A desert lncRNA HIDEN regulates human endoderm differentiation via interacting with IMP1 and stabilizing FZD5 mRNA [0.03%]
长链非编码RNA HIDEN通过与IMP1相互作用并稳定FZD5 mRNA来调节人内胚层分化
Pei Lu,Jie Yang,Mao Li et al.
Pei Lu et al.
Background: Extensive studies have revealed the function and mechanism of lncRNAs in development and differentiation, but the majority have focused on those lncRNAs adjacent to protein-coding genes. In contrast, lncRNAs l...
Author Correction: mbDenoise: microbiome data denoising using zero-inflated probabilistic principal components analysis [0.03%]
作者更正：mbDenoise：使用零膨胀概率主成分分析进行微生物组数据去噪
Yanyan Zeng,Jing Li,Chaochun Wei et al.
Yanyan Zeng et al.
Published Erratum
Genome biology. 2023 Apr 21;24(1):84. DOI:10.1186/s13059-023-02940-x 2023
CasKAS: direct profiling of genome-wide dCas9 and Cas9 specificity using ssDNA mapping [0.03%]
利用ssDNA图谱直接分析dCas9和Cas9全基因组特异性的CasKAS系统
Georgi K Marinov,Samuel H Kim,S Tansu Bagdatli et al.
Georgi K Marinov et al.
Detecting and mitigating off-target activity is critical to the practical application of CRISPR-mediated genome and epigenome editing. While numerous methods have been developed to map Cas9 binding specificity genome-wide, they are generall...
YY1 lactylation in microglia promotes angiogenesis through transcription activation-mediated upregulation of FGF2 [0.03%]
小胶质细胞中YY1乳酰化通过转录激活介导FGF2上调促进血管生成
Xiaotang Wang,Wei Fan,Na Li et al.
Xiaotang Wang et al.
Background: Ocular neovascularization is a leading cause of blindness. Retinal microglia have been implicated in hypoxia-induced angiogenesis and vasculopathy, but the underlying mechanisms are not entirely clear. Lactyla...
Publisher Correction: FIPRESCI: droplet microfluidics based combinatorial indexing for massive-scale 5'-end single-cell RNA sequencing [0.03%]
出版更正：FIPRESCI：基于液滴微流体组合索引的大量5'端单细胞RNA测序
Yun Li,Zheng Huang,Zhaojun Zhang et al.
Yun Li et al.
Published Erratum
Genome biology. 2023 Apr 21;24(1):88. DOI:10.1186/s13059-023-02944-7 2023
Consequences and opportunities arising due to sparser single-cell RNA-seq datasets [0.03%]
更稀疏的单细胞RNA测序数据集带来的挑战与机遇
Gerard A Bouland,Ahmed Mahfouz,Marcel J T Reinders
Gerard A Bouland
With the number of cells measured in single-cell RNA sequencing (scRNA-seq) datasets increasing exponentially and concurrent increased sparsity due to more zero counts being measured for many genes, we demonstrate here that downstream analy...
satmut_utils: a simulation and variant calling package for multiplexed assays of variant effect [0.03%]
用于变异效应复式测定的模拟和变体调用软件包（SATMUT_UTILS）
Ian Hoskins,Song Sun,Atina Cote et al.
Ian Hoskins et al.
The impact of millions of individual genetic variants on molecular phenotypes in coding sequences remains unknown. Multiplexed assays of variant effect (MAVEs) are scalable methods to annotate relevant variants, but existing software lacks ...
pycoMeth: a toolbox for differential methylation testing from Nanopore methylation calls [0.03%]
pycoMeth：一个基于纳米孔甲基化数据的差异甲基化检测工具包
Rene Snajder,Adrien Leger,Oliver Stegle et al.
Rene Snajder et al.
We present pycoMeth, a toolbox to store, manage and analyze DNA methylation calls from long-read sequencing data obtained using the Oxford Nanopore Technologies sequencing platform. Building on a novel, rapid-access, read-level and referenc...
PAUSE: principled feature attribution for unsupervised gene expression analysis [0.03%]
基于原理的特征归因在无监督基因表达分析中的应用
Joseph D Janizek,Anna Spiro,Safiye Celik et al.
Joseph D Janizek et al.
As interest in using unsupervised deep learning models to analyze gene expression data has grown, an increasing number of methods have been developed to make these models more interpretable. These methods can be separated into two groups: p...
The ENCODE Imputation Challenge: a critical assessment of methods for cross-cell type imputation of epigenomic profiles [0.03%]
_ENCODE直面挑战：对表观基因组图谱跨细胞类型填补方法进行批评式评估
Jacob Schreiber,Carles Boix,Jin Wook Lee et al.
Jacob Schreiber et al.
A promising alternative to comprehensively performing genomics experiments is to, instead, perform a subset of experiments and use computational methods to impute the remainder. However, identifying the best imputation methods and what meas...