Genome-Wide Association Analyses in the Model Rhizobium Ensifer meliloti

Weak Epistasis May Drive Adaptation in Recombining Bacteria

(2018) Brian J. Arnold et al.   GENETICS

Select and resequence reveals relative fitness of bacteria in symbiotic and free-living environments

(2018) Liana T. Burghardt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Weak Epistasis May Drive Adaptation in Recombining Bacteria

(2018) Brian J. Arnold et al.   GENETICS

What can genome-wide association studies tell us about the evolutionary forces maintaining genetic variation for quantitative traits?

(2017) Emily B. Josephs et al.   NEW PHYTOLOGIST

Association mapping reveals novel serpentine adaptation gene clusters in a population of symbiotic Mesorhizobium

(2016) Stephanie S Porter et al.   ISME Journal

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

Bacterial GWAS: not just gilding the lily

(2016) John A. Lees et al.   NATURE REVIEWS MICROBIOLOGY

Not So Simple After All: Bacteria, Their Population Genetics, and Recombination

(2016) William P. Hanage   Cold Spring Harbor Perspectives in Biology

Adaptive radiation by waves of gene transfer leads to fine-scale resource partitioning in marine microbes

(2016) Jan-Hendrik Hehemann 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

A genome-wide association study identifies a horizontally transferred bacterial surface adhesin gene associated with antimicrobial resistant strains

(2016) Masato Suzuki et al.   Scientific Reports

The advent of genome-wide association studies for bacteria

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

Sporadic, Global Linkage Disequilibrium Between Unlinked Segregating Sites

(2015) D. A. Skelly et al.   GENETICS

Genomic analysis of cyclic-di-GMP-related genes in rhizobial type strains and functional analysis in Rhizobium etli

(2014) Shanjun Gao et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

Why are some microbes more ubiquitous than others? Predicting the habitat breadth of soil bacteria

(2014) Albert Barberán et al.   ECOLOGY LETTERS

Genomic Signature of Adaptation to Climate inMedicago truncatula

(2014) Jeremy B. Yoder et al.   GENETICS

Detecting epistasis in human complex traits

(2014) Wen-Hua Wei et al.   NATURE REVIEWS GENETICS

Responses to Elevated c-di-GMP Levels in Mutualistic and Pathogenic Plant-Interacting Bacteria

(2014) Daniel Pérez-Mendoza et al.   PLoS One

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

(2014) Claire Chewapreecha et al.   PLoS Genetics

Genome-wide association study of sleep in Drosophila melanogaster

(2013) Susan T Harbison et al.   BMC GENOMICS

Pitfalls of predicting complex traits from SNPs

(2013) Naomi R. Wray et al.   NATURE REVIEWS GENETICS

The advantages and limitations of trait analysis with GWAS: a review

(2013) Arthur Korte et al.   Plant Methods

Queuosine Biosynthesis Is Required for Sinorhizobium meliloti-Induced Cytoskeletal Modifications on HeLa Cells and Symbiosis with Medicago truncatula

(2013) Marta Marchetti et al.   PLoS One

Candidate Genes and Genetic Architecture of Symbiotic and Agronomic Traits Revealed by Whole-Genome, Sequence-Based Association Genetics in Medicago truncatula

(2013) John Stanton-Geddes et al.   PLoS One

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

Polygenic Modeling with Bayesian Sparse Linear Mixed Models

(2013) Xiang Zhou et al.   PLoS Genetics

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Genome-wide association study in a Swedish population yields support for greater CNV and MHC involvement in schizophrenia compared with bipolar disorder

(2012) S E Bergen et al.   MOLECULAR PSYCHIATRY

Genome-wide efficient mixed-model analysis for association studies

(2012) Xiang Zhou et al.   NATURE GENETICS

Rare and common variants: twenty arguments

(2012) Greg Gibson   NATURE REVIEWS GENETICS

Population Genomics of the Facultatively Mutualistic Bacteria Sinorhizobium meliloti and S. medicae

(2012) Brendan Epstein et al.   PLoS Genetics

The Rules of Engagement in the Legume-Rhizobial Symbiosis

(2011) Giles E.D. Oldroyd et al.   Annual Review of Genetics

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

THE QTN PROGRAM AND THE ALLELES THAT MATTER FOR EVOLUTION: ALL THAT'S GOLD DOES NOT GLITTER

(2011) Matthew V. Rockman   EVOLUTION

Population genomics of Sinorhizobium medicae based on low-coverage sequencing of sympatric isolates

(2011) Xavier Bailly et al.   ISME Journal

Genome-wide association studies for feedlot and growth traits in cattle1

(2011) S. Bolormaa et al.   JOURNAL OF ANIMAL SCIENCE

Population Genomics in Bacteria: A Case Study of Staphylococcus aureus

(2011) S. Takuno et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genome-wide nested association mapping of quantitative resistance to northern leaf blight in maize

(2011) J. A. Poland et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Aminoglycoside modifying enzymes

(2010) Maria S. Ramirez et al.   DRUG RESISTANCE UPDATES

Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines

(2010) Susanna Atwell et al.   NATURE

Statistical analysis strategies for association studies involving rare variants

(2010) Vikas Bansal et al.   NATURE REVIEWS GENETICS

Impact of recombination on bacterial evolution

(2010) Xavier Didelot et al.   TRENDS IN MICROBIOLOGY

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Pathway of  -Aminobutyrate Metabolism in Rhizobium leguminosarum 3841 and Its Role in Symbiosis

(2009) J. Prell et al.   JOURNAL OF BACTERIOLOGY

A comparison of homologous recombination rates in bacteria and archaea

(2008) Michiel Vos et al.   ISME Journal

Global inputs of biological nitrogen fixation in agricultural systems

(2008) David F. Herridge et al.   PLANT AND SOIL