ArticleNucleic acids research2023
MGnify: the microbiome sequence data analysis resource in 2023.
Article in Nucleic acids research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 247 papers, 1 of them a synthesis that pooled it.
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Who cites it
247 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Protein Sequence Analysis landscape: A Systematic Review of Task Types, Databases, Datasets, Word Embeddings Methods, and Language Models.Database : the journal of biological databases and curation · 2025Pooled it
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- The Biotechnological Applications of Marine Bacteria.Biology · 2026Review
- AI semantics for biomedical data integration.bioRxiv : the preprint server for biology · 2026Article
- Methods for the establishment of enzymatic mechanisms - from QM to ML.Chemical science · 2026Review
- From functional annotation to functional meaning in microbiome research.Environmental microbiome · 2026Review
- Foundation Models for Microbiome Research: From Sequence Semantics to Community Dynamics and Multimodal World Models.Advanced genetics (Hoboken, N.J.) · 2026Review
- Complete genomes from a xenicMicrobiology spectrum · 2026Article
- Community-driven updates for comprehensive long-read metagenomics and enhanced binning in nf-core/mag v5.Bioinformatics (Oxford, England) · 2026Article
- Highly Sensitive Spatial Host-Microbiome Transcriptomics in FFPE Tissues via Iterative Hydrogel Expansion.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Characterization of microbial dark matter at scale with MetaSBT and taxonomy-aware Sequence Bloom Trees.Nature biotechnology · 2026Article
- Fine-grained structural classification of biosynthetic gene cluster-encoded products.Bioinformatics (Oxford, England) · 2026Article
- Synthetic sequence alignments as programmable probes of learned conformational landscapes in deep learning protein structure predictors.Bioinformatics (Oxford, England) · 2026Article
- A trimodal protein language model enables advanced protein searches.Nature biotechnology · 2026Article
- Data of annotated draft genome assemblies of three bacterial isolates from the 'Panchabrihi' rice, soybean, and bean-associated niches in Bangladesh.Data in brief · 2026Article
- Review
- Engineering Plant-Associated Soil Microbiomes for Sustainable and Climate-Resilient Agriculture: Mechanisms, Technologies, and Applications.Microorganisms · 2026Review
- Advancing FAIR data towards comparable, organized, predictive AI-ready data for community validation.Communications biology · 2026Review
187 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
21 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The MGnify platform (https://www.ebi.ac.uk/metagenomics) facilitates the assembly, analysis and archiving of microbiome-derived nucleic acid sequences. The platform provides access to taxonomic assignments and functional annotations for nearly half a million analyses covering metabarcoding, metatranscriptomic, and metagenomic datasets, which are derived from a wide range of different environments. Over the past 3 years, MGnify has not only grown in terms of the number of datasets contained but also increased the breadth of analyses provided, such as the analysis of long-read sequences. The MGnify protein database now exceeds 2.4 billion non-redundant sequences predicted from metagenomic assemblies. This collection is now organised into a relational database making it possible to understand the genomic context of the protein through navigation back to the source assembly and sample metadata, marking a major improvement. To extend beyond the functional annotations already provided in MGnify, we have applied deep learning-based annotation methods. The technology underlying MGnify's Application Programming Interface (API) and website has been upgraded, and we have enabled the ability to perform downstream analysis of the MGnify data through the introduction of a coupled Jupyter Lab environment.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.