Benchmarking the performance of Pool‐seq SNP callers using simulated and real sequencing data

A whole-genome scan for association with invasion success in the fruit fly Drosophila suzukii using contrasts of allele frequencies corrected for population structure

(2020) Laure Olazcuaga et al.   MOLECULAR BIOLOGY AND EVOLUTION

Strong selective effects of mitochondrial DNA on the nuclear genome

(2020) Timothy M. Healy et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comparative study of population genomic approaches for mapping colony-level traits

(2020) Shani Inbar et al.   PLoS Computational Biology

Minor allele frequency thresholds strongly affect population structure inference with genomic datasets

(2019) Ethan Linck et al.   Molecular Ecology Resources

A guinea fowl genome assembly provides new evidence on evolution following domestication and selection in galliformes

(2019) Alain Vignal et al.   Molecular Ecology Resources

Genetic analyses of diverse populations improves discovery for complex traits

(2019) Genevieve L. Wojcik et al.   NATURE

Effects of Host, Sample, and in vitro Culture on Genomic Diversity of Pathogenic Mycobacteria

(2019) Abigail C. Shockey et al.   Frontiers in Genetics

Accurate Allele Frequencies from Ultra-low Coverage Pool-Seq Samples in Evolve-and-Resequence Experiments

(2019) Susanne Tilk et al.   G3-Genes Genomes Genetics

Rare variants contribute disproportionately to quantitative trait variation in yeast

(2019) Joshua S Bloom et al.   eLife

Extensive impact of low-frequency variants on the phenotypic landscape at population-scale

(2019) Téo Fournier et al.   eLife

Selection signatures in goats reveal copy number variants underlying breed-defining coat color phenotypes

(2019) Jan Henkel et al.   PLoS Genetics

Utility of pooled sequencing for association mapping in nonmodel organisms

(2018) Steven J. Micheletti et al.   Molecular Ecology Resources

Effective discovery of rare variants by pooled target capture sequencing: A comparative analysis with individually indexed target capture sequencing

(2018) Seungjin Ryu et al.   MUTATION RESEARCH-FUNDAMENTAL AND MOLECULAR MECHANISMS OF MUTAGENESIS

A Genomic Map of Climate Adaptation in Arabidopsis thaliana at a Micro-Geographic Scale

(2018) Léa Frachon et al.   Frontiers in Plant Science

The Genomic Basis of Color Pattern Polymorphism in the Harlequin Ladybird

(2018) Mathieu Gautier et al.   CURRENT BIOLOGY

Measuring Genetic Differentiation from Pool-seq Data

(2018) Valentin Hivert et al.   GENETICS

Relaxed Selection During a Recent Human Expansion

(2017) Stephan Peischl et al.   GENETICS

Porcine Y-chromosome variation is consistent with the occurrence of paternal gene flow from non-Asian to Asian populations

(2017) Sara Guirao-Rico et al.   HEREDITY

Investigating the genomic basis of discrete phenotypes using a Pool-Seq-only approach: New insights into the genetics underlying colour variation in diverse taxa

(2017) Ramprasad Neethiraj et al.   MOLECULAR ECOLOGY

Parallel adaptive evolution of geographically distant herring populations on both sides of the North Atlantic Ocean

(2017) Sangeet Lamichhaney et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Relaxed Selection During a Recent Human Expansion

(2017) Stephan Peischl et al.   GENETICS

Single nucleotide variant discovery of highly inbred Leghorn and Fayoumi chicken breeds using pooled whole genome resequencing data reveals insights into phenotype differences

(2016) D. S. Fleming et al.   BMC GENOMICS

Genetic Basis for Red Coloration in Birds

(2016) Ricardo J. Lopes et al.   CURRENT BIOLOGY

Natural Selection and Genetic Diversity in the Butterfly Heliconius melpomene

(2016) Simon H. Martin et al.   GENETICS

Estimating the Effective Population Size from Temporal Allele Frequency Changes in Experimental Evolution

(2016) A. Jonas et al.   GENETICS

The genomic basis of circadian and circalunar timing adaptations in a midge

(2016) Tobias S. Kaiser et al.   NATURE

The genetic basis for ecological adaptation of the Atlantic herring revealed by genome sequencing

(2016) Alvaro Martinez Barrio et al.   eLife

Natural Selection and Genetic Diversity in the Butterfly Heliconius melpomene

(2016) Simon H. Martin et al.   GENETICS

Next Generation Sequencing of Pooled Samples: Guideline for Variants’ Filtering

(2016) Santosh Anand et al.   Scientific Reports

Evaluation of variant detection software for pooled next-generation sequence data

(2015) Howard W. Huang et al.   BMC BIOINFORMATICS

A Composite-Likelihood Method for Detecting Incomplete Selective Sweep from Population Genomic Data

(2015) Ha My T. Vy et al.   GENETICS

Single Nucleotide Polymorphism Identification in Polyploids: A Review, Example, and Recommendations

(2015) Josh Clevenger et al.   Molecular Plant

Validation of Pooled Whole-Genome Re-Sequencing in Arabidopsis lyrata

(2015) Marco Fracassetti et al.   PLoS One

The vgll3 Locus Controls Age at Maturity in Wild and Domesticated Atlantic Salmon (Salmo salar L.) Males

