ArticleNature methods2019
Learning representations of microbe-metabolite interactions.
Article in Nature methods, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 162 papers, 1 of them a synthesis that pooled it.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
162 citing papers in PubMed, 1 synthesis or guideline pooled it.
- A meta-analysis study of the robustness and universality of gut microbiome-metabolome associations.Microbiome · 2021Pooled it
- Sialidase inhibitor modulates gut microbiota and enhances mucosal protection in the treatment of ulcerative colitis.mSystems · 2026Trial
- Pleiotropic roles of microbial bile acid metabolism in intestinal health and diseases.Cell host & microbe · 2026Review
- The Mycorrhizal Fungal Species Funneliformis mosseae Reshapes Rhizosphere Microbial Metabolic Pathways of Soybeans Under Tetracycline Stress.MicrobiologyOpen · 2026Article
- Integrating multi-omics technologies to decipher microbiome functions.Nature communications · 2026Review
- Joint-RPCA: domain-aware multi-omics integration for systems microbiology.Molecular systems biology · 2026Article
- Bridging complexity and accessibility in metabolomics with MetaboApps.Nature methods · 2026Article
- Tobacco smoking disrupts bile acid and tryptophan metabolism in multiple sclerosis.Multiple sclerosis (Houndmills, Basingstoke, England) · 2026Article
- Gut Microbiomes of Rainbow Trout and Atlantic Salmon: Nutritional Modulation, Mucosal Immunity, and Resistome Risk.Biology · 2026Review
- Integrating host-microbiome multi-omics with machine learning: methods, benchmarks, and translational applications.Science China. Life sciences · 2026Review
- Omics-based decoding of molecular and metabolic crosstalk in the skin barrier ecosystem.Cell death and differentiation · 2026Review
- Review
- Article
- Water kefir as a paradigm for multi-omics and genome-scale metabolic modelling in fermented food.NPJ biofilms and microbiomes · 2026Review
- Decoding immunotherapy response through computational modeling.Nature communications · 2026Review
- A triangulation and neural network approach reveals the microbe-metabolite-sensory associations of fermented milk.Current research in food science · 2026Article
- Decoding the rhizosphere microbiome againstFrontiers in microbiomes · 2026Review
- Microbial Omics.Progress in molecular and subcellular biology · 2026Review
- Bayesian inference captures metabolite-bacteria interactions in a microbial community.ISME communications · 2026Article
- Decoding the reproductive microbiome: enabling clinical and biological insights through machine and deep learning.Frontiers in endocrinology · 2026Review
102 more citing papers are in PubMed but not listed here.
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Authors and funding
17 authors.
Funding
Abstract
Integrating multiomics datasets is critical for microbiome research; however, inferring interactions across omics datasets has multiple statistical challenges. We solve this problem by using neural networks (https://github.com/biocore/mmvec) to estimate the conditional probability that each molecule is present given the presence of a specific microorganism. We show with known environmental (desert soil biocrust wetting) and clinical (cystic fibrosis lung) examples, our ability to recover microbe-metabolite relationships, and demonstrate how the method can discover relationships between microbially produced metabolites and inflammatory bowel disease.
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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.