Nucleic Acids Research最新文献_第10页

MOBIDB in 2025: integrating ensemble properties and function annotations for intrinsically disordered proteins. 2025 年的 MOBIDB：整合内在无序蛋白质的集合属性和功能注释。

IF 16.6 2区生物学

Nucleic Acids Research Pub Date : 2025-01-06 DOI: 10.1093/nar/gkae969

Damiano Piovesan, Alessio Del Conte, Mahta Mehdiabadi, Maria Cristina Aspromonte, Matthias Blum, Giulio Tesei, Sören von Bülow, Kresten Lindorff-Larsen, Silvio C E Tosatto

{"title":"MOBIDB in 2025: integrating ensemble properties and function annotations for intrinsically disordered proteins.","authors":"Damiano Piovesan, Alessio Del Conte, Mahta Mehdiabadi, Maria Cristina Aspromonte, Matthias Blum, Giulio Tesei, Sören von Bülow, Kresten Lindorff-Larsen, Silvio C E Tosatto","doi":"10.1093/nar/gkae969","DOIUrl":"10.1093/nar/gkae969","url":null,"abstract":"The MobiDB database (URL: https://mobidb.org/) aims to provide structural and functional information about intrinsic protein disorder, aggregating annotations from the literature, experimental data, and predictions for all known protein sequences. Here, we describe the improvements made to our resource to capture more information, simplify access to the aggregated data, and increase documentation of all MobiDB features. Compared to the previous release, all underlying pipeline modules were updated. The prediction module is ten times faster and can detect if a predicted disordered region is structurally extended or compact. The PDB component is now able to process large cryo-EM structures extending the number of processed entries. The entry page has been restyled to highlight functional aspects of disorder and all graphical modules have been completely reimplemented for better flexibility and faster rendering. The server has been improved to optimise bulk downloads. Annotation provenance has been standardised by adopting ECO terms. Finally, we propagated disorder function (IDPO and GO terms) from the DisProt database exploiting sequence similarity and protein embeddings. These improvements, along with the addition of comprehensive training material, offer a more intuitive interface and novel functional knowledge about intrinsic disorder.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":" ","pages":"D495-D503"},"PeriodicalIF":16.6,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11701742/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142522582","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

PolyASite v3.0: a multi-species atlas of polyadenylation sites inferred from single-cell RNA-sequencing data. PolyASite v3.0：从单细胞 RNA 序列数据推断出的多腺苷酸化位点多物种图谱。

IF 16.6 2区生物学

Nucleic Acids Research Pub Date : 2025-01-06 DOI: 10.1093/nar/gkae1043

Youngbin Moon, Christina J Herrmann, Aleksei Mironov, Mihaela Zavolan

{"title":"PolyASite v3.0: a multi-species atlas of polyadenylation sites inferred from single-cell RNA-sequencing data.","authors":"Youngbin Moon, Christina J Herrmann, Aleksei Mironov, Mihaela Zavolan","doi":"10.1093/nar/gkae1043","DOIUrl":"10.1093/nar/gkae1043","url":null,"abstract":"The broadly used 10X Genomics technology for single-cell RNA sequencing (scRNA-seq) captures RNA 3' ends. Thus, some reads contain part of the non-templated polyadenosine tails, providing direct evidence for the sites of 3' end cleavage and polyadenylation on the respective RNAs. Taking advantage of this property, we recently developed the SCINPAS workflow to infer polyadenylation sites (PASs) from scRNA-seq data. Here, we used this workflow to construct version 3.0 (v3.0, https://polyasite.unibas.ch/) of the PolyASite Atlas from a big compendium of publicly available human, mouse and worm scRNA-seq datasets obtained from healthy tissues. As the resolution of scRNA-seq was too low for robust detection of cell-level differences in PAS usage, we aggregated samples based on their tissue-of-origin to construct tissue-level catalogs of PASs. These provide qualitatively new information about PAS usage, in comparison to the previous PAS catalogs that were based on bulk 3' end sequencing experiments primarily in cell lines. In the new version, we document stringency levels associated with each PAS so that users can balance sensitivity and specificity in their analysis. We also upgraded the integration with the UCSC Genome Browser and developed track hubs conveniently displaying pooled and tissue-specific expression of PASs.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":" ","pages":"D197-D204"},"PeriodicalIF":16.6,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11701536/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142624782","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

