Benchmarking bacterial genome-wide association study methods using simulated genomes and phenotypes

Genome-wide association analyses of invasive pneumococcal isolates identify a missense bacterial mutation associated with meningitis

(2019) Yuan Li et al.   Nature Communications

Fast and flexible bacterial genomic epidemiology with PopPUNK

(2019) John A. Lees et al.   GENOME RESEARCH

GWAS for quantitative resistance phenotypes in Mycobacterium tuberculosis reveals resistance genes and regulatory regions

(2019) Maha R. Farhat et al.   Nature Communications

Bacmeta: simulator for genomic evolution in bacterial metapopulations

(2018) Aleksi Sipola et al.   BIOINFORMATICS

pyseer: a comprehensive tool for microbial pangenome-wide association studies

(2018) John A Lees et al.   BIOINFORMATICS

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

(2018) Caitlin Collins et al.   PLoS Computational Biology

A GWAS on Helicobacter pylori strains points to genetic variants associated with gastric cancer risk

(2018) Elvire Berthenet et al.   BMC BIOLOGY

The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019

(2018) Annalisa Buniello et al.   NUCLEIC ACIDS RESEARCH

A fast and agnostic method for bacterial genome-wide association studies: Bridging the gap between k-mers and genetic events

(2018) Magali Jaillard et al.   PLoS Genetics

A standardised method for interpreting the association between mutations and phenotypic drug resistance in Mycobacterium tuberculosis

(2017) Paolo Miotto et al.   EUROPEAN RESPIRATORY JOURNAL

Efficient Inference of Recent and Ancestral Recombination within Bacterial Populations

(2017) Rafal Mostowy et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genome-wide identification of lineage and locus specific variation associated with pneumococcal carriage duration

(2017) John A Lees et al.   eLife

How Can We Explain Very Low Odds Ratios in GWAS? I. Polygenic Models

(2016) Susan E. Hodge et al.   HUMAN HEREDITY

Genomic and functional analyses of Mycobacterium tuberculosis strains implicate ald in D-cycloserine resistance

(2016) Christopher A Desjardins et al.   NATURE GENETICS

Uncovering Listeria monocytogenes hypervirulence by harnessing its biodiversity

(2016) Mylène M Maury et al.   NATURE GENETICS

Microbial genome-wide association studies: lessons from human GWAS

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

CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database

(2016) Baofeng Jia et al.   NUCLEIC ACIDS RESEARCH

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

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

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

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

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

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

The advent of genome-wide association studies for bacteria

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

Dissecting Vancomycin-Intermediate Resistance in Staphylococcus aureus Using Genome-Wide Association

(2014) Md Tauqeer Alam et al.   Genome Biology and Evolution

Predicting the virulence of MRSA from its genome sequence

(2014) M. Laabei et al.   GENOME RESEARCH

Large-scale genomic sequencing of extraintestinal pathogenicEscherichia colistrains

(2014) Stephen J. Salipante et al.   GENOME RESEARCH

Dense genomic sampling identifies highways of pneumococcal recombination

(2014) Claire Chewapreecha et al.   NATURE GENETICS

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

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

(2014) Claire Chewapreecha et al.   PLoS Genetics

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

(2013) Maha R Farhat et al.   NATURE GENETICS

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

A genome-to-genome analysis of associations between human genetic variation, HIV-1 sequence diversity, and viral control

(2013) István Bartha et al.   eLife

Genome-wide efficient mixed-model analysis for association studies

(2012) Xiang Zhou et al.   NATURE GENETICS

ART: a next-generation sequencing read simulator

(2011) Weichun Huang et al.   BIOINFORMATICS

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

ALF—A Simulation Framework for Genome Evolution

(2011) Daniel A. Dalquen et al.   MOLECULAR BIOLOGY AND EVOLUTION

FaST linear mixed models for genome-wide association studies

(2011) Christoph Lippert et al.   NATURE METHODS

GCTA: A Tool for Genome-wide Complex Trait Analysis

(2010) Jian Yang et al.   AMERICAN JOURNAL OF HUMAN GENETICS

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Enhanced Bayesian modelling in BAPS software for learning genetic structures of populations

(2008) Jukka Corander et al.   BMC BIOINFORMATICS

The conditioned reconstructed process

(2008) Tanja Gernhard   JOURNAL OF THEORETICAL BIOLOGY