Global atlas of enhancer-promoter interactome in cotton genome revealed by profiling RNA-RNA spatial interactions [0.03%]
棉花基因组中调控元件与转录起始位点互作的全局图谱——通过表征RNA-RNA空间构象解析棉属物种组织发育和驯化的遗传基础
Miaomiao Wen,Xiaodong Liang,Keke Shi et al.
Miaomiao Wen et al.
Background: RNA-RNA spatial interactions play crucial roles in various cellular processes, including gene transcriptional and post-transcriptional regulations. However, research on this area of RNA regulation remains limi...
Unravelling the progression of the zebrafish primary body axis with reconstructed spatiotemporal transcriptomics [0.03%]
具有时空转录组学的重建斑马鱼主轴进展解析
Yang Dong,Tao Cheng,Xiang Liu et al.
Yang Dong et al.
Background: Elucidating the spatiotemporal dynamics of gene expression is essential for understanding complex physiological and pathological processes. Current spatial transcriptomics techniques are hindered by low read d...
The repetitive genome of the Ixodes ricinus tick reveals transposable elements have driven genome evolution in ticks [0.03%]
Ixodes ricinus的重复基因组表明转座元件驱动了全基因组的进化
Isobel Ronai,Rodrigo de Paula Baptista,Nicole S Paulat et al.
Isobel Ronai et al.
Background: Ticks are obligate blood-feeding parasites associated with a huge diversity of diseases globally. The hard tick Ixodes ricinus is the key vector of Lyme borreliosis and tick-borne encephalitis in Western Euras...
Coordinated single-nucleus responses for quantitative disease resistance involve a calcium-associated switch in transcriptional noise [0.03%]
定量抗病性涉及钙相关的转录噪声开关的协调单核响应
Darcy A B Jones,Florent Delplace,Mehdi Khafif et al.
Darcy A B Jones et al.
Background: Efficient plant immune response requires concerted reprogramming of cellular transcriptomes both globally and locally at the site of infection. Upon inoculation by the fungal pathogen Sclerotinia sclerotiorum,...
Biogeography influences plant-microbe interactions and natural soil suppressiveness to black root rot disease of tobacco [0.03%]
生物地理学影响植物-微生物相互作用和烟草黑根腐病的自然土壤抑病性
Alix Catry,Danis Abrouk,Nicolas Fierling et al.
Alix Catry et al.
Background: In disease-suppressive soils, the rhizosphere microbiota protects plants from root disease(s). However, the soil microbiome follows distinct spatial patterns, and the biogeographic factors shaping plant-microb...
BASCULE: bayesian inference and clustering of mutational signatures leveraging biological priors [0.03%]
基于生物先验的突变特征的贝叶斯推断和聚类(BASCULE)
Elena Buscaroli,Azad Sadr,Riccardo Bergamin et al.
Elena Buscaroli et al.
Mutational signatures provide key insights into cancer mutational processes, but the availability of signature catalogues generated by different groups using distinct methodologies underscores a need for standardization. We introduce a Baye...
HUBMet: an integrative database and analytical platform for human blood metabolites and metabolite-protein associations [0.03%]
HUBMet代谢物和代谢物-蛋白质关联的整合型数据库和分析平台
Xingyue Wang,Xiangyu Qiao,Alberto Zenere et al.
Xingyue Wang et al.
Understanding human blood metabolites is essential for deciphering systemic physiology and disease mechanisms, yet remains challenging due to diverse origins and dynamic regulation. In this study, we develop HUBMet (https://hubmet.app.bio-i...
The differential subcellular localization of soybean transcripts, an additional regulatory mechanism of gene activity [0.03%]
大豆转录本的不同亚细胞定位及其作为基因活性的额外调节机制
Sutton Tennant,Erik J Amezquita,Yaohua Li et al.
Sutton Tennant et al.
Background: Our understanding of gene function is often driven by its expression and, a fortiori, based on its RNA abundance in a cell, a tissue, or an organ. This assumption often neglects the limited correlation between...
Sinian Xing,Kunling Chen,Haocheng Zhu et al.
Sinian Xing et al.
Published Erratum
Genome biology. 2025 Dec 24;26(1):435. DOI:10.1186/s13059-025-03894-y 2025
PepQueryMHC: rapid and comprehensive tumor antigen prioritization from immunopeptidomics data [0.03%]
PepQueryMHC：从免疫肽组学数据中快速而全面地优先确定肿瘤抗原
Seunghyuk Choi,Bing Zhang
Seunghyuk Choi
Determining tumor-specificity of MHC-bound peptides is crucial for cancer immunotherapy development, yet current methods struggle with class II peptides and non-reference sequences. We introduce PepQueryMHC, an ultra-fast tool that integrat...