SPathDB: a comprehensive database of spatial pathway activity atlas. SPathDB：空间通路活动图集综合数据库。

IF 16.6 2区生物学

Nucleic Acids Research Pub Date : 2025-01-06 DOI: 10.1093/nar/gkae1041

Feng Li, Xinyu Song, Wenli Fan, Liying Pei, Jiaqi Liu, Rui Zhao, Yifang Zhang, Mengyue Li, Kaiyue Song, Yu Sun, Chunlong Zhang, Yunpeng Zhang, Yanjun Xu

{"title":"SPathDB: a comprehensive database of spatial pathway activity atlas.","authors":"Feng Li, Xinyu Song, Wenli Fan, Liying Pei, Jiaqi Liu, Rui Zhao, Yifang Zhang, Mengyue Li, Kaiyue Song, Yu Sun, Chunlong Zhang, Yunpeng Zhang, Yanjun Xu","doi":"10.1093/nar/gkae1041","DOIUrl":"10.1093/nar/gkae1041","url":null,"abstract":"Spatial transcriptomics sequencing technology deepens our understanding of the diversity of cell behaviors, fates and states within complex tissue, which is often determined by the fine-tuning of regulatory network functional activities. Therefore, characterizing the functional activity within tissue space is helpful for revealing the functional features that drive spatial heterogeneity, and understanding complex biological processes. Here, we describe a database, SPathDB (http://bio-bigdata.hrbmu.edu.cn/SPathDB/), which aims to dissect the pathway-mediated multidimensional spatial heterogeneity in the context of functional activity. We manually curated spatial transcriptomics datasets and biological pathways from public data resources. SPathDB consists of 1689 868 spatial spots of 695 slices from 84 spatial transcriptome datasets of human and mouse, which involves 36 tissues, and also diseases such as cancer, and provides interactive analysis and visualization of the functional activities of 114 998 pathways across these spatial spots. SPathDB provides five flexible interfaces to retrieve and analyze pathways with highly variable functional activity across spatial spots, the distribution of pathway functional activities along pseudo-space axis, pathway-mediated spatial intercellular communications and the associations between spatial pathway functional activity and the occurrence of cell types. SPathDB will serve as a foundational resource for identifying functional features and elucidating underlying mechanisms of spatial heterogeneity.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":" ","pages":"D1205-D1214"},"PeriodicalIF":16.6,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11701687/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142639452","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Complex portal 2025: predicted human complexes and enhanced visualisation tools for the comparison of orthologous and paralogous complexes. 复合物门户网站 2025：预测的人类复合物以及用于比较同源和旁系复合物的增强型可视化工具。

IF 16.6 2区生物学

Nucleic Acids Research Pub Date : 2025-01-06 DOI: 10.1093/nar/gkae1085

Sucharitha Balu, Susie Huget, Juan Jose Medina Reyes, Eliot Ragueneau, Kalpana Panneerselvam, Samantha N Fischer, Erin R Claussen, Savvas Kourtis, Colin W Combe, Birgit H M Meldal, Livia Perfetto, Juri Rappsilber, Georg Kustatscher, Kevin Drew, Sandra Orchard, Henning Hermjakob

{"title":"Complex portal 2025: predicted human complexes and enhanced visualisation tools for the comparison of orthologous and paralogous complexes.","authors":"Sucharitha Balu, Susie Huget, Juan Jose Medina Reyes, Eliot Ragueneau, Kalpana Panneerselvam, Samantha N Fischer, Erin R Claussen, Savvas Kourtis, Colin W Combe, Birgit H M Meldal, Livia Perfetto, Juri Rappsilber, Georg Kustatscher, Kevin Drew, Sandra Orchard, Henning Hermjakob","doi":"10.1093/nar/gkae1085","DOIUrl":"10.1093/nar/gkae1085","url":null,"abstract":"The Complex Portal (www.ebi.ac.uk/complexportal) is a manually curated reference database for molecular complexes. It is a unifying web resource linking aggregated data on composition, topology and the function of macromolecular complexes from 28 species. In addition to significantly extending the number of manually curated complexes, we have massively extended the coverage of the human complexome through the incorporation of high confidence assemblies predicted by machine-learning algorithms trained on large-scale experimental data. The current content of the portal comprising 2150 human complexes has been augmented by 14 964 machine-learning (ML) predicted complexes from hu.MAP3.0. We have refactored the website to enable easy search and filtering of these different classes of protein complexes and have implemented the Complex Navigator, a visualisation tool to facilitate comparison of related complexes in the context of orthology or paralogy. We have embedded the Rhea reaction visualisation tool into the website to enable users to view the catalytic activity of enzyme complexes.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":" ","pages":"D644-D650"},"PeriodicalIF":16.6,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11701666/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142668263","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

