• 文献检索
  • 文档翻译
  • 深度研究
  • 学术资讯
  • Suppr Zotero 插件Zotero 插件
  • 邀请有礼
  • 套餐&价格
  • 历史记录
应用&插件
Suppr Zotero 插件Zotero 插件浏览器插件Mac 客户端Windows 客户端微信小程序
定价
高级版会员购买积分包购买API积分包
服务
文献检索文档翻译深度研究API 文档MCP 服务
关于我们
关于 Suppr公司介绍联系我们用户协议隐私条款
关注我们

Suppr 超能文献

核心技术专利：CN118964589B侵权必究
粤ICP备2023148730 号-1Suppr @ 2026

文献检索

告别复杂PubMed语法，用中文像聊天一样搜索，搜遍4000万医学文献。AI智能推荐，让科研检索更轻松。

立即免费搜索

文件翻译

保留排版，准确专业，支持PDF/Word/PPT等文件格式，支持 12+语言互译。

免费翻译文档

深度研究

AI帮你快速写综述，25分钟生成高质量综述，智能提取关键信息，辅助科研写作。

立即免费体验

真核病原体基因组数据库资源（EuPathDB）

EuPathDB: The Eukaryotic Pathogen Genomics Database Resource.

作者信息

Warrenfeltz Susanne, Basenko Evelina Y, Crouch Kathryn, Harb Omar S, Kissinger Jessica C, Roos David S, Shanmugasundram Achchuthan, Silva-Franco Fatima

机构信息

Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, USA.

Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Liverpool, UK.

出版信息

Methods Mol Biol. 2018;1757:69-113. doi: 10.1007/978-1-4939-7737-6_5.

DOI:10.1007/978-1-4939-7737-6_5
PMID:29761457
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC7124890/
Abstract

Fighting infections and developing novel drugs and vaccines requires advanced knowledge of pathogen's biology. Readily accessible genomic, functional genomic, and population data aids biological and translational discovery. The Eukaryotic Pathogen Database Resources ( http://eupathdb.org ) are data mining resources that support hypothesis driven research by facilitating the discovery of meaningful biological relationships from large volumes of data. The resource encompasses 13 sites that support over 170 species including pathogenic protists, oomycetes, and fungi as well as evolutionarily related nonpathogenic species. EuPathDB integrates preanalyzed data with advanced search capabilities, data visualization, analysis tools and a comprehensive record system in a graphical interface that does not require prior computational skills. This chapter describes guiding concepts common across EuPathDB sites and illustrates the powerful data mining capabilities of some of the available tools and features.

摘要

对抗感染以及研发新型药物和疫苗需要深入了解病原体的生物学特性。易于获取的基因组、功能基因组和群体数据有助于生物学和转化医学研究的发现。真核病原体数据库资源（http://eupathdb.org）是数据挖掘资源，通过促进从大量数据中发现有意义的生物学关系来支持假设驱动的研究。该资源涵盖13个网站，支持170多种物种，包括致病性原生生物、卵菌和真菌以及进化相关的非致病性物种。EuPathDB将预先分析的数据与高级搜索功能、数据可视化、分析工具和一个全面的记录系统集成在一个图形界面中，无需事先具备计算技能。本章描述了EuPathDB各网站共有的指导概念，并展示了一些可用工具和功能强大的数据挖掘能力。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/81af/7124890/a273c9aa10be/EMS86149-f022.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/81af/7124890/9a7f6d9725a0/EMS86149-f001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/81af/7124890/d129e578e428/EMS86149-f002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/81af/7124890/f19135a3272b/EMS86149-f003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/81af/7124890/4a2ad7f7be08/EMS86149-f004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/81af/7124890/564f0379e855/EMS86149-f005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/81af/7124890/94c0497bb31d/EMS86149-f006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/81af/7124890/9779980441ac/EMS86149-f007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/81af/7124890/c47a24652d49/EMS86149-f008.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/81af/7124890/a2ed75b1e79d/EMS86149-f009.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/81af/7124890/d6ff1be82f02/EMS86149-f010.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/81af/7124890/37f59d882dda/EMS86149-f011.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/81af/7124890/dd4e567b1dc1/EMS86149-f012.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/81af/7124890/24a80c3e86d5/EMS86149-f013.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/81af/7124890/3fba1f2f23c1/EMS86149-f014.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/81af/7124890/9db752f0fc46/EMS86149-f015.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/81af/7124890/b8eab97961c5/EMS86149-f016.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/81af/7124890/da83e4c802fd/EMS86149-f017.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/81af/7124890/65bbbc48efaf/EMS86149-f018.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/81af/7124890/4dd186f208ac/EMS86149-f019.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/81af/7124890/53a79f45666f/EMS86149-f020.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/81af/7124890/416a454fbf63/EMS86149-f021.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/81af/7124890/a273c9aa10be/EMS86149-f022.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/81af/7124890/9a7f6d9725a0/EMS86149-f001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/81af/7124890/d129e578e428/EMS86149-f002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/81af/7124890/f19135a3272b/EMS86149-f003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/81af/7124890/4a2ad7f7be08/EMS86149-f004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/81af/7124890/564f0379e855/EMS86149-f005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/81af/7124890/94c0497bb31d/EMS86149-f006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/81af/7124890/9779980441ac/EMS86149-f007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/81af/7124890/c47a24652d49/EMS86149-f008.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/81af/7124890/a2ed75b1e79d/EMS86149-f009.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/81af/7124890/d6ff1be82f02/EMS86149-f010.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/81af/7124890/37f59d882dda/EMS86149-f011.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/81af/7124890/dd4e567b1dc1/EMS86149-f012.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/81af/7124890/24a80c3e86d5/EMS86149-f013.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/81af/7124890/3fba1f2f23c1/EMS86149-f014.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/81af/7124890/9db752f0fc46/EMS86149-f015.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/81af/7124890/b8eab97961c5/EMS86149-f016.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/81af/7124890/da83e4c802fd/EMS86149-f017.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/81af/7124890/65bbbc48efaf/EMS86149-f018.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/81af/7124890/4dd186f208ac/EMS86149-f019.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/81af/7124890/53a79f45666f/EMS86149-f020.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/81af/7124890/416a454fbf63/EMS86149-f021.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/81af/7124890/a273c9aa10be/EMS86149-f022.jpg

