Analysis of genetic recombination and the pan-genome of a highly recombinogenic bacteriophage species

Prophage Hunter: an integrative hunting tool for active prophages

(2019) Wenchen Song et al.   NUCLEIC ACIDS RESEARCH

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

(2018) Gabriel Ramírez-Vargas et al.   Frontiers in Microbiology

Phylogeographic diversity and mosaicism of the Helicobacter pylori tfs integrative and conjugative elements

(2018) Robin M. Delahay et al.   Mobile DNA

Investigation of recombination-intense viral groups and their genes in the Earth’s virome

(2018) Jan P. Meier-Kolthoff et al.   Scientific Reports

Genomics of Helicobacter pylori

(2017) Kaisa Thorell et al.   HELICOBACTER

Phylogeographic agreement between prophage and bacterial housekeeping genes in Helicobacter pylori strains from The Gambia

(2017) Ousman Secka et al.   HELICOBACTER

The expression of Helicobacter pylori tfs plasticity zone cluster is regulated by pH and adherence, and its composition is associated with differential gastric IL-8 secretion

(2017) Bruno Silva et al.   HELICOBACTER

Rapid evolution of distinct Helicobacter pylori subpopulations in the Americas

(2017) Kaisa Thorell et al.   PLoS Genetics

Identification and genomic comparison of temperate bacteriophages derived from emetic Bacillus cereus

(2017) Peiling Geng et al.   PLoS One

Genomic structure and insertion sites of Helicobacter pylori prophages from various geographical origins

(2017) Filipa F. Vale et al.   Scientific Reports

Genome-wide survey of codons under diversifying selection in a highly recombining bacterial species,Helicobacter pylori

(2016) Koji Yahara et al.   DNA RESEARCH

Recent “omics” advances inHelicobacter pylori

(2016) Elvire Berthenet et al.   HELICOBACTER

Uncovering Earth’s virome

(2016) David Paez-Espino et al.   NATURE

A Novel Approach to Helicobacter pylori Pan-Genome Analysis for Identification of Genomic Islands

(2016) Ikuo Uchiyama et al.   PLoS One

Roary: rapid large-scale prokaryote pan genome analysis

(2015) Andrew J. Page et al.   BIOINFORMATICS

The Presence of Phage Orthologous Genes inHelicobacter pyloriCorrelates with the Presence of the Virulence FactorsCagAandVacA

(2015) Alexandra Kyrillos et al.   HELICOBACTER

CRISPR Immunity Drives Rapid Phage Genome Evolution in Streptococcus thermophilus

(2015) David Paez-Espino et al.   mBio

Dormant phages of Helicobacter pylori reveal distinct populations in Europe

(2015) F. F. Vale et al.   Scientific Reports

Pan-Genome Analysis of Human Gastric PathogenH. pylori: Comparative Genomics and Pathogenomics Approaches to Identify Regions Associated with Pathogenicity and Prediction of Potential Core Therapeutic Targets

(2015) Amjad Ali et al.   Biomed Research International

Whole genome comparison of a large collection of mycobacteriophages reveals a continuum of phage genetic diversity

(2015) Welkin H Pope et al.   eLife

Efficient Inference of Recombination Hot Regions in Bacterial Genomes

(2014) Koji Yahara et al.   MOLECULAR BIOLOGY AND EVOLUTION

Comparative genomics defines the core genome of the growing N4-like phage genus and identifies N4-like Roseophage specific genes

(2014) Jacqueline Z.-M. Chan et al.   Frontiers in Microbiology

Characterization of Helicobacter pylori Bacteriophage KHP30

(2013) Jumpei Uchiyama et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Proteome variability amongHelicobacter pyloriisolates clustered according to genomic methylation

(2013) I. Vitoriano et al.   JOURNAL OF APPLIED MICROBIOLOGY

Chromosome Painting In Silico in a Bacterial Species Reveals Fine Population Structure

(2013) Koji Yahara et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

Complete Genome Sequences of Two Helicobacter pylori Bacteriophages Isolated from Japanese Patients

(2012) J. Uchiyama et al.   JOURNAL OF VIROLOGY

Genome, Integration, and Transduction of a Novel Temperate Phage of Helicobacter pylori

(2012) Cheng-Hung Luo et al.   JOURNAL OF VIROLOGY

Inference of Population Structure using Dense Haplotype Data

(2012) Daniel John Lawson et al.   PLoS Genetics

Age of the Association between Helicobacter pylori and Man

(2012) Yoshan Moodley et al.   PLoS Pathogens

Pathogen comparative genomics in the next-generation sequencing era: genome alignments, pangenomics and metagenomics

(2011) B. Hu et al.   Briefings in Functional Genomics

Genome Sequencing Reveals a Phage in Helicobacter pylori

(2011) P. Lehours et al.   mBio

Bacteriophages and their genomes

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

Genomes of the T4-related bacteriophages as windows on microbial genome evolution

(2010) Vasiliy M Petrov et al.   Virology Journal

DnaSP v5: a software for comprehensive analysis of DNA polymorphism data

(2009) P. Librado et al.   BIOINFORMATICS

Geographic distribution of methyltransferases of Helicobacter pylori: evidence of human host population isolation and migration

(2009) Filipa F Vale et al.   BMC MICROBIOLOGY

Diversity of Prophages in Dominant Staphylococcus aureus Clonal Lineages

(2009) C. Goerke et al.   JOURNAL OF BACTERIOLOGY

PGEToolbox: A Matlab Toolbox for Population Genetics and Evolution

(2008) J. J. Cai   JOURNAL OF HEREDITY

Helicobacter pylori Phage Screening

(2008) Filipa F. Vale et al.   MICROSCOPY AND MICROANALYSIS