Whole-genome sequencing approaches for conservation biology: Advantages, limitations and practical recommendations

Genome graphs and the evolution of genome inference

(2017) Benedict Paten et al.   GENOME RESEARCH

New advances in sequence assembly

(2017) Adam M. Phillippy   GENOME RESEARCH

RADseq provides unprecedented insights into molecular ecology and evolutionary genetics: comment on Breaking RAD by Lowry et al . (2016)

(2017) Garrett J. McKinney et al.   Molecular Ecology Resources

Tracing the peopling of the world through genomics

(2017) Rasmus Nielsen et al.   NATURE

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

Whole genome sequencing data and de novo draft assemblies for 66 teleost species

(2017) Martin Malmstrøm et al.   Scientific Data

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

(2016) Sean Hoban et al.   AMERICAN NATURALIST

Estimating IBD tracts from low coverage NGS data

(2016) Filipe G. Vieira et al.   BIOINFORMATICS

How and how much does RAD-seq bias genetic diversity estimates?

(2016) Marie Cariou et al.   BMC EVOLUTIONARY BIOLOGY

Atlantic salmon populations reveal adaptive divergence of immune related genes - a duplicated genome under selection

(2016) Erik Kjærner-Semb et al.   BMC GENOMICS

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

Detecting polygenic selection in marine populations by combining population genomics and quantitative genetics approaches

(2016) Pierre-Alexandre Gagnaire et al.   Current Zoology

Forest genetic monitoring: an overview of concepts and definitions

(2016) Barbara Fussi et al.   ENVIRONMENTAL MONITORING AND ASSESSMENT

Genomics advances the study of inbreeding depression in the wild

(2016) Marty Kardos et al.   Evolutionary Applications

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

(2016) A. Jonas et al.   GENETICS

Efficient Genome-Wide Sequencing and Low-Coverage Pedigree Analysis from Noninvasively Collected Samples

(2016) N. Snyder-Mackler et al.   GENETICS

The sequence of sequencers: The history of sequencing DNA

(2016) James M. Heather et al.   GENOMICS

From next-generation resequencing reads to a high-quality variant data set

(2016) S P Pfeifer   HEREDITY

Estimating contemporary effective population size in non-model species using linkage disequilibrium across thousands of loci

(2016) R K Waples et al.   HEREDITY

From population genomics to conservation and management: a workflow for targeted analysis of markers identified using genome-wide approaches in Atlantic salmonSalmo salar

(2016) T. Aykanat et al.   JOURNAL OF FISH BIOLOGY

On the maintenance of genetic variation and adaptation to environmental change: considerations from population genomics in fishes

(2016) L. Bernatchez   JOURNAL OF FISH BIOLOGY

Applying SNP-Derived Molecular Coancestry Estimates to Captive Breeding Programs

(2016) Jamie A. Ivy et al.   JOURNAL OF HEREDITY

LaGomiCs—Lagomorph Genomics Consortium: An International Collaborative Effort for Sequencing the Genomes of an Entire Mammalian Order

(2016) Luca Fontanesi et al.   JOURNAL OF HEREDITY

Next-generation biology: Sequencing and data analysis approaches for non-model organisms

(2016) Rute R. da Fonseca et al.   Marine Genomics

Whole-Genome Sequencing of Native Sheep Provides Insights into Rapid Adaptations to Extreme Environments

(2016) Ji Yang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evolution of GOUNDRY, a cryptic subgroup of Anopheles gambiae s.l ., and its impact on susceptibility to Plasmodium infection

(2016) Jacob E. Crawford et al.   MOLECULAR ECOLOGY

Genomewide ancestry and divergence patterns from low-coverage sequencing data reveal a complex history of admixture in wild baboons

(2016) Jeffrey D. Wall et al.   MOLECULAR ECOLOGY

Pooled ecotype sequencing reveals candidate genetic mechanisms for adaptive differentiation and reproductive isolation

(2016) Billie A. Gould et al.   MOLECULAR ECOLOGY

Adaptive genomic divergence under high gene flow between freshwater and brackish-water ecotypes of prickly sculpin (Cottus asper) revealed by Pool-Seq

(2016) Stefan Dennenmoser et al.   MOLECULAR ECOLOGY

PSMC analysis of effective population sizes in molecular ecology and its application to black-and-whiteFicedulaflycatchers

