ArticleThe ISME journal2019
'NetShift': a methodology for understanding 'driver microbes' from healthy and disease microbiome datasets.
Article in The ISME journal, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 87 papers, 1 of them a synthesis that pooled it.
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Who cites it
87 citing papers in PubMed, 1 synthesis or guideline pooled it.
- A Risk Score for Polycystic Ovary Syndrome Based on Meta-Analysis and Machine Learning of Gut Microbiota Signatures.Reproductive sciences (Thousand Oaks, Calif.) · 2026Pooled it
- Lifestyle modifications result in alterations in the gut microbiota in obese children.BMC microbiology · 2021Trial
- ssNetShift: single-sample metabolic network rewiring reveals hidden prognostic subtypes beyond clinical staging in gastric cancer.Briefings in bioinformatics · 2026Article
- Unraveling the relationship between the vaginal microbiome and return to estrus in post-weaning sows.BMC veterinary research · 2026Article
- Phenolic acid biosynthesis is associated with deleterious microbiome changes during Plasmodiophora brassicae-induced clubroot in pakchoi.Microbiome · 2026Article
- Sex-biased associations between gut microbiota and hematologic toxicity of neoadjuvant chemoradiotherapy in locally advanced rectal cancer.International journal of surgery (London, England) · 2026Article
- Identifying Differential Network Properties and Driver Microbes in Microbial Association Networks Using CompNet and NetShift.Methods in molecular biology (Clifton, N.J.) · 2026Article
- MNetClass: a control-free microbial network clustering framework for identifying central subcommunities across ecological niches.mSystems · 2025Article
- Integrative multi-omics analysis of autism spectrum disorder reveals unique microbial macromolecules interactions.Journal of advanced research · 2025Article
- Sedative co-medication patterns across frailty states in people with HIV: a network-based study.International journal of clinical pharmacy · 2025Article
- Identification and validation of intratumoral microbiome associated with sensitization to immune checkpoint inhibitors.Cell reports. Medicine · 2025Article
- Integrated Microbiome Data Analysis Reveals Potential Pneumonia Microbial Biomarkers in ICU Patients: A Machine Learning Approach.Current microbiology · 2025Article
- DnaK of Parvimonas micra extracellular vesicles interacts with the host fibroblasts BAG3-IKK-γ axis to accelerate TNF-α secretion in oral lichen planus.Microbiome · 2025Article
- Metagenomics reveals an increased proportion of anJournal of Zhejiang University. Science. B · 2025Article
- Application of fungal inoculants enhances colonization of secondary bacterial degraders during in situ paddy straw degradation: a genomic insights into cross-domain synergism.International microbiology : the official journal of the Spanish Society for Microbiology · 2025Article
- Ironing out the conflicts: iron supplementation reduces negatives bacterial interactions in the rhizosphere of an Atacama-endemic perennial grass.Environmental microbiome · 2025Article
- A Generalized Bayesian Stochastic Block Model for Microbiome Community Detection.Statistics in medicine · 2025Article
- Identification of stress-alleviating strains from the core drought-responsive microbiome of Arabidopsis ecotypes.The ISME journal · 2025Article
- Machine learning integrates region-specific microbial signatures to distinguish geographically adjacent populations within a province.Frontiers in microbiology · 2025Article
- Synthetic communities derived from the core endophytic microbiome of hyperaccumulators and their role in cadmium phytoremediation.Microbiome · 2024Article
27 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors.
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No grant is acknowledged in the PubMed record.
Abstract
The combined effect of mutual association within the co-inhabiting microbes in human body is known to play a major role in determining health status of individuals. The differential taxonomic abundance between healthy and disease are often used to identify microbial markers. However, in order to make a microbial community based inference, it is important not only to consider microbial abundances, but also to quantify the changes observed among inter microbial associations. In the present study, we introduce a method called 'NetShift' to quantify rewiring and community changes in microbial association networks between healthy and disease. Additionally, we devise a score to identify important microbial taxa which serve as 'drivers' from the healthy to disease. We demonstrate the validity of our score on a number of scenarios and apply our methodology on two real world metagenomic datasets. The 'NetShift' methodology is also implemented as a web-based application available at https://web.rniapps.net/netshift.
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