ArticleMolecular biology and evolution2018
Bipartite Network Analysis of Gene Sharings in the Microbial World.
Article in Molecular biology and evolution, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 20 papers.
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.
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Who cites it
20 citing papers in PubMed, 41 citations in OpenAlex.
- A generative model for bipartite gene-sharing networks.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
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- Genetic Transfer in Action: Uncovering DNA Flow in an Extremophilic Microbial Community.Environmental microbiology · 2025Article
- The ageing virus hypothesis: Epigenetic ageing beyond the Tree of Life.BioEssays : news and reviews in molecular, cellular and developmental biology · 2025Review
- Unveiling microbial diversity: harnessing long-read sequencing technology.Nature methods · 2024Review
- Large-Scale Identification of Known and Novel RRNPP Quorum-Sensing Systems by RRNPP_Detector Captures Novel Features of Bacterial, Plasmidic, and Viral Coevolution.Molecular biology and evolution · 2023Article
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- Mining and the sustainable development goals: Prioritizing SDG targets for proper environmental governance.Ambio · 2023Article
- Dissecting the HGT network of carbon metabolic genes in soil-borne microbiota.Frontiers in microbiology · 2023Article
- Bioinformatic Analysis of a Set of 14 Temperate Bacteriophages Isolated from Staphylococcus aureus Strains Highlights Their Massive Genetic Diversity.Microbiology spectrum · 2022Article
- High Arsenic Levels Increase Activity Rather than Diversity or Abundance of Arsenic Metabolism Genes in Paddy Soils.Applied and environmental microbiology · 2021Article
- Entropic measure unveils country competitiveness and product specialization in the World trade web.Scientific reports · 2021Article
- Coevolving Plasmids Drive Gene Flow and Genome Plasticity in Host-Associated Intracellular Bacteria.Current biology : CB · 2021Article
- A network approach to elucidate and prioritize microbial dark matter in microbial communities.The ISME journal · 2021Article
- Antibiotic resistance gene sharing networks and the effect of dietary nutritional content on the canine and feline gut resistome.Animal microbiome · 2020Article
- Viruses as key reservoirs of antibiotic resistance genes in the environment.The ISME journal · 2019Article
- Article
- MultiTwin: A Software Suite to Analyze Evolution at Multiple Levels of Organization Using Multipartite Graphs.Genome biology and evolution · 2018Article
- Towards a Dynamic Interaction Network of Life to unify and expand the evolutionary theory.BMC biology · 2018Review
Corrections and comments
- Erratum issued
Authors and funding
6 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Extensive microbial gene flows affect how we understand virology, microbiology, medical sciences, genetic modification, and evolutionary biology. Phylogenies only provide a narrow view of these gene flows: plasmids and viruses, lacking core genes, cannot be attached to cellular life on phylogenetic trees. Yet viruses and plasmids have a major impact on cellular evolution, affecting both the gene content and the dynamics of microbial communities. Using bipartite graphs that connect up to 149,000 clusters of homologous genes with 8,217 related and unrelated genomes, we can in particular show patterns of gene sharing that do not map neatly with the organismal phylogeny. Homologous genes are recycled by lateral gene transfer, and multiple copies of homologous genes are carried by otherwise completely unrelated (and possibly nested) genomes, that is, viruses, plasmids and prokaryotes. When a homologous gene is present on at least one plasmid or virus and at least one chromosome, a process of "gene externalization," affected by a postprocessed selected functional bias, takes place, especially in Bacteria. Bipartite graphs give us a view of vertical and horizontal gene flow beyond classic taxonomy on a single very large, analytically tractable, graph that goes beyond the cellular Web of Life.
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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.