slow5tools灵活高效地处理纳米孔测序信号数据
Hiruna Samarakoon,James M Ferguson,Sasha P Jenner et al.
Hiruna Samarakoon et al.
Nanopore sequencing is being rapidly adopted in genomics. We recently developed SLOW5, a new file format with advantages for storage and analysis of raw signal data from nanopore experiments. Here we introduce slow5tools, an intuitive toolk...
Reading and writing of mRNA m6A modification orchestrate maternal-to-zygotic transition in mice [0.03%]
阅读和写作mRNA m6A修饰调控小鼠从卵母细胞到合子的过渡
Wencheng Zhu,Yufeng Ding,Juan Meng et al.
Wencheng Zhu et al.
N6-methyladenosine (m6A) modification has been shown to regulate RNA metabolism. Here, we investigate m6A dynamics during maternal-to-zygotic transition (MZT) in mice through multi-omic analysis. Our results show that m6A can be maternally ...