Genome sequence of the progenitor of wheat A subgenome Triticum urartu

Hybrid assembly of the large and highly repetitive genome ofAegilops tauschii, a progenitor of bread wheat, with the MaSuRCA mega-reads algorithm

(2017) Aleksey V. Zimin et al.   GENOME RESEARCH

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

Reconstructing the genome of the most recent common ancestor of flowering plants

(2017) Florent Murat et al.   NATURE GENETICS

iTAK: A Program for Genome-wide Prediction and Classification of Plant Transcription Factors, Transcriptional Regulators, and Protein Kinases

(2016) Yi Zheng et al.   Molecular Plant

Haplotyping germline and cancer genomes with high-throughput linked-read sequencing

(2016) Grace X Y Zheng et al.   NATURE BIOTECHNOLOGY

Physiological, biochemical and proteomics analysis reveals the adaptation strategies of the alpine plant Potentilla saundersiana at altitude gradient of the Northwestern Tibetan Plateau

(2015) Lan Ma et al.   Journal of Proteomics

proovread : large-scale high-accuracy PacBio correction through iterative short read consensus

(2014) Thomas Hackl et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

A maize wall-associated kinase confers quantitative resistance to head smut

(2014) Weiliang Zuo et al.   NATURE GENETICS

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

Structural and functional partitioning of bread wheat chromosome 3B

(2014) F. Choulet et al.   SCIENCE

The MaSuRCA genome assembler

(2013) Aleksey V. Zimin et al.   BIOINFORMATICS

An evaluation of the PacBio RS platform for sequencing and de novo assembly of a chloroplast genome

(2013) Marco Ferrarini et al.   BMC GENOMICS

Shared Subgenome Dominance Following Polyploidization Explains Grass Genome Evolutionary Plasticity from a Seven Protochromosome Ancestor with 16K Protogenes

(2013) Florent Murat et al.   Genome Biology and Evolution

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

Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory

(2012) Mark J Chaisson et al.   BMC BIOINFORMATICS

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

(2012) Rachel Brenchley et al.   NATURE

Genome mapping on nanochannel arrays for structural variation analysis and sequence assembly

(2012) Ernest T Lam et al.   NATURE BIOTECHNOLOGY

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

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

Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology

(2012) Adam C. English et al.   PLoS One

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

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

MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

(2011) K. Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

Domestication evolution, genetics and genomics in wheat

(2011) Junhua H. Peng et al.   MOLECULAR BREEDING

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Scaffolding pre-assembled contigs using SSPACE

(2010) Marten Boetzer et al.   BIOINFORMATICS

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

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

Infernal 1.0: inference of RNA alignments

(2009) E. P. Nawrocki et al.   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

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

The B73 Maize Genome: Complexity, Diversity, and Dynamics

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

LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons

(2008) David Ellinghaus et al.   BMC BIOINFORMATICS

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

(2008) J. Salse et al.   PLANT CELL

The plant B3 superfamily

(2008) K SWAMINATHAN et al.   TRENDS IN PLANT SCIENCE

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

(2008) Yonghui Wu et al.   PLoS Genetics