(2015) Fernando Ayllon et al.   PLoS Genetics

A Composite-Likelihood Method for Detecting Incomplete Selective Sweep from Population Genomic Data

(2015) Ha My T. Vy et al.   GENETICS

A Deep Catalog of Autosomal Single Nucleotide Variation in the Pig

(2015) Erica Bianco et al.   PLoS One

ANGSD: Analysis of Next Generation Sequencing Data

(2014) Thorfinn Sand Korneliussen et al.   BMC BIOINFORMATICS

Population-Genetic Inference from Pooled-Sequencing Data

(2014) Michael Lynch et al.   Genome Biology and Evolution

Insights into the origin and distribution of biodiversity in the Brazilian Atlantic forest hot spot: a statistical phylogeographic study using a low-dispersal organism

(2014) M Álvarez-Presas et al.   HEREDITY

Pipeliner: software to evaluate the performance of bioinformatics pipelines for next-generation resequencing

(2014) B. Nevado et al.   Molecular Ecology Resources

Sequencing pools of individuals — mining genome-wide polymorphism data without big funding

(2014) Christian Schlötterer et al.   NATURE REVIEWS GENETICS

Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication

(2014) M. Carneiro et al.   SCIENCE

The Impact of Population Demography and Selection on the Genetic Architecture of Complex Traits

(2014) Kirk E. Lohmueller   PLoS Genetics

Genomic Evidence of Rapid and Stable Adaptive Oscillations over Seasonal Time Scales in Drosophila

(2014) Alan O. Bergland et al.   PLoS Genetics

Dissecting structural and nucleotide genome-wide variation in inbred Iberian pigs

(2013) Anna Esteve-Codina et al.   BMC GENOMICS

Learning Natural Selection from the Site Frequency Spectrum

(2013) R. Ronen et al.   GENETICS

Estimating inbreeding coefficients from NGS data: Impact on genotype calling and allele frequency estimation

(2013) Filipe G. Vieira et al.   GENOME RESEARCH

Estimation of population allele frequencies from next-generation sequencing data: pool-versus individual-based genotyping

(2013) Mathieu Gautier et al.   MOLECULAR ECOLOGY

Population genomics from pool sequencing

(2013) Luca Ferretti et al.   MOLECULAR ECOLOGY

Population genomic footprints of selection and associations with climate in natural populations ofArabidopsis hallerifrom the Alps

(2013) Martin C. Fischer et al.   MOLECULAR ECOLOGY

Next-generation sequencing for molecular ecology: a caveat regarding pooled samples

(2013) Eric C. Anderson et al.   MOLECULAR ECOLOGY

Validation of SNP Allele Frequencies Determined by Pooled Next-Generation Sequencing in Natural Populations of a Non-Model Plant Species

(2013) Christian Rellstab et al.   PLoS One

Evolutionary change during experimental ocean acidification

(2013) M. H. Pespeni et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Robust Demographic Inference from Genomic and SNP Data

(2013) Laurent Excoffier et al.   PLoS Genetics

SNP calling by sequencing pooled samples

(2012) Emanuele Raineri et al.   BMC BIOINFORMATICS

Demographic Inference Reveals African and European Admixture in the North American Drosophila melanogaster Population

(2012) P. Duchen et al.   GENETICS

The Drosophila melanogaster Genetic Reference Panel

(2012) Trudy F. C. Mackay et al.   NATURE

LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets

(2012) Andreas Wilm et al.   NUCLEIC ACIDS RESEARCH

Empirical Validation of Pooled Whole Genome Population Re-Sequencing in Drosophila melanogaster

(2012) Yuan Zhu et al.   PLoS One

An Abundance of Rare Functional Variants in 202 Drug Target Genes Sequenced in 14,002 People

(2012) M. R. Nelson et al.   SCIENCE

Recent Explosive Human Population Growth Has Resulted in an Excess of Rare Genetic Variants

(2012) A. Keinan et al.   SCIENCE

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

SNVer: a statistical tool for variant calling in analysis of pooled or individual next-generation sequencing data

(2011) Zhi Wei et al.   NUCLEIC ACIDS RESEARCH

Lack of Low Frequency Variants Masks Patterns of Non-Neutral Evolution following Domestication

(2011) Céline H. Frère et al.   PLoS One

Demographic history and rare allele sharing among human populations

(2011) S. Gravel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A statistical method for the detection of variants from next-generation resequencing of DNA pools

(2010) V. Bansal   BIOINFORMATICS

To Pool, or Not to Pool?

(2010) David J. Cutler et al.   GENETICS

The Next Generation of Molecular Markers From Massively Parallel Sequencing of Pooled DNA Samples

(2010) Andreas Futschik et al.   GENETICS

Signatures of positive selection apparent in a small sample of human exomes

(2010) J. A. Tennessen et al.   GENOME RESEARCH

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

(2010) A. McKenna et al.   GENOME RESEARCH

VarScan: variant detection in massively parallel sequencing of individual and pooled samples

(2009) Daniel C. Koboldt et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Quantification of rare allelic variants from pooled genomic DNA

(2009) Todd E Druley et al.   NATURE METHODS

Inferring the Joint Demographic History of Multiple Populations from Multidimensional SNP Frequency Data

(2009) Ryan N. Gutenkunst et al.   PLoS Genetics