CellMemory: hierarchical interpretation of out-of-distribution cells using bottlenecked transformer [0.03%]
基于瓶颈变压器的异常单元的层次化解释(CellMemory)
Qifei Wang,He Zhu,Yiwen Hu et al.
Qifei Wang et al.
Machine learning methods, especially Transformer architectures, have been widely employed in single-cell omics studies. However, interpretability and accurate representation of out-of-distribution (OOD) cells remains challenging. Inspired b...
Loop Catalog: a comprehensive HiChIP database of human and mouse samples [0.03%]
循环目录：人类和小鼠样本的全面HiChIP数据库
Joaquin Reyna,Kyra Fetter,Romeo Ignacio et al.
Joaquin Reyna et al.
HiChIP enables cost-effective and high-resolution profiling of chromatin loops. To leverage the increasing number of HiChIP datasets, we develop Loop Catalog ( https://loopcatalog.lji.org ), a web-based database featuring loop calls from ov...
Comparison of spatial transcriptomics technologies using tumor cryosections [0.03%]
基于肿瘤冷冻切片的类空间转录组技术比较研究
Anne Rademacher,Alik Huseynov,Michele Bortolomeazzi et al.
Anne Rademacher et al.
Background: Spatial transcriptomics technologies are revolutionizing our understanding of intra-tumor heterogeneity and the tumor microenvironment by revealing single-cell molecular profiles within their spatial tissue co...
scExtract: leveraging large language models for fully automated single-cell RNA-seq data annotation and prior-informed multi-dataset integration [0.03%]
基于大型语言模型的单细胞RNA序列数据全自动注释和先验知识引导多数据集集成工具scExtract
Yuxuan Wu,Fuchou Tang
Yuxuan Wu
Single-cell RNA sequencing has revolutionized cellular heterogeneity research, but analyzing the abundance of unannotated public datasets remains challenging. We present scExtract, a framework leveraging large language models to automate sc...
KPop: accurate and scalable comparative analysis of microbial genomes by sequence embeddings [0.03%]
基于序列嵌入的准确可扩展的微生物基因组比较分析(KPop)
Xavier Didelot,Paolo Ribeca
Xavier Didelot
Here we introduce KPop, a novel versatile method based on full k-mer spectra and dataset-specific transformations, through which thousands of assembled or unassembled microbial genomes can be quickly compared. Unlike MinHash-based methods t...
Comparative Study
Genome biology. 2025 Jun 18;26(1):170. DOI:10.1186/s13059-025-03585-8 2025
k-mer-based GWAS in a wheat collection reveals novel and diverse sources of powdery mildew resistance [0.03%]
基于k-mer的小麦群体全基因组关联分析揭示了多种新的抗白粉病资源
Benjamin Jaegle,Yoav Voichek,Max Haupt et al.
Benjamin Jaegle et al.
Wheat genetic resources hold the diversity required to mitigate agricultural challenges from climate change and reduced inputs. Using DArTseq, we genotype 461 wheat landraces and cultivars and evaluate them for powdery mildew resistance. By...
Intragenomic conflict associated with extreme phenotypic plasticity in queen-worker caste determination in honey bees (Apis mellifera) [0.03%]
与极端表型可塑性相关的种内基因组冲突：蜜蜂蜂后和工蜂品级决定中的现象
Sean T Bresnahan,Shaun Mahony,Kate Anton et al.
Sean T Bresnahan et al.
Background: Caste determination of honey bees (Apis mellifera) exemplifies developmental plasticity, where differences in larval diet result in identical genotypes yielding either long-lived, reproductive queens or short-...
Vispro improves imaging analysis for Visium spatial transcriptomics [0.03%]
Vispro改善了Visium空间转录组学的成像分析
Huifang Ma,Xingyuan Zhang,Yilong Qu et al.
Huifang Ma et al.
Spatial transcriptomics enables spatially resolved gene expression analysis, but accompanying histology images are often degraded by fiducial markers and background regions, hindering interpretation. To address this, we introduce Vispro, an...
Vikram S Shivakumar,Ben Langmead
Vikram S Shivakumar
Aligning genomes into common coordinates is central to pangenome construction, though computationally expensive. Multi-sequence maximal unique matches (multi-MUMs) help to frame and solve the multiple alignment problem. We introduce Mumemto...
Abundant and metabolically flexible bacterial lineages underlie a vast potential for rubisco-mediated carbon fixation in the dark ocean [0.03%]
暗淡海洋中丰富的代谢灵活的细菌谱系构成了核糖体依赖性碳固定的巨大潜力
Alexander L Jaffe,Rebecca S R Salcedo,Anne E Dekas
Alexander L Jaffe
Background: Rubisco is among the most abundant enzymes on Earth and is a critical conduit for inorganic carbon into the biosphere. Despite this, the full extent of rubisco diversity and the biology of organisms that emplo...