Developing insights into the mechanisms of evolution of bacterial pathogens from whole-genome sequences

Behavior and Target Site Selection of Conjugative Transposon Tn916in Two Different Strains of Toxigenic Clostridium difficile

(2012) Peter Mullany et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

A novel non-homologous recombination-mediated mechanism for Escherichia coli unilateral flagellar phase variation

(2012) Bin Liu et al.   NUCLEIC ACIDS RESEARCH

Population Genomics of Early Events in the Ecological Differentiation of Bacteria

(2012) B. J. Shapiro et al.   SCIENCE

Whole-Genome Sequencing of Sordaria macrospora Mutants Identifies Developmental Genes

(2012) Minou Nowrousian et al.   G3-Genes Genomes Genetics

Genetic Diversity of Tn916-Related Transposons among Drug-Resistant Streptococcus pneumoniae Isolates Colonizing Healthy Children in Venezuela

(2011) Beatríz Quintero et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Heterogeneity of Tn5253-Like Composite Elements in ClinicalStreptococcus pneumoniaeIsolates

(2011) Marina Mingoia et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Assessing the benefits of using mate-pairs to resolve repeats in de novo short-read prokaryotic assemblies

(2011) Joshua Wetzel et al.   BMC BIOINFORMATICS

The genome sequence of Brucella pinnipedialis B2/94 sheds light on the evolutionary history of the genus Brucella

(2011) Stéphane Audic et al.   BMC EVOLUTIONARY BIOLOGY

Identification, variation and transcription of pneumococcal repeat sequences

(2011) Nicholas J Croucher et al.   BMC GENOMICS

Enterococcus faecalis from patients with chronic periodontitis: virulence and antimicrobial resistance traits and determinants

(2011) J. Sun et al.   EUROPEAN JOURNAL OF CLINICAL MICROBIOLOGY & INFECTIOUS DISEASES

Impact of Small Repeat Sequences on Bacterial Genome Evolution

(2011) Nicholas Delihas   Genome Biology and Evolution

Antibiotic and antiseptic resistance genes are linked on a novel mobile genetic element: Tn6087

(2011) Lena Ciric et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Population structure in the Neisseria, and the biological significance of fuzzy species

(2011) J. Corander et al.   Journal of the Royal Society Interface

Targeted Bacterial Immunity Buffers Phage Diversity

(2011) J. O. Haerter et al.   JOURNAL OF VIROLOGY

Molecular Mechanisms of Tetracycline and Macrolide Resistance and emm Characterization of Streptococcus pyogenes Isolates in Tunisia

(2011) Manel Hraoui et al.   Microbial Drug Resistance

Evidence for several waves of global transmission in the seventh cholera pandemic

(2011) Ankur Mutreja et al.   NATURE

Parallel bacterial evolution within multiple patients identifies candidate pathogenicity genes

(2011) Tami D Lieberman et al.   NATURE GENETICS

Evolutionary paths to antibiotic resistance under dynamically sustained drug selection

(2011) Erdal Toprak et al.   NATURE GENETICS

Use of whole genome sequencing to estimate the mutation rate of Mycobacterium tuberculosis during latent infection

(2011) Christopher B Ford et al.   NATURE GENETICS

Whole-genome sequencing of rifampicin-resistant Mycobacterium tuberculosis strains identifies compensatory mutations in RNA polymerase genes

(2011) Iñaki Comas et al.   NATURE GENETICS

Genome structural variation discovery and genotyping

(2011) Can Alkan et al.   NATURE REVIEWS GENETICS

Detection of recombination events in bacterial genomes from large population samples

(2011) Pekka Marttinen et al.   NUCLEIC ACIDS RESEARCH

Whole Genome Sequencing and Complete Genetic Analysis Reveals Novel Pathways to Glycopeptide Resistance in Staphylococcus aureus

(2011) Adriana Renzoni et al.   PLoS One

Selection in Coastal Synechococcus (Cyanobacteria) Populations Evaluated from Environmental Metagenomes

(2011) Vera Tai et al.   PLoS One

Gene Decay in Shigella as an Incipient Stage of Host-Adaptation

(2011) Ye Feng et al.   PLoS One

Second-Order Selection for Evolvability in a Large Escherichia coli Population

(2011) R. J. Woods et al.   SCIENCE

Rapid Pneumococcal Evolution in Response to Clinical Interventions

(2011) N. J. Croucher et al.   SCIENCE

Genome-Scale Identification of Resistance Functions in Pseudomonas aeruginosa Using Tn-seq

(2011) L. A. Gallagher et al.   mBio

Recombination and Population Structure in Salmonella enterica

(2011) Xavier Didelot et al.   PLoS Genetics

Salmonella bongori Provides Insights into the Evolution of the Salmonellae

(2011) Maria Fookes et al.   PLoS Pathogens

Citrobacter rodentium is an Unstable Pathogen Showing Evidence of Significant Genomic Flux

(2011) Nicola K. Petty et al.   PLoS Pathogens

Diversity and Mobility of Integrative and Conjugative Elements in Bovine Isolates of Streptococcus agalactiae, S. dysgalactiae subsp. dysgalactiae, and S. uberis

