Utility of pooled sequencing for association mapping in nonmodel organisms

Landscape features along migratory routes influence adaptive genomic variation in anadromous steelhead (Oncorhynchus mykiss )

(2017) Steven J. Micheletti et al.   MOLECULAR ECOLOGY

Accounting for linkage disequilibrium in genome scans for selection without individual genotypes: The local score approach

(2017) María Inés Fariello et al.   MOLECULAR ECOLOGY

Haplotyping RAD loci: an efficient method to filter paralogs and account for physical linkage

(2017) Stuart C. Willis et al.   Molecular Ecology Resources

Finding the Genomic Basis of Local Adaptation: Pitfalls, Practical Solutions, and Future Directions

(2016) Sean Hoban et al.   AMERICAN NATURALIST

Impact of post-alignment processing in variant discovery from whole exome data

(2016) Shulan Tian et al.   BMC BIOINFORMATICS

Practical low-coverage genomewide sequencing of hundreds of individually barcoded samples for population and evolutionary genomics in nonmodel species

(2016) Nina Overgaard Therkildsen et al.   Molecular Ecology Resources

Identification of Sex and Female’s Reproductive Stage in Commercial Fish Species through the Quantification of Ribosomal Transcripts in Gonads

(2016) Iratxe Rojo-Bartolomé et al.   PLoS One

Intestinal Fluid Permeability in Atlantic Salmon (Salmo salar L.) Is Affected by Dietary Protein Source

(2016) Haibin Hu et al.   PLoS One

Unique evolutionary trajectories in repeated adaptation to hydrogen sulphide-toxic habitats of a neotropical fish (Poecilia mexicana)

(2015) Markus Pfenninger et al.   MOLECULAR ECOLOGY

The impact of library preparation protocols on the consistency of allele frequency estimates in Pool-Seq data

(2015) Robert Kofler et al.   Molecular Ecology Resources

Whole-genome resequencing of extreme phenotypes in collared flycatchers highlights the difficulty of detecting quantitative trait loci in natural populations

(2015) Marty Kardos et al.   Molecular Ecology Resources

Evolution of Darwin’s finches and their beaks revealed by genome sequencing

(2015) Sangeet Lamichhaney et al.   NATURE

Sex-dependent dominance at a single locus maintains variation in age at maturity in salmon

(2015) Nicola J. Barson et al.   NATURE

A Sex-Determining Gene (sdY) Assay Shows Discordance between Phenotypic and Genotypic Sex in Wild Populations of Chinook Salmon

(2015) Timothy D. Cavileer et al.   TRANSACTIONS OF THE AMERICAN FISHERIES SOCIETY

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

(2015) Fernando Ayllon et al.   PLoS Genetics

SAMBLASTER: fast duplicate marking and structural variant read extraction

(2014) G. G. Faust et al.   BIOINFORMATICS

Genotyping-in-Thousands by sequencing (GT-seq): A cost effective SNP genotyping method based on custom amplicon sequencing

(2014) Nathan R. Campbell 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

Non-random DNA fragmentation in next-generation sequencing

(2014) Maria S. Poptsova et al.   Scientific Reports

LUMPY: a probabilistic framework for structural variant discovery

(2014) Ryan M Layer et al.   GENOME BIOLOGY

Ontogeny of melanophore photosensitivity in rainbow trout (Oncorhynchus mykiss)

(2014) S.-C. Chen et al.   Biology Open

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

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

The genomic signature of dog domestication reveals adaptation to a starch-rich diet

(2013) Erik Axelsson et al.   NATURE

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

An Extensive Evaluation of Read Trimming Effects on Illumina NGS Data Analysis

(2013) Cristian Del Fabbro et al.   PLoS One

Genome sequencing and population genomics in non-model organisms

(2013) Hans Ellegren   TRENDS IN ECOLOGY & EVOLUTION

DELLY: structural variant discovery by integrated paired-end and split-read analysis

(2012) T. Rausch et al.   BIOINFORMATICS

An Immune-Related Gene Evolved into the Master Sex-Determining Gene in Rainbow Trout, Oncorhynchus mykiss

(2012) Ayaka Yano et al.   CURRENT BIOLOGY

The sexually dimorphic on the Y-chromosome gene (sdY) is a conserved male-specific Y-chromosome sequence in many salmonids

(2012) Ayaka Yano et al.   Evolutionary Applications

Genome-wide patterns of natural variation reveal strong selective sweeps and ongoing genomic conflict in Drosophila mauritiana

(2012) V. Nolte et al.   GENOME RESEARCH

Supportive breeding boosts natural population abundance with minimal negative impacts on fitness of a wild population of Chinook salmon

(2012) Maureen A. Hess et al.   MOLECULAR ECOLOGY

Adaptation ofDrosophilato a novel laboratory environment reveals temporally heterogeneous trajectories of selected alleles

(2012) PABLO OROZCO-terWENGEL et al.   MOLECULAR ECOLOGY

Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing

(2012) Li Ding et al.   NATURE

LDx: Estimation of Linkage Disequilibrium from High-Throughput Pooled Resequencing Data

(2012) Alison F. Feder et al.   PLoS One

Population-scale sequencing reveals genetic differentiation due to local adaptation in Atlantic herring

(2012) S. Lamichhaney et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Strong signatures of selection in the domestic pig genome

(2012) C.-J. Rubin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Sequencing of Pooled DNA Samples (Pool-Seq) Uncovers Complex Dynamics of Transposable Element Insertions in Drosophila melanogaster

(2012) Robert Kofler et al.   PLoS Genetics

PoPoolation2: identifying differentiation between populations using sequencing of pooled DNA samples (Pool-Seq)

(2011) R. Kofler 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

Regulation and expression of sexual differentiation factors in embryonic and extragonadal tissues of Atlantic salmon

(2011) Kristian R von Schalburg et al.   BMC GENOMICS

Identification of the Sex Chromosomes of Brown Trout (Salmo trutta) and Their Comparison with the Corresponding Chromosomes in Atlantic Salmon (Salmo salar) and Rainbow Trout (Oncorhynchus mykiss)

(2011) J. Li et al.   CYTOGENETIC AND GENOME RESEARCH

Genome structural variation discovery and genotyping

(2011) Can Alkan et al.   NATURE REVIEWS GENETICS

The Genetics of Human Adaptation: Hard Sweeps, Soft Sweeps, and Polygenic Adaptation

(2010) Jonathan K. Pritchard et al.   CURRENT BIOLOGY

Detecting Selection in Population Trees: The Lewontin and Krakauer Test Extended

(2010) Maxime Bonhomme et al.   GENETICS

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

(2010) A. McKenna et al.   GENOME RESEARCH

Applications of next generation sequencing in molecular ecology of non-model organisms

(2010) R Ekblom et al.   HEREDITY

Whole-genome resequencing reveals loci under selection during chicken domestication

(2010) Carl-Johan Rubin et al.   NATURE

Principles and challenges of genome-wide DNA methylation analysis

(2010) Peter W. Laird   NATURE REVIEWS GENETICS

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

Finding the missing heritability of complex diseases

(2009) Teri A. Manolio et al.   NATURE

Design of a High Density SNP Genotyping Assay in the Pig Using SNPs Identified and Characterized by Next Generation Sequencing Technology

(2009) Antonio M. Ramos et al.   PLoS One

Genetic diagnosis by whole exome capture and massively parallel DNA sequencing

(2009) Murim Choi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Single SNP in an Evolutionary Conserved Region within Intron 86 of the HERC2 Gene Determines Human Blue-Brown Eye Color

(2008) Richard A. Sturm et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS