miRglmm: a generalized linear mixed model of isomiR-level counts improves estimation of miRNA-level differential expression and uncovers variable differential expression between isomiRs [0.03%]
miRglmm：一种基于异构体水平计数的miRNA混合线性模型可改善差异表达估计，并揭示isomiR之间的变量差异表达
Andrea M Baran,Arun H Patil,Ernesto Aparicio-Puerta et al.
Andrea M Baran et al.
MicroRNA-seq data is produced by aligning small RNA sequencing reads of different microRNA transcript isoforms, called isomiRs, to known microRNAs. Aggregation to microRNA-level counts discards information and violates core assumptions of d...
Variant effect predictor correlation with functional assays is reflective of clinical classification performance [0.03%]
变异效应预测与功能分析的吻合程度反映了临床分类性能
Benjamin J Livesey,Joseph A Marsh
Benjamin J Livesey
Background: Understanding the relationship between protein sequence and function is crucial for accurate classification of missense variants. Variant effect predictors (VEPs) play a vital role in deciphering this complex ...
Weighted 2D-kernel density estimations provide a new probabilistic measure for epigenetic age [0.03%]
加权二维核密度估计可提供表观遗传年龄的新概率衡量标准
Juan-Felipe Perez-Correa,Thomas Stiehl,Riccardo E Marioni et al.
Juan-Felipe Perez-Correa et al.
Epigenetic aging signatures provide insights into human aging, but traditional clocks rely on linear regression of DNA methylation levels, assuming linear trajectories. This study explores a non-parametric approach using 2D-kernel density e...
Zero-shot evaluation reveals limitations of single-cell foundation models [0.03%]
零样本评估揭示单细胞基础模型的局限性
Kasia Z Kedzierska,Lorin Crawford,Ava P Amini et al.
Kasia Z Kedzierska et al.
Foundation models such as scGPT and Geneformer have not been rigorously evaluated in a setting where they are used without any further training (i.e., zero-shot). Understanding the performance of models in zero-shot settings is critical to ...
Hmgb2 improves astrocyte to neuron conversion by increasing the chromatin accessibility of genes associated with neuronal maturation in a proneuronal factor-dependent manner [0.03%]
Hmgb2通过增加与神经元成熟相关的基因的染色质可及性来依赖于促神经元因子的方式改善星形胶质细胞向神经元的转化
Priya Maddhesiya,Tjasa Lepko,Andrea Steiner-Mezzardi et al.
Priya Maddhesiya et al.
Background: Direct conversion of reactive glial cells to neurons is a promising avenue for neuronal replacement therapies after brain injury or neurodegeneration. The overexpression of neurogenic fate determinants in glia...
DNA methylation dynamics play crucial roles in shaping the distinct transcriptomic profiles for different root-type initiation in rice [0.03%]
DNA甲基化动力学在塑造水稻不同根型起始的独特转录组特征中起关键作用
Wei Jiang,Zhou Zhou,Xiaoying Li et al.
Wei Jiang et al.
Background: Monocots possess a fibrous root system comprising an embryonic root, crown roots, and lateral roots. The distinct cellular origins highlight the diversity of the initiation mechanism. To date, the distinct ini...
Bayesian multi-study non-negative matrix factorization for mutational signatures [0.03%]
用于突变特征的多研究非负矩阵因子分解的贝叶斯方法
Isabella N Grabski,Lorenzo Trippa,Giovanni Parmigiani
Isabella N Grabski
Mutational signatures are typically identified from tumor genome sequencing data using non-negative matrix factorization (NMF). However, existing NMF techniques only decompose a single dataset, limiting rigorous comparisons of signatures ac...
Benjamin J Livesey,Mihaly Badonyi,Mafalda Dias et al.
Benjamin J Livesey et al.
Computational methods for assessing the likely impacts of mutations, known as variant effect predictors (VEPs), are widely used in the assessment and interpretation of human genetic variation, as well as in other applications like protein e...
Extracellular vesicle-derived miRNA-mediated cell-cell communication inference for single-cell transcriptomic data with miRTalk [0.03%]
基于miRTalk的单细胞转录组数据的外泌体衍生miRNA介导的细胞间通讯推断方法
Xin Shao,Lingqi Yu,Chengyu Li et al.
Xin Shao et al.
MicroRNAs are released from cells in extracellular vesicles (EVs), representing an essential mode of cell-cell communication (CCC) via a regulatory effect on gene expression. Single-cell RNA-sequencing technologies have ushered in an era of...
Post-cleavage target residence determines asymmetry in non-homologous end joining of Cas12a-induced DNA double strand breaks [0.03%]
crispr-cas12a介导的dna双链断裂非同源末端连接修复途径中非对称性形成机制研究
Ruo-Dan Chen,Yi Yang,Kun-Ming Liu et al.
Ruo-Dan Chen et al.
Background: After Cas12a cleaves its DNA target, it generates a DNA double strand break (DSB) with two compatible 5'-staggered ends. The Cas12a-gRNA complex remains at the protospacer adjacent motif (PAM)-proximal end (PP...