Nucleic Acids Research最新文献

SDMap: a comprehensive database of spatial drug perturbation maps. SDMap：空间药物摄动图的综合数据库。

IF 14.9 2区生物学

Nucleic Acids Research Pub Date : 2025-10-22 DOI: 10.1093/nar/gkaf1046

Feng Li,Zhe Chen,Yifang Zhang,Xinguo Ye,Wenli Fan,Anhui Kang,Xinyu Song,Liying Pei,Quan Qi,Wensong Liu,Zhengliang Zha,Yunpeng Zhang,Chunlong Zhang,Yanjun Xu

{"title":"SDMap: a comprehensive database of spatial drug perturbation maps.","authors":"Feng Li,Zhe Chen,Yifang Zhang,Xinguo Ye,Wenli Fan,Anhui Kang,Xinyu Song,Liying Pei,Quan Qi,Wensong Liu,Zhengliang Zha,Yunpeng Zhang,Chunlong Zhang,Yanjun Xu","doi":"10.1093/nar/gkaf1046","DOIUrl":"https://doi.org/10.1093/nar/gkaf1046","url":null,"abstract":"The arrangement patterns and spatial distribution features of cells within tissues are key regulators of drug actions and cellular responses; however, the specific spatial microenvironment that mediates drug actions and efficacy remains to be elucidated. Here, we introduce SDMap (http://bio-bigdata.hrbmu.edu.cn/SDMap/), a database to dissect the spatial distributions of drug-associated cells and spatial contexts that contribute to drug actions. SDMap establishes connections between 5 490 079 spatial locations (spots/cells) derived from 989 slices of 35 human tissues (including disease-state slices) and 538 419 instances across 33 149 drugs. It also offers 10 user-friendly tools for retrieving and analyzing: (i) associations between drug-associated instances and spatial spots/cells, niches, or cell types; (ii) the influence of spatial drug target activity on drug actions; (iii) drug-associated instances exhibiting highly variable spatial perturbation effects; (iv) the perturbation effects of drug dosage and duration on the spatial microenvironment; (v) spatial differentiation trajectories of drug-perturbed cells; (vi) the impact of spatial cellular functional activity on drug perturbation; (vii) spatial perturbation effect maps of drug combinations; and (viii) 3D maps of drug perturbation effects within spatial tissue contexts. SDMap is anticipated to yield critical insights into how spatial heterogeneity influences drug actions, and serve as a comprehensive database for identifying spatially resolved precision therapy targets and elucidating drug-associated mechanisms.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"21 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2025-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145338693","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Spatial2GWAS: a database for linking spatial transcriptomic regions with GWAS traits. Spatial2GWAS：连接空间转录组区域与GWAS性状的数据库。

IF 14.9 2区生物学

Nucleic Acids Research Pub Date : 2025-10-22 DOI: 10.1093/nar/gkaf1047

Xi Hu,Aoqi Wang,Huan Yu,Pora Kim,Xiaobo Zhou

{"title":"Spatial2GWAS: a database for linking spatial transcriptomic regions with GWAS traits.","authors":"Xi Hu,Aoqi Wang,Huan Yu,Pora Kim,Xiaobo Zhou","doi":"10.1093/nar/gkaf1047","DOIUrl":"https://doi.org/10.1093/nar/gkaf1047","url":null,"abstract":"Spatial heterogeneity of gene expression within tissue regions has a critical influence on biological functions, thereby affecting disease pathogenesis. However, systematic associations between spatially resolved transcriptomes and phenotypes, especially in complex diseases, remain underexplored. Here, we developed spatial2GWAS (http://www.spatial2gwas.cn), a comprehensive resource linking spatial transcriptomic (ST) regions with GWAS traits. In the database, we collected 1196 ST slices (human and mouse) from five technologies and 812 GWAS traits spanning 18 phenotype categories and identified 29 701 ST slice-GWAS trait pairs containing 47 492 significant regions. Functional analyses reveal distinct patterns of cell type composition, gene expression, GO/KEGG pathway activation, and cell-cell communication direction between trait-related and unrelated spatial regions. The database provides a user-friendly interface for visualization of spatial regions and GWAS trait associations, supporting advanced queries by slice and GWAS information, genes co-expressed with GWAS trait-associated genes, and spatial regions. Spatial2GWAS aims to enable systematic exploration of spatial mechanisms underlying complex traits and offer insights into region-specific biological functions and potential therapeutic targets. This database bridges ST and high-level phenotypes, advancing the understanding of tissue heterogeneity in complex human diseases.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"108 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2025-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145338698","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

CIRCpedia v3: an interactive database for circular RNA characterization and functional exploration. CIRCpedia v3：用于环状RNA表征和功能探索的交互式数据库。

