ArticleCells2020
MicrobioLink: An Integrated Computational Pipeline to Infer Functional Effects of Microbiome-Host Interactions.
Article in Cells, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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
23 citing papers in PubMed, 39 citations in OpenAlex.
- Integrating host-microbiome multi-omics with machine learning: methods, benchmarks, and translational applications.Science China. Life sciences · 2026Review
- Microbial Omics.Progress in molecular and subcellular biology · 2026Review
- Article
- mimicINT: A workflow for microbe-host protein interaction inference.F1000Research · 2025Article
- Integrating multi-omics to unravel host-microbiome interactions in inflammatory bowel disease.Cell reports. Medicine · 2024Review
- Individual-network based predictions of microbial interaction signatures for response to biological therapies in IBD patients.Frontiers in molecular biosciences · 2024Article
- Microbiome modeling: a beginner's guide.Frontiers in microbiology · 2024Review
- Multidimensional outlook on the pathophysiology of cervical cancer invasion and metastasis.Molecular and cellular biochemistry · 2023Review
- HMI-PRED 2.0: a biologist-oriented web application for prediction of host-microbe protein-protein interaction by interface mimicry.Bioinformatics (Oxford, England) · 2022Article
- A Framework for the Systematic Selection of Biosensor Chassis for Environmental Synthetic Biology.ACS synthetic biology · 2022Review
- Multilayered Networks of SalmoNet2 Enable Strain Comparisons of the Salmonella Genus on a Molecular Level.mSystems · 2022Article
- Article
- Artificial Intelligence for Disease Assessment in Inflammatory Bowel Disease: How Will it Change Our Practice?Gastroenterology · 2022Review
- Investigation of fiber utilization in the rumen of dairy cows based on metagenome-assembled genomes and single-cell RNA sequencing.Microbiome · 2022Article
- Computational prediction and experimental validation ofFrontiers in cellular and infection microbiology · 2022Article
- Extracellular vesicles produced by the human commensal gut bacterium Bacteroides thetaiotaomicron affect host immune pathways in a cell-type specific manner that are altered in inflammatory bowel disease.Journal of extracellular vesicles · 2022Article
- Forest and Trees: Exploring Bacterial Virulence with Genome-wide Association Studies and Machine Learning.Trends in microbiology · 2021Review
- Plant-Microbiome Crosstalk: Dawning from Composition and Assembly of Microbial Community to Improvement of Disease Resilience in Plants.International journal of molecular sciences · 2021Review
- Integrated intra- and intercellular signaling knowledge for multicellular omics analysis.Molecular systems biology · 2021Article
- ViralLink: An integrated workflow to investigate the effect of SARS-CoV-2 on intracellular signalling and regulatory pathways.PLoS computational biology · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 3 institutions in 4 countries.
Funding
Abstract
Microbiome-host interactions play significant roles in health and in various diseases including autoimmune disorders. Uncovering these inter-kingdom cross-talks propels our understanding of disease pathogenesis and provides useful leads on potential therapeutic targets. Despite the biological significance of microbe-host interactions, there is a big gap in understanding the downstream effects of these interactions on host processes. Computational methods are expected to fill this gap by generating, integrating, and prioritizing predictions-as experimental detection remains challenging due to feasibility issues. Here, we present MicrobioLink, a computational pipeline to integrate predicted interactions between microbial and host proteins together with host molecular networks. Using the concept of network diffusion, MicrobioLink can analyse how microbial proteins in a certain context are influencing cellular processes by modulating gene or protein expression. We demonstrated the applicability of the pipeline using a case study. We used gut metaproteomic data from Crohn's disease patients and healthy controls to uncover the mechanisms by which the microbial proteins can modulate host genes which belong to biological processes implicated in disease pathogenesis. MicrobioLink, which is agnostic of the microbial protein sources (bacterial, viral, etc.), is freely available on GitHub.
Indexed as
Identifiers
What OpenQuestion holds
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.