(2010) M. Haenni et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Comparative genomics of the bacterial genus Listeria: Genome evolution is characterized by limited gene acquisition and limited gene loss

(2010) Henk C den Bakker et al.   BMC GENOMICS

Continuing Evolution of Burkholderia mallei Through Genome Reduction and Large-Scale Rearrangements

(2010) Liliana Losada et al.   Genome Biology and Evolution

Diversity of CRISPR loci in Escherichia coli

(2010)   MICROBIOLOGY-SGM

The CRISPR System: Small RNA-Guided Defense in Bacteria and Archaea

(2010) Fedor V. Karginov et al.   MOLECULAR CELL

Antagonistic coevolution accelerates molecular evolution

(2010) Steve Paterson et al.   NATURE

Next-generation sequencing: adjusting to data overload

(2010) Monya Baker   NATURE METHODS

Limitations of next-generation genome sequence assembly

(2010) Can Alkan et al.   NATURE METHODS

CRISPR interference: RNA-directed adaptive immunity in bacteria and archaea

(2010) Luciano A. Marraffini et al.   NATURE REVIEWS GENETICS

Evolutionary microbial genomics: insights into bacterial host adaptation

(2010) Christina Toft et al.   NATURE REVIEWS GENETICS

The phage-related chromosomal islands of Gram-positive bacteria

(2010) Richard P. Novick et al.   NATURE REVIEWS MICROBIOLOGY

A universal TagModule collection for parallel genetic analysis of microorganisms

(2010) Julia Oh et al.   NUCLEIC ACIDS RESEARCH

Evolutionary dynamics of Clostridium difficile over short and long time scales

(2010) M. He et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Population Dynamics and Control of Tuberculosis

(2010) C. Dye et al.   SCIENCE

Evolution of MRSA During Hospital Transmission and Intercontinental Spread

(2010) S. R. Harris et al.   SCIENCE

CRISPR/Cas, the Immune System of Bacteria and Archaea

(2010) P. Horvath et al.   SCIENCE

Evidence That Mutation Is Universally Biased towards AT in Bacteria

(2010) Ruth Hershberg et al.   PLoS Genetics

The Early Stage of Bacterial Genome-Reductive Evolution in the Host

(2010) Han Song et al.   PLoS Pathogens

Molecular diversity and transferability of the tetracycline resistance gene tet(M), carried on Tn916-1545 family transposons, in enterococci from a total food chain

(2009) Lucia Rizzotti et al.   ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY

Phylogeographic reconstruction of a bacterial species with high levels of lateral gene transfer

(2009) Talima Pearson et al.   BMC BIOLOGY

Co-evolution of genomes and plasmids within Chlamydia trachomatis and the emergence in Sweden of a new variant strain

(2009) Helena MB Seth-Smith et al.   BMC GENOMICS

Simultaneous assay of every Salmonella Typhi gene using one million transposon mutants

(2009) G. C. Langridge et al.   GENOME RESEARCH

Rapidly evolving genes in pathogens: Methods for detecting positive selection and examples among fungi, bacteria, viruses and protists

(2009) Gabriela Aguileta et al.   INFECTION GENETICS AND EVOLUTION

Diversity of the tetracycline resistance gene tet(M) and identification of Tn916- and Tn5801-like (Tn6014) transposons in Staphylococcus aureus from humans and animals

(2009) L. E. de Vries et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Short-Term Signatures of Evolutionary Change in the Salmonella enterica Serovar Typhimurium 14028 Genome

(2009) T. Jarvik et al.   JOURNAL OF BACTERIOLOGY

Transcription Profile of Thermus thermophilus CRISPR Systems after Phage Infection

(2009) Yoshihiro Agari et al.   JOURNAL OF MOLECULAR BIOLOGY

Computational methods for discovering structural variation with next-generation sequencing

(2009) Paul Medvedev et al.   NATURE METHODS

Rapid Evolution of Virulence and Drug Resistance in the Emerging Zoonotic Pathogen Streptococcus suis

(2009) Matthew T. G. Holden et al.   PLoS One

Use of high throughput sequencing to observe genome dynamics at a single cell level

(2009) D. Parkhomchuk et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High frequency of hotspot mutations in core genes of Escherichia coli due to short-term positive selection

(2009) S. Chattopadhyay et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Tracking insertion mutants within libraries by deep sequencing and a genome-wide screen for Haemophilus genes required in the lung

(2009) J. D. Gawronski et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Hyper-Recombination, Diversity, and Antibiotic Resistance in Pneumococcus

(2009) W. P. Hanage et al.   SCIENCE

Genome flexibility in Neisseria meningitidis

(2009) Christoph Schoen et al.   VACCINE

Bayesian modeling of recombination events in bacterial populations

(2008) Pekka Marttinen et al.   BMC BIOINFORMATICS

Whole-genome mutational biases in bacteria

(2008) P. A. Lind et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome assembly forensics: finding the elusive mis-assembly

(2008) Adam M Phillippy et al.   GENOME BIOLOGY

The impact of the neisserial DNA uptake sequences on genome evolution and stability

(2008) Todd J Treangen et al.   GENOME BIOLOGY