Reduced representation approaches to interrogate genome diversity in large repetitive plant genomes

Multiphasic analysis of whole exome sequencing data identifies a novel mutation of ACTG1 in a nonsyndromic hearing loss family

(2013) Gibeom Park et al.   BMC GENOMICS

The Norway spruce genome sequence and conifer genome evolution

(2013) Björn Nystedt et al.   NATURE

Genotyping by RAD sequencing enables mapping of fatty acid composition traits in perennial ryegrass (Lolium perenne(L.))

(2013) Matthew Hegarty et al.   PLANT BIOTECHNOLOGY JOURNAL

Barley whole exome capture: a tool for genomic research in the genusHordeumand beyond

(2013) Martin Mascher et al.   PLANT JOURNAL

Whole-exome targeted sequencing of the uncharacterized pine genome

(2013) Leandro G. Neves et al.   PLANT JOURNAL

The advantages and limitations of trait analysis with GWAS: a review

(2013) Arthur Korte et al.   Plant Methods

Comparative Studies of Copy Number Variation Detection Methods for Next-Generation Sequencing Technologies

(2013) Junbo Duan et al.   PLoS One

Linkage Analysis and QTL Mapping Using SNP Dosage Data in a Tetraploid Potato Mapping Population

(2013) Christine A. Hackett et al.   PLoS One

Bridging the genotyping gap: using genotyping by sequencing (GBS) to add high-density SNP markers and new value to traditional bi-parental mapping and breeding populations

(2013) Jennifer Spindel et al.   THEORETICAL AND APPLIED GENETICS

Genomic Prediction in Maize Breeding Populations with Genotyping-by-Sequencing

(2013) José Crossa et al.   G3-Genes Genomes Genetics

Sequence Diversity in Coding Regions of Candidate Genes in the Glycoalkaloid Biosynthetic Pathway of Wild Potato Species

(2013) Norma C. Manrique-Carpintero et al.   G3-Genes Genomes Genetics

Retrospective View of North American Potato ( Solanum tuberosum L.) Breeding in the 20 th and 21 st Centuries

(2013) Candice N. Hirsch 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

Prevalence of single nucleotide polymorphism among 27 diverse alfalfa genotypes as assessed by transcriptome sequencing

(2012) Xuehui Li et al.   BMC GENOMICS

Targeted enrichment of the black cottonwood (Populus trichocarpa) gene space using sequence capture

(2012) Lecong Zhou et al.   BMC GENOMICS

The tomato genome sequence provides insights into fleshy fruit evolution

(2012)   NATURE

Comparative population genomics of maize domestication and improvement

(2012) Matthew B Hufford et al.   NATURE GENETICS

De novo mutations in human genetic disease

(2012) Joris A. Veltman et al.   NATURE REVIEWS GENETICS

Targeted re-sequencing of the allohexaploid wheat exome

(2012) Mark O. Winfield et al.   PLANT BIOTECHNOLOGY JOURNAL

Enrichment of genomic DNA for polymorphism detection in a non-model highly polyploid crop plant

(2012) Peter C. Bundock et al.   PLANT BIOTECHNOLOGY JOURNAL

Transcriptome analysis and gene expression atlas for Panicum hallii var. filipes, a diploid model for biofuel research

(2012) Eli Meyer et al.   PLANT JOURNAL

Structural Variants in the Soybean Genome Localize to Clusters of Biotic Stress-Response Genes

(2012) L. K. McHale et al.   PLANT PHYSIOLOGY

Maize (Zea mays L.) Genome Diversity as Revealed by RNA-Sequencing

(2012) Candice N. Hansey et al.   PLoS One

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

Gene Mapping via Bulked Segregant RNA-Seq (BSR-Seq)

(2012) Sanzhen Liu et al.   PLoS One

Integration of Two Diploid Potato Linkage Maps with the Potato Genome Sequence

(2012) Kimberly J. Felcher et al.   PLoS One

A RAD Tag Derived Marker Based Eggplant Linkage Map and the Location of QTLs Determining Anthocyanin Pigmentation

(2012) Lorenzo Barchi et al.   PLoS One

Development of a Large SNP Genotyping Array and Generation of High-Density Genetic Maps in Tomato

(2012) Sung-Chur Sim et al.   PLoS One

Development of Transcriptomic Resources for Interrogating the Biosynthesis of Monoterpene Indole Alkaloids in Medicinal Plant Species

(2012) Elsa Góngora-Castillo et al.   PLoS One

Single Nucleotide Polymorphism Discovery in Cultivated Tomato via Sequencing by Synthesis

