ArticleComputational and structural biotechnology journal2022
FunOMIC: Pipeline with built-in fungal taxonomic and functional databases for human mycobiome profiling.
Article in Computational and structural biotechnology journal, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 47 citations in OpenAlex.
- Benchmarking methods for extracting microbial signal from host-dominated metatranscriptomes.Briefings in bioinformatics · 2026Article
- Metagenomic sequencing reveals the dynamic changes of pig gut fungal composition following the ages and identifies fungal species associated with diarrhea in piglets.Animal microbiome · 2026Article
- Interpreting fungal ecological contributions through taxonomic and functional profiling of metatranscriptomics.IMA fungus · 2026Review
- Article
- The Functional Role of Fungi and Bacteria in Sulfur Cycling During Kelp (Ecklonia Radiata) Degradation: Unconventional Use of PiCrust2.Environmental microbiology reports · 2025Article
- Exploring diet-microbiota interactions and therapeutic nutrition management in inflammatory bowel disease.Biophysics reports · 2025Article
- The Role of Intestinal Fungi in the Pathogenesis and Treatment of Ulcerative Colitis.Microorganisms · 2025Review
- Challenges in capturing the mycobiome from shotgun metagenome data: lack of software and databases.Microbiome · 2025Article
- Early-Life Host-Microbial Interactions and Asthma Development: A Lifelong Impact?Immunological reviews · 2025Review
- Implication of Gut Mycobiome and Virome in Type-2 Diabetes Mellitus: Uncovering the Hidden Players.Phenomics (Cham, Switzerland) · 2025Review
- Article
- Shotgun metagenomics reveals interkingdom association between intestinal bacteria and fungi involving competition for nutrients.Microbiome · 2023Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
While analysis of the bacterial microbiome has become routine, that of the fungal microbiome is still hampered by the lack of robust databases and bioinformatic pipelines. Here, we present FunOMIC, a pipeline with built-in taxonomic (1.6 million marker genes) and functional (3.4 million non-redundant fungal proteins) databases for the identification of fungi. Applied to more than 2,600 human metagenomic samples, the tool revealed fungal species associated with geography, body sites, and diseases. Correlation network analysis provided new insights into inter-kingdom interactions. With this pipeline and two of the most comprehensive fungal databases, we foresee a fast-growing resource for mycobiome studies.
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