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

Ancient hybridizations among the ancestral genomes of bread wheat

(2014) T. Marcussen et al.   SCIENCE

Genome interplay in the grain transcriptome of hexaploid bread wheat

(2014) M. Pfeifer et al.   SCIENCE

Structural and functional partitioning of bread wheat chromosome 3B

(2014) F. Choulet et al.   SCIENCE

Cadmium uptake and partitioning in durum wheat during grain filling

(2013) Neil S Harris et al.   BMC PLANT BIOLOGY

Next-Generation Survey Sequencing and the Molecular Organization of Wheat Chromosome 6B

(2013) T. Tanaka et al.   DNA RESEARCH

Proteogenomic Database Construction Driven from Large Scale RNA-seq Data

(2013) Sunghee Woo et al.   JOURNAL OF PROTEOME RESEARCH

An Automated Proteogenomic Method Uses Mass Spectrometry to Reveal Novel Genes inZea mays

(2013) Natalie E. Castellana et al.   MOLECULAR & CELLULAR PROTEOMICS

Draft genome of the wheat A-genome progenitor Triticum urartu

(2013) Hong-Qing Ling et al.   NATURE

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

(2013) Jizeng Jia et al.   NATURE

Reticulate Evolution of the Rye Genome

(2013) M. M. Martis et al.   PLANT CELL

Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ)

(2013) Martin Mascher et al.   PLANT JOURNAL

Sequence-Based Analysis of Translocations and Inversions in Bread Wheat (Triticum aestivum L.)

(2013) Jian Ma et al.   PLoS One

Reticulated Origin of Domesticated Emmer Wheat Supports a Dynamic Model for the Emergence of Agriculture in the Fertile Crescent

(2013) Peter Civáň et al.   PLoS One

A 4-gigabase physical map unlocks the structure and evolution of the complex genome of Aegilops tauschii, the wheat D-genome progenitor

(2013) M.-C. Luo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-wide comparative diversity uncovers multiple targets of selection for improvement in hexaploid wheat landraces and cultivars

(2013) C. R. Cavanagh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Sequence-Based Mapping of the Polyploid Wheat Genome

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

Genomic expression dominance in allopolyploids

(2012) Ryan A Rapp et al.   BMC BIOLOGY

Genome-wide classification and expression analysis of MYB transcription factor families in rice and Arabidopsis

(2012) Amit Katiyar et al.   BMC GENOMICS

Optimizing illumina next-generation sequencing library preparation for extremely at-biased genomes

(2012) Samuel O Oyola et al.   BMC GENOMICS

Rapid, Repeated, and Clustered Loss of Duplicate Genes in Allopolyploid Plant Populations of Independent Origin

(2012) Richard J.A. Buggs et al.   CURRENT BIOLOGY

Subgenomic analysis of microRNAs in polyploid wheat

(2012) Melda Kantar et al.   FUNCTIONAL & INTEGRATIVE GENOMICS

Transcriptome survey reveals increased complexity of the alternative splicing landscape inArabidopsis

(2012) Yamile Marquez et al.   GENOME RESEARCH

Homoeolog expression bias and expression level dominance in allopolyploid cotton

(2012) M-J Yoo et al.   HEREDITY

Flow cytometric chromosome sorting in plants: The next generation

(2012) Jan Vrána et al.   METHODS

Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres

(2012) Andrew H. Paterson et al.   NATURE

The tomato genome sequence provides insights into fleshy fruit evolution

(2012)   NATURE

Analysis of the bread wheat genome using whole-genome shotgun sequencing

(2012) Rachel Brenchley et al.   NATURE

Reference genome sequence of the model plant Setaria

(2012) Jeffrey L Bennetzen et al.   NATURE BIOTECHNOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Prevalence of gene expression additivity in genetically stable wheat allohexaploids

(2012) Houda Chelaifa et al.   NEW PHYTOLOGIST

PsRobot: a web-based plant small RNA meta-analysis toolbox

(2012) Hua-Jun Wu et al.   NUCLEIC ACIDS RESEARCH

Discovery and development of exome-based, co-dominant single nucleotide polymorphism markers in hexaploid wheat (Triticum aestivumL.)