(2016) Krystyna Nadachowska-Brzyska et al.   MOLECULAR ECOLOGY

Conservation genomics of natural and managed populations: building a conceptual and practical framework

(2016) Laura Marilyn Benestan et al.   MOLECULAR ECOLOGY

Breaking RAD: an evaluation of the utility of restriction site-associated DNA sequencing for genome scans of adaptation

(2016) David B. Lowry et al.   Molecular Ecology Resources

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

The Power of Inbreeding: NGS-Based GWAS of Rice Reveals Convergent Evolution during Rice Domestication

(2016) Hongru Wang et al.   Molecular Plant

Real-time, portable genome sequencing for Ebola surveillance

(2016) Joshua Quick et al.   NATURE

The Atlantic salmon genome provides insights into rediploidization

(2016) Sigbjørn Lien et al.   NATURE

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

(2016) Tobias S. Kaiser et al.   NATURE

Harnessing the power of RADseq for ecological and evolutionary genomics

(2016) Kimberly R. Andrews et al.   NATURE REVIEWS GENETICS

Coming of age: ten years of next-generation sequencing technologies

(2016) Sara Goodwin et al.   NATURE REVIEWS GENETICS

Genomes OnLine Database (GOLD) v.6: data updates and feature enhancements

(2016) Supratim Mukherjee et al.   NUCLEIC ACIDS RESEARCH

Are We There Yet? Reliably Estimating the Completeness of Plant Genome Sequences

(2016) Elisabeth Veeckman et al.   PLANT CELL

Detection of human adaptation during the past 2000 years

(2016) Yair Field et al.   SCIENCE

Comparison of Target-Capture and Restriction-Site Associated DNA Sequencing for Phylogenomics: A Test in Cardinalid Tanagers (Aves, Genus:Piranga)

(2016) Joseph D. Manthey et al.   SYSTEMATIC BIOLOGY

Genome-culture coevolution promotes rapid divergence of killer whale ecotypes

(2016) Andrew D. Foote et al.   Nature Communications

Discovery of 20,000 RAD–SNPs and development of a 52-SNP array for monitoring river otters

(2016) Jeffrey B. Stetz et al.   Conservation Genetics Resources

Bioinformatic processing of RAD-seq data dramatically impacts downstream population genetic inference

(2016) Aaron B. A. Shafer et al.   Methods in Ecology and Evolution

Investigation of rare and low-frequency variants using high-throughput sequencing with pooled DNA samples

(2016) Jingwen Wang et al.   Scientific Reports

Inferring Population Size History from Large Samples of Genome-Wide Molecular Data - An Approximate Bayesian Computation Approach

(2016) Simon Boitard et al.   PLoS Genetics

Detecting polygenic selection in marine populations by combining population genomics and quantitative genetics approaches

(2016) Pierre-Alexandre Gagnaire et al.   Current Zoology

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

(2016) Alvaro Martinez Barrio et al.   eLife

Whole-genome sequence analysis shows that two endemic species of North American wolf are admixtures of the coyote and gray wolf

(2016) B. M. vonHoldt et al.   Science Advances

Library construction for next-generation sequencing: Overviews and challenges

(2016) Steven R. Head et al.   BIOTECHNIQUES

Alignment of Next-Generation Sequencing Reads

(2015) Knut Reinert et al.   Annual Review of Genomics and Human Genetics

Denoising DNA deep sequencing data—high-throughput sequencing errors and their correction

(2015) David Laehnemann et al.   BRIEFINGS IN BIOINFORMATICS

The conservation genetics juggling act: integrating genetics and ecology, science and policy

(2015) Susan M. Haig et al.   Evolutionary Applications

High-throughput gene targeting and phenotyping in zebrafish using CRISPR/Cas9

(2015) Gaurav K. Varshney et al.   GENOME RESEARCH

Gene-associated markers can assign origin in a weakly structured fish, Atlantic herring

(2015) Dorte Bekkevold et al.   ICES JOURNAL OF MARINE SCIENCE

Transatlantic secondary contact in Atlantic Salmon, comparing microsatellites, a single nucleotide polymorphism array and restriction-site associated DNA sequencing for the resolution of complex spatial structure