IF 14.9 2区生物学

Nucleic Acids Research Pub Date : 2025-10-22 DOI: 10.1093/nar/gkaf1039

Si-Nan Zhai,Yu-Yao Zhang,Mo-Han Chen,Zhi-Can Fu,Ling-Ling Chen,Xu-Kai Ma,Li Yang

{"title":"CIRCpedia v3: an interactive database for circular RNA characterization and functional exploration.","authors":"Si-Nan Zhai,Yu-Yao Zhang,Mo-Han Chen,Zhi-Can Fu,Ling-Ling Chen,Xu-Kai Ma,Li Yang","doi":"10.1093/nar/gkaf1039","DOIUrl":"https://doi.org/10.1093/nar/gkaf1039","url":null,"abstract":"Recent advances on genome-wide profiling and characterization of circular RNAs have suggested their versatile roles in diverse biological processes, yet systematic elucidation of their molecular characteristics and functional mechanisms remains challenging. Here, we introduce CIRCpedia v3 (https://bits.fudan.edu.cn/circpediav3), an expanded repository to annotate both circular RNAs from back-splicing of exons (circRNAs) and circular RNAs from intron lariats (ciRNAs) by profiling 2413 sequencing datasets across 20 species. Building upon the previous version of CIRCpedia, this release identifies >2 million circular RNAs and introduces transformative advances to facilitate circular RNA research: (i) community-recommended nomenclature with enhanced molecular profiling, enabling quantitative comparison of circular/linear isoform dynamics; (ii) an interactive platform with real-time comparative analyses of circRNAs and visualizations; and (iii) integrated toolkits to identify base-editable sites, predict circRNA subcellular localization, detect circRNA degradation signals for stability optimization, predict m6A modification sites, assess circRNA coding potential, and design divergent polymerase chain reaction primers and small interfering RNAs (siRNAs). By integrating insights from cross-species expression, molecular characterization, and functional predictions, CIRCpedia v3 empowers researchers to prioritize context-specific circular RNA candidates in biological or disease conditions and to accelerate mechanistic discovery and therapeutic development.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"44 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2025-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145338691","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

GTDB release 10: a complete and systematic taxonomy for 715 230 bacterial and 17 245 archaeal genomes. GTDB release 10: 715230个细菌基因组和17245个古细菌基因组的完整系统分类。

IF 14.9 2区生物学

Nucleic Acids Research Pub Date : 2025-10-22 DOI: 10.1093/nar/gkaf1040

Donovan H Parks,Pierre-Alain Chaumeil,Aaron J Mussig,Christian Rinke,Maria Chuvochina,Philip Hugenholtz

引用次数: 0

riboCIRC v2.0: an expanded resource for translatable CircRNAs. riboCIRC v2.0：可翻译circrna的扩展资源。

IF 14.9 2区生物学

Nucleic Acids Research Pub Date : 2025-10-21 DOI: 10.1093/nar/gkaf1022

Yunhao Xu,Lei Yang,Yuewen Tang,Yan Wang,Hongwei Wang

{"title":"riboCIRC v2.0: an expanded resource for translatable CircRNAs.","authors":"Yunhao Xu,Lei Yang,Yuewen Tang,Yan Wang,Hongwei Wang","doi":"10.1093/nar/gkaf1022","DOIUrl":"https://doi.org/10.1093/nar/gkaf1022","url":null,"abstract":"riboCIRC (http://www.ribocirc.com) is a translatome data-oriented database dedicated to cataloging translatable circRNAs and their encoded peptides across six model species, including Homo sapiens, Mus musculus, Rattus norvegicus, Caenorhabditis elegans, Drosophila melanogaster, and Danio rerio. Here, we present riboCIRC v2.0, a major update featuring expanded content and enhanced functionality to facilitate and accelerate research into circRNA translation and function characterization. Key improvements include (i) expanded data coverage: now documenting 5212 computationally predicted translatable circRNAs and 7563 predicted finite ORF-encoded peptides, representing a substantial increase from the initial release (2247 and 2234 entries, respectively); (ii) enhanced evidence integration: incorporation of new evidence layers supporting translation of circRNAs, including RNA editing sites and RBP interactions, supplementing existing evidence from ribosome profiling, mass spectrometry, IRES elements, and m6A modifications; (iii) comprehensive peptide annotation: systematic in silico characterization of finite ORF-encoded peptides, detailing their physicochemical properties, predicted structures, and potential functions; and (iv) optimized user interface: improved navigation and dedicated modules for streamlined data exploration, retrieval, and visualization. Collectively, these enhancements establish riboCIRC v2.0 as a more powerful resource for investigating the functional roles of translatable circRNAs and their products across diverse biological systems.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"2 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2025-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145338570","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

SmallBARNA 2026: a kingdom-wide bacterial sRNA resource. SmallBARNA 2026：全细菌sRNA资源。

