Shifting the limits in wheat research and breeding using a fully annotated reference genome

Features of the organization of bread wheat chromosome 5BS based on physical mapping

(2018) Elena A. Salina et al.   BMC GENOMICS

Integrated physical map of bread wheat chromosome arm 7DS to facilitate gene cloning and comparative studies

(2018) Zuzana Tulpová et al.   New Biotechnology

High throughput SNP discovery and genotyping in hexaploid wheat

(2018) Hélène Rimbert et al.   PLoS One

Independent assessment and improvement of wheat genome sequence assemblies using Fosill jumping libraries

(2018) Fu-Hao Lu et al.   GigaScience

The transcriptional landscape of polyploid wheat

(2018) R. H. Ramírez-González et al.   SCIENCE

Leveraging multiple transcriptome assembly methods for improved gene structure annotation

(2018) Luca Venturini et al.   GigaScience

Genome mapping of seed-borne allergens and immunoresponsive proteins in wheat

(2018) Angéla Juhász et al.   Science Advances

An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations

(2017) Bernardo J. Clavijo et al.   GENOME RESEARCH

Rice Expression Database (RED): An integrated RNA-Seq-derived gene expression database for rice

(2017) Lin Xia et al.   Journal of Genetics and Genomics

Exploiting the ZIP4 homologue within the wheat Ph1 locus has identified two lines exhibiting homoeologous crossover in wheat-wild relative hybrids

(2017) María-Dolores Rey et al.   MOLECULAR BREEDING

Exploring the genetics of fertility restoration controlled by Rf1 in common wheat (Triticum aestivum L.) using high-density linkage maps

(2017) Manuel Geyer et al.   MOLECULAR GENETICS AND GENOMICS

Improved maize reference genome with single-molecule technologies

(2017) Yinping Jiao et al.   NATURE

Genome sequence of the progenitor of the wheat D genome Aegilops tauschii

(2017) Ming-Cheng Luo et al.   NATURE

A chromosome conformation capture ordered sequence of the barley genome

(2017) Martin Mascher et al.   NATURE

Genomic prediction unifies animal and plant breeding programs to form platforms for biological discovery

(2017) John M Hickey et al.   NATURE GENETICS

Towards a whole-genome sequence for rye (Secale cerealeL.)

(2017) Eva Bauer et al.   PLANT JOURNAL

Copy number variations ofCBFgenes at theFr-A2locus are essential components of winter hardiness in wheat

(2017) Tobias Würschum et al.   PLANT JOURNAL

Cytological and Transcriptomic Analyses Reveal Important Roles ofCLE19in Pollen Exine Formation

(2017) Shuangshuang Wang et al.   PLANT PHYSIOLOGY

Uncovering hidden variation in polyploid wheat

(2017) Ksenia V. Krasileva et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Wild emmer genome architecture and diversity elucidate wheat evolution and domestication

(2017) Raz Avni et al.   SCIENCE

Physical Map of the Short Arm of Bread Wheat Chromosome 3D

(2017) Kateřina Holušová et al.   Plant Genome

Assembly and Annotation of Transcriptome Provided Evidence of miRNA Mobility between Wheat and Wheat Stem Sawfly

(2017) Halise B. Cagirici et al.   Frontiers in Plant Science

Haplotype Analysis of the Pre-harvest Sprouting Resistance Locus Phs-A1 Reveals a Causal Role of TaMKK3-A in Global Germplasm

(2017) Oluwaseyi Shorinola et al.   Frontiers in Plant Science

Estimating the total number of phosphoproteins and phosphorylation sites in eukaryotic proteomes

(2017) Panayotis Vlastaridis et al.   GigaScience

Rapid breeding and varietal replacement are critical to adaptation of cropping systems in the developing world to climate change

(2017) Gary N. Atlin et al.   Global Food Security-Agriculture Policy Economics and Environment

Construction of a map-based reference genome sequence for barley, Hordeum vulgare L.

(2017) Sebastian Beier et al.   Scientific Data

High density mapping and haplotype analysis of the major stem-solidness locus SSt1 in durum and common wheat

(2017) Kirby T. Nilsen et al.   PLoS One

Ancient WGD events as drivers of key innovations in angiosperms

(2016) Pamela S Soltis et al.   CURRENT OPINION IN PLANT BIOLOGY

ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data

(2016) Jaime Huerta-Cepas et al.   MOLECULAR BIOLOGY AND EVOLUTION

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown

(2016) Mihaela Pertea et al.   Nature Protocols

Using intron position conservation for homology-based gene prediction

(2016) Jens Keilwagen et al.   NUCLEIC ACIDS RESEARCH

Expansion of the Gene Ontology knowledgebase and resources

(2016)   NUCLEIC ACIDS RESEARCH

UniProt: the universal protein knowledgebase

(2016)   NUCLEIC ACIDS RESEARCH

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees

(2016) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

BioNano genome mapping of individual chromosomes supports physical mapping and sequence assembly in complex plant genomes

