Identification of genetic variants that impact gene co-expression relationships using large-scale single-cell data [0.03%]
利用大规模单细胞数据识别影响基因共表达关系的遗传变异体
Shuang Li,Katharina T Schmid,Dylan H de Vries et al.
Shuang Li et al.
Background: Expression quantitative trait loci (eQTL) studies show how genetic variants affect downstream gene expression. Single-cell data allows reconstruction of personalized co-expression networks and therefore the id...
Meta-Analysis
Genome biology. 2023 Apr 18;24(1):80. DOI:10.1186/s13059-023-02897-x 2023
Metabolic independence drives gut microbial colonization and resilience in health and disease [0.03%]
代谢独立驱动健康和疾病状态下肠道微生物定植及稳定性的建立
Andrea R Watson,Jessika Füssel,Iva Veseli et al.
Andrea R Watson et al.
Background: Changes in microbial community composition as a function of human health and disease states have sparked remarkable interest in the human gut microbiome. However, establishing reproducible insights into the de...
GBC: a parallel toolkit based on highly addressable byte-encoding blocks for extremely large-scale genotypes of species [0.03%]
基于高度寻址字节编码块的并行工具包GBC用于物种极其大规模基因型
Liubin Zhang,Yangyang Yuan,Wenjie Peng et al.
Liubin Zhang et al.
Whole -genome sequencing projects of millions of subjects contain enormous genotypes, entailing a huge memory burden and time for computation. Here, we present GBC, a toolkit for rapidly compressing large-scale genotypes into highly address...
JBrowse 2: a modular genome browser with views of synteny and structural variation [0.03%]
JBrowse 2：一种具有同线型和结构变化视图的模块化基因组浏览器
Colin Diesh,Garrett J Stevens,Peter Xie et al.
Colin Diesh et al.
We present JBrowse 2, a general-purpose genome annotation browser offering enhanced visualization of complex structural variation and evolutionary relationships. It retains core features of JBrowse while adding new views for synteny, dotplo...
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...