(2012) Alexandra M. Allen et al.   PLANT BIOTECHNOLOGY JOURNAL

Comparative Analysis of Syntenic Genes in Grass Genomes Reveals Accelerated Rates of Gene Structure and Coding Sequence Evolution in Polyploid Wheat

(2012) E. D. Akhunov et al.   PLANT PHYSIOLOGY

Copy Number Variation Affecting the Photoperiod-B1 and Vernalization-A1 Genes Is Associated with Altered Flowering Time in Wheat (Triticum aestivum)

(2012) Aurora Díaz 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

Biased Gene Fractionation and Dominant Gene Expression among the Subgenomes of Brassica rapa

(2012) Feng Cheng et al.   PLoS One

Sorting the Wheat from the Chaff: Identifying miRNAs in Genomic Survey Sequences of Triticum aestivum Chromosome 1AL

(2012) Stuart J. Lucas et al.   PLoS One

A high-density consensus map of A and B wheat genomes

(2012) Daniela Marone et al.   THEORETICAL AND APPLIED GENETICS

Identification of novel transcripts in annotated genomes using RNA-Seq

(2011) A. Roberts et al.   BIOINFORMATICS

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

Sequence-based marker development in wheat: Advances and applications to breeding

(2011) Etienne Paux et al.   BIOTECHNOLOGY ADVANCES

Multigenic phylogeny and analysis of tree incongruences in Triticeae (Poaceae)

(2011) Juan S Escobar et al.   BMC EVOLUTIONARY BIOLOGY

Reconstruction of the Synthetic W7984 × Opata M85 wheat reference population

(2011) Mark E. Sorrells et al.   GENOME

Ectopic expression of a wheat MYB transcription factor gene, TaMYB73, improves salinity stress tolerance in Arabidopsis thaliana

(2011) Yanan He et al.   JOURNAL OF EXPERIMENTAL BOTANY

Solutions for a cultivated planet

(2011) Jonathan A. Foley et al.   NATURE

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Whole-genome sequencing of multiple Arabidopsis thaliana populations

(2011) Jun Cao et al.   NATURE GENETICS

The Pfam protein families database

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

Sequencing and assembly of low copy and genic regions of isolated Triticum aestivum chromosome arm 7DS

(2011) Paul J. Berkman et al.   PLANT BIOTECHNOLOGY JOURNAL

Frequent Gene Movement and Pseudogene Evolution Is Common to the Large and Complex Genomes of Wheat, Barley, and Their Relatives

(2011) Thomas Wicker 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

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

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

Climate Trends and Global Crop Production Since 1980

(2011) D. B. Lobell et al.   SCIENCE

Sequencing wheat chromosome arm 7BS delimits the 7BS/4AL translocation and reveals homoeologous gene conservation

(2011) Paul J. Berkman et al.   THEORETICAL AND APPLIED GENETICS

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Development of Chromosome-Specific BAC Resources for Genomics of Bread Wheat

(2010) J. Šafář et al.   CYTOGENETIC AND GENOME RESEARCH

Function annotation of the rice transcriptome at single-nucleotide resolution by RNA-seq

(2010) T. Lu et al.   GENOME RESEARCH

Proteogenomics of Pristionchus pacificus reveals distinct proteome structure of nematode models

(2010) N. Borchert et al.   GENOME RESEARCH

Proteogenomics to discover the full coding content of genomes: A computational perspective

(2010) Natalie Castellana et al.   Journal of Proteomics

Genome sequencing and analysis of the model grass Brachypodium distachyon

(2010) John P. Vogel et al.   NATURE

AgBase: supporting functional modeling in agricultural organisms

(2010) Fiona M. McCarthy et al.   NUCLEIC ACIDS RESEARCH

Megabase Level Sequencing Reveals Contrasted Organization and Evolution Patterns of the Wheat Gene and Transposable Element Spaces

