Two Novel Myoviruses from the North of Iraq Reveal Insights into Clostridium difficile Phage Diversity and Biology

CRISPR Diversity and Microevolution inClostridium difficile

(2016) Joakim M. Andersen et al.   Genome Biology and Evolution

Bacteriophage Combinations Significantly Reduce Clostridium difficile GrowthIn Vitroand ProliferationIn Vivo

(2015) Janet Y. Nale et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Diversity and Evolution in the Genome of Clostridium difficile

(2015) Daniel R. Knight et al.   CLINICAL MICROBIOLOGY REVIEWS

A Taxonomic Review of Clostridium difficile Phages and Proposal of a Novel Genus, “Phimmp04likevirus”

(2015) Katherine Hargreaves et al.   Viruses-Basel

Mechanisms of DNA Packaging by Large Double-Stranded DNA Viruses

(2015) Venigalla B. Rao et al.   Annual Review of Virology

Strain Types and Antimicrobial Resistance Patterns of Clostridium difficile Isolates from the United States, 2011 to 2013

(2014) Isabella A. Tickler et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Characterization of Temperate Phages Infecting Clostridium difficile Isolates of Human and Animal Origins

(2014) Ognjen Sekulovic et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Bacteriophage recombination systems and biotechnical applications

(2014) Nafiseh Nafissi et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

Epidemic Clostridium difficile Strains Demonstrate Increased Competitive Fitness Compared to Nonepidemic Isolates

(2014) Catherine D. Robinson et al.   INFECTION AND IMMUNITY

Intra- and inter-generic transfer of pathogenicity island-encoded virulence genes by cos phages

(2014) John Chen et al.   ISME Journal

What Does the Talking?: Quorum Sensing Signalling Genes Discovered in a Bacteriophage Genome

(2014) Katherine R. Hargreaves et al.   PLoS One

Abundant and Diverse Clustered Regularly Interspaced Short Palindromic Repeat Spacers in Clostridium difficile Strains and Prophages Target Multiple Phage Types within This Pathogen

(2014) K. R. Hargreaves et al.   mBio

Genetically Diverse Clostridium difficile Strains Harboring Abundant Prophages in an Estuarine Environment

(2013) K. R. Hargreaves et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Infernal 1.1: 100-fold faster RNA homology searches

(2013) E. P. Nawrocki et al.   BIOINFORMATICS

Molecular Aspects and Comparative Genomics of Bacteriophage Endolysins

(2013) H. Oliveira et al.   JOURNAL OF VIROLOGY

Variations in Virulence and Molecular Biology among Emerging Strains of Clostridium difficile

(2013) J. J. Hunt et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)

(2013) Ross Overbeek et al.   NUCLEIC ACIDS RESEARCH

CRISPRTarget

(2013) Ambarish Biswas et al.   RNA Biology

Phage  C2 Mediates Transduction of Tn6215, Encoding Erythromycin Resistance, between Clostridium difficile Strains

(2013) S. Goh et al.   mBio

Genome-Wide Identification of Regulatory RNAs in the Human Pathogen Clostridium difficile

(2013) Olga A. Soutourina et al.   PLoS Genetics

Evidence ofIn VivoProphage Induction during Clostridium difficile Infection

(2012) Mathieu Meessen-Pinard et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Prophage Carriage and Diversity within Clinically Relevant Strains of Clostridium difficile

(2012) Jinyu Shan et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse et al.   BIOINFORMATICS

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

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

Gegenees: Fragmented Alignment of Multiple Genomes for Determining Phylogenomic Distances and Genetic Signatures Unique for Specified Target Groups

(2012) Joakim Ågren et al.   PLoS One

Easyfig: a genome comparison visualizer

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

BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons

(2011) Nabil-Fareed Alikhan et al.   BMC GENOMICS

The human gut virome: Inter-individual variation and dynamic response to diet

(2011) S. Minot et al.   GENOME RESEARCH

Profound Alterations of Intestinal Microbiota following a Single Dose of Clindamycin Results in Sustained Susceptibility to Clostridium difficile-Induced Colitis

(2011) Charlie G. Buffie et al.   INFECTION AND IMMUNITY

Prophage-Stimulated Toxin Production in Clostridium difficile NAP1/027 Lysogens

(2011) O. Sekulovic et al.   JOURNAL OF BACTERIOLOGY

RAxML and FastTree: Comparing Two Methods for Large-Scale Maximum Likelihood Phylogeny Estimation

(2011) Kevin Liu et al.   PLoS One

Bacteriophage treatment significantly reduces viable Clostridium difficile and prevents toxin production in an in vitro model system

(2010) Emma Meader et al.   ANAEROBE

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Genome analysis of the Clostridium difficile phage ΦCD6356, a temperate phage of the Siphoviridae family

(2010) Marianne Horgan et al.   GENE

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

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

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

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Classification of Myoviridae bacteriophages using protein sequence similarity

(2009) Rob Lavigne et al.   BMC MICROBIOLOGY

De novo assembly of human genomes with massively parallel short read sequencing

(2009) R. Li et al.   GENOME RESEARCH

SOAP: short oligonucleotide alignment program

(2008) R. Li et al.   BIOINFORMATICS

Molecular Characterization of a Clostridium difficile Bacteriophage and Its Cloned Biologically Active Endolysin

(2008) M. J. Mayer et al.   JOURNAL OF BACTERIOLOGY