SAKURA: a knowledge-guided approach to recovering important, rare signals from single-cell data [0.03%]
SAKURA：一种知识引导的方法，从单细胞数据中恢复重要且稀有的信号
Zhenghao Zhang,Jiamin Chen,Haoran Wu et al.
Zhenghao Zhang et al.
Dimensionality reduction is routinely applied to single-cell transcriptomic data to improve interpretability, remove noise and redundancy, and enable visualization. Most existing methods aim at preserving the most prominent data properties,...
Haplotype-resolved and near telomere-to-telomere assembly of the autotetraploid potato genome [0.03%]
基于单倍体型的自四倍体马铃薯基因组高解析度全端到端完整组装
Pei-Xuan Xiao,Lei Tan,Jianke Dong et al.
Pei-Xuan Xiao et al.
Background: Potato (Solanum tuberosum) breeding is severely hindered by its highly heterozygous autotetraploid genome, where complex allelic interactions impede precise trait selection. Reconstructing complete haplotype-r...
Self-supervised pretraining with NuSPIRe unlocks nuclear morphology-driven insights in spatial omics [0.03%]
基于NuSPIRe的自监督预训练解锁空间组学中的核形态驱动见解
Yuwei Hua,Shiyu Li,Yong Zhang
Yuwei Hua
Nuclear morphology encodes rich phenotypic information critical for understanding cellular states, yet its full potential remains untapped in biomedical analysis. This study introduces NuSPIRe, a self-supervised deep learning model designed...
Sex-specific nonlinear DNA methylation aging trajectories reveal biomarkers of cancer risk and inflammation [0.03%]
性别特异性非线性DNA甲基化衰老轨迹揭示了癌症风险和炎症的生物标志物
Robin Grolaux,Macsue Jacques,Bernadette Jones-Freeman et al.
Robin Grolaux et al.
Background: Aging is a multi-modal process, leaving distinct molecular signatures across the epigenome. DNA methylation is among the most robust biomarkers of biological aging, yet most studies assume linear age relations...
A comprehensive functional atlas of ALK kinase domain variants reveals resistance landscape to ALK inhibitors [0.03%]
ALK激酶结构域变异功能图谱的综合分析揭示了ROS1抑制剂耐药机制
Hyeong-Cheol Oh,Yeonseung Han,Yoojin Chang et al.
Hyeong-Cheol Oh et al.
Background: ALK gene fusions are key oncogenic drivers in cancers such as non-small cell lung cancer, where they define a molecular subtype responsive to ALK tyrosine kinase inhibitors (TKIs). However, resistance commonly...
smoppix: unified nonparametric analysis of single-molecule spatial omics data using probabilistic indices [0.03%]
SMOppyx：使用概率指标统一分析单分子空间组学数据的非参数方法
Stijn Hawinkel,Xilan Yang,Ward Poelmans et al.
Stijn Hawinkel et al.
Spatial omics technologies localize individual molecules at subcellular resolution, yet growing numbers of molecules, features and replicates set analysis challenges. We present smoppix, a nonparametric analysis method based on the probabil...
Functional correction and genome integrity with duplex base editing of β-thalassemic hematopoietic stem cells [0.03%]
功能性校正和基因组完整性与β型地中海贫血造血干细胞的双链基编辑
Nikoletta Y Papaioannou,Petros Patsali,Julia Klermund et al.
Nikoletta Y Papaioannou et al.
Background: Beta-thalassemia is among the most common monogenic disorders, posing a major global health challenge. Editing of genetic modifiers, such as BCL11A erythroid enhancer and HBG promoters, enhances fetal hemoglob...
The evolutionary history of the field vole species complex revealed by modern and ancient genomes [0.03%]
现代和古代基因组揭示的田鼠物种复合体的进化历史
Mateusz Baca,Barbara Bujalska,Danijela Popović et al.
Mateusz Baca et al.
Background: The field vole, an abundant and widespread microtine rodent, is a complex comprised of three cryptic species: the short-tailed field vole (Microtus agrestis) which is present over much of Eurasia, the Mediterr...
PolyAseqTrap: a universal tool for genome-wide identification and quantification of polyadenylation sites from different 3' end sequencing data [0.03%]
PolyAseqTrap：一种用于从不同3'端测序数据鉴定和量化多聚腺苷酸化位点的通用工具
Wenbin Ye,Xin Cheng,Xingyu Bi et al.
Wenbin Ye et al.
Alternative polyadenylation (APA) is a pervasive RNA-processing mechanism in eukaryotes that significantly promotes transcriptome and proteome diversity. Here we proposed PolyAseqTrap, an R package for probing polyA sites from diverse 3' se...
MER57E3 transposable elements regulate gene expression in a human cell model of neural development [0.03%]
MER57E3转座元件通过人体神经发育细胞模型调节基因表达
Michelle Almeida da Paz,Umut Yildiz,Minyoung Kim et al.
Michelle Almeida da Paz et al.
Background: Long dismissed as mere genomic parasites, transposable elements (TEs) are now recognized as major drivers of genome evolution. TEs serve as a source of cell-type specific cis-regulatory elements, influencing g...