(2016) Helena Staňková et al.   PLANT BIOTECHNOLOGY JOURNAL

A whole-genome, radiation hybrid mapping resource of hexaploid wheat

(2016) Vijay K. Tiwari et al.   PLANT JOURNAL

Large-scale atlas of microarray data reveals the distinct expression landscape of different tissues in Arabidopsis

(2016) Fei He et al.   PLANT JOURNAL

A Flowering Locus C Homolog Is a Vernalization-Regulated Repressor in Brachypodium and Is Cold Regulated in Wheat

(2016) Neha Sharma et al.   PLANT PHYSIOLOGY

expVIP: a Customizable RNA-seq Data Analysis and Visualization Platform

(2016) Philippa Borrill et al.   PLANT PHYSIOLOGY

Homoeologs: What Are They and How Do We Infer Them?

(2016) Natasha M. Glover et al.   TRENDS IN PLANT 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

De Novo Centromere Formation and Centromeric Sequence Expansion in Wheat and its Wide Hybrids

(2016) Xiang Guo et al.   PLoS Genetics

LHP1 Regulates H3K27me3 Spreading and Shapes the Three-Dimensional Conformation of the Arabidopsis Genome

(2016) Alaguraj Veluchamy et al.   PLoS One

Evolutionary plasticity of restorer-of-fertility-like proteins in rice

(2016) Joanna Melonek et al.   Scientific Reports

A multi-objective optimization approach accurately resolves protein domain architectures

(2015) J.S. Bernardes et al.   BIOINFORMATICS

Functional Gene Networks: R/Bioc package to generate and analyse gene networks derived from functional enrichment and clustering

(2015) Sara Aibar et al.   BIOINFORMATICS

ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes

(2015) Siavash Mirarab et al.   BIOINFORMATICS

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

The physical map of wheat chromosome 5DS revealed gene duplications and small rearrangements

(2015) Bala Ani Akpinar et al.   BMC GENOMICS

A high-resolution physical map integrating an anchored chromosome with the BAC physical maps of wheat chromosome 6B

(2015) Fuminori Kobayashi et al.   BMC GENOMICS

Single-molecule real-time transcript sequencing facilitates common wheat genome annotation and grain transcriptome research

(2015) Lingli Dong et al.   BMC GENOMICS

Root precursors of microRNAs in wild emmer and modern wheats show major differences in response to drought stress

(2015) Bala Ani Akpinar et al.   FUNCTIONAL & INTEGRATIVE GENOMICS

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Genomics as the key to unlocking the polyploid potential of wheat

(2015) Philippa Borrill et al.   NEW PHYTOLOGIST

The draft genome of Tibetan hulless barley reveals adaptive patterns to the high stressful Tibetan Plateau

(2015) Xingquan Zeng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The human transcriptome across tissues and individuals

(2015) M. Mele et al.   SCIENCE

Physical Mapping of Bread Wheat Chromosome 5A: An Integrated Approach

(2015) Delfina Barabaschi et al.   Plant Genome

Deep transcriptome sequencing provides new insights into the structural and functional organization of the wheat genome

(2015) Lise Pingault et al.   GENOME BIOLOGY

Ultra-large alignments using phylogeny-aware profiles

(2015) Nam-phuong D. Nguyen et al.   GENOME BIOLOGY

A haplotype map of allohexaploid wheat reveals distinct patterns of selection on homoeologous genomes

(2015) Katherine W Jordan et al.   GENOME BIOLOGY

A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome

(2015) Jarrod A Chapman et al.   GENOME BIOLOGY

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

The genome of Eucalyptus grandis

(2014) Alexander A. Myburg et al.   NATURE

Whole-genome profiling and shotgun sequencing delivers an anchored, gene-decorated, physical map assembly of bread wheat chromosome 6A

(2014) Naser Poursarebani et al.   PLANT JOURNAL

Ancient hybridizations among the ancestral genomes of bread wheat

(2014) T. Marcussen et al.   SCIENCE

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

(2014) 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

Utilization of deletion bins to anchor and order sequences along the wheat 7B chromosome

(2014) Tatiana Belova et al.   THEORETICAL AND APPLIED GENETICS

Reannotation and extended community resources for the genome of the non-seed plant Physcomitrella patens provide insights into the evolution of plant gene structures and functions

(2013) Andreas D Zimmer et al.   BMC GENOMICS

Genetic analysis and molecular mapping of a new fertility restorer gene Rf8 for Triticum timopheevi cytoplasm in wheat (Triticum aestivum L.) using SSR markers

