UnionLoops: a workflow for calling chromatin loops across related Hi-C datasets with improved specificity, precision, and sensitivity [0.03%]
联合循环：一种用于跨相关Hi-C数据集调用染色质环的工作流程，具有更高的特异性和灵敏度
Jiangyuan Liu,Johan H Gibcus,Job Dekker
Jiangyuan Liu
Chromatin loop calling from chromatin interaction data often exhibits substantial variability across related samples. We present UnionLoops, a computational workflow for chromatin loop calling across multiple related samples. UnionLoops int...
Spatiotemporal transcriptomic analysis during cold ischemic injury to the murine kidney reveals compartment-specific changes [0.03%]
冷缺血损伤下小鼠肾脏时空转录组分析揭示隔室特异性变化
Srujan Singh,Shishir Kumar Patel,Ryo Matsuura et al.
Srujan Singh et al.
Background: Kidney transplantation is the preferred treatment strategy for end-stage kidney disease. Deceased donor kidneys usually undergo cold storage until kidney transplantation, leading to cold ischemia injury that m...
GenOT: generative optimal transport enables spatiotemporal interpolation and generation in cross-platform spatial transcriptomics [0.03%]
基于生成最优传输的跨平台空间转录组时空插值和生成方法研究
Rui Wang,Xinxin Liu,Linlin Zhuo et al.
Rui Wang et al.
Spatial transcriptomics technologies have revolutionized the analysis of spatial gene expression, yet integrating spatial information and generating data across heterogeneous samples remain challenging. We present GenOT, a generative framew...
Deciphering the mosaic genome of sugarcane cultivars through polyploid admixture inference with AdmixPoly [0.03%]
通过AdmixPoly进行甘蔗栽培品种多倍体杂交推断以解读其镶嵌基因组
Simon Rio,Franck Gauthier,Olivier Garsmeur et al.
Simon Rio et al.
Background: Characterizing population structure and admixture events between ancestral groups plays a key role in understanding the evolutionary history of species and crops. Most tools for inferring admixture have been d...
OTTR-seq profiling reveals dynamic tRNA modification landscapes across diverse archaeal species [0.03%]
基于OTTR-seq的表征揭示了广泛古菌种类中动态tRNA修饰图谱
Jesse S Leavitt,Henry T Moore,Thomas J Santangelo et al.
Jesse S Leavitt et al.
Background: Transfer RNA (tRNA) modifications are essential for structural integrity, decoding fidelity, and stress adaptation, yet their evolutionary dynamics remain poorly characterized in archaea. Here, we apply Ordere...
James M Holt,Christopher T Saunders,Egor Dolzhenko et al.
James M Holt et al.
Variant benchmarking is critical in assessing the accuracy of genomic secondary pipelines. However, traditional benchmarking tools that require exact genotype matches inject biases from variant representation and are ill-suited for tandem r...
Gapless and phased genome assembly reveals post-allopolyploidization subgenomic diversification of tobacco centromeres [0.03%]
连续性和阶段性的基因组组装揭示了烟草半保持染色体在全四倍体化后的分化
Weikai Chen,Shaoying Chen,Jingxuan Wang et al.
Weikai Chen et al.
Common tobacco (Nicotiana tabacum) is an economically important crop worldwide whose allotetraploid genome remains incompletely assembled. We present a 4.2-Gb telomere-to-telomere, gap-free, and phased genome assembly. This assembly reveals...
SINTER3D: continuous 3D reconstruction of spatial transcriptomics via implicit neural representations [0.03%]
基于隐式神经表示的连续三维空间转录组重建（SINTER3D）
Tianjiao Zhang,Shenghe Li,Hongfei Zhang et al.
Tianjiao Zhang et al.
Spatial transcriptomics enables gene-expression profiling while preserving spatial context, but three-dimensional reconstruction from discrete tissue sections remains limited by large inter-section gaps and gene-wise independent interpolati...
Taxonomy-aware, disorder-matched benchmarking of phase-separating protein predictors [0.03%]
基于_taxonomy_的干扰素紊乱匹配基准相分离蛋白质预测器
Shuang Hou,Hexin Shen,Yong Zhang
Shuang Hou
Background: Biomolecular condensates formed via liquid-liquid phase separation (LLPS) play vital roles in cellular organization and function. Computational prediction of phase-separating proteins (PSPs) is increasingly us...
A cytoplasmic index for quantifying immune-related A-to-I RNA editing [0.03%]
一种定量免疫相关的A到I RNA编辑的细胞质指数
Roni Cohen-Fultheim,Itamar Twersky,Haim Krupkin et al.
Roni Cohen-Fultheim et al.
Background: Distinguishing self from non-self is a major challenge for the immune system. Endogenous cytoplasmic double-stranded RNA (dsRNA) can mimic viral RNA and activate immune sensors like MDA5. ADAR1-mediated adenos...