Agus Salim,Dharmesh D Bhuva,Carissa Chen et al.
Agus Salim et al.
Normalization of spatial transcriptomics data is challenging due to spatial association between region-specific library size and biology. We develop SpaNorm, the first spatially-aware normalization method that concurrently models library si...
Rewiring of SINE-MIR enhancer topology and Esrrb modulation in expanded and naive pluripotency [0.03%]
扩增和初始多能性中的SINE-MIR增强子拓扑结构的重新布线和Esrrb调节
Nadia Omega Cipta,Yingying Zeng,Ka Wai Wong et al.
Nadia Omega Cipta et al.
Background: The interplay between 3D genomic structure and transposable elements (TE) in regulating cell state-specific gene expression program is largely unknown. Here, we explore the utilization of TE-derived enhancers ...
Multi-ancestry whole genome sequencing analysis of lean body mass [0.03%]
多祖先全基因组序列分析 lean body mass
Xiaoyu Zhang,Kuan-Jui Su,Bodhisattwa Banerjee et al.
Xiaoyu Zhang et al.
Background: Lean body mass is a crucial physiological component of body composition. Although lean body mass has a high heritability, studies evaluating the genetic determinants of lean mass (LM) have to date been limited...
Meta-Analysis
Genome biology. 2025 Apr 28;26(1):106. DOI:10.1186/s13059-025-03520-x 2025
Medieval genomes from eastern Iberia illuminate the role of Morisco mass deportations in dismantling a long-standing genetic bridge with North Africa [0.03%]
来自伊比利亚半岛东部的中世纪基因组揭示摩尔人的大规模流放如何拆除了与北非长期存在的遗传联系
Gonzalo Oteo-Garcia,Marina Silva,M George B Foody et al.
Gonzalo Oteo-Garcia et al.
Background: The Islamic influence on the Iberian Peninsula left an enduring cultural and linguistic legacy. However, the demographic impact is less well understood. This study aims to explore the dynamics of gene flow and...
InSituCor: exploring spatially correlated genes conditional on the cell type landscape [0.03%]
基于细胞类型景观探索空间相关的基因(InSituCor)
Patrick Danaher,Dan McGuire,Lidan Wu et al.
Patrick Danaher et al.
In spatial transcriptomics data, spatially correlated genes promise to reveal high-interest phenomena like cell-cell interactions and latent variables. But in practice, most spatial correlations arise from the spatial arrangement of cell ty...
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...