The Novel Phages phiCD5763 and phiCD2955 Represent Two Groups of Big Plasmidial Siphoviridae Phages of Clostridium difficile

Virulence factors of Clostridium difficile and their role during infection

(2016) Claire Janoir   ANAEROBE

CRISPR Diversity and Microevolution inClostridium difficile

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

Prophages mediate defense against phage infection through diverse mechanisms

(2016) Joseph Bondy-Denomy et al.   ISME Journal

InterPro in 2017—beyond protein family and domain annotations

(2016) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Temperate phages both mediate and drive adaptive evolution in pathogen biofilms

(2016) Emily V. Davies et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Predominance and high antibiotic resistance of the emerging Clostridium difficile genotypes NAPCR1 and NAP9 in a Costa Rican hospital over a 2-year period without outbreaks

(2016) Diana López-Ureña et al.   Emerging Microbes & Infections

Roary: rapid large-scale prokaryote pan genome analysis

(2015) Andrew J. Page et al.   BIOINFORMATICS

Emergence of an Outbreak-Associated Clostridium difficile Variant with Increased Virulence

(2015) Carlos Quesada-Gómez et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Small acid-soluble spore proteins of Clostridium acetobutylicum are able to protect DNA in vitro and are specifically cleaved by germination protease GPR and spore protease YyaC

(2015) Daniela Wetzel et al.   MICROBIOLOGY-SGM

A prophage-encoded actin-like protein required for efficient viral DNA replication in bacteria

(2015) Catriona Donovan et al.   NUCLEIC ACIDS RESEARCH

A Modified R-Type Bacteriocin Specifically Targeting Clostridium difficile Prevents Colonization of Mice without Affecting Gut Microbiota Diversity

(2015) Dana Gebhart et al.   mBio

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Characterization of the core and accessory genomes of Pseudomonas aeruginosa using bioinformatic tools Spine and AGEnt

(2014) Egon A Ozer et al.   BMC GENOMICS

Automated classification of tailed bacteriophages according to their neck organization

(2014) Anne Lopes et al.   BMC GENOMICS

CDD: NCBI's conserved domain database

(2014) Aron Marchler-Bauer et al.   NUCLEIC ACIDS RESEARCH

SMART: recent updates, new developments and status in 2015

(2014) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

UniProt: a hub for protein information

(2014)   NUCLEIC ACIDS RESEARCH

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

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

CasA mediates Cas3-catalyzed target degradation during CRISPR RNA-guided interference

(2014) M. L. Hochstrasser et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phages Preying on Bacillus anthracis, Bacillus cereus, and Bacillus thuringiensis: Past, Present and Future

(2014) Annika Gillis et al.   Viruses-Basel

GET_HOMOLOGUES, a Versatile Software Package for Scalable and Robust Microbial Pangenome Analysis

(2013) Bruno Contreras-Moreira et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

A giant Pseudomonas phage from Poland

(2013) Zuzanna Drulis-Kawa et al.   ARCHIVES OF VIROLOGY

A bioinformatic analysis of ribonucleotide reductase genes in phage genomes and metagenomes

(2013) Bhakti Dwivedi et al.   BMC EVOLUTIONARY BIOLOGY

Evolutionary History of the Clostridium difficile Pathogenicity Locus

(2013) Kate E. Dingle et al.   Genome Biology and Evolution

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

(2013) Ross Overbeek et al.   NUCLEIC ACIDS RESEARCH

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Horizontal gene transfer converts non-toxigenic Clostridium difficile strains into toxin producers

(2013) Michael S.M. Brouwer et al.   Nature Communications

Enterococcus faecalis Prophage Dynamics and Contributions to Pathogenic Traits

(2013) Renata C. Matos et al.   PLoS Genetics

Novel High-Molecular-Weight, R-Type Bacteriocins of Clostridium difficile

(2012) D. Gebhart et al.   JOURNAL OF BACTERIOLOGY

Easyfig: a genome comparison visualizer

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

Phamerator: a bioinformatic tool for comparative bacteriophage genomics

(2011) Steven G Cresawn et al.   BMC BIOINFORMATICS

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

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

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

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

Bacteriophage Crosstalk: Coordination of Prophage Induction by Trans-Acting Antirepressors

(2011) Sébastien Lemire et al.   PLoS Genetics

The impact of bacteriophages on probiotic bacteria and gut microbiota diversity

(2010) Marco Ventura et al.   Genes and Nutrition

Inhibition of Superinfection and the Evolution of Viral Latency

(2010) T. W. Berngruber et al.   JOURNAL OF VIROLOGY

Acyl-Homoserine Lactones Can Induce Virus Production in Lysogenic Bacteria: an Alternative Paradigm for Prophage Induction

(2009) D. Ghosh et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Emergence of Clostridium difficile NAP1 in Latin America

(2009) C. Quesada-Gomez et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Bacteriophage-Mediated Toxin Gene Regulation in Clostridium difficile

(2009) R. Govind et al.   JOURNAL OF VIROLOGY

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

De novo bacterial genome sequencing: Millions of very short reads assembled on a desktop computer

(2008) D. Hernandez et al.   GENOME RESEARCH

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH