Identifying lineage effects when controlling for population structure improves power in bacterial association studies (Q37309101)

19 August 2017

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

1 reference

19 August 2017

1 reference

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27572646%20AND%20SRC:MED&resulttype=core&format=json

13 June 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27572646%20AND%20SRC:MED&resulttype=core&format=json

13 June 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27572646%20AND%20SRC:MED&resulttype=core&format=json

13 June 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27572646%20AND%20SRC:MED&resulttype=core&format=json

13 June 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27572646%20AND%20SRC:MED&resulttype=core&format=json

13 June 2020

A Sarah Walker

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27572646%20AND%20SRC:MED&resulttype=core&format=json

13 June 2020

Derrick W Crook

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27572646%20AND%20SRC:MED&resulttype=core&format=json

13 June 2020

Tim E Peto

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27572646%20AND%20SRC:MED&resulttype=core&format=json

13 June 2020

Timothy M Walker

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27572646%20AND%20SRC:MED&resulttype=core&format=json

13 June 2020

Nazir Ismail

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27572646%20AND%20SRC:MED&resulttype=core&format=json

13 June 2020

Jane Charlesworth

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27572646%20AND%20SRC:MED&resulttype=core&format=json

13 June 2020

Chris C A Spencer

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27572646%20AND%20SRC:MED&resulttype=core&format=json

13 June 2020

Sarah G Earle

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27572646%20AND%20SRC:MED&resulttype=core&format=json

13 June 2020

David A Clifton

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27572646%20AND%20SRC:MED&resulttype=core&format=json

13 June 2020

Katie L Hopkins

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27572646%20AND%20SRC:MED&resulttype=core&format=json

13 June 2020

E Grace Smith

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27572646%20AND%20SRC:MED&resulttype=core&format=json

13 June 2020

Gil McVean

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27572646%20AND%20SRC:MED&resulttype=core&format=json

13 June 2020

Daniel J Wilson

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27572646%20AND%20SRC:MED&resulttype=core&format=json

13 June 2020

Neil Woodford

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27572646%20AND%20SRC:MED&resulttype=core&format=json

13 June 2020

publication date

4 April 2016

1 reference

19 August 2017

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27572646%20AND%20SRC:MED&resulttype=core&format=json

13 June 2020

volume

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27572646%20AND%20SRC:MED&resulttype=core&format=json

13 June 2020

page(s)

16041

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27572646%20AND%20SRC:MED&resulttype=core&format=json

Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis

13 June 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5049680

Whole-genome sequencing for prediction of Mycobacterium tuberculosis drug susceptibility and resistance: a retrospective cohort study

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5049680

Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance in Klebsiella pneumoniae, an urgent threat to public health

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5049680

The advent of genome-wide association studies for bacteria.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5049680

ClonalFrameML: efficient inference of recombination in whole bacterial genomes

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5049680

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5049680

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5049680

Bacterial phylogenetic reconstruction from whole genomes is robust to recombination but demographic inference is not.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5049680

Large-scale genomic sequencing of extraintestinal pathogenic Escherichia coli strains

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5049680

UniProt: a hub for protein information

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5049680

Comprehensive identification of single nucleotide polymorphisms associated with beta-lactam resistance within pneumococcal mosaic genes

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5049680

Mobile elements drive recombination hotspots in the core genome of Staphylococcus aureus.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5049680

Dissecting vancomycin-intermediate resistance in staphylococcus aureus using genome-wide association.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5049680

Predicting the virulence of MRSA from its genome sequence

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5049680

Trimmomatic: a flexible trimmer for Illumina sequence data

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5049680

Explaining microbial genomic diversity in light of evolutionary ecology

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5049680

SNP-associations and phenotype predictions from hundreds of microbial genomes without genome alignments

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5049680

Efficient inference of recombination hot regions in bacterial genomes.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5049680

Prediction of Staphylococcus aureus antimicrobial resistance by whole-genome sequencing.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5049680

Advantages and pitfalls in the application of mixed-model association methods

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5049680

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5049680

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5049680

Predicting antimicrobial susceptibilities for Escherichia coli and Klebsiella pneumoniae isolates using whole genomic sequence data.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5049680

DSK: k-mer counting with very low memory usage

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5049680

A pilot study of rapid benchtop sequencing of Staphylococcus aureus and Clostridium difficile for outbreak detection and surveillance

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5049680

Improved linear mixed models for genome-wide association studies

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5049680

Fast gapped-read alignment with Bowtie 2

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5049680

Five years of GWAS discovery

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5049680

Stampy: a statistical algorithm for sensitive and fast mapping of Illumina sequence reads

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5049680

Origins and evolution of antibiotic resistance

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5049680

New approaches to population stratification in genome-wide association studies

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5049680

Prodigal: prokaryotic gene recognition and translation initiation site identification

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5049680

Variance component model to account for sample structure in genome-wide association studies

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5049680

BLAST+: architecture and applications

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5049680

A genealogical interpretation of principal components analysis

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5049680

Bayesian statistical methods for genetic association studies

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5049680

The microbial engines that drive Earth's biogeochemical cycles.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5049680

Efficient control of population structure in model organism association mapping

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5049680

Velvet: algorithms for de novo short read assembly using de Bruijn graphs

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5049680

Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5049680

Principal components analysis corrects for stratification in genome-wide association studies

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5049680

Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5049680

Population genetics of microbial pathogens estimated from multilocus sequence typing (MLST) data

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5049680

A unified mixed-model method for association mapping that accounts for multiple levels of relatedness

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5049680

Recombination and the population structures of bacterial pathogens

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5049680

A fast algorithm for joint reconstruction of ancestral amino acid sequences

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5049680

Prokaryotes: the unseen majority

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5049680

The Phylogenetic Regression

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5049680

Molecular evolution of the Escherichia coli chromosome. III. Clonal frames

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5049680

Genome-wide efficient mixed-model analysis for association studies

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5049680

Genetic basis of resistance to fusidic acid in staphylococci.

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5049680

FaST linear mixed models for genome-wide association studies

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5049680

Contribution of gene amplification to evolution of increased antibiotic resistance in Salmonella typhimurium

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5049680

A comparison of homologous recombination rates in bacteria and archaea

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5049680

Genome-wide association mapping in bacteria?

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5049680

Phylogenies and the Comparative Method: A General Approach to Incorporating Phylogenetic Information into the Analysis of Interspecific Data

2 September 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMICROBIOL.2016.41

Estimation of the Medians for Dependent Variables

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMICROBIOL.2016.41

Population Structure and Cryptic Relatedness in Genetic Association Studies

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMICROBIOL.2016.41

Tests of statistical hypotheses concerning several parameters when the number of observations is large

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMICROBIOL.2016.41

inferred from DOI database lookup

7 January 2021

based on heuristic

Identifiers

DOI

10.1038/NMICROBIOL.2016.41

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27572646%20AND%20SRC:MED&resulttype=core&format=json

13 June 2020

1 reference

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27572646%20AND%20SRC:MED&resulttype=core&format=json

13 June 2020

PubMed publication ID

27572646

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27572646%20AND%20SRC:MED&resulttype=core&format=json