Pseudomonas Phage MD8: Genetic Mosaicism and Challenges of Taxonomic Classification of Lambdoid Bacteriophages

Stop that plasmid

(2020) Ursula Hofer   NATURE REVIEWS MICROBIOLOGY

Structural Insights Into the Transcriptional Regulation of HigBA Toxin–Antitoxin System by Antitoxin HigA in Pseudomonas aeruginosa

(2020) Ying Liu et al.   Frontiers in Microbiology

Autographivirinae Bacteriophage Arno 160 Infects Pectobacterium carotovorum via Depolymerization of the Bacterial O-Polysaccharide

(2020) Mikhail M. Shneider et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

The new scope of virus taxonomy: partitioning the virosphere into 15 hierarchical ranks

(2020)   Nature Microbiology

Molecular Characterization and Comparative Genomic Analysis of vB_PaeP_YA3, a Novel Temperate Bacteriophage of Pseudomonas aeruginosa

(2020) Xinyan Yu et al.   Frontiers in Microbiology

Classifying the Unclassified: A Phage Classification Method

(2019) Cynthia Maria Chibani et al.   Viruses-Basel

Evaluation of a concatenated protein phylogeny for classification of tailed double-stranded DNA viruses belonging to the order Caudovirales

(2019) Soo Jen Low et al.   Nature Microbiology

The role of 3D genome organization in development and cell differentiation

(2019) Hui Zheng et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Temperate Bacteriophages from Chronic Pseudomonas aeruginosa Lung Infections Show Disease-Specific Changes in Host Range and Modulate Antimicrobial Susceptibility

(2019) Mohammad A. Tariq et al.   mSystems

ModelTest-NG: A New and Scalable Tool for the Selection of DNA and Protein Evolutionary Models

(2019) Diego Darriba et al.   MOLECULAR BIOLOGY AND EVOLUTION

Changing Rates of Chronic Pseudomonas aeruginosa Infections in Cystic Fibrosis: A Population-Based Cohort Study

(2018) Matthew R Crull et al.   CLINICAL INFECTIOUS DISEASES

A Completely Reimplemented MPI Bioinformatics Toolkit with a New HHpred Server at its Core

(2018) Lukas Zimmermann et al.   JOURNAL OF MOLECULAR BIOLOGY

Gene Co-occurrence Networks Reflect Bacteriophage Ecology and Evolution

(2018) Jason W. Shapiro et al.   mBio

A Reference Viral Database (RVDB) To Enhance Bioinformatics Analysis of High-Throughput Sequencing for Novel Virus Detection

(2018) Norman Goodacre et al.   mSphere

Pelagiphages in the Podoviridae family integrate into host genomes

(2018) Yanlin Zhao et al.   ENVIRONMENTAL MICROBIOLOGY

Cryo-EM structure of the bacteriophage T4 isometric head at 3.3-Å resolution and its relevance to the assembly of icosahedral viruses

(2017) Zhenguo Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

OrthoANI: An improved algorithm and software for calculating average nucleotide identity

(2016) Imchang Lee et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Emerging Roles of Toxin-Antitoxin Modules in Bacterial Pathogenesis

(2016) Barbara Kędzierska et al.   MOLECULES

Common Evolutionary Origin of Procapsid Proteases, Phage Tail Tubes, and Tubes of Bacterial Type VI Secretion Systems

(2016) Andrei Fokine et al.   STRUCTURE

Chronic wound infections: the role ofPseudomonas aeruginosaandStaphylococcus aureus

(2015) Raffaele Serra et al.   Expert Review of Anti-Infective Therapy

The Phyre2 web portal for protein modeling, prediction and analysis

(2015) Lawrence A Kelley et al.   Nature Protocols

Bacteriophage lambda: Early pioneer and still relevant

(2015) Sherwood R. Casjens et al.   VIROLOGY

Phage ΦPan70, a Putative Temperate Phage, Controls Pseudomonas aeruginosa in Planktonic, Biofilm and Burn Mouse Model Assays

(2015) Angela Holguín et al.   Viruses-Basel

Phylogenetic Distribution of CRISPR-Cas Systems in Antibiotic-Resistant Pseudomonas aeruginosa

(2015) Alex van Belkum et al.   mBio

Comparative Genomic and Phylogenomic Analyses Reveal a Conserved Core Genome Shared by Estuarine and Oceanic Cyanopodoviruses

(2015) Sijun Huang et al.   PLoS One

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Phage lysis: Three steps, three choices, one outcome

(2014) Ryland Young   JOURNAL OF MICROBIOLOGY

A novel Pseudomonas aeruginosa Bacteriophage, Ab31, a Chimera Formed from Temperate Phage PAJU2 and P. putida Lytic Phage AF: Characteristics and Mechanism of Bacterial Resistance

(2014) Libera Latino et al.   PLoS One

Capsid expansion mechanism of bacteriophage T7 revealed by multistate atomic models derived from cryo-EM reconstructions

(2014) F. Guo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Phylogenetic Likelihood Library

(2014) T. Flouri et al.   SYSTEMATIC BIOLOGY

Phage cluster relationships identified through single gene analysis

(2013) Kyle C Smith et al.   BMC GENOMICS

Functional Domains of the HK97 Capsid Maturation Protease and the Mechanisms of Protein Encapsidation

(2013) Robert L. Duda et al.   JOURNAL OF MOLECULAR BIOLOGY

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

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

Isolation and characterization of novel soilborne lytic bacteriophages infectingDickeyaspp. biovar 3 (‘D. solani’)

(2013) R. Czajkowski et al.   PLANT PATHOLOGY

Phage Lambda P Protein: Trans-Activation, Inhibition Phenotypes and their Suppression

(2013) Sidney Hayes et al.   Viruses-Basel

Expanding the Marine Virosphere Using Metagenomics

(2013) Carolina Megumi Mizuno et al.   PLoS Genetics

Genomes of marine cyanopodoviruses reveal multiple origins of diversity

(2012) S. J. Labrie et al.   ENVIRONMENTAL MICROBIOLOGY

The Spanin Complex Is Essential for Lambda Lysis

(2012) J. Berry et al.   JOURNAL OF BACTERIOLOGY

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Easyfig: a genome comparison visualizer

(2011) M. J. Sullivan et al.   BIOINFORMATICS

Structure of the Three N-Terminal Immunoglobulin Domains of the Highly Immunogenic Outer Capsid Protein from a T4-Like Bacteriophage

(2011) A. Fokine et al.   JOURNAL OF VIROLOGY

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Assembly and Maturation of the Bacteriophage Lambda Procapsid: gpC Is the Viral Protease

(2010) Elizabeth Medina et al.   JOURNAL OF MOLECULAR BIOLOGY

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

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

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

FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix

(2009) M. N. Price et al.   MOLECULAR BIOLOGY AND EVOLUTION

An Improved General Amino Acid Replacement Matrix

(2008) S. Q. Le et al.   MOLECULAR BIOLOGY AND EVOLUTION

Functional domains of the bacteriophage P2 scaffolding protein: Identification of residues involved in assembly and protease activity

(2008) Jenny R. Chang et al.   VIROLOGY