The limited role of differential fractionation in genome content variation and function in maize (Zea mays L .) inbred lines

Gene Fractionation and Function in the Ancient Subgenomes of Maize

(2017) Simon Renny-Byfield et al.   MOLECULAR BIOLOGY AND EVOLUTION

Draft Assembly of Elite Inbred Line PH207 Provides Insights into Genomic and Transcriptome Diversity in Maize

(2016) Candice N. Hirsch et al.   PLANT CELL

Integration of omic networks in a developmental atlas of maize

(2016) J. W. Walley et al.   SCIENCE

An Expanded Maize Gene Expression Atlas based on RNA Sequencing and its Use to Explore Root Development

(2016) Scott C. Stelpflug et al.   Plant Genome

Sambamba: fast processing of NGS alignment formats

(2015) Artem Tarasov et al.   BIOINFORMATICS

Nested radiations and the pulse of angiosperm diversification: increased diversification rates often follow whole genome duplications

(2015) David C. Tank et al.   NEW PHYTOLOGIST

High-resolution genetic mapping of maize pan-genome sequence anchors

(2015) Fei Lu et al.   Nature Communications

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Insights into the Maize Pan-Genome and Pan-Transcriptome

(2014) C. N. Hirsch et al.   PLANT CELL

Association Mapping across Numerous Traits Reveals Patterns of Functional Variation in Maize

(2014) Jason G. Wallace et al.   PLoS Genetics

Increased copy number at the HvFT1 locus is associated with accelerated flowering time in barley

(2013) Rebecca Nitcher et al.   MOLECULAR GENETICS AND GENOMICS

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

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Genome-Wide Analysis of Syntenic Gene Deletion in the Grasses

(2012) James C. Schnable et al.   Genome Biology and Evolution

Maize HapMap2 identifies extant variation from a genome in flux

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

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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

(2012) Sanzhen Liu et al.   PLANT JOURNAL

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

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

A Papaver somniferum 10-Gene Cluster for Synthesis of the Anticancer Alkaloid Noscapine

(2012) T. Winzer et al.   SCIENCE

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

(2012) D. E. Cook et al.   SCIENCE

Adaptive seeds tame genomic sequence comparison

(2011) S. M. Kielbasa et al.   GENOME RESEARCH

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

Ancestral polyploidy in seed plants and angiosperms

(2011) Yuannian Jiao et al.   NATURE

Identification of a functional transposon insertion in the maize domestication gene tb1

(2011) Anthony Studer et al.   NATURE GENETICS

Genes Identified by Visible Mutant Phenotypes Show Increased Bias toward One of Two Subgenomes of Maize

(2011) James C. Schnable et al.   PLoS One

Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss

(2011) J. C. Schnable et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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-wide patterns of genetic variation among elite maize inbred lines

(2010) Jinsheng Lai et al.   NATURE GENETICS

Following Tetraploidy in Maize, a Short Deletion Mechanism Removed Genes Preferentially from One of the Two Homeologs

(2010) Margaret R. Woodhouse et al.   PLOS BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

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

The Value of Nonmodel Genomes and an Example Using SynMap Within CoGe to Dissect the Hexaploidy that Predates the Rosids

(2008) Eric Lyons et al.   Tropical Plant Biology