Causes and Consequences of Bacteriophage Diversification via Genetic Exchanges across Lifestyles and Bacterial Taxa

Phage diversity, genomics and phylogeny

(2020) Moïra B. Dion et al.   NATURE REVIEWS MICROBIOLOGY

Expansion of known ssRNA phage genomes: From tens to over a thousand

(2020) J. Callanan et al.   Science Advances

Bacterial NHEJ: a never ending story

(2019) Claire Bertrand et al.   MOLECULAR MICROBIOLOGY

A matter of background: DNA repair pathways as a possible cause for the sparse distribution of CRISPR-Cas systems in bacteria

(2019) Aude Bernheim et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Bacteriophages benefit from generalized transduction

(2019) Alfred Fillol-Salom et al.   PLoS Pathogens

HH-suite3 for fast remote homology detection and deep protein annotation

(2019) Martin Steinegger et al.   BMC BIOINFORMATICS

Widespread anti-CRISPR proteins in virulent bacteriophages inhibit a range of Cas9 proteins

(2018) Alexander P. Hynes et al.   Nature Communications

Sak4 of Phage HK620 Is a RecA Remote Homolog With Single-Strand Annealing Activity Stimulated by Its Cognate SSB Protein

(2018) Geoffrey Hutinet et al.   Frontiers in Microbiology

The smallest ssDNA phage infecting a marine bacterium

(2018) Yuanchao Zhan et al.   ENVIRONMENTAL MICROBIOLOGY

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses

(2018) Jaime Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database in 2019

(2018) Sara El-Gebali et al.   NUCLEIC ACIDS RESEARCH

Phage Mu Gam protein promotes NHEJ in concert with Escherichia coli ligase

(2018) Sudipta Bhattacharyya et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets

(2017) Martin Steinegger et al.   NATURE BIOTECHNOLOGY

ModelFinder: fast model selection for accurate phylogenetic estimates

(2017) Subha Kalyaanamoorthy et al.   NATURE METHODS

Bacteriophage evolution differs by host, lifestyle and genome

(2017) Travis N. Mavrich et al.   Nature Microbiology

Genetic and life-history traits associated with the distribution of prophages in bacteria

(2016) Marie Touchon et al.   ISME Journal

Prokaryotic Virus Orthologous Groups (pVOGs): a resource for comparative genomics and protein family annotation

(2016) Ana Laura Grazziotin et al.   NUCLEIC ACIDS RESEARCH

Linking Virus Genomes with Host Taxonomy

(2016) Tomoko Mihara et al.   Viruses-Basel

Bacteriophage-mediated spread of bacterial virulence genes

(2015) José R Penadés et al.   CURRENT OPINION IN MICROBIOLOGY

CRISPR-Cas immunity in prokaryotes

(2015) Luciano A. Marraffini   NATURE

VirSorter: mining viral signal from microbial genomic data

(2015) Simon Roux et al.   PeerJ

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Temperate Phages Acquire DNA from Defective Prophages by Relaxed Homologous Recombination: The Role of Rad52-Like Recombinases

(2014) Marianne De Paepe et al.   PLoS Genetics

Diversity and evolutionary relationships of T7-like podoviruses infecting marine cyanobacteria

(2013) Naama P. Dekel-Bird et al.   ENVIRONMENTAL MICROBIOLOGY

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

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

PHACTS, a computational approach to classifying the lifestyle of phages

(2012) Katelyn McNair et al.   BIOINFORMATICS

DO PHAGES EFFICIENTLY SHUTTLE TRANSPOSABLE ELEMENTS AMONG PROKARYOTES?

(2011) Sébastien Leclercq et al.   EVOLUTION

Analysing recombination in nucleotide sequences

(2011) DARREN P. MARTIN et al.   Molecular Ecology Resources

Phage auxiliary metabolic genes and the redirection of cyanobacterial host carbon metabolism

(2011) L. R. Thompson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bacteriophages and their genomes

(2011) Graham F Hatfull et al.   Current Opinion in Virology

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

DendroPy: a Python library for phylogenetic computing

(2010) J. Sukumaran et al.   BIOINFORMATICS

Predicting Plasmid Promiscuity Based on Genomic Signature

(2010) H. Suzuki et al.   JOURNAL OF BACTERIOLOGY

Detection of novel recombinases in bacteriophage genomes unveils Rad52, Rad51 and Gp2.5 remote homologs

(2010) Anne Lopes et al.   NUCLEIC ACIDS RESEARCH

Infernal 1.0: inference of RNA alignments

(2009) E. P. Nawrocki et al.   BIOINFORMATICS

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

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

Genomic Characterization of Mycobacteriophage Giles: Evidence for Phage Acquisition of Host DNA by Illegitimate Recombination

(2008) P. Morris et al.   JOURNAL OF BACTERIOLOGY

Fast unfolding of communities in large networks

(2008) Vincent D Blondel et al.   JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT

Reticulate Representation of Evolutionary and Functional Relationships between Phage Genomes

(2008) G. Lima-Mendez et al.   MOLECULAR BIOLOGY AND EVOLUTION

Determination of cell fate selection during phage lambda infection

(2008) F. St-Pierre et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Characterization of 1706, a virulent phage from Lactococcus lactis with similarities to prophages from other Firmicutes

(2008) Josiane E. Garneau et al.   VIROLOGY

The λ Red Proteins Promote Efficient Recombination between Diverged Sequences: Implications for Bacteriophage Genome Mosaicism

(2008) Jann T. Martinsohn et al.   PLoS Genetics