TASSEL-GBS: A High Capacity Genotyping by Sequencing Analysis Pipeline

Discovering motifs that induce sequencing errors

(2013) Manuel Allhoff et al.   BMC BIOINFORMATICS

Digital genotyping of sorghum -- a diverse plant species with a large repeat-rich genome

(2013) Daryl T Morishige et al.   BMC GENOMICS

Relatedness and Genotype × Environment Interaction Affect Prediction Accuracies in Genomic Selection: A Study in Cassava

(2013) Delphine Ly et al.   CROP SCIENCE

The population structure and recent colonization history of Oregon threespine stickleback determined using restriction-site associated DNA-sequencing

(2013) Julian Catchen et al.   MOLECULAR ECOLOGY

Adaptive evolution during an ongoing range expansion: the invasive bank vole (Myodes glareolus) in Ireland

(2013) Thomas A. White et al.   MOLECULAR ECOLOGY

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

(2013) B. Arnold et al.   MOLECULAR ECOLOGY

Genotyping-by-sequencing in ecological and conservation genomics

(2013) Shawn R. Narum et al.   MOLECULAR ECOLOGY

Identification of SNPs in Closely Related Temperate Japonica Rice Cultivars Using Restriction Enzyme-Phased Sequencing

(2013) Sang-Ic Kim et al.   PLoS One

An Improved Genotyping by Sequencing (GBS) Approach Offering Increased Versatility and Efficiency of SNP Discovery and Genotyping

(2013) Humira Sonah et al.   PLoS One

Genotyping-by-Sequencing (GBS): A Novel, Efficient and Cost-Effective Genotyping Method for Cattle Using Next-Generation Sequencing

(2013) Marcos De Donato et al.   PLoS One

A Filtering Method to Generate High Quality Short Reads Using Illumina Paired-End Technology

(2013) A. Murat Eren et al.   PLoS One

RESTseq – Efficient Benchtop Population Genomics with RESTriction Fragment SEQuencing

(2013) Eckart Stolle et al.   PLoS One

Genotyping by Genome Reducing and Sequencing for Outbred Animals

(2013) Qiang Chen et al.   PLoS One

Application of Genotyping-by-Sequencing on Semiconductor Sequencing Platforms: A Comparison of Genetic and Reference-Based Marker Ordering in Barley

(2013) Martin Mascher et al.   PLoS One

Aluminum tolerance in maize is associated with higher MATE1 gene copy number

(2013) L. G. Maron et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Imputation of Unordered Markers and the Impact on Genomic Selection Accuracy

(2013) Jessica E. Rutkoski et al.   G3-Genes Genomes Genetics

Sequence-Based Mapping of the Polyploid Wheat Genome

(2013) Cyrille Saintenac et al.   G3-Genes Genomes Genetics

Switchgrass Genomic Diversity, Ploidy, and Evolution: Novel Insights from a Network-Based SNP Discovery Protocol

(2013) Fei Lu et al.   PLoS Genetics

BioJava: an open-source framework for bioinformatics in 2012

(2012) A. Prlic et al.   BIOINFORMATICS

Reference genome-independent assessment of mutation density using restriction enzyme-phased sequencing

(2012) Jennifer Monson-Miller et al.   BMC GENOMICS

GemSIM: general, error-model based simulator of next-generation sequencing data

(2012) Kerensa E McElroy et al.   BMC GENOMICS

The effect of RAD allele dropout on the estimation of genetic variation within and between populations

(2012) Mathieu Gautier et al.   MOLECULAR ECOLOGY

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

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

An integrated map of genetic variation from 1,092 human genomes

(2012)   NATURE

The expanding scope of DNA sequencing

(2012) Jay Shendure et al.   NATURE BIOTECHNOLOGY

Maize HapMap2 identifies extant variation from a genome in flux

(2012) Jer-Ming Chia et al.   NATURE GENETICS

2b-RAD: a simple and flexible method for genome-wide genotyping

(2012) Shi Wang et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Sustainable plant breeding

(2012) Wallace A. Cowling   PLANT BREEDING

Development of High-Density Genetic Maps for Barley and Wheat Using a Novel Two-Enzyme Genotyping-by-Sequencing Approach

(2012) Jesse A. Poland et al.   PLoS One

Sequence-Based Genotyping for Marker Discovery and Co-Dominant Scoring in Germplasm and Populations

(2012) Hoa T. Truong et al.   PLoS One

Population genomic and genome-wide association studies of agroclimatic traits in sorghum

(2012) G. P. Morris et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Accessing complex crop genomes with next-generation sequencing

(2012) David Edwards et al.   THEORETICAL AND APPLIED GENETICS

How next-generation sequencing is transforming complex disease genetics

(2012) Helena Kilpinen et al.   TRENDS IN GENETICS

Genotyping-by-Sequencing for Plant Breeding and Genetics

(2012) Jesse A. Poland et al.   Plant Genome

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Multiplexed shotgun genotyping for rapid and efficient genetic mapping

(2011) P. Andolfatto et al.   GENOME RESEARCH

Inference of human population history from individual whole-genome sequences

(2011) Heng Li et al.   NATURE

Genome-wide association study of leaf architecture in the maize nested association mapping population

(2011) Feng Tian et al.   NATURE GENETICS

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

(2011) Mark A DePristo et al.   NATURE GENETICS

Genome-wide genetic marker discovery and genotyping using next-generation sequencing

(2011) John W. Davey et al.   NATURE REVIEWS GENETICS

A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species

(2011) Robert J. Elshire et al.   PLoS One

Genotype Imputation with Thousands of Genomes

(2011) Bryan Howie et al.   G3-Genes Genomes Genetics

Stacks : Building and Genotyping Loci De Novo From Short-Read Sequences

(2011) Julian M. Catchen et al.   G3-Genes Genomes Genetics

Association genetics in crop improvement

(2010) J Antoni Rafalski   CURRENT OPINION IN PLANT BIOLOGY

Effect of crop improvement on genetic diversity in oilseedBrassica rapa (turnip-rape) cultivars, detected by SSR markers

(2010) Atta Ofori et al.   JOURNAL OF APPLIED GENETICS

Ascertainment Biases in SNP Chips Affect Measures of Population Divergence

(2010) A. Albrechtsen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genotype imputation for genome-wide association studies

(2010) Jonathan Marchini et al.   NATURE REVIEWS GENETICS

Parent-independent genotyping for constructing an ultrahigh-density linkage map based on population sequencing

(2010) W. Xie et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

SNP detection for massively parallel whole-genome resequencing

(2009) R. Li et al.   GENOME RESEARCH

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

Genetic Properties of the Maize Nested Association Mapping Population

(2009) M. D. McMullen et al.   SCIENCE

SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries

(2008) Curtis P Van Tassell et al.   NATURE METHODS

Substantial biases in ultra-short read data sets from high-throughput DNA sequencing

(2008) J. C. Dohm et al.   NUCLEIC ACIDS RESEARCH

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

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