(2015) Ian R. Bradbury et al.   MOLECULAR ECOLOGY

Targeted capture in evolutionary and ecological genomics

(2015) Matthew R. Jones et al.   MOLECULAR ECOLOGY

The relative power of genome scans to detect local adaptation depends on sampling design and statistical method

(2015) Katie E. Lotterhos et al.   MOLECULAR ECOLOGY

Fifteen years of genomewide scans for selection: trends, lessons and unaddressed genetic sources of complication

(2015) Ryan J. Haasl et al.   MOLECULAR ECOLOGY

Detection of selective sweeps in structured populations: a comparison of recent methods

(2015) Alexandra I. Vatsiou et al.   MOLECULAR ECOLOGY

The past, present and future of genomic scans for selection

(2015) Jeffrey D. Jensen et al.   MOLECULAR ECOLOGY

Bird sequencing project takes off

(2015) Guojie Zhang   NATURE

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 global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

Assembling large genomes with single-molecule sequencing and locality-sensitive hashing

(2015) Konstantin Berlin et al.   NATURE BIOTECHNOLOGY

Structural genomic changes underlie alternative reproductive strategies in the ruff (Philomachus pugnax)

(2015) Sangeet Lamichhaney et al.   NATURE GENETICS

Recurrent somatic mutations in regulatory regions of human cancer genomes

(2015) Collin Melton et al.   NATURE GENETICS

Genomic variant annotation and prioritization with ANNOVAR and wANNOVAR

(2015) Hui Yang et al.   Nature Protocols

Haplotype-resolved genome sequencing: experimental methods and applications

(2015) Matthew W. Snyder et al.   NATURE REVIEWS GENETICS

Examining the cause of high inbreeding depression: analysis of whole-genome sequence data in 28 selfed progeny of Eucalyptus grandis

(2015) Philip W. Hedrick et al.   NEW PHYTOLOGIST

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

(2015) Marco Fracassetti et al.   PLoS One

Whole-genome sequencing is more powerful than whole-exome sequencing for detecting exome variants

(2015) Aziz Belkadi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mountain gorilla genomes reveal the impact of long-term population decline and inbreeding

(2015) Y. Xue et al.   SCIENCE

Third generation sequencing: technology and its potential impact on evolutionary biodiversity research

(2015) Christoph Bleidorn   SYSTEMATICS AND BIODIVERSITY

Genomics and the challenging translation into conservation practice

(2015) Aaron B.A. Shafer et al.   TRENDS IN ECOLOGY & EVOLUTION

Rare variant discovery by deep whole-genome sequencing of 1,070 Japanese individuals

(2015) Masao Nagasaki et al.   Nature Communications

Towards the identification of the loci of adaptive evolution

(2015) Carolina Pardo-Diaz et al.   Methods in Ecology and Evolution

Rare variant association studies: considerations, challenges and opportunities

(2015) Paul L Auer et al.   Genome Medicine

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

(2015) Fernando Ayllon et al.   PLoS Genetics

The Power of Gene-Based Rare Variant Methods to Detect Disease-Associated Variation and Test Hypotheses About Complex Disease

(2015) Loukas Moutsianas et al.   PLoS Genetics

The Genome 10K Project: A Way Forward

(2015) Klaus-Peter Koepfli et al.   Annual Review of Animal Biosciences

The genetic architecture of gene expression levels in wild baboons

(2015) Jenny Tung et al.   eLife

Alignment of Short Reads: A Crucial Step for Application of Next-Generation Sequencing Data in Precision Medicine

(2015) Hao Ye et al.   Pharmaceutics

Inexpensive Multiplexed Library Preparation for Megabase-Sized Genomes

(2015) Michael Baym et al.   PLoS One

Reduced SNP Panels for Genetic Identification and Introgression Analysis in the Dark Honey Bee (Apis mellifera mellifera)

(2015) Irene Muñoz et al.   PLoS One

Rare-Variant Association Analysis: Study Designs and Statistical Tests

(2014) Seunggeung Lee et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Fast and accurate site frequency spectrum estimation from low coverage sequence data

(2014) Eunjung Han et al.   BIOINFORMATICS

ngsTools: methods for population genetics analyses from next-generation sequencing data

(2014) Matteo Fumagalli et al.   BIOINFORMATICS

Toward better understanding of artifacts in variant calling from high-coverage samples

(2014) Heng Li   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

ANGSD: Analysis of Next Generation Sequencing Data

(2014) Thorfinn Sand Korneliussen et al.   BMC BIOINFORMATICS

How and why should we implement genomics into conservation?