(2010) Frédéric Choulet et al.   PLANT CELL

Molecular Basis of Plant Cold Acclimation: Insights Gained from Studying the CBF Cold Response Pathway

(2010) M. F. Thomashow   PLANT PHYSIOLOGY

Targeted mapping of Cdu1, a major locus regulating grain cadmium concentration in durum wheat (Triticum turgidum L. var durum)

(2010) K. Wiebe et al.   THEORETICAL AND APPLIED GENETICS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

HHMMiR: efficient de novo prediction of microRNAs using hierarchical hidden Markov models

(2009) Sabah Kadri et al.   BMC BIOINFORMATICS

A new method to compute K-mer frequencies and its application to annotate large repetitive plant genomes

(2009) Stefan Kurtz et al.   BMC GENOMICS

Discovery and mapping of single feature polymorphisms in wheat using Affymetrix arrays

(2009) Amy N Bernardo et al.   BMC GENOMICS

Identification of conserved Aquilegia coerulea microRNAs and their targets

(2009) Joshua R. Puzey et al.   GENE

Reciprocal Silencing, Transcriptional Bias and Functional Divergence of Homeologs in Polyploid Cotton (Gossypium)

(2009) B. Chaudhary et al.   GENETICS

Chromosomal location of the cadmium uptake gene (Cdu1) in durum wheat

(2009) R. E. Knox et al.   GENOME

Epigenetic silencing of transposable elements: A trade-off between reduced transposition and deleterious effects on neighboring gene expression

(2009) J. D. Hollister et al.   GENOME RESEARCH

ABySS: A parallel assembler for short read sequence data

(2009) J. T. Simpson et al.   GENOME RESEARCH

The Sorghum bicolor genome and the diversification of grasses

(2009) Andrew H. Paterson et al.   NATURE

TriFLDB: A Database of Clustered Full-Length Coding Sequences from Triticeae with Applications to Comparative Grass Genomics

(2009) K. Mochida et al.   PLANT PHYSIOLOGY

Gene Content and Virtual Gene Order of Barley Chromosome 1H

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

The B73 Maize Genome: Complexity, Diversity, and Dynamics

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

Computational identification of microRNAs and their targets in wheat (Triticum aestivum L.)

(2009) YouSheng Han et al.   Science in China. Series C, Life sciences / Chinese Academy of Sciences

A novel resource for genomics of Triticeae: BAC library specific for the short arm of rye (Secale cereale L.) chromosome 1R (1RS)

(2008) Hana Šimková et al.   BMC GENOMICS

Nonadditive Expression of Homoeologous Genes Is Established Upon Polyploidization in Hexaploid Wheat

(2008) M. Pumphrey et al.   GENETICS

Data mining for miRNAs and their targets in the Triticeae

(2008) Ani Dryanova et al.   GENOME

Comparative proteogenomics: Combining mass spectrometry and comparative genomics to analyze multiple genomes

(2008) N. Gupta et al.   GENOME RESEARCH

Structure–function analysis of the NB-ARC domain of plant disease resistance proteins

(2008) Gerben van Ooijen et al.   JOURNAL OF EXPERIMENTAL BOTANY

Spectral Probabilities and Generating Functions of Tandem Mass Spectra: A Strike against Decoy Databases

(2008) Sangtae Kim et al.   JOURNAL OF PROTEOME RESEARCH

An integrated DArT-SSR linkage map of durum wheat

(2008) Paola Mantovani et al.   MOLECULAR BREEDING

Discovery and revision of Arabidopsis genes by proteogenomics

(2008) N. E. Castellana et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Surveying expression level polymorphism and single-feature polymorphism in near-isogenic wheat lines differing for the Yr5 stripe rust resistance locus

(2008) Tristan E. Coram et al.   THEORETICAL AND APPLIED GENETICS

Proteomics studies confirm the presence of alternative protein isoforms on a large scale

(2008) Michael L Tress et al.   GENOME BIOLOGY