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...
A survey of computational approaches for characterizing microbial interactions in microbial mats [0.03%]
用于表征微生物被膜中微生物相互作用的计算方法综述
Vanesa L Perillo,Michael Nute,Nicolae Sapoval et al.
Vanesa L Perillo et al.
In this review, we use microbial mat communities as a general model system to highlight the strengths and limitations of current computational methods for analyzing interactions between members of microbial ecosystems. We describe the facto...
cuteFC: regenotyping structural variants through an accurate and efficient force-calling method [0.03%]
cuteFC：通过准确高效的强制调用方法对结构变异进行重分型
Tao Jiang,Shuqi Cao,Yadong Liu et al.
Tao Jiang et al.
Long-read sequencing technologies have great potential for the comprehensive discovery of structural variations (SVs). However, accurate genotype assignment for SVs remains challenging due to unavoidable sequencing errors, limited coverage,...
Cancer gene identification from RNA variant allelic frequencies using RVdriver [0.03%]
基于RNA变异等位基因频率的癌症驱动基因识别算法RVdriver
James R M Black,Thomas P Jones,Carlos Martínez-Ruiz et al.
James R M Black et al.
Existing approaches to identifying cancer genes rely overwhelmingly on DNA sequencing data. Here, we introduce RVdriver, a computational tool that leverages paired bulk genomic and transcriptomic data to classify RNA variant allele frequenc...
Engineering novel CRISPRi repressors for highly efficient mammalian gene regulation [0.03%]
高效的哺乳动物基因调控的新型CRISPR干扰阻遏物工程化
Andrew Kristof,Krithika Karunakaran,Christopher Allen et al.
Andrew Kristof et al.
Background: CRISPR interference (CRISPRi), the repurposing of the RNA-guided endonuclease dCas9 as a programmable transcriptional repressor, allows highly specific repression (knockdown) of gene expression. CRISPRi platfo...
MINGLE: a mutual information-based interpretable framework for automatic cell type annotation in single-cell chromatin accessibility data [0.03%]
Siyu Li,Yifan Huang,Shengquan Chen
Siyu Li
Single-cell chromatin accessibility sequencing (scCAS) has proven invaluable for investigating the intricate landscape of epigenomic heterogeneity. We propose MINGLE, a mutual information-based interpretable framework that leverages cellula...