Relating Phage Genomes to Helicobacter pylori Population Structure: General Steps Using Whole-Genome Sequencing Data

Population genetic structure of Helicobacter pylori strains from Portuguese-speaking countries

(2017) Mónica Oleastro et al.   HELICOBACTER

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

(2017) Ousman Secka et al.   HELICOBACTER

Application of next generation sequencing in clinical microbiology and infection prevention

(2017) Ruud H. Deurenberg et al.   JOURNAL OF BIOTECHNOLOGY

Rapid evolution of distinct Helicobacter pylori subpopulations in the Americas

(2017) Kaisa Thorell et al.   PLoS Genetics

Revisiting Antibiotic Resistance Spreading in Wastewater Treatment Plants – Bacteriophages as a Much Neglected Potential Transmission Vehicle

(2017) Rolf Lood et al.   Frontiers in Microbiology

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

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

The history of Helicobacter pylori : from phylogeography to paleomicrobiology

(2016) F. Mégraud et al.   CLINICAL MICROBIOLOGY AND INFECTION

Phage Therapy in Bacterial Infections Treatment: One Hundred Years After the Discovery of Bacteriophages

(2016) Agata Anna Cisek et al.   CURRENT MICROBIOLOGY

Cryptic prophages as targets for drug development

(2016) Xiaoxue Wang et al.   DRUG RESISTANCE UPDATES

Recent “omics” advances inHelicobacter pylori

(2016) Elvire Berthenet et al.   HELICOBACTER

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

(2016) Marie Touchon et al.   ISME Journal

Human migration: Climate and the peopling of the world

(2016) Peter B. deMenocal et al.   NATURE

PHASTER: a better, faster version of the PHAST phage search tool

(2016) David Arndt et al.   NUCLEIC ACIDS RESEARCH

GenBank

(2016) Dennis A. Benson et al.   NUCLEIC ACIDS RESEARCH

The 5300-year-old Helicobacter pylori genome of the Iceman

(2016) F. Maixner et al.   SCIENCE

Genome-wide analysis of chromosomal import patterns after natural transformation of Helicobacter pylori

(2016) Sebastian Bubendorfer et al.   Nature Communications

Dissemination of Antimicrobial Resistance in Microbial Ecosystems through Horizontal Gene Transfer

(2016) Christian J. H. von Wintersdorff et al.   Frontiers in Microbiology

Comparative analysis of prophage-like elements inHelicobactersp. genomes

(2016) Xiangyu Fan et al.   PeerJ

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

(2015) Alexandra Kyrillos et al.   HELICOBACTER

A new perspective on lysogeny: prophages as active regulatory switches of bacteria

(2015) Ron Feiner et al.   NATURE REVIEWS MICROBIOLOGY

Dormant phages of Helicobacter pylori reveal distinct populations in Europe

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

VirSorter: mining viral signal from microbial genomic data

(2015) Simon Roux et al.   PeerJ

Comparative Genomics of a Helicobacter pylori Isolate from a Chinese Yunnan Naxi Ethnic Aborigine Suggests High Genetic Divergence and Phage Insertion

(2015) Yuanhai You et al.   PLoS One

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

DNA transfer in the gastric pathogen Helicobacter pylori

(2014) Esther Fernandez-Gonzalez et al.   JOURNAL OF GASTROENTEROLOGY

Pervasive domestication of defective prophages by bacteria

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

Characterization of Helicobacter pylori Bacteriophage KHP30

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

Explaining microbial phenotypes on a genomic scale: GWAS for microbes

(2013) B. E. Dutilh et al.   Briefings in Functional Genomics

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

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

(2013) Ross Overbeek et al.   NUCLEIC ACIDS RESEARCH

Temperate Bacterial Viruses as Double-Edged Swords in Bacterial Warfare

(2013) João Alves Gama et al.   PLoS One

Sequence Divergence and Conservation in Genomes of Helicobacter cetorum Strains from a Dolphin and a Whale

(2013) Dangeruta Kersulyte et al.   PLoS One

Next-Generation Sequence Assembly: Four Stages of Data Processing and Computational Challenges

(2013) Sara El-Metwally et al.   PLoS Computational Biology

PHACTS, a computational approach to classifying the lifestyle of phages

(2012) Katelyn McNair et al.   BIOINFORMATICS

Coevolution of bacteria and their viruses

(2012) František Golais et al.   FOLIA MICROBIOLOGICA

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

PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies

(2012) Sajia Akhter et al.   NUCLEIC ACIDS RESEARCH

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

Phamerator: a bioinformatic tool for comparative bacteriophage genomics

(2011) Steven G Cresawn et al.   BMC BIOINFORMATICS

Comparative Genomics of Helicobacter pylori and the human-derived Helicobacter bizzozeronii CIII-1 strain reveal the molecular basis of the zoonotic nature of non-pylori gastric Helicobacter infections in humans

(2011) Thomas Schott et al.   BMC GENOMICS

Comparative Whole Genome Sequence Analysis of the Carcinogenic Bacterial Model Pathogen Helicobacter felis

(2011) Isabelle C. Arnold et al.   Genome Biology and Evolution

Molecular epidemiology, population genetics, and pathogenic role of Helicobacter pylori

(2011) Rumiko Suzuki et al.   INFECTION GENETICS AND EVOLUTION

PHAST: A Fast Phage Search Tool

(2011) Y. Zhou et al.   NUCLEIC ACIDS RESEARCH

Evolutionary History of Helicobacter pylori Sequences Reflect Past Human Migrations in Southeast Asia

(2011) Sebastien Breurec et al.   PLoS One

Genome Sequencing Reveals a Phage in Helicobacter pylori

(2011) P. Lehours et al.   mBio

From array-based hybridization of Helicobacter pylori isolates to the complete genome sequence of an isolate associated with MALT lymphoma

(2010) Jean-Michel Thiberge et al.   BMC GENOMICS

Ongoing and future developments at the Universal Protein Resource

(2010)   NUCLEIC ACIDS RESEARCH

Cryptic prophages help bacteria cope with adverse environments

(2010) Xiaoxue Wang et al.   Nature Communications

Genome (re-)annotation and open-source annotation pipelines

(2010) Roland J. Siezen et al.   Microbial Biotechnology

A Global Overview of the Genetic and Functional Diversity in the Helicobacter pylori cag Pathogenicity Island

(2010) Patrick Olbermann et al.   PLoS Genetics

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

(2009) Filipa F Vale et al.   BMC MICROBIOLOGY

Composite system mediates two-step DNA uptake into Helicobacter pylori

(2009) K. Stingl et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Peopling of the Pacific from a Bacterial Perspective

(2009) Y. Moodley et al.   SCIENCE

Prophinder: a computational tool for prophage prediction in prokaryotic genomes

(2008) Gipsi Lima-Mendez et al.   BIOINFORMATICS

Bacteriophage genomics

(2008) Graham F Hatfull   CURRENT OPINION IN MICROBIOLOGY

Helicobacter pylori Phage Screening

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