(2014) Barry J. McMahon et al.   Evolutionary Applications

A field guide to whole-genome sequencing, assembly and annotation

(2014) Robert Ekblom et al.   Evolutionary Applications

Resequencing studies of nonmodel organisms using closely related reference genomes: optimal experimental designs and bioinformatics approaches for population genomics

(2014) B. Nevado et al.   MOLECULAR ECOLOGY

The genome of Eucalyptus grandis

(2014) Alexander A. Myburg et al.   NATURE

Whole-genome sequencing of the snub-nosed monkey provides insights into folivory and evolutionary history

(2014) Xuming Zhou et al.   NATURE GENETICS

Inferring human population size and separation history from multiple genome sequences

(2014) Stephan Schiffels et al.   NATURE GENETICS

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

(2014) Christian Schlötterer et al.   NATURE REVIEWS GENETICS

Sequencing depth and coverage: key considerations in genomic analyses

(2014) David Sims et al.   NATURE REVIEWS GENETICS

Comparative genomics reveals insights into avian genome evolution and adaptation

(2014) G. Zhang et al.   SCIENCE

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

(2014) M. Carneiro et al.   SCIENCE

Advances and limits of using population genetics to understand local adaptation

(2014) Peter Tiffin et al.   TRENDS IN ECOLOGY & EVOLUTION

A Population Genetic Signal of Polygenic Adaptation

(2014) Jeremy J. Berg et al.   PLoS Genetics

Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies

(2014) David B Neale et al.   GENOME BIOLOGY

Gene Prediction and Annotation inPenstemon(Plantaginaceae): A Workflow for Marker Development from Extremely Low-Coverage Genome Sequencing

(2014) Paul D. Blischak et al.   Applications in Plant Sciences

Detecting Natural Selection in Genomic Data

(2013) Joseph J. Vitti et al.   Annual Review of Genetics

Major Histocompatibility Complex Genomics and Human Disease

(2013) John Trowsdale et al.   Annual Review of Genomics and Human Genetics

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

Fragmentation of DNA affects the accuracy of the DNA quantitation by the commonly used methods

(2013) Tatiana Sedlackova et al.   BIOLOGICAL PROCEDURES ONLINE

Next-generation phylogenomics

(2013) Cheong Xin Chan et al.   Biology Direct

Benchmarking short sequence mapping tools

(2013) Ayat Hatem et al.   BMC BIOINFORMATICS

The application of genetics to marine management and conservation: examples from the Indo-Pacific

(2013) Sophie von der Heyden et al.   BULLETIN OF MARINE SCIENCE

Oceanographic connectivity and environmental correlates of genetic structuring in Atlantic herring in the Baltic Sea

(2013) Amber GF Teacher et al.   Evolutionary Applications

Learning Natural Selection from the Site Frequency Spectrum

(2013) R. Ronen et al.   GENETICS

Quantifying Population Genetic Differentiation from Next-Generation Sequencing Data

(2013) Matteo Fumagalli et al.   GENETICS

Estimating Individual Admixture Proportions from Next Generation Sequencing Data

(2013) Line Skotte 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

The Global Invertebrate Genomics Alliance (GIGA): Developing Community Resources to Study Diverse Invertebrate Genomes

(2013)   JOURNAL OF HEREDITY

The i5K Initiative: Advancing Arthropod Genomics for Knowledge, Human Health, Agriculture, and the Environment

(2013)   JOURNAL OF HEREDITY

The promise of whole-exome sequencing in medical genetics

(2013) Bahareh Rabbani et al.   JOURNAL OF HUMAN GENETICS

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

RADseq underestimates diversity and introduces genealogical biases due to nonrandom haplotype sampling

(2013) B. Arnold 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

The haplotype-resolved genome and epigenome of the aneuploid HeLa cancer cell line