(2013) Pallavi Sinha et al.   GENETICA

Maize centromeres expand and adopt a uniform size in the genetic background of oat

(2013) K. Wang et al.   GENOME RESEARCH

Hybrid breeding in wheat: technologies to improve hybrid wheat seed production

(2013) Ryan Whitford et al.   JOURNAL OF EXPERIMENTAL BOTANY

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

Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions

(2013) Joshua N Burton et al.   NATURE BIOTECHNOLOGY

DIALIGN at GOBICS—multiple sequence alignment using various sources of external information

(2013) Layal Al Ait et al.   NUCLEIC ACIDS RESEARCH

Physical Mapping Integrated with Syntenic Analysis to Characterize the Gene Space of the Long Arm of Wheat Chromosome 1A

(2013) Stuart J. Lucas et al.   PLoS One

A Physical Map of the Short Arm of Wheat Chromosome 1A

(2013) James Breen 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

Molecular Dating, Evolutionary Rates, and the Age of the Grasses

(2013) P.-A. Christin et al.   SYSTEMATIC BIOLOGY

The physical map of wheat chromosome 1BS provides insights into its gene space organization and evolution

(2013) Dina Raats et al.   GENOME BIOLOGY

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

A physical, genetic and functional sequence assembly of the barley genome

(2012)   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity

(2012) Y. Wang et al.   NUCLEIC ACIDS RESEARCH

The Plant Ontology as a Tool for Comparative Plant Anatomy and Genomic Analyses

(2012) Laurel Cooper et al.   PLANT AND CELL PHYSIOLOGY

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

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

Gene duplication as a mechanism of genomic adaptation to a changing environment

(2012) F. A. Kondrashov   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

TriAnnot: A Versatile and High Performance Pipeline for the Automated Annotation of Plant Genomes

(2012) Philippe Leroy et al.   Frontiers in Plant Science

Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications

(2011) Felix Krueger et al.   BIOINFORMATICS

BamTools: a C++ API and toolkit for analyzing and managing BAM files

(2011) D. W. Barnett et al.   BIOINFORMATICS

Reconstruction of the Synthetic W7984 × Opata M85 wheat reference population

(2011) Mark E. Sorrells et al.   GENOME

Sequence-based physical mapping of complex genomes by whole genome profiling

(2011) J. van Oeveren et al.   GENOME RESEARCH

Genome architectures revealed by tethered chromosome conformation capture and population-based modeling

(2011) Reza Kalhor et al.   NATURE BIOTECHNOLOGY

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

GOSemSim: an R package for measuring semantic similarity among GO terms and gene products

(2010) G. Yu et al.   BIOINFORMATICS

GLay: community structure analysis of biological networks

(2010) G. Su et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

LTC: a novel algorithm to improve the efficiency of contig assembly for physical mapping in complex genomes

(2010) Zeev Frenkel et al.   BMC BIOINFORMATICS

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

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

Efficient Plant Gene Identification Based on Interspecies Mapping of Full-Length cDNAs

(2010) N. Amano et al.   DNA RESEARCH

Genome-Wide Phylogenetic Comparative Analysis of Plant Transcriptional Regulation: A Timeline of Loss, Gain, Expansion, and Correlation with Complexity

(2010) Daniel Lang et al.   Genome Biology and Evolution

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

miRBase: integrating microRNA annotation and deep-sequencing data

(2010) A. Kozomara et al.   NUCLEIC ACIDS RESEARCH

Insertion site-based polymorphism markers open new perspectives for genome saturation and marker-assisted selection in wheat

(2010) Etienne Paux et al.   PLANT BIOTECHNOLOGY JOURNAL

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

(2010) Frédéric Choulet et al.   PLANT CELL

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

KaKs_Calculator 2.0: A Toolkit Incorporating Gamma-Series Methods and Sliding Window Strategies

(2010) Dapeng Wang et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

The Sorghum bicolor genome and the diversification of grasses

(2009) Andrew H. Paterson et al.   NATURE

The evolutionary significance of ancient genome duplications

(2009) Yves Van de Peer et al.   NATURE REVIEWS GENETICS

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

(2009) K. Mochida et al.   PLANT PHYSIOLOGY

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

The B73 Maize Genome: Complexity, Diversity, and Dynamics

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

Comparative genomic analysis of C4 photosynthetic pathway evolution in grasses

(2009) Xiyin Wang et al.   GENOME BIOLOGY

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

A Physical Map of the 1-Gigabase Bread Wheat Chromosome 3B

(2008) E. Paux et al.   SCIENCE

Intergenic Locations of Rice Centromeric Chromatin

(2008) Huihuang Yan et al.   PLOS BIOLOGY

Efficient and Accurate Construction of Genetic Linkage Maps from the Minimum Spanning Tree of a Graph

(2008) Yonghui Wu et al.   PLoS Genetics