PubChem 2025 update. PubChem 2025 更新。

IF 16.6 2区生物学

Nucleic Acids Research Pub Date : 2025-01-06 DOI: 10.1093/nar/gkae1059

Sunghwan Kim, Jie Chen, Tiejun Cheng, Asta Gindulyte, Jia He, Siqian He, Qingliang Li, Benjamin A Shoemaker, Paul A Thiessen, Bo Yu, Leonid Zaslavsky, Jian Zhang, Evan E Bolton

{"title":"PubChem 2025 update.","authors":"Sunghwan Kim, Jie Chen, Tiejun Cheng, Asta Gindulyte, Jia He, Siqian He, Qingliang Li, Benjamin A Shoemaker, Paul A Thiessen, Bo Yu, Leonid Zaslavsky, Jian Zhang, Evan E Bolton","doi":"10.1093/nar/gkae1059","DOIUrl":"10.1093/nar/gkae1059","url":null,"abstract":"PubChem (https://pubchem.ncbi.nlm.nih.gov) is a large and highly-integrated public chemical database resource at NIH. In the past two years, significant updates were made to PubChem. With additions from over 130 new sources, PubChem contains >1000 data sources, 119 million compounds, 322 million substances and 295 million bioactivities. New interfaces, such as the consolidated literature panel and the patent knowledge panel, were developed. The consolidated literature panel combines all references about a compound into a single list, allowing users to easily find, sort, and export all relevant articles for a chemical in one place. The patent knowledge panels for a given query chemical or gene display chemicals, genes, and diseases co-mentioned with the query in patent documents, helping users to explore relationships between co-occurring entities within patent documents. PubChemRDF was expanded to include the co-occurrence data underlying the literature knowledge panel, enabling users to exploit semantic web technologies to explore entity relationships based on the co-occurrences in the scientific literature. The usability and accessibility of information on chemicals with non-discrete structures (e.g. biologics, minerals, polymers, UVCBs and glycans) were greatly improved with dedicated web pages that provide a comprehensive view of all available information in PubChem for these chemicals.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":" ","pages":"D1516-D1525"},"PeriodicalIF":16.6,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11701573/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142668525","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The Immune Epitope Database (IEDB): 2024 update. 免疫表位数据库（IEDB）：2024 年更新。

IF 16.6 2区生物学

Nucleic Acids Research Pub Date : 2025-01-06 DOI: 10.1093/nar/gkae1092

Randi Vita, Nina Blazeska, Daniel Marrama, Sebastian Duesing, Jason Bennett, Jason Greenbaum, Marcus De Almeida Mendes, Jarjapu Mahita, Daniel K Wheeler, Jason R Cantrell, James A Overton, Darren A Natale, Alessandro Sette, Bjoern Peters

引用次数: 0

PanKB: An interactive microbial pangenome knowledgebase for research, biotechnological innovation, and knowledge mining. PanKB：用于研究、生物技术创新和知识挖掘的交互式微生物泛基因组知识库。

IF 16.6 2区生物学

Nucleic Acids Research Pub Date : 2025-01-06 DOI: 10.1093/nar/gkae1042

Binhuan Sun, Liubov Pashkova, Pascal Aldo Pieters, Archana Sanjay Harke, Omkar Satyavan Mohite, Alberto Santos, Daniel C Zielinski, Bernhard O Palsson, Patrick Victor Phaneuf

