ReviewTrends in microbiology2016
Network-Thinking: Graphs to Analyze Microbial Complexity and Evolution.
Review in Trends in microbiology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 48 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.
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.
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Who cites it
48 citing papers in PubMed.
- Reconstructing the Network of Horizontal Gene Exchange in Bacteria to Differentiate Direct and Indirect Transfers.Genome biology and evolution · 2026Article
- MicroSSNet: an R package for microbial network construction and analysis at the single-sample and aggregated levels.BMC bioinformatics · 2026Article
- Metatranscriptomes-based sequence similarity networks uncover genetic signatures within parasitic freshwater microbial eukaryotes.Microbiome · 2025Article
- Challenges in Assembling the Dated Tree of Life.Genome biology and evolution · 2024Article
- A Novel Slope-Matrix-Graph Algorithm to Analyze Compositional Microbiome Data.Microorganisms · 2024Article
- Article
- Classes of explicit phylogenetic networks and their biological and mathematical significance.Journal of mathematical biology · 2022Review
- Hundreds of Out-of-Frame Remodeled Gene Families in the Escherichia coli Pangenome.Molecular biology and evolution · 2022Article
- Article
- Evolutionary Pathways and Trajectories in Antibiotic Resistance.Clinical microbiology reviews · 2021Article
- Applicability of several rooted phylogenetic network algorithms for representing the evolutionary history of SARS-CoV-2.BMC ecology and evolution · 2021Article
- From Trees to Clouds: PhageClouds for Fast Comparison of ∼640,000 Phage Genomic Sequences and Host-Centric Visualization Using Genomic Network Graphs.PHAGE (New Rochelle, N.Y.) · 2021Article
- Horizontal gene transfer and recombination analysis of SARS-CoV-2 genes helps discover its close relatives and shed light on its origin.BMC ecology and evolution · 2021Article
- Mode and dynamics of vanA-type vancomycin resistance dissemination in Dutch hospitals.Genome medicine · 2021Article
- Unraveling gene content variation across eukaryotic giant viruses based on network analyses and host associations.Virus evolution · 2021Article
- Gene Similarity Networks Unveil a Potential Novel Unicellular Group Closely Related to Animals from the Tara Oceans Expedition.Genome biology and evolution · 2020Article
- Should Networks Supplant Tree Building?Microorganisms · 2020Review
- Large-scale network analysis captures biological features of bacterial plasmids.Nature communications · 2020Article
- Ab Initio Construction and Evolutionary Analysis of Protein-Coding Gene Families with Partially Homologous Relationships: Closely Related Drosophila Genomes as a Case Study.Genome biology and evolution · 2020Article
- Antibiotic resistance gene sharing networks and the effect of dietary nutritional content on the canine and feline gut resistome.Animal microbiome · 2020Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The tree model and tree-based methods have played a major, fruitful role in evolutionary studies. However, with the increasing realization of the quantitative and qualitative importance of reticulate evolutionary processes, affecting all levels of biological organization, complementary network-based models and methods are now flourishing, inviting evolutionary biology to experience a network-thinking era. We show how relatively recent comers in this field of study, that is, sequence-similarity networks, genome networks, and gene families-genomes bipartite graphs, already allow for a significantly enhanced usage of molecular datasets in comparative studies. Analyses of these networks provide tools for tackling a multitude of complex phenomena, including the evolution of gene transfer, composite genes and genomes, evolutionary transitions, and holobionts.
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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.