ArticlePLoS computational biology2016
Visualization of Metabolic Interaction Networks in Microbial Communities Using VisANT 5.0.
Article in PLoS computational biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 33 citations in OpenAlex.
- Exploring interspecific interaction variability in microbiota: A review.Engineering microbiology · 2024Review
- BioNexusSentinel: a visual tool for bioregulatory network and cytohistological RNA-seq genetic expression profiling within the context of multicellular simulation research using ChatGPT-augmented software engineering.Bioinformatics advances · 2024Article
- CAVE: a cloud-based platform for analysis and visualization of metabolic pathways.Nucleic acids research · 2023Article
- Molecular landscapes of glioblastoma cell lines revealed a group of patients that do not benefit fromFrontiers in neuroscience · 2023Article
- Unravelling potential biomarkers for acute and chronic brucellosis through proteomic and bioinformatic approaches.Frontiers in cellular and infection microbiology · 2023Article
- NetCom: A Network-Based Tool for Predicting Metabolic Activities of Microbial Communities Based on Interpretation of Metagenomics Data.Microorganisms · 2021Article
- Metabolic modelling approaches for describing and engineering microbial communities.Computational and structural biotechnology journal · 2021Review
- Trem2 promotes anti-inflammatory responses in microglia and is suppressed under pro-inflammatory conditions.Human molecular genetics · 2020Article
- Regularized S-Map Reveals Varying Bacterial Interactions.Applied and environmental microbiology · 2020Article
- Metabolomics as an Emerging Tool in the Search for Astrobiologically Relevant Biomarkers.Astrobiology · 2020Review
- Metabolic Modeling of Microbial Community Interactions for Health, Environmental and Biotechnological Applications.Current genomics · 2018Review
- Analysis of Microbial Functions in the Rhizosphere Using a Metabolic-Network Based Framework for Metagenomics Interpretation.Frontiers in microbiology · 2017Article
- Interactions between host genetics and gut microbiome in diabetes and metabolic syndrome.Molecular metabolism · 2016Review
- Review
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
Abstract
The complexity of metabolic networks in microbial communities poses an unresolved visualization and interpretation challenge. We address this challenge in the newly expanded version of a software tool for the analysis of biological networks, VisANT 5.0. We focus in particular on facilitating the visual exploration of metabolic interaction between microbes in a community, e.g. as predicted by COMETS (Computation of Microbial Ecosystems in Time and Space), a dynamic stoichiometric modeling framework. Using VisANT's unique metagraph implementation, we show how one can use VisANT 5.0 to explore different time-dependent ecosystem-level metabolic networks. In particular, we analyze the metabolic interaction network between two bacteria previously shown to display an obligate cross-feeding interdependency. In addition, we illustrate how a putative minimal gut microbiome community could be represented in our framework, making it possible to highlight interactions across multiple coexisting species. We envisage that the "symbiotic layout" of VisANT can be employed as a general tool for the analysis of metabolism in complex microbial communities as well as heterogeneous human tissues. VisANT is freely available at: http://visant.bu.edu and COMETS at http://comets.bu.edu.
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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.