(2013) Andrew Adey et al.   NATURE

Evaluating empirical bounds on complex disease genetic architecture

(2013) Vineeta Agarwala et al.   NATURE GENETICS

MycoCosm portal: gearing up for 1000 fungal genomes

(2013) Igor V. Grigoriev et al.   NUCLEIC ACIDS RESEARCH

Assessing the Effect of Sequencing Depth and Sample Size in Population Genetics Inferences

(2013) Matteo Fumagalli   PLoS One

De Novo SNP Discovery in the Scandinavian Brown Bear (Ursus arctos)

(2013) Anita J. Norman et al.   PLoS One

Population genomics of rapid adaptation by soft selective sweeps

(2013) Philipp W. Messer et al.   TRENDS IN ECOLOGY & EVOLUTION

Genome sequencing and population genomics in non-model organisms

(2013) Hans Ellegren   TRENDS IN ECOLOGY & EVOLUTION

Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing

(2013) Jason O'Rawe et al.   Genome Medicine

Conservation Genomics of Threatened Animal Species

(2013) Cynthia C. Steiner et al.   Annual Review of Animal Biosciences

Characterizing and measuring bias in sequence data

(2013) Michael G Ross et al.   GENOME BIOLOGY

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

(2013) Keith R Bradnam et al.   GigaScience

Accurate estimation of short read mapping quality for next-generation genome sequencing

(2012) M. Ruffalo et al.   BIOINFORMATICS

Tools for mapping high-throughput sequencing data

(2012) Nuno A. Fonseca et al.   BIOINFORMATICS

SNP calling by sequencing pooled samples

(2012) Emanuele Raineri et al.   BMC BIOINFORMATICS

Whole mitochondrial genome scan for population structure and selection in the Atlantic herring

(2012) Amber GF Teacher et al.   BMC EVOLUTIONARY BIOLOGY

Transcriptome-based exon capture enables highly cost-effective comparative genomic data collection at moderate evolutionary scales

(2012) Ke Bi et al.   BMC GENOMICS

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing

(2012) D. C. Koboldt et al.   GENOME RESEARCH

Environmental selection on transcriptome-derived SNPs in a high gene flow marine fish, the Atlantic herring (Clupea harengus)

(2012) MORTEN T. LIMBORG et al.   MOLECULAR ECOLOGY

Population genomics based on low coverage sequencing: how low should we go?

(2012) C. Alex Buerkle et al.   MOLECULAR ECOLOGY

The simple fool's guide to population genomics via RNA-Seq: an introduction to high-throughput sequencing data analysis

(2012) Pierre De Wit et al.   Molecular Ecology Resources

Mutations in DMRT3 affect locomotion in horses and spinal circuit function in mice

(2012) Lisa S. Andersson et al.   NATURE

Extremely low-coverage sequencing and imputation increases power for genome-wide association studies

(2012) Bogdan Pasaniuc et al.   NATURE GENETICS

Whole-genome sequencing of giant pandas provides insights into demographic history and local adaptation

(2012) Shancen Zhao et al.   NATURE GENETICS

De novo genome assembly: what every biologist should know

(2012) Monya Baker   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

SNP Calling, Genotype Calling, and Sample Allele Frequency Estimation from New-Generation Sequencing Data

(2012) Rasmus Nielsen 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

Harnessing genomics for delineating conservation units

(2012) W. Chris Funk et al.   TRENDS IN ECOLOGY & EVOLUTION

Tissue sampling methods and standards for vertebrate genomics

(2012) Pamela BY Wong et al.   GigaScience

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

(2012) Ruibang Luo et al.   GigaScience

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

(2011) R. Kofler et al.   BIOINFORMATICS

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Estimation of allele frequency and association mapping using next-generation sequencing data

(2011) Su Kim et al.   BMC BIOINFORMATICS

Building a model: developing genomic resources for common milkweed (Asclepias syriaca) with low coverage genome sequencing

(2011) Shannon CK Straub et al.   BMC GENOMICS

cis-regulatory mutations are a genetic cause of human limb malformations

(2011) Julia E. VanderMeer et al.   DEVELOPMENTAL DYNAMICS

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

(2011) Matthew V. Rockman   EVOLUTION

Genomic toolboxes for conservation biologists

(2011) Francesco Angeloni et al.   Evolutionary Applications

Assemblathon 1: A competitive assessment of de novo short read assembly methods

(2011) D. Earl et al.   GENOME RESEARCH

GAGE: A critical evaluation of genome assemblies and assembly algorithms

(2011) S. L. Salzberg et al.   GENOME RESEARCH

A conserved haplotype controls parallel adaptation in geographically distant salmonid populations

