HebQTLs reveal intra-subgenome regulation inducing unbalanced expression and function among bread wheat homoeologs [0.03%]
HebQTLs揭示了诱导一维表达和功能的面包小麦同源学调节不平衡的亚基因组 регуляция
Xiaoming Wang,Yuxiu Liu,Peng Zhao et al.
Xiaoming Wang et al.
Background: Polyploidy contains multiple gene copies, known as homoeologs. Differential expression of homoeologs confers expression plasticity and facilitates the adaptation and domestication of major polyploid crops. How...
FedscGen: privacy-preserving federated batch effect correction of single-cell RNA sequencing data [0.03%]
FedscGen：单细胞RNA测序数据的隐私保护联合批次效应校正
Mohammad Bakhtiari,Stefan Bonn,Fabian Theis et al.
Mohammad Bakhtiari et al.
Single-cell RNA-seq data from clinical samples often suffer from batch effects, but data sharing is limited due to genomic privacy concerns. We present FedscGen, a privacy-preserving communication-efficient federated method built upon the s...
Irene Perotti,Laura Broglia,Gian Gaetano Tartaglia et al.
Irene Perotti et al.
X-chromosome inactivation (XCI) is a crucial mechanism of dosage compensation in female mammals ensuring that genes from only one X chromosome are expressed, initiated through expression of the long noncoding RNA Xist. Recent evidence under...
Epigenetic priming of mammalian embryonic enhancer elements coordinates developmental gene networks [0.03%]
表观遗传学预示哺乳动物胚胎增强子元件协调发育基因网络
Christopher D Todd,Jannat Ijaz,Fereshteh Torabi et al.
Christopher D Todd et al.
Background: Embryonic development requires the accurate spatiotemporal execution of cell lineage-specific gene expression programs, which are controlled by transcriptional enhancers. Developmental enhancers adopt a primed...
STHD: probabilistic cell typing of single spots in whole transcriptome spatial data with high definition [0.03%]
基于单点概率细胞类型的高精度全转录组空间数据细胞亚型鉴定算法研究
Chuhanwen Sun,Yi Zhang
Chuhanwen Sun
Recent advances in spatial transcriptomics technologies have enabled gene expression profiling across the transcriptome in spots with subcellular resolution, but high sparsity and dimensionality present significant computational challenges....
Direct genetic transformation bypasses tumor-associated DNA methylation alterations [0.03%]
直接基因转化绕过了与肿瘤相关的DNA甲基化改变
Sara Hetzel,Eran Hodis,Elena Torlai Triglia et al.
Sara Hetzel et al.
Background: Tumors represent dynamically evolving populations of mutant cells, and many advances have been made in understanding the biology of their progression. However, there are key unresolved questions about the cond...
Sceptic: pseudotime analysis for time-series single-cell sequencing and imaging data [0.03%]
Skeptic：时间序列单细胞测序和成像数据的伪时间分析
Gang Li,Hyeon-Jin Kim,Sriram Pendyala et al.
Gang Li et al.
Several computational methods have been developed to construct single-cell pseudotime embeddings for extracting the temporal order of transcriptional cell states from time-series scRNA-seq datasets. However, existing methods suffer from low...
scPDA: denoising protein expression in droplet-based single-cell data [0.03%]
基于droplet的单细胞数据去噪蛋白质表达.scPDA
Ouyang Zhu,Jun Li
Ouyang Zhu
Droplet-based profiling techniques such as CITE-seq are often contaminated by technical noise. Current computational denoising methods have serious limitations, including a strong reliance on often-unavailable empty droplets or null control...
Multi-ancestry genome-wide meta-analysis of 56,241 individuals identifies known and novel cross-population and ancestry-specific associations as novel risk loci for Alzheimer's disease [0.03%]
基于56,241人的跨祖先队列的全基因组元分析鉴定出已知和新的阿尔茨海默病风险位点
Farid Rajabli,Penelope Benchek,Giuseppe Tosto et al.
Farid Rajabli et al.
Background: Limited ancestral diversity has impaired our ability to detect risk variants more prevalent in ancestry groups of predominantly non-European ancestral background in genome-wide association studies (GWAS). We c...
Meta-Analysis
Genome biology. 2025 Jul 17;26(1):210. DOI:10.1186/s13059-025-03564-z 2025
HELLS is required for maintaining proper DNA modification at human satellite repeats [0.03%]
HELLS在维持人类卫星重复序列适当的DNA修饰中是必需的
Philine Guckelberger,Leah Haut,Rosaria Tornisiello et al.
Philine Guckelberger et al.
DNA methylation regulation involves multi-layered chromatin interactions that require remodeling proteins like the helicase, lymphoid-specific (HELLS). Here, we generate HELLS and DNA methyltransferase 3A and B (DNMT3A/B) knockout human plu...