相似文献

1
EuPathDB: The Eukaryotic Pathogen Genomics Database Resource.真核病原体基因组数据库资源（EuPathDB）
Methods Mol Biol. 2018;1757:69-113. doi: 10.1007/978-1-4939-7737-6_5.
2
EuPathDB: the eukaryotic pathogen genomics database resource.EuPathDB：真核病原体基因组数据库资源。
Nucleic Acids Res. 2017 Jan 4;45(D1):D581-D591. doi: 10.1093/nar/gkw1105. Epub 2016 Nov 29.
3
The Eukaryotic Pathogen Databases: a functional genomic resource integrating data from human and veterinary parasites.真核病原体数据库：整合来自人类和兽医寄生虫数据的功能基因组资源。
Methods Mol Biol. 2015;1201:1-18. doi: 10.1007/978-1-4939-1438-8_1.
4
Accessing Cryptosporidium Omic and Isolate Data via CryptoDB.org.通过CryptoDB.org访问隐孢子虫组学和分离株数据。
Methods Mol Biol. 2020;2052:139-192. doi: 10.1007/978-1-4939-9748-0_10.
5
FungiDB: An Integrated Bioinformatic Resource for Fungi and Oomycetes.真菌数据库（FungiDB）：真菌和卵菌的综合生物信息资源。
J Fungi (Basel). 2018 Mar 20;4(1):39. doi: 10.3390/jof4010039.
6
EuPathDB: a portal to eukaryotic pathogen databases.EuPathDB：真核病原体数据库门户。
Nucleic Acids Res. 2010 Jan;38(Database issue):D415-9. doi: 10.1093/nar/gkp941. Epub 2009 Nov 13.
7
Bovine Genome Database: Tools for Mining the Bos taurus Genome.牛基因组数据库：挖掘牛基因组的工具。
Methods Mol Biol. 2018;1757:211-249. doi: 10.1007/978-1-4939-7737-6_9.
8
EuPathDB: the eukaryotic pathogen database.EuPathDB：真核病原体数据库。
Nucleic Acids Res. 2013 Jan;41(Database issue):D684-91. doi: 10.1093/nar/gks1113. Epub 2012 Nov 21.
9
Geneious plugins for the access of PlasmoDB and PiroplasmaDB databases.用于访问疟原虫数据库（PlasmoDB）和梨形虫数据库（PiroplasmaDB）的Geneious插件。
Parasitol Int. 2013 Apr;62(2):134-6. doi: 10.1016/j.parint.2012.11.003. Epub 2012 Nov 24.
10
The Evolution of Soybean Knowledge Base (SoyKB).大豆知识库（SoyKB）的发展历程。
Methods Mol Biol. 2017;1533:149-159. doi: 10.1007/978-1-4939-6658-5_7.

引用本文的文献

1
The molecular basis of coordinated antigen switching enabling chronic infection by human malaria parasites.人类疟原虫实现慢性感染的协同抗原转换的分子基础。
bioRxiv. 2025 Jul 16:2025.07.16.665170. doi: 10.1101/2025.07.16.665170.
2
P21 Ablation Unveils Strain-Specific Transcriptional Reprogramming in Amastigotes.P21基因敲除揭示无鞭毛体中特定菌株的转录重编程
Int J Microbiol. 2025 Jul 4;2025:9919200. doi: 10.1155/ijm/9919200. eCollection 2025.
3
scRNA-seq reveals transcriptional plasticity of var gene expression in Plasmodium falciparum for host immune avoidance.

