ArticlemSystems2021
Microbiome Search Engine 2: a Platform for Taxonomic and Functional Search of Global Microbiomes on the Whole-Microbiome Level.
Article in mSystems, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- CAM-Net: a context-aware network for identifying reliable microbial relations via optimal consortium.Briefings in bioinformatics · 2026Article
- ResMicroDb: a comprehensive database and analysis platform for the human respiratory microbiome.Nucleic acids research · 2026Article
- Coordinated Meta-Storms enables comparison of million-level microbiomes.Bioinformatics (Oxford, England) · 2025Article
- OMD Curation Toolkit: a workflow for in-house curation of public omics datasets.BMC bioinformatics · 2024Article
- Novel order-level lineage of ammonia-oxidizing archaea widespread in marine and terrestrial environments.The ISME journal · 2024Article
- Comprehensive Assessment of 16S rRNA Gene Amplicon Sequencing for Microbiome Profiling across Multiple Habitats.Microbiology spectrum · 2023Article
- Construction of a caries diagnosis model based on microbiome novelty score.Hua xi kou qiang yi xue za zhi = Huaxi kouqiang yixue zazhi = West China journal of stomatology · 2023Article
- Airborne antibiotic resistome and human health risk in railway stations during COVID-19 pandemic.Environment international · 2023Article
- Single-cell Raman-activated sorting and cultivation (scRACS-Culture) for assessing and mining in situ phosphate-solubilizing microbes from nature.ISME communications · 2022Article
- Microbiomes in the Challenger Deep slope and bottom-axis sediments.Nature communications · 2022Article
- Parallel-Meta Suite: Interactive and rapid microbiome data analysis on multiple platforms.iMeta · 2022Article
- Autonomous schema markups based on intelligent computing for search engine optimization.PeerJ. Computer science · 2022Article
- Elucidating the Beta-Diversity of the Microbiome: from Global Alignment to Local Alignment.mSystems · 2021Article
- A Scale-Free, Fully Connected Global Transition Network Underlies Known Microbiome Diversity.mSystems · 2021Article
- The predictive power of saliva electrolytes exceeds that of saliva microbiomes in diagnosing early childhood caries.Journal of oral microbiology · 2021Article
- Towards multi-label classification: Next step of machine learning for microbiome research.Computational and structural biotechnology journal · 2021Review
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Authors and funding
12 authors.
Funding
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Abstract
Metagenomic data sets from diverse environments have been growing rapidly. To ensure accessibility and reusability, tools that quickly and informatively correlate new microbiomes with existing ones are in demand. Here, we introduce Microbiome Search Engine 2 (MSE 2), a microbiome database platform for searching query microbiomes in the global metagenome data space based on the taxonomic or functional similarity of a whole microbiome to those in the database. MSE 2 consists of (i) a well-organized and regularly updated microbiome database that currently contains over 250,000 metagenomic shotgun and 16S rRNA gene amplicon samples associated with unified metadata collected from 798 studies, (ii) an enhanced search engine that enables real-time and fast (<0.5 s per query) searches against the entire database for best-matched microbiomes using overall taxonomic or functional profiles, and (iii) a Web-based graphical user interface for user-friendly searching, data browsing, and tutoring. MSE 2 is freely accessible via http://mse.ac.cn For standalone searches of customized microbiome databases, the kernel of the MSE 2 search engine is provided at GitHub (https://github.com/qibebt-bioinfo/meta-storms).
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