ArticleGigaScience2024
gNOMO2: a comprehensive and modular pipeline for integrated multi-omics analyses of microbiomes.
Article in GigaScience, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- Integrating multi-omics technologies to decipher microbiome functions.Nature communications · 2026Review
- Water kefir as a paradigm for multi-omics and genome-scale metabolic modelling in fermented food.NPJ biofilms and microbiomes · 2026Review
- MADRe: Strain-level metagenomic classification through assembly-driven database reduction.GigaScience · 2026Article
- Computational and multi-omics systems biology for precision microbiome therapeutics.Frontiers in microbiomes · 2026Review
- Microbial Omics.Progress in molecular and subcellular biology · 2026Review
- Gut-Brain Axis Dysregulation in Inflammatory Bowel Disease: Implications for Coagulation Abnormalities and Extraintestinal Manifestations.International journal of general medicine · 2026Review
- Artificial intelligence empowers gut microbiota research in neurodegenerative diseases molecular mechanisms and precision therapy.iScience · 2025Review
- gNOMO2: a comprehensive and modular pipeline for integrated multi-omics analyses of microbiomes.GigaScience · 2024Article
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Authors and funding
2 authors.
Funding
Abstract
backgroundIn recent years, omics technologies have offered an exceptional chance to gain a deeper insight into the structural and functional characteristics of microbial communities. As a result, there is a growing demand for user-friendly, reproducible, and versatile bioinformatic tools that can effectively harness multi-omics data to provide a holistic understanding of microbiomes. Previously, we introduced gNOMO, a bioinformatic pipeline tailored to analyze microbiome multi-omics data in an integrative manner. In response to the evolving demands within the microbiome field and the growing necessity for integrated multi-omics data analysis, we have implemented substantial enhancements to the gNOMO pipeline.
resultsHere, we present gNOMO2, a comprehensive and modular pipeline that can seamlessly manage various omics combinations, ranging from 2 to 4 distinct omics data types, including 16S ribosomal RNA (rRNA) gene amplicon sequencing, metagenomics, metatranscriptomics, and metaproteomics. Furthermore, gNOMO2 features a specialized module for processing 16S rRNA gene amplicon sequencing data to create a protein database suitable for metaproteomics investigations. Moreover, it incorporates new differential abundance, integration, and visualization approaches, enhancing the toolkit for a more insightful analysis of microbiomes. The functionality of these new features is showcased through the use of 4 microbiome multi-omics datasets encompassing various ecosystems and omics combinations. gNOMO2 not only replicated most of the primary findings from these studies but also offered further valuable perspectives.
conclusionsgNOMO2 enables the thorough integration of taxonomic and functional analyses in microbiome multi-omics data, offering novel insights in both host-associated and free-living microbiome research. gNOMO2 is available freely at https://github.com/muzafferarikan/gNOMO2.
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