sciMET-cap: high-throughput single-cell methylation analysis with a reduced sequencing burden [0.03%]
具有降低的测序负担的高通量单细胞甲基化分析（sciMET-cap）
Sonia N Acharya,Ruth V Nichols,Lauren E Rylaarsdam et al.
Sonia N Acharya et al.
DNA methylation is a key component of the mammalian epigenome, playing a regulatory role in development, disease, and other processes. Robust, high-throughput single-cell DNA methylation assays are now possible (sciMET); however, the genome...
TFscope: systematic analysis of the sequence features involved in the binding preferences of transcription factors [0.03%]
TFSCOPE：转录因子结合偏好的序列特征的系统分析
Raphaël Romero,Christophe Menichelli,Christophe Vroland et al.
Raphaël Romero et al.
Characterizing the binding preferences of transcription factors (TFs) in different cell types and conditions is key to understand how they orchestrate gene expression. Here, we develop TFscope, a machine learning approach that identifies se...
Author Correction: CelFiE-ISH: a probabilistic model for multi-cell type deconvolution from single-molecule DNA methylation haplotypes [0.03%]
作者更正：CelFiE-ISH：单分子DNA甲基化单倍型多细胞类型的概率模型分解
Irene Unterman,Dana Avrahami,Efrat Katsman et al.
Irene Unterman et al.
Published Erratum
Genome biology. 2024 Jul 8;25(1):182. DOI:10.1186/s13059-024-03330-7 2024
Di Huang,Ivan Ovcharenko
Di Huang
Background: Although disease-causal genetic variants have been found within silencer sequences, we still lack a comprehensive analysis of the association of silencers with diseases. Here, we profiled GWAS variants in 2.8 ...
Detection of allele-specific expression in spatial transcriptomics with spASE [0.03%]
基于spASE的空间转录组学等位基因特异性表达检测方法
Luli S Zou,Dylan M Cable,Irving A Barrera-Lopez et al.
Luli S Zou et al.
Spatial transcriptomics technologies permit the study of the spatial distribution of RNA at near-single-cell resolution genome-wide. However, the feasibility of studying spatial allele-specific expression (ASE) from these data remains uncha...
Panpipes: a pipeline for multiomic single-cell and spatial transcriptomic data analysis [0.03%]
Panpipes：单细胞和空间转录组多组学数据的分析管道
Fabiola Curion,Charlotte Rich-Griffin,Devika Agarwal et al.
Fabiola Curion et al.
Single-cell multiomic analysis of the epigenome, transcriptome, and proteome allows for comprehensive characterization of the molecular circuitry that underpins cell identity and state. However, the holistic interpretation of such datasets ...
Massively integrated coexpression analysis reveals transcriptional regulation, evolution and cellular implications of the yeast noncanonical translatome [0.03%]
大规模共表达分析揭示了酵母非规范转译组的转录调控、演化及细胞影响
April Rich,Omer Acar,Anne-Ruxandra Carvunis
April Rich
Background: Recent studies uncovered pervasive transcription and translation of thousands of noncanonical open reading frames (nORFs) outside of annotated genes. The contribution of nORFs to cellular phenotypes is difficu...
TaqTth-hpRNA: a novel compact RNA-targeting tool for specific silencing of pathogenic mRNA [0.03%]
TaqTth-hpRNA：一种新颖的针对病原mRNA高效沉默的RNA靶向工具
Chong Xu,Jiyanuo Cao,Huanran Qiang et al.
Chong Xu et al.
Pathogenic allele silencing is a promising treatment for genetic hereditary diseases. Here, we develop an RNA-cleaving tool, TaqTth-hpRNA, consisting of a small, chimeric TaqTth, and a hairpin RNA guiding probe. With a minimal flanking sequ...
Author Correction: The shaky foundations of simulating single-cell RNA sequencing data [0.03%]
作者更正：单细胞RNA测序数据模拟的摇摇欲坠的基础
Helena L Crowell,Sarah X Morillo Leonardo,Charlotte Soneson et al.
Helena L Crowell et al.
Published Erratum
Genome biology. 2024 Jul 5;25(1):178. DOI:10.1186/s13059-024-03329-0 2024
VirRep: a hybrid language representation learning framework for identifying viruses from human gut metagenomes [0.03%]
VirRep：一种用于从人体肠道元基因组中识别病毒的混合语言表示学习框架
Yanqi Dong,Wei-Hua Chen,Xing-Ming Zhao
Yanqi Dong
Identifying viruses from metagenomes is a common step to explore the virus composition in the human gut. Here, we introduce VirRep, a hybrid language representation learning framework, for identifying viruses from human gut metagenomes. Vir...