Nucleotide polymorphism and copy number variant detection using exome capture and next-generation sequencing in the polyploid grassPanicum virgatum

Generation of Transcript Assemblies and Identification of Single Nucleotide Polymorphisms from Seven Lowland and Upland Cultivars of Switchgrass

(2014) Kevin L. Childs et al.   Plant Genome

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

Development of an integrated transcript sequence database and a gene expression atlas for gene discovery and analysis in switchgrass (Panicum virgatumL.)

(2013) Ji-Yi Zhang et al.   PLANT JOURNAL

Copy number variation in potato - an asexually propagated autotetraploid species

(2013) Marina Iovene et al.   PLANT JOURNAL

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

(2013) Junbo Duan et al.   PLoS One

A Next-Generation Sequencing Method for Genotyping-by-Sequencing of Highly Heterozygous Autotetraploid Potato

(2013) Jan G. A. M. L. Uitdewilligen et al.   PLoS One

Reference genome sequence of the model plant Setaria

(2012) Jeffrey L Bennetzen et al.   NATURE BIOTECHNOLOGY

Maize HapMap2 identifies extant variation from a genome in flux

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

Targeted re-sequencing of the allohexaploid wheat exome

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

Changes in genome content generated via segregation of non-allelic homologs

(2012) Sanzhen Liu 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

Exploring the Switchgrass Transcriptome Using Second-Generation Sequencing Technology

(2012) Yixing Wang et al.   PLoS One

A Genome-Wide Survey of Switchgrass Genome Structure and Organization

(2012) Manoj K. Sharma et al.   PLoS One

Copy Number Variation of Multiple Genes at Rhg1 Mediates Nematode Resistance in Soybean

(2012) D. E. Cook et al.   SCIENCE

A High-Density Simple Sequence Repeat-Based Genetic Linkage Map of Switchgrass

(2012) Linglong Liu et al.   G3-Genes Genomes Genetics

Next-Generation Sequencing of Crown and Rhizome Transcriptome from an Upland, Tetraploid Switchgrass

(2011) Nathan A. Palmer et al.   BioEnergy Research

The Pfam protein families database

(2011) M. Punta et al.   NUCLEIC ACIDS RESEARCH

Phenotypic and Genomic Analyses of a Fast Neutron Mutant Population Resource in Soybean

(2011) Y.-T. Bolon et al.   PLANT PHYSIOLOGY

Genome-Wide Comparison of Nucleotide-Binding Site-Leucine-Rich Repeat-Encoding Genes in Arabidopsis

(2011) Y.-L. Guo et al.   PLANT PHYSIOLOGY

The Switchgrass Genome: Tools and Strategies

(2011) Michael D. Casler et al.   Plant Genome

Genome-wide patterns of genetic variation in sweet and grain sorghum (Sorghum bicolor)

(2011) Lei-Ying Zheng et al.   GENOME BIOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Pervasive gene content variation and copy number variation in maize and its undomesticated progenitor

(2010) R. A. Swanson-Wagner et al.   GENOME RESEARCH

Genome sequencing and analysis of the model grass Brachypodium distachyon

(2010) John P. Vogel et al.   NATURE

Rice structural variation: a comparative analysis of structural variation between rice and three of its closest relatives in the genus Oryza

(2010) Bonnie L. Hurwitz et al.   PLANT JOURNAL

Detection of inherited mutations for breast and ovarian cancer using genomic capture and massively parallel sequencing

(2010) Tom Walsh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Hierarchical classification of switchgrass genotypes using SSR and chloroplast sequences: ecotypes, ploidies, gene pools, and cultivars

(2010) J. E. Zalapa et al.   THEORETICAL AND APPLIED GENETICS

Genome-size Variation in Switchgrass (Panicum virgatum): Flow Cytometry and Cytology Reveal Rampant Aneuploidy

(2010) Denise E. Costich et al.   Plant Genome

Whole exome capture in solution with 3 Gbp of data

(2010) Matthew N Bainbridge et al.   GENOME BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

The Sorghum bicolor genome and the diversification of grasses

(2009) Andrew H. Paterson et al.   NATURE

Genomewide SNP variation reveals relationships among landraces and modern varieties of rice

(2009) K. L. McNally et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The B73 Maize Genome: Complexity, Diversity, and Dynamics

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

Maize Inbreds Exhibit High Levels of Copy Number Variation (CNV) and Presence/Absence Variation (PAV) in Genome Content

(2009) Nathan M. Springer et al.   PLoS Genetics

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Net energy of cellulosic ethanol from switchgrass

(2008) M. R. Schmer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comparative Genomics in Switchgrass Using 61,585 High-Quality Expressed Sequence Tags

(2008) Christian M. Tobias et al.   Plant Genome