G-quadruplex structural motifs modulate protein-RNA interactions within the transcriptome [0.03%]
转录组中G-四链体结构基序调节蛋白质-RNA相互作用
Uditi Bhatt,Cameron W Evans,Anne Cucchiarini et al.
Uditi Bhatt et al.
Background: RNA secondary structures, including G-quadruplexes (G4s), have emerged as vital players in protein-RNA interactions. The RNA-binding protein Fused in Sarcoma (FUS), which is strongly implicated in both neurode...
[Formula: see text] -Space: continuous phenotyping of single-cell multi-omics data [0.03%]
[公式：请参见文本]空间：单细胞多组学数据的连续表型分析
Jiadong Mao,Yidi Deng,Kim-Anh Lê Cao
Jiadong Mao
The prevalence of single-cell multi-omics datasets calls for automated cell type annotation methods that can characterize novel cell states. We developed Φ -Space, a computational framework for the continuous phenotyping of single-cell...
The distinct roles of genome, methylation, transcription, and translation on protein expression in Arabidopsis thaliana resolve the Central Dogma's information flow [0.03%]
拟南芥蛋白质表达中基因组、甲基化、转录和翻译的不同作用解析了中心法则的信息流
Ziming Zhong,Mark Bailey,Yong-In Kim et al.
Ziming Zhong et al.
Background: We investigate the flow of genetic information from DNA to RNA to protein as described by the Central Dogma in molecular biology, to determine the impact of intermediate genomic levels on plant protein express...
TrueSpot: a robust automated tool for quantifying signal puncta in fluorescent imaging [0.03%]
稳健的荧光显微图像信号斑点量化自动化工具TrueSpot
Blythe G Hospelhorn,Benjamin K Kesler,Hossein Jashnsaz et al.
Blythe G Hospelhorn et al.
Characterizing the movement of biomolecules in single cells quantitatively is essential to understanding fundamental biological mechanisms. RNA fluorescent in situ hybridization (RNA-FISH) is a technique for visualizing RNA in fixed cells u...
DeepWheat: predicting the effects of genomic variants on gene expression and regulatory activities across tissues and varieties in wheat using deep learning [0.03%]
基于深度学习的预测小麦基因组变异对跨组织和品种基因表达及调控活性影响的新模型
Zhigang Ma,Jiazi Zhang,Hongcui Pei et al.
Zhigang Ma et al.
Spatiotemporal gene expression shapes key agronomic traits, yet tissue-specific prediction remains challenging in complex crops. We present DeepWheat, a broadly applicable deep learning framework comprising DeepEXP and DeepEPI, for accurate...
Benchmarking multi-slice integration and downstream applications in spatial transcriptomics data analysis [0.03%]
空间转录组学数据分析中多切片积分和下游应用的基准测试
Kejing Dong,Yicheng Gao,Qi Zou et al.
Kejing Dong et al.
Background: Spatial transcriptomics preserves spatial context of tissues while capturing gene expression. As the technology advances, researchers are increasingly generating data from multiple tissue sections, creating a ...
Variable efficiency of nonsense-mediated mRNA decay across human tissues, tumors and individuals [0.03%]
人类组织、肿瘤和个体中无意义介导的mRNA降解的效率不同
Guillermo Palou-Márquez,Fran Supek
Guillermo Palou-Márquez
Background: Nonsense-mediated mRNA decay (NMD) is a quality-control pathway that degrades mRNA bearing premature termination codons (PTCs) resulting from mutation or mis-splicing, and that additionally participates in gen...
Characterization of the transposable element landscape shaping the Ectocarpus genome [0.03%]
表征转座子景观塑造Ectocarpus基因组的特性
Erica Dinatale,Rory J Craig,Claudia Martinho et al.
Erica Dinatale et al.
Background: Comprising up to 90% of eukaryotic genomes, transposable elements (TEs) are mobile genetic units that play fundamental roles in evolution. Brown algae, one of the most complex multicellular eukaryotic groups t...
Codon-specific ribosome stalling reshapes translational dynamics during branched-chain amino acid starvation [0.03%]
支链氨基酸饥饿期间密码子特异性核糖体停滞重塑了翻译动力学
Lina Worpenberg,Cédric Gobet,Felix Naef
Lina Worpenberg
Background: Cells regulate protein synthesis in response to fluctuating nutrient availability through mechanisms that affect both translation initiation and elongation. Branched-chain amino acids, leucine, isoleucine, and...
Hybrid BAG-seq: DNA and RNA from the same single nucleus reveals interactions between genomic and transcriptomic landscapes in human tumor samples [0.03%]
混合BAG-seq：来自同一单个细胞核的DNA和RNA揭示了人类肿瘤样本中基因组和转录组景观之间的相互作用
Siran Li,Joan Alexander,Jude Kendall et al.
Siran Li et al.
We introduce hybrid BAG-seq: a high-throughput, multi-omic method that simultaneously captures DNA and RNA from single nuclei. We apply this protocol to 65,499 single nuclei from samples of five uterine cancer patients and validate the clus...