Genome interplay in the grain transcriptome of hexaploid bread wheat

A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome

(2014) et al.   SCIENCE

The gene space in wheat: the complete γ-gliadin gene family from the wheat cultivar Chinese Spring

(2013) Olin D. Anderson et al.   FUNCTIONAL & INTEGRATIVE GENOMICS

Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation

(2013) Jizeng Jia et al.   NATURE

Epigenetic modification contributes to the expression divergence of threeTaEXPA1homoeologs in hexaploid wheat (Triticum aestivum)

(2013) Zhaorong Hu et al.   NEW PHYTOLOGIST

Comprehensive developmental profiles of gene activity in regions and subregions of the Arabidopsis seed

(2013) M. F. Belmonte et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomic asymmetry in allopolyploid plants: wheat as a model

(2012) M. Feldman et al.   JOURNAL OF EXPERIMENTAL BOTANY

Gene expression in the developing aleurone and starchy endosperm of wheat

(2012) Susan A. Gillies et al.   PLANT BIOTECHNOLOGY JOURNAL

Unlocking the Barley Genome by Chromosomal and Comparative Genomics

(2011) Klaus F.X. Mayer et al.   PLANT CELL

Next-generation sequencing and syntenic integration of flow-sorted arms of wheat chromosome 4A exposes the chromosome structure and gene content

(2011) Pilar Hernandez et al.   PLANT JOURNAL

Cell Walls of Developing Wheat Starchy Endosperm: Comparison of Composition and RNA-Seq Transcriptome

(2011) T. K. Pellny et al.   PLANT PHYSIOLOGY

A 3,000-Loci Transcription Map of Chromosome 3B Unravels the Structural and Functional Features of Gene Islands in Hexaploid Wheat

(2011) C. Rustenholz et al.   PLANT PHYSIOLOGY

REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms

(2011) Fran Supek et al.   PLoS One

Deciphering the complexities of the wheat flour proteome using quantitative two-dimensional electrophoresis, three proteases and tandem mass spectrometry

(2011) Frances M Dupont et al.   Proteome Science

Circoletto: visualizing sequence similarity with Circos

(2010) N. Darzentas   BIOINFORMATICS

Homoeolog-specific transcriptional bias in allopolyploid wheat

(2010) Alina R Akhunova et al.   BMC GENOMICS

Genome sequencing and analysis of the model grass Brachypodium distachyon

(2010) John P. Vogel et al.   NATURE

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Jalview Version 2--a multiple sequence alignment editor and analysis workbench

(2009) A. M. Waterhouse et al.   BIOINFORMATICS

The wheat ω-gliadin genes: structure and EST analysis

(2009) Olin D. Anderson et al.   FUNCTIONAL & INTEGRATIVE GENOMICS

The Sorghum bicolor genome and the diversification of grasses

(2009) Andrew H. Paterson et al.   NATURE

Gene Content and Virtual Gene Order of Barley Chromosome 1H

(2009) K. F.X. Mayer et al.   PLANT PHYSIOLOGY

Nucleotide Polymorphism in the Wheat Transcriptional Activator Spa Influences Its Pattern of Expression and Has Pleiotropic Effects on Grain Protein Composition, Dough Viscoelasticity, and Grain Hardness

(2009) C. Ravel et al.   PLANT PHYSIOLOGY

The B73 Maize Genome: Complexity, Diversity, and Dynamics

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

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

The ‘inner circle’ of the cereal genomes

(2008) Stéphanie Bolot et al.   CURRENT OPINION IN PLANT BIOLOGY

Identification and genetic mapping of variant forms of puroindoline b expressed in developing wheat grain

(2008) Mark Wilkinson et al.   JOURNAL OF CEREAL SCIENCE

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

Identification and Characterization of Shared Duplications between Rice and Wheat Provide New Insight into Grass Genome Evolution

(2008) J. Salse et al.   PLANT CELL

Barley Grain Maturation and Germination: Metabolic Pathway and Regulatory Network Commonalities and Differences Highlighted by New MapMan/PageMan Profiling Tools

(2008) N. Sreenivasulu et al.   PLANT PHYSIOLOGY

Geometric Interpretation of Gene Coexpression Network Analysis

(2008) Steve Horvath et al.   PLoS Computational Biology