ArticleJournal of computational biology : a journal of computational molecular cell biology2010
Mosaic graphs and comparative genomics in phage communities.
Article in Journal of computational biology : a journal of computational molecular cell biology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 20 citations in OpenAlex.
- LAMBDA: a prophage detection benchmark for genomic language models.NAR genomics and bioinformatics · 2026Article
- LAMBDA: A Prophage Detection Benchmark for Genomic Language Models.bioRxiv : the preprint server for biology · 2026Article
- Computational Microbial and Viral Ecology Analysis.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Novel Escherichia coli phages representing a distinct genus within the subfamily Stephanstirmvirinae: genome and host range characteristics.Archives of virology · 2025Article
- CheekAge: a next-generation buccal epigenetic aging clock associated with lifestyle and health.GeroScience · 2024Article
- A Novel Subcluster of Closely RelatedViruses · 2023Article
- Phables: from fragmented assemblies to high-quality bacteriophage genomes.Bioinformatics (Oxford, England) · 2023Article
- Phables: from fragmented assemblies to high-quality bacteriophage genomes.bioRxiv : the preprint server for biology · 2023Article
- Whole-genome analysis showed the promotion of genetic diversity and coevolution inFrontiers in microbiology · 2023Article
- Isolation and Characterization of a Novel Phage SaGU1 that Infects Staphylococcus aureus Clinical Isolates from Patients with Atopic Dermatitis.Current microbiology · 2021Article
- Evaluation of a concatenated protein phylogeny for classification of tailed double-stranded DNA viruses belonging to the order Caudovirales.Nature microbiology · 2019Article
- Prevalence ofFrontiers in microbiology · 2019Article
- Phage spanins: diversity, topological dynamics and gene convergence.BMC bioinformatics · 2018Article
- Multidimensional metrics for estimating phage abundance, distribution, gene density, and sequence coverage in metagenomes.Frontiers in microbiology · 2015Article
- The Staphylococci phages family: an overview.Viruses · 2012Review
- Staphylococcus aureus temperate bacteriophage: carriage and horizontal gene transfer is lineage associated.Frontiers in cellular and infection microbiology · 2012Article
- The evolution of the tape measure protein: units, duplications and losses.BMC bioinformatics · 2011Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
Abstract
Comparing the genomes of two closely related viruses often produces mosaics where nearly identical sequences alternate with sequences that are unique to each genome. When several closely related genomes are compared, the unique sequences are likely to be shared with third genomes, leading to virus mosaic communities. Here we present comparative analysis of sets of Staphylococcus aureus phages that share large identical sequences with up to three other genomes, and with different partners along their genomes. We introduce mosaic graphs to represent these complex recombination events, and use them to illustrate the breath and depth of sequence sharing: some genomes are almost completely made up of shared sequences, while genomes that share very large identical sequences can adopt alternate functional modules. Mosaic graphs also allow us to identify breakpoints that could eventually be used for the construction of recombination networks. These findings have several implications on phage metagenomics assembly, on the horizontal gene transfer paradigm, and more generally on the understanding of the composition and evolutionary dynamics of virus communities.
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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.