IF 14.9 2区生物学

Nucleic Acids Research Pub Date : 2025-10-21 DOI: 10.1093/nar/gkaf999

Shusruto Rishik,Leidy Alejandra G Molano,Syed Mohammed Khalid,Tiniko Babalashvili,Fadlilah Nur Hasanah,Md Mobashir Rahman,Pascal Hirsch,Friederike Grandke,Emma S Hoffmann,Tobias W Wolff,Georges P Schmartz,Andreas Keller

{"title":"SmallBARNA 2026: a kingdom-wide bacterial sRNA resource.","authors":"Shusruto Rishik,Leidy Alejandra G Molano,Syed Mohammed Khalid,Tiniko Babalashvili,Fadlilah Nur Hasanah,Md Mobashir Rahman,Pascal Hirsch,Friederike Grandke,Emma S Hoffmann,Tobias W Wolff,Georges P Schmartz,Andreas Keller","doi":"10.1093/nar/gkaf999","DOIUrl":"https://doi.org/10.1093/nar/gkaf999","url":null,"abstract":"Bacterial small RNA are important context-sensitive regulators of gene expression, especially in highly pathogenic bacteria, often controlling virulence. The number of predicted small RNA (sRNA) entries in public repositories has grown exponentially, contrasting with the linear growth of functionally validated sRNAs. While there are databases maintaining sRNA records from single bacterial species or taxonomic groups, a central repository of bona fide sRNAs for all bacteria with evidence, alignment, and RNA expression information is missing. Such a repository is a critical starting point for both wet lab biologists validating sRNA function as well as bioinformaticians creating new models for sRNA prediction. In this paper, we hand-curate 1117 articles from the literature to find 746 sRNAs that have been confirmed by northern blotting, quantitative polymerase chain reaction (qPCR), mutagenesis, or other functional validation methods. We map these sRNA sequences to QC-filtered bacterial genomic assemblies from NCBI, obtaining 3.8 million hits from 44 789 chromosomes and 10 884 plasmids. Finally, we also quantify these sRNAs in a filtered subset of 5292 isolates with available RNA-seq data from the Sequence Read Archive. The bona fide set, alignment, and expression information is available for download and interactive exploration at https://web.ccb.uni-saarland.de/smallbarna/.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"52 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2025-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145338568","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

MouseOmics: a multi-omics database for mouse biological study. MouseOmics：用于小鼠生物学研究的多组学数据库。

IF 14.9 2区生物学

Nucleic Acids Research Pub Date : 2025-10-21 DOI: 10.1093/nar/gkaf1031

Xin Tian,Yifan Teng,Miaomiao Huang,Qian Zhang,Juan Huang,Yong Chen,Ao Wu,Qishan Wang,Jingyin Yu,Jie Feng

{"title":"MouseOmics: a multi-omics database for mouse biological study.","authors":"Xin Tian,Yifan Teng,Miaomiao Huang,Qian Zhang,Juan Huang,Yong Chen,Ao Wu,Qishan Wang,Jingyin Yu,Jie Feng","doi":"10.1093/nar/gkaf1031","DOIUrl":"https://doi.org/10.1093/nar/gkaf1031","url":null,"abstract":"Mouse represents a pivotal model and indispensable resource in medical and life sciences, widely used for developmental biology and multi-omics studies. Yet, a comprehensive, integrated mouse multi-omics database remains lacking. Here, we established a mouse multi-omics database, MouseOmics, by integrating 21 genomes distributed among five species within the genus Mus, transcriptomes in 584 tissue samples, proteomes in 285 tissue samples, metabolomes in 143 tissue samples, metallomes in 296 tissue samples, and three variomes covering 52 mouse inbred strains. All mouse multi-omics data can be explored through multiple functional modules with user-friendly web interface. Furthermore, we embedded several useful tools, like MISAweb, for the identification of microsatellite DNAs, and specifically developed the enrichment analysis modules of InterPro, Gene Ontology, and Pathway for mouse. The mouse multi-omics data can be downloaded online conveniently. MouseOmics will be updated regularly with the newly released mouse multi-omics data and can be accessed freely via the address https://www.varnatech.cn/MouseOmics.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"1 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2025-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145338567","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Structure of Bacillus subtilis Ku-mediated DNA synaptic complex. 枯草芽孢杆菌ku介导的DNA突触复合体的结构。

IF 14.9 2区生物学

Nucleic Acids Research Pub Date : 2025-10-21 DOI: 10.1093/nar/gkaf1036

Whan-Jong Kim,Jieun Kim,Mingyu Jo,Youngjin Kim,Min-Sung Kim

引用次数: 0

Ribocentre-aptamer: an integrative, structure-focused database for RNA aptamers. 核糖中心-适体：一个整合的，以结构为中心的RNA适体数据库。

