Phylogenomic networks reveal limited phylogenetic range of lateral gene transfer by transduction

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VirSorter: mining viral signal from microbial genomic data

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Location of the unique integration site on an Escherichia coli chromosome by bacteriophage lambda DNA in vivo

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Pervasive domestication of defective prophages by bacteria

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Sulfur Oxidation Genes in Diverse Deep-Sea Viruses

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The Comprehensive Antibiotic Resistance Database

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MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

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Using networks to measure similarity between genes: association index selection

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A Tight Link between Orthologs and Bidirectional Best Hits in Bacterial and Archaeal Genomes

(2012) Yuri I. Wolf et al.   Genome Biology and Evolution

Genomic characterization of the Bacillus cereus sensu lato species: Backdrop to the evolution of Bacillus anthracis

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Multi-scale structure and geographic drivers of cross-infection within marine bacteria and phages

(2012) Cesar O Flores et al.   ISME Journal

The Adaptation of Temperate Bacteriophages to Their Host Genomes

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Structure, function and diversity of the healthy human microbiome

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PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies

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Population Genomics of Early Events in the Ecological Differentiation of Bacteria

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Contrasting Life Strategies of Viruses that Infect Photo- and Heterotrophic Bacteria, as Revealed by Viral Tagging

(2012) L. Deng et al.   mBio

PanDaTox

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Directed networks reveal genomic barriers and DNA repair bypasses to lateral gene transfer among prokaryotes

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Ecology drives a global network of gene exchange connecting the human microbiome

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Association between translation efficiency and horizontal gene transfer within microbial communities

(2011) Tamir Tuller et al.   NUCLEIC ACIDS RESEARCH

PHAST: A Fast Phage Search Tool

(2011) Y. Zhou et al.   NUCLEIC ACIDS RESEARCH

Horizontal Transfer, Not Duplication, Drives the Expansion of Protein Families in Prokaryotes

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High-frequency phage-mediated gene transfer in freshwater environments determined at single-cell level

(2010) Takehiko Kenzaka et al.   ISME Journal

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

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Photosystem I gene cassettes are present in marine virus genomes

(2009) Itai Sharon et al.   NATURE

Network analyses structure genetic diversity in independent genetic worlds

(2009) S. Halary et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phage-Mediated Intergeneric Transfer of Toxin Genes

(2009) J. Chen et al.   SCIENCE