{"title":"PanKB: An interactive microbial pangenome knowledgebase for research, biotechnological innovation, and knowledge mining.","authors":"Binhuan Sun, Liubov Pashkova, Pascal Aldo Pieters, Archana Sanjay Harke, Omkar Satyavan Mohite, Alberto Santos, Daniel C Zielinski, Bernhard O Palsson, Patrick Victor Phaneuf","doi":"10.1093/nar/gkae1042","DOIUrl":"10.1093/nar/gkae1042","url":null,"abstract":"The exponential growth of microbial genome data presents unprecedented opportunities for unlocking the potential of microorganisms. The burgeoning field of pangenomics offers a framework for extracting insights from this big biological data. Recent advances in microbial pangenomic research have generated substantial data and literature, yielding valuable knowledge across diverse microbial species. PanKB (pankb.org), a knowledgebase designed for microbial pangenomics research and biotechnological applications, was built to capitalize on this wealth of information. PanKB currently includes 51 pangenomes from 8 industrially relevant microbial families, comprising 8402 genomes, over 500 000 genes and over 7M mutations. To describe this data, PanKB implements four main components: (1) Interactive pangenomic analytics to facilitate exploration, intuition, and potential discoveries; (2) Alleleomic analytics, a pangenomic-scale analysis of variants, providing insights into intra-species sequence variation and potential mutations for applications; (3) A global search function enabling broad and deep investigations across pangenomes to power research and bioengineering workflows; (4) A bibliome of 833 open-access pangenomic papers and an interface with an LLM that can answer in-depth questions using its knowledge. PanKB empowers researchers and bioengineers to harness the potential of microbial pangenomics and serves as a valuable resource bridging the gap between pangenomic data and practical applications.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":" ","pages":"D806-D818"},"PeriodicalIF":16.6,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11701538/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142687524","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Correction to 'Plant Metabolic Network 16: expansion of underrepresented plant groups and experimentally supported enzyme data'. 修正“植物代谢网络16：未被充分代表的植物群的扩展和实验支持的酶数据”。

IF 16.6 2区生物学

Nucleic Acids Research Pub Date : 2025-01-06 DOI: 10.1093/nar/gkae1231

引用次数: 0

Correction to 'MolluscDB 2.0: a comprehensive functional and evolutionary genomics database for over 1400 molluscan species'. 修正“MolluscDB 2.0：超过1400种软体动物物种的综合功能和进化基因组数据库”。

IF 16.6 2区生物学

Nucleic Acids Research Pub Date : 2025-01-06 DOI: 10.1093/nar/gkae1232

引用次数: 0

metsDB: a knowledgebase of cancer metastasis at bulk, single-cell and spatial levels. metsDB：大体、单细胞和空间层面的癌症转移知识库。

IF 16.6 2区生物学

Nucleic Acids Research Pub Date : 2025-01-06 DOI: 10.1093/nar/gkae916

Sijia Wu, Jiajin Zhang, Yanfei Wang, Xinyu Qin, Zhaocan Zhang, Zhennan Lu, Pora Kim, Xiaobo Zhou, Liyu Huang

{"title":"metsDB: a knowledgebase of cancer metastasis at bulk, single-cell and spatial levels.","authors":"Sijia Wu, Jiajin Zhang, Yanfei Wang, Xinyu Qin, Zhaocan Zhang, Zhennan Lu, Pora Kim, Xiaobo Zhou, Liyu Huang","doi":"10.1093/nar/gkae916","DOIUrl":"10.1093/nar/gkae916","url":null,"abstract":"Cancer metastasis, the process by which tumour cells migrate and colonize distant organs from a primary site, is responsible for the majority of cancer-related deaths. Understanding the cellular and molecular mechanisms underlying this complex process is essential for developing effective metastasis prevention and therapy strategies. To this end, we systematically analysed 1786 bulk tissue samples from 13 cancer types, 988 463 single cells from 17 cancer types, and 40 252 spots from 45 spatial slides across 10 cancer types. The results of these analyses are compiled in the metsDB database, accessible at https://relab.xidian.edu.cn/metsDB/. This database provides insights into alterations in cell constitutions, cell relationships, biological pathways, molecular biomarkers, and drug responses during cancer metastasis at bulk, single-cell, and spatial levels. Users can perform cell or gene searches to obtain multi-view and multi-scale metastasis-related data. This comprehensive resource is invaluable for understanding the metastasis process and for designing molecular therapies.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":" ","pages":"D1427-D1434"},"PeriodicalIF":16.6,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11701579/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142471260","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0