(2012) John P. Hamilton et al.   Plant Genome

Current challenges in de novo plant genome sequencing and assembly

(2012) Michael C Schatz et al.   GENOME BIOLOGY

Exome sequencing-based copy-number variation and loss of heterozygosity detection: ExomeCNV

(2011) Jarupon Fah Sathirapongsasuti et al.   BIOINFORMATICS

SeqGene: a comprehensive software solution for mining exome- and transcriptome- sequencing data

(2011) Xutao Deng   BMC BIOINFORMATICS

Using RNA-Seq for gene identification, polymorphism detection and transcript profiling in two alfalfa genotypes with divergent cell wall composition in stems

(2011) S Samuel Yang et al.   BMC GENOMICS

Single nucleotide polymorphism discovery in elite north american potato germplasm

(2011) John P Hamilton et al.   BMC GENOMICS

Construction and application for QTL analysis of a Restriction Site Associated DNA (RAD) linkage map in barley

(2011) Yada Chutimanitsakun et al.   BMC GENOMICS

From RNA-seq to large-scale genotyping - genomics resources for rye (Secale cereale L.)

(2011) Grit Haseneyer et al.   BMC PLANT BIOLOGY

Multiple reference genomes and transcriptomes for Arabidopsis thaliana

(2011) Xiangchao Gan et al.   NATURE

Genome sequence and analysis of the tuber crop potato

(2011) Xun Xu et al.   NATURE

Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes

(2011) Xun Xu et al.   NATURE BIOTECHNOLOGY

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

(2011) Feng Tian et al.   NATURE GENETICS

Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasm

(2011) Xuehui Huang et al.   NATURE GENETICS

Exome sequencing as a tool for Mendelian disease gene discovery

(2011) Michael J. Bamshad et al.   NATURE REVIEWS GENETICS

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

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

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

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

RNA-Seq analysis and de novo transcriptome assembly of Hevea brasiliensis

(2011) Zhihui Xia et al.   PLANT MOLECULAR BIOLOGY

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

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

Mapping with RAD (restriction-site associated DNA) markers to rapidly identify QTL for stem rust resistance in Lolium perenne

(2011) W. F. Pfender et al.   THEORETICAL AND APPLIED GENETICS

Genome-wide association mapping of agronomic and morphologic traits in highly structured populations of barley cultivars

(2011) Minghui Wang et al.   THEORETICAL AND APPLIED GENETICS

Molecular genetic studies of complex phenotypes

(2011) Ali J. Marian   Translational Research

The draft genome and transcriptome of Cannabis sativa

(2011) Harm van Bakel et al.   GENOME BIOLOGY

Mutation discovery in mice by whole exome sequencing

(2011) Heather Fairfield et al.   GENOME BIOLOGY

Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines

(2010) Susanna Atwell et al.   NATURE

Genome sequence of the palaeopolyploid soybean

(2010) Jeremy Schmutz et al.   NATURE

Genome-wide patterns of genetic variation among elite maize inbred lines

(2010) Jinsheng Lai et al.   NATURE GENETICS

Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection

(2010) Hon-Ming Lam et al.   NATURE GENETICS

Repeat subtraction-mediated sequence capture from a complex genome

(2010) Yan Fu et al.   PLANT JOURNAL

The Composition and Origins of Genomic Variation among Individuals of the Soybean Reference Cultivar Williams 82

(2010) W. J. Haun et al.   PLANT PHYSIOLOGY

Rapid Genomic Characterization of the Genus Vitis

(2010) Sean Myles et al.   PLoS One

The study of eQTL variations by RNA-seq: from SNPs to phenotypes

(2010) Jacek Majewski et al.   TRENDS IN GENETICS

Whole exome capture in solution with 3 Gbp of data

(2010) Matthew N Bainbridge et al.   GENOME BIOLOGY

High-throughput genotyping by whole-genome resequencing

(2009) X. Huang et al.   GENOME RESEARCH

Targeted capture and massively parallel sequencing of 12 human exomes

(2009) Sarah B. Ng et al.   NATURE

Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing

(2009) Andreas Gnirke et al.   NATURE BIOTECHNOLOGY

Genome comparisons reveal a dominant mechanism of chromosome number reduction in grasses and accelerated genome evolution in Triticeae

(2009) M. C. Luo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A First-Generation Haplotype Map of Maize

(2009) M. A. Gore et al.   SCIENCE

The B73 Maize Genome: Complexity, Diversity, and Dynamics

(2009) P. S. Schnable et al.   SCIENCE

The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus)

(2008) Ray Ming et al.   NATURE

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

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