Methylation-directed regulatory networks determine enhancing and silencing of mutation disease driver genes and explain inter-patient expression variation [0.03%]
甲基化导向的调控网络决定了对突变疾病驱动基因的增强和沉默作用并解释了患者间的表达差异
Yifat Edrei,Revital Levy,Daniel Kaye et al.
Yifat Edrei et al.
Background: Common diseases manifest differentially between patients, but the genetic origin of this variation remains unclear. To explore possible involvement of gene transcriptional-variation, we produce a DNA methylati...
Acute expression of human APOBEC3B in mice results in RNA editing and lethality [0.03%]
小鼠急性表达人APOBEC3B会导致RNA编辑并致死
Alicia Alonso de la Vega,Nuri Alpay Temiz,Rafail Tasakis et al.
Alicia Alonso de la Vega et al.
Background: RNA editing has been described as promoting genetic heterogeneity, leading to the development of multiple disorders, including cancer. The cytosine deaminase APOBEC3B is implicated in tumor evolution through D...
CREaTor: zero-shot cis-regulatory pattern modeling with attention mechanisms [0.03%]
基于注意力机制的零样本建模工具CREaTor
Yongge Li,Fusong Ju,Zhiyuan Chen et al.
Yongge Li et al.
Linking cis-regulatory sequences to target genes has been a long-standing challenge. In this study, we introduce CREaTor, an attention-based deep neural network designed to model cis-regulatory patterns for genomic elements up to 2 Mb from ...
Multi-omics analysis reveals the molecular response to heat stress in a "red tide" dinoflagellate [0.03%]
多组学分析揭示了造成赤潮的原生动物对高温胁迫的分子响应
Katherine E Dougan,Zhi-Luo Deng,Lars Wöhlbrand et al.
Katherine E Dougan et al.
Background: "Red tides" are harmful algal blooms caused by dinoflagellate microalgae that accumulate toxins lethal to other organisms, including humans via consumption of contaminated seafood. These algal blooms are drive...
Yuqiu Yang,Kaiwen Wang,Zeyu Lu et al.
Yuqiu Yang et al.
Recently, many analysis tools have been devised to offer insights into data generated via cytometry by time-of-flight (CyTOF). However, objective evaluations of these methods remain absent as most evaluations are conducted against real data...
N-of-one differential gene expression without control samples using a deep generative model [0.03%]
无需对照样本的单例差异基因表达分析的深度生成模型方法
Iñigo Prada-Luengo,Viktoria Schuster,Yuhu Liang et al.
Iñigo Prada-Luengo et al.
Differential analysis of bulk RNA-seq data often suffers from lack of good controls. Here, we present a generative model that replaces controls, trained solely on healthy tissues. The unsupervised model learns a low-dimensional representati...
Dissecting the autism-associated 16p11.2 locus identifies multiple drivers in neuroanatomical phenotypes and unveils a male-specific role for the major vault protein [0.03%]
分析自闭症相关的16p11.2位点确定神经解剖表型中的多个驱动因素并揭示主要 Vault 蛋白的男性特异性作用
Perrine F Kretz,Christel Wagner,Anna Mikhaleva et al.
Perrine F Kretz et al.
Background: Using mouse genetic studies and systematic assessments of brain neuroanatomical phenotypes, we set out to identify which of the 30 genes causes brain defects at the autism-associated 16p11.2 locus. ...
Fake IDs? Widespread misannotation of DNA transposons as a general transcription factor [0.03%]
假冒身份？DNA转座子被广泛误标为一般转录因子
Nozhat T Hassan,David L Adelson
Nozhat T Hassan
Accurate annotation of genes and transposable elements (TEs) is vital for understanding genomes, but current annotation pipelines often misannotate TEs as genes. This study reveals how the general transcription factor II-I repeat domain-con...
Evaluation of deep learning-based feature selection for single-cell RNA sequencing data analysis [0.03%]
基于深度学习的特征选择在单细胞RNA测序数据分析中的评估
Hao Huang,Chunlei Liu,Manoj M Wagle et al.
Hao Huang et al.
Background: Feature selection is an essential task in single-cell RNA-seq (scRNA-seq) data analysis and can be critical for gene dimension reduction and downstream analyses, such as gene marker identification and cell typ...
Statistical learning quantifies transposable element-mediated cis-regulation [0.03%]
统计学习量化转座元件介导的顺式调控
Cyril Pulver,Delphine Grun,Julien Duc et al.
Cyril Pulver et al.
Background: Transposable elements (TEs) have colonized the genomes of most metazoans, and many TE-embedded sequences function as cis-regulatory elements (CREs) for genes involved in a wide range of biological processes fr...