IF 14.9 2区生物学

Nucleic Acids Research Pub Date : 2025-10-21 DOI: 10.1093/nar/gkaf1016

Zhizhong Lu,Hao Sun,Bo Fu,Ying Ao,Jiali Wang,Ke Chen,Yuhang Luo,Linfei Li,Zhaoji Qiu,Jiaxin Zhao,Yuxuan Sun,Zhijie Tan,Qiaozhen Liu,Yangyi Ren,Ziyu Guo,Xiaoxue Chen,Yuanlin He,Yingying Zhao,Yixin Chen,Mengxiao Li,Xuemei Peng,Baowei Huang,Shuang Zhu,Lin Huang,Zhichao Miao

{"title":"Ribocentre-aptamer: an integrative, structure-focused database for RNA aptamers.","authors":"Zhizhong Lu,Hao Sun,Bo Fu,Ying Ao,Jiali Wang,Ke Chen,Yuhang Luo,Linfei Li,Zhaoji Qiu,Jiaxin Zhao,Yuxuan Sun,Zhijie Tan,Qiaozhen Liu,Yangyi Ren,Ziyu Guo,Xiaoxue Chen,Yuanlin He,Yingying Zhao,Yixin Chen,Mengxiao Li,Xuemei Peng,Baowei Huang,Shuang Zhu,Lin Huang,Zhichao Miao","doi":"10.1093/nar/gkaf1016","DOIUrl":"https://doi.org/10.1093/nar/gkaf1016","url":null,"abstract":"RNA aptamers function as 'chemical antibodies' with advantages in binding to diverse ligands, enabling transformative applications in diagnostics, therapeutics, and biosensing. Despite these potential and existing databases, rational aptamer design is hindered by the lack of integrated resources coupling experimentally determined structural data with ligand-binding mechanisms. Here, we present Ribocentre-aptamer (https://aptamer.ribocentre.org/), a manually curated database to capture the molecular mechanism of RNA aptamer binding. Our resource systematically catalogues 191 aptamer types across 669 publications, unifying 510 sequences, 123 small-molecule ligands, and 344 protein ligands with experimentally resolved secondary/tertiary structures, ligand-binding pockets, affinity metrics, and functional annotations. Ribocentre-aptamer aims to bridge molecular mechanism discovery with translational engineering, providing an indispensable platform for advancing aptamer science.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"71 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2025-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145338566","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

RNAPaceDB: a dedicated database to dissect RNA velocity across diverse cell types. RNAPaceDB：一个专门分析不同细胞类型的RNA速度的数据库。

IF 14.9 2区生物学

Nucleic Acids Research Pub Date : 2025-10-21 DOI: 10.1093/nar/gkaf1045

Hui Liu,Honghan Zhou,Siru Yang,Weicheng Ma,Jun Wang,Nan Zhang,Huicheng Zhang,Wen Huang,Xin Zhong,Chaohan Xu,Shuyuan Wang

{"title":"RNAPaceDB: a dedicated database to dissect RNA velocity across diverse cell types.","authors":"Hui Liu,Honghan Zhou,Siru Yang,Weicheng Ma,Jun Wang,Nan Zhang,Huicheng Zhang,Wen Huang,Xin Zhong,Chaohan Xu,Shuyuan Wang","doi":"10.1093/nar/gkaf1045","DOIUrl":"https://doi.org/10.1093/nar/gkaf1045","url":null,"abstract":"RNA velocity, which reflects the balance between nascent RNA synthesis and mature RNA degradation, provides a kinetic perspective to explore gene expression dynamics and cellular state transitions, offering profound insights into diverse biological processes and disease mechanisms. Deciphering RNA velocity patterns across cell types and contexts will deepen our understanding of the temporal logic of gene regulation and facilitating the discovery of novel biomarkers and therapeutic targets. Here, we present RNAPaceDB (http://biocclab.cn/RNAPaceDB/), a dedicated database to dissect RNA velocity across diverse cell types. RNAPaceDB integrates single-cell RNA sequencing profiles from 144 datasets, encompassing over 2.1 million cells across 81 cell types and 41 diseases, and offers 4380 velocity stream plots derived from six computational models. Using RNAPaceDB, users can explore RNA velocity profiles of >18 000 genes across cell development processes. Additionally, RNAPaceDB provides integrated online interfaces to retrieve and analyze cell cluster distribution, cell development trajectories, cell type-specific differential velocity genes, and functional enrichments under varying conditions. Collectively, RNAPaceDB serves as a valuable resource for deciphering the temporal logic of gene expression dynamics, facilitating discoveries of regulatory mechanisms, biomarkers, and therapeutic targets in precision medicine and systems biology.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"41 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2025-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145338569","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0