本文引用的文献

1
EuPaGDT: a web tool tailored to design CRISPR guide RNAs for eukaryotic pathogens.EuPaGDT：一种专门为真核病原体设计CRISPR引导RNA的网络工具。
Microb Genom. 2015 Oct 30;1(4):e000033. doi: 10.1099/mgen.0.000033. eCollection 2015 Oct.
2
EuPathDB: the eukaryotic pathogen genomics database resource.EuPathDB：真核病原体基因组数据库资源。
Nucleic Acids Res. 2017 Jan 4;45(D1):D581-D591. doi: 10.1093/nar/gkw1105. Epub 2016 Nov 29.
3
InterPro in 2017-beyond protein family and domain annotations.2017年的InterPro——超越蛋白质家族和结构域注释
单细胞RNA测序揭示恶性疟原虫中var基因表达的转录可塑性以逃避宿主免疫。
Nat Microbiol. 2025 May 16. doi: 10.1038/s41564-025-02008-5.
4
Transformer-based deep learning enables improved B-cell epitope prediction in parasitic pathogens: A proof-of-concept study on Fasciola hepatica.基于Transformer的深度学习可改善对寄生性病原体中B细胞表位的预测：对肝片吸虫的概念验证研究
PLoS Negl Trop Dis. 2025 Apr 29;19(4):e0012985. doi: 10.1371/journal.pntd.0012985. eCollection 2025 Apr.
5
NGS-based Aspergillus detection in plasma and lung lavage of children with invasive pulmonary aspergillosis.基于二代测序技术检测侵袭性肺曲霉病患儿血浆及肺灌洗液中的曲霉
NPJ Genom Med. 2025 Mar 17;10(1):24. doi: 10.1038/s41525-025-00482-8.
6
Protective targets of PfSPZ vaccines identified from whole-genome sieve analysis of isolates from malaria vaccine efficacy trials in West Africa.从西非疟疾疫苗效力试验分离株的全基因组筛选分析中确定的PfSPZ疫苗的保护性靶点。
medRxiv. 2025 Mar 6:2025.03.04.25323352. doi: 10.1101/2025.03.04.25323352.
7
Harnessing the power of new genetic tools to illuminate Giardia biology and pathogenesis.利用新的遗传工具的力量来阐明贾第虫生物学和发病机制。
Genetics. 2024 Jun 5;227(2). doi: 10.1093/genetics/iyae038.
8
Transcriptional plasticity of virulence genes provides malaria parasites with greater adaptive capacity for avoiding host immunity.毒力基因的转录可塑性为疟原虫提供了更强的逃避宿主免疫的适应能力。
bioRxiv. 2024 Mar 9:2024.03.08.584127. doi: 10.1101/2024.03.08.584127.
9
, the Outlier When It Comes to Protein Synthesis.当涉及到蛋白质合成时， 是一个异常值。
Biomolecules. 2023 Dec 29;14(1):46. doi: 10.3390/biom14010046.
10
Major data analysis errors invalidate cancer microbiome findings.主要数据分析错误使癌症微生物组研究结果无效。
mBio. 2023 Oct 31;14(5):e0160723. doi: 10.1128/mbio.01607-23. Epub 2023 Oct 9.
Nucleic Acids Res. 2017 Jan 4;45(D1):D190-D199. doi: 10.1093/nar/gkw1107. Epub 2016 Nov 29.
4
Integrated transcriptomic and proteomic analyses of P. falciparum gametocytes: molecular insight into sex-specific processes and translational repression.恶性疟原虫配子体的转录组和蛋白质组综合分析：对性别特异性过程和翻译抑制的分子洞察
Nucleic Acids Res. 2016 Jul 27;44(13):6087-101. doi: 10.1093/nar/gkw536. Epub 2016 Jun 13.
5
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update.用于可访问、可重复和协作式生物医学分析的Galaxy平台：2016年更新
Nucleic Acids Res. 2016 Jul 8;44(W1):W3-W10. doi: 10.1093/nar/gkw343. Epub 2016 May 2.
6
Companion: a web server for annotation and analysis of parasite genomes.Companion：一个用于寄生虫基因组注释和分析的网络服务器。
Nucleic Acids Res. 2016 Jul 8;44(W1):W29-34. doi: 10.1093/nar/gkw292. Epub 2016 Apr 21.
7
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases.代谢途径与酶的MetaCyc数据库以及途径/基因组数据库的BioCyc集合。
Nucleic Acids Res. 2016 Jan 4;44(D1):D471-80. doi: 10.1093/nar/gkv1164. Epub 2015 Nov 2.
8
KEGG as a reference resource for gene and protein annotation.KEGG作为基因和蛋白质注释的参考资源。
Nucleic Acids Res. 2016 Jan 4;44(D1):D457-62. doi: 10.1093/nar/gkv1070. Epub 2015 Oct 17.
9
Cytoscape.js: a graph theory library for visualisation and analysis.Cytoscape.js：一个用于可视化和分析的图论库。
Bioinformatics. 2016 Jan 15;32(2):309-11. doi: 10.1093/bioinformatics/btv557. Epub 2015 Sep 28.
10
Gene Ontology Consortium: going forward.基因本体论联盟：展望未来。
Nucleic Acids Res. 2015 Jan;43(Database issue):D1049-56. doi: 10.1093/nar/gku1179. Epub 2014 Nov 26.