TORC: Target-Oriented Reference Construction for supervised cell-type identification in scRNA-seq [0.03%]
基于目标导向参考构建的单细胞转录组监督分类方法研究
Xin Wei,Wenjing Ma,Zhijin Wu et al.
Xin Wei et al.
Cell-type identification is a crucial step in single cell RNA-seq (scRNA-seq) data analysis, for which supervised methods are preferred due to their accuracy and efficiency. Performance is highly dependent on the quality of the reference da...
DNA G-quadruplex structures act as functional elements in α- and β-globin enhancers [0.03%]
DNA G-四链体结构作为α-和β-血红蛋白增强子中的功能元件
Colm Doyle,Krzysztof Herka,Sean M Flynn et al.
Colm Doyle et al.
Background: Enhancer elements interact with target genes at a distance to modulate their expression, but the molecular details of enhancer-promoter interaction are incompletely understood. G-quadruplex DNA secondary struc...
Identifying associations of de novo noncoding variants with autism through integration of gene expression, sequence, and sex information [0.03%]
通过基因表达、序列和性别信息的整合来识别自闭症的新发非编码变异关联
Runjia Li,Jason Ernst
Runjia Li
Background: Whole-genome sequencing (WGS) data has facilitated genome-wide identification of rare noncoding variants. However, elucidating these variants' associations with complex diseases remains challenging. A previous...
Transcriptional analysis of metastatic hormone-naïve prostate cancer primary tumor biopsies reveals a relevant role for SOX11 in prostate cancer cell dissemination [0.03%]
转录分析转移性非去势前列腺癌的活检标本发现SOX11在前列腺癌细胞播散中具有相关作用
Natalia Martin-Martin,Saioa Garcia-Longarte,Jon Corres-Mendizabal et al.
Natalia Martin-Martin et al.
Background: Metastatic hormone-naïve prostate cancer (mHNPC) is an infrequent form of this tumor type that is characterized by metastasis at the time of diagnosis and accounts for up to 50% of prostate cancer-related dea...
A resource for whole-body gene expression map of human tissues based on integration of single cell and bulk transcriptomics [0.03%]
基于单细胞和批量转录组学整合的人类组织全基因表达图谱资源
Mengnan Shi,Loren Méar,Max Karlsson et al.
Mengnan Shi et al.
New technologies enable single-cell transcriptome analysis, mapping genome-wide expression across the human body. Here, we present an extended analysis of protein-coding genes in all major human tissues and organs, combining single-cell and...
DeepGFT: identifying spatial domains in spatial transcriptomics of complex and 3D tissue using deep learning and graph Fourier transform [0.03%]
基于深度学习和图傅里叶变换的复杂及三维组织空间转录组学区域识别
Shuli Sun,Jixin Liu,Guojun Li et al.
Shuli Sun et al.
The rapid advancements in spatially resolved transcriptomics (SRT) enable the characterization of gene expressions while preserving spatial information. However, high dropout rates and noise hinder accurate spatial domain identification for...
Publisher Correction: Analyzing the relationship of RNA and DNA methylation with gene expression [0.03%]
出版更正：分析RNA和DNA甲基化与基因表达之间的关系
Shangqian Xie,Darren Hagen,Gabrielle M Becker et al.
Shangqian Xie et al.
Published Erratum
Genome biology. 2025 Jun 3;26(1):151. DOI:10.1186/s13059-025-03632-4 2025
Yi Wang,Kyla Woyshner,Chaichontat Sriworarat et al.
Yi Wang et al.
Analyzing multi-sample spatial transcriptomics data requires accounting for biological variation. We present multi-sample non-negative spatial factorization (mNSF), an alignment-free framework extending single-sample spatial factorization t...
Differential epigenetic regulation by blue and UV-A light reveals the key role of CsSDG36-mediated H3K4 methylation in leaf development and secondary metabolism in Camellia sinensis [0.03%]
蓝光和UV-A光的差异表观调控揭示了CsSDG36介导的H3K4甲基化在茶树叶片发育及次生代谢中的关键作用
Pu Wang,Hong Zhang,Yongli Yin et al.
Pu Wang et al.
Background: There is a Chinese proverb that good tea comes from high mountains with clouds and mists, suggesting the important impact of environmental factors on the development and secondary metabolism in tea plants. How...
Microbial inoculants modulate the rhizosphere microbiome, alleviate plant stress responses, and enhance maize growth at field scale [0.03%]
微生物制剂可以调节根际微生态系统，缓解植物应对逆境的生理反应，并在田间尺度上增加玉米产量
Davide Francioli,Ioannis D Kampouris,Theresa Kuhl-Nagel et al.
Davide Francioli et al.
Background: Field inoculation of crops with beneficial microbes is a promising sustainable strategy to enhance plant fitness and nutrient acquisition. However, effectiveness can vary due to environmental factors, microbia...