A phylogenetic method to perform genome-wide association studies in microbes that accounts for population structure and recombination

Bayesian Inference of the Evolution of a Phenotype Distribution on a Phylogenetic Tree

(2016) M. Azim Ansari et al.   GENETICS

Microbial genome-wide association studies: lessons from human GWAS

(2016) Robert A. Power et al.   NATURE REVIEWS GENETICS

Comprehensive Identification of Meningococcal Genes and Small Noncoding RNAs Required for Host Cell Colonization

(2016) Elena Capel et al.   mBio

Sequence element enrichment analysis to determine the genetic basis of bacterial phenotypes

(2016) John A. Lees et al.   Nature Communications

Bayesian Inference of the Evolution of a Phenotype Distribution on a Phylogenetic Tree

(2016) M. Azim Ansari et al.   GENETICS

Identifying lineage effects when controlling for population structure improves power in bacterial association studies

(2016) Sarah G. Earle et al.   Nature Microbiology

From Genomes to Phenotypes: Traitar, the Microbial Trait Analyzer

(2016) Aaron Weimann et al.   mSystems

Genome-Wide Association Study of HIV Whole Genome Sequences Validated using Drug Resistance

(2016) Robert A. Power et al.   PLoS One

Automatic selection of partitioning schemes for phylogenetic analyses using iterative k-means clustering of site rates

(2015) Paul B Frandsen et al.   BMC EVOLUTIONARY BIOLOGY

The advent of genome-wide association studies for bacteria

(2015) Peter E Chen et al.   CURRENT OPINION IN MICROBIOLOGY

Ten years of pan-genome analyses

(2015) George Vernikos et al.   CURRENT OPINION IN MICROBIOLOGY

Neisseria meningitidis: pathogenesis and immunity

(2015) Mariagrazia Pizza et al.   CURRENT OPINION IN MICROBIOLOGY

Genomic signatures of human and animal disease in the zoonotic pathogen Streptococcus suis

(2015) Lucy A. Weinert et al.   Nature Communications

ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes

(2015) Xavier Didelot et al.   PLoS Computational Biology

The use of genome wide association methods to investigate pathogenicity, population structure and serovar in Haemophilus parasuis

(2015) Kate J Howell et al.   BMC GENOMICS

Cellular and molecular biology ofNeisseria meningitidiscolonization and invasive disease

(2015) Darryl J. Hill et al.   CLINICAL SCIENCE

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

(2014) Nicholas J. Croucher et al.   NUCLEIC ACIDS RESEARCH

A phylogeny-based sampling strategy and power calculator informs genome-wide associations study design for microbial pathogens

(2014) Maha R Farhat et al.   Genome Medicine

Characterizing the genetic basis of bacterial phenotypes using genome-wide association studies: a new direction for bacteriology

(2014) Timothy D Read et al.   Genome Medicine

Comprehensive Identification of Single Nucleotide Polymorphisms Associated with Beta-lactam Resistance within Pneumococcal Mosaic Genes

(2014) Claire Chewapreecha et al.   PLoS Genetics

A genomic portrait of the emergence, evolution, and global spread of a methicillin-resistant Staphylococcus aureus pandemic

(2013) M. T. G. Holden et al.   GENOME RESEARCH

Genomic analysis identifies targets of convergent positive selection in drug-resistant Mycobacterium tuberculosis

(2013) Maha R Farhat et al.   NATURE GENETICS

The NHGRI GWAS Catalog, a curated resource of SNP-trait associations

(2013) Danielle Welter et al.   NUCLEIC ACIDS RESEARCH

Genome-wide association study identifies vitamin B5 biosynthesis as a host specificity factor in Campylobacter

(2013) S. K. Sheppard et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Uncovering the co-evolutionary network among prokaryotic genes

(2012) Ofir Cohen et al.   BIOINFORMATICS

Progressive genome-wide introgression in agriculturalCampylobacter coli

(2012) Samuel K. Sheppard et al.   MOLECULAR ECOLOGY

BIGSdb: Scalable analysis of bacterial genome variation at the population level

(2011) Keith A Jolley et al.   BMC BIOINFORMATICS

In the NadR Regulon, Adhesins and Diverse Meningococcal Functions Are Regulated in Response to Signals in Human Saliva

(2011) L. Fagnocchi et al.   JOURNAL OF BACTERIOLOGY

Discriminant analysis of principal components: a new method for the analysis of genetically structured populations

(2010) Thibaut Jombart et al.   BMC GENETICS

The role of glyceraldehyde 3-phosphate dehydrogenase (GapA-1) in Neisseria meningitidis adherence to human cells

(2010) Sarfraz A Tunio et al.   BMC MICROBIOLOGY

Inference of Homologous Recombination in Bacteria Using Whole-Genome Sequences

(2010) X. Didelot et al.   GENETICS

Evolutionary Genomics of Staphylococcus aureus Reveals Insights into the Origin and Molecular Basis of Ruminant Host Adaptation

(2010) Caitriona M. Guinane et al.   Genome Biology and Evolution

Impact of recombination on bacterial evolution

(2010) Xavier Didelot et al.   TRENDS IN MICROBIOLOGY

Comparative analysis of two Neisseria gonorrhoeae genome sequences reveals evidence of mobilization of Correia Repeat Enclosed Elements and their role in regulation

(2009) Lori AS Snyder et al.   BMC GENOMICS

Epidemiological Evidence for the Role of the Hemoglobin Receptor, HmbR, in Meningococcal Virulence

(2009) Odile B. Harrison et al.   JOURNAL OF INFECTIOUS DISEASES

Recent human-to-poultry host jump, adaptation, and pandemic spread of Staphylococcus aureus

(2009) B. V. Lowder et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fast NJ-like algorithms to deal with incomplete distance matrices

(2008) Alexis Criscuolo et al.   BMC BIOINFORMATICS

Accounting for ancestry: population substructure and genome-wide association studies

(2008) C. Tian et al.   HUMAN MOLECULAR GENETICS

A comparison of homologous recombination rates in bacteria and archaea

(2008) Michiel Vos et al.   ISME Journal