(2011) MICHAEL R. MILLER et al.   MOLECULAR ECOLOGY

Chromosomal rearrangements maintain a polymorphic supergene controlling butterfly mimicry

(2011) Mathieu Joron et al.   NATURE

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Cis-regulatory elements: molecular mechanisms and evolutionary processes underlying divergence

(2011) Patricia J. Wittkopp et al.   NATURE REVIEWS GENETICS

Haplotype phasing: existing methods and new developments

(2011) Sharon R. Browning et al.   NATURE REVIEWS GENETICS

Genotype and SNP calling from next-generation sequencing data

(2011) Rasmus Nielsen et al.   NATURE REVIEWS GENETICS

Repetitive DNA and next-generation sequencing: computational challenges and solutions

(2011) Todd J. Treangen et al.   NATURE REVIEWS GENETICS

Genome structural variation discovery and genotyping

(2011) Can Alkan et al.   NATURE REVIEWS GENETICS

Molecular spandrels: tests of adaptation at the genetic level

(2011) Rowan D. H. Barrett et al.   NATURE REVIEWS GENETICS

PoPoolation: A Toolbox for Population Genetic Analysis of Next Generation Sequencing Data from Pooled Individuals

(2011) Robert Kofler et al.   PLoS One

Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries

(2011) Daniel Aird et al.   GENOME BIOLOGY

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

Challenges and opportunities of genetic approaches to biological conservation

(2010) Richard Frankham   BIOLOGICAL CONSERVATION

What Role Does Heritable Epigenetic Variation Play in Phenotypic Evolution?

(2010) Christina L. Richards et al.   BIOSCIENCE

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

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

(2010) G. Lunter 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

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

RNA sequencing: advances, challenges and opportunities

(2010) Fatih Ozsolak et al.   NATURE REVIEWS GENETICS

Genomics and the future of conservation genetics

(2010) Fred W. Allendorf et al.   NATURE REVIEWS GENETICS

Conservation genetics in transition to conservation genomics

(2010) N. Joop Ouborg et al.   TRENDS IN GENETICS

Population Genomics of Parallel Adaptation in Threespine Stickleback using Sequenced RAD Tags

(2010) Paul A. Hohenlohe et al.   PLoS Genetics

From Conservation Genetics to Conservation Genomics

(2009) Craig R. Primmer   Annals of the New York Academy of Sciences

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

Perspective: conservation genetics enters the genomics era

(2009) John C. Avise   CONSERVATION GENETICS

ADAPTIONISM-30 YEARS AFTER GOULD AND LEWONTIN

(2009) Rasmus Nielsen   EVOLUTION

SNP detection for massively parallel whole-genome resequencing

(2009) R. Li et al.   GENOME RESEARCH

Temporally stable genetic structure of heavily exploited Atlantic herring (Clupea harengus) in Swedish waters

(2009) L C Larsson et al.   HEREDITY

Divergent selection and heterogeneous genomic divergence

(2009) PATRIK NOSIL et al.   MOLECULAR ECOLOGY

Genetics in geographically structured populations: defining, estimating and interpreting FST

(2009) Kent E. Holsinger et al.   NATURE REVIEWS GENETICS

The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants

(2009) Peter J. A. Cock et al.   NUCLEIC ACIDS RESEARCH

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

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

Revisiting the Impact of Inversions in Evolution: From Population Genetic Markers to Drivers of Adaptive Shifts and Speciation?

(2008) Ary A. Hoffmann et al.   Annual Review of Ecology Evolution and Systematics

Mapping short DNA sequencing reads and calling variants using mapping quality scores

(2008) H. Li et al.   GENOME RESEARCH

Generations of sequencing technologies

(2008) Erik Pettersson et al.   GENOMICS

Next-generation DNA sequencing

(2008) Jay Shendure et al.   NATURE BIOTECHNOLOGY

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

(2008) Nathan A. Baird et al.   PLoS One