MaskGraphene: an advanced framework for interpretable joint representation for multi-slice, multi-condition spatial transcriptomics [0.03%]
MaskGraphene：一种用于多层、多条件空间转录组学的可解释联合表示的先进框架
Yunfei Hu,Zhenhan Lin,Manfei Xie et al.
Yunfei Hu et al.
Recent advances in spatial transcriptomics (ST) highlight the need to integrate multiple slices for joint analysis. A key challenge is generating interpretable embeddings that preserve spatial geometry while correcting batch effects. We pre...
ERV3-MLT1 provides cis-regulatory elements for human placental functioning and are commonly dysregulated in human-specific preeclampsia [0.03%]
ERV3-MLT1为人类胎盘功能提供顺式调控元件，并且在人类特有的子痫前期中通常被共同调节紊乱
Rabia Anwar,Amit Pande,Manvendra Singh et al.
Rabia Anwar et al.
Background: Owing to their transcription factor binding sites, endogenous retroviruses (ERVs) can act as cis-regulatory-elements (CREs). By invading genomes in waves, ERVs offer a substrate for lineage-specific adaptation...
Transposable elements drive species-specific and tissue-specific transcriptomes in human development [0.03%]
转座元件驱动人类发育中物种特异性和组织特异性转录组
Yun Zhang,Jianqi She,Xueyan Hu et al.
Yun Zhang et al.
Background: Transposable elements (TEs) are an abundant and crucial regulatory resource in the human genome. Serving as alternative promoters, TEs can be reactivated and produce TE-initiated transcripts, which play import...
Comprehensive evaluation of diverse massively parallel reporter assays to functionally characterize human enhancers genome-wide [0.03%]
全面评估多种大规模并行报告基因检测方法以功能表征全基因组范围内的增强子元件
Junke Zhang,Alden King-Yung Leung,Yutong Zhu et al.
Junke Zhang et al.
Background: Massively parallel reporter assays (MPRAs) and self-transcribing active regulatory region sequencing (STARR-seq) have revolutionized enhancer characterization by enabling high-throughput functional assessment ...
Natural language processing of gene descriptions for overrepresentation analysis with GeneTEA [0.03%]
基于GeneTEA的基因描述文本的自然语言处理及富集分析方法
Isabella A Boyle,Nayeem Akram Aquib,Mustafa Kocak et al.
Isabella A Boyle et al.
Overrepresentation analysis is used to identify biological enrichment in a list of genes. Here, we introduce GeneTEA, a model that ingests free-text gene descriptions and incorporates natural language processing methods to learn a sparse ge...
Lactate-binding protein DNMT3A in HRMECs promotes angiogenesis by upregulating VEGFA through HIF-1α lactylation [0.03%]
乳酸结合蛋白DNMT3A通过HIF-1α乳酰化在HRMECs中促进血管生成以上调VEGFA
Xiaotang Wang,Jiaxing Huang,Wei Fan et al.
Xiaotang Wang et al.
Background: Ocular neovascularization is a leading cause of blindness. Hypoxia is associated with retinal angiogenesis. Hypoxia results in lactate accumulation, which typically precedes protein lactylation, and this plays...
Minkyoung Lee,Ilhan E Acar,Davide Eletto et al.
Minkyoung Lee et al.
Background: Subcellular RNA localization is crucial for the spatio-temporal control of protein synthesis and underlies key processes during development, homeostasis, and disease. In epithelial cells, RNA can localize asym...
Stratifying variant deleteriousness and trait-modulating effect under human recent adaptation using the FIND model [0.03%]
基于FIND模型的有害突变分层及近期选择作用分析
Xutong Fan,Dandan Huang,Zhikun Wu et al.
Xutong Fan et al.
Existing methods to distinguish deleterious/pathogenic from neutral variants still inadequately capture the full spectrum of genetic variant impact on fitness and disease susceptibility. We introduce the FIND model, which stratifies genetic...
Cross-expression meta-analysis of mouse brain slices reveals coordinated gene expression across spatially adjacent cells [0.03%]
小鼠脑切片的跨表达元分析揭示了空间相邻细胞间的协调基因表达
Ameer Sarwar,Mara Rue,Leon French et al.
Ameer Sarwar et al.
Background: Spatial transcriptomics allow us to ask a fundamental question: how do nearby cells orchestrate their gene expression? Rather than focus on how these cells (samples) communicate with each other, we reframe the...
Meta-Analysis
Genome biology. 2025 Oct 29;26(1):373. DOI:10.1186/s13059-025-03747-8 2025
The role of FRUITFULL controlling cell cycle during early flower development revealed by time-series snRNA-seq experiments [0.03%]
利用时间序列单细胞核转录组测序揭示FRUITFULL在花早期发育中调控细胞周期的作用
Peilin Chen,Xiaocai Xu,Cezary Smaczniak et al.
Peilin Chen et al.
Background: Starting from pools of undifferentiated cells, plants generate new organs postembryonically in response to external and endogenous signals. This requires a dynamic coordination of cell division with cellular g...