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

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

Sequencing and comparative analyses of Aegilops tauschii chromosome arm 3DS reveal rapid evolution of Triticeae genomes

(2017) Jingzhong Xie et al.   Journal of Genetics and Genomics

A chromosome conformation capture ordered sequence of the barley genome

(2017) Martin Mascher et al.   NATURE

RGAugury: a pipeline for genome-wide prediction of resistance gene analogs (RGAs) in plants

(2016) Pingchuan Li et al.   BMC GENOMICS

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

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

Rapid evolutionary dynamics in a 2.8-Mb chromosomal region containing multiple prolamin and resistance gene families inAegilops tauschii

(2016) Lingli Dong et al.   PLANT JOURNAL

Tools and pipelines for BioNano data: molecule assembly pipeline and FASTA super scaffolding tool

(2015) Jennifer M. Shelton et al.   BMC GENOMICS

Rapid detection of structural variation in a human genome using nanochannel-based genome mapping technology

(2015) Hongzhi Cao et al.   GigaScience

HelitronScanner uncovers a large overlooked cache of Helitron transposons in many plant genomes

(2014) W. Xiong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2014) et al.   SCIENCE

MCScanX-transposed: detecting transposed gene duplications based on multiple colinearity scans

(2013) Yupeng Wang et al.   BIOINFORMATICS

The MaSuRCA genome assembler

(2013) Aleksey V. Zimin et al.   BIOINFORMATICS

The Norway spruce genome sequence and conifer genome evolution

(2013) Björn Nystedt et al.   NATURE

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

(2013) Jizeng Jia et al.   NATURE

Aegilops tauschiisingle nucleotide polymorphisms shed light on the origins of wheat D-genome genetic diversity and pinpoint the geographic origin of hexaploid wheat

(2013) Jirui Wang et al.   NEW PHYTOLOGIST

Insular Organization of Gene Space in Grass Genomes

(2013) Andrea Gottlieb 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

The Gene Sr33, an Ortholog of Barley Mla Genes, Encodes Resistance to Wheat Stem Rust Race Ug99

(2013) S. Periyannan et al.   SCIENCE

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

(2012) Ernest T Lam et al.   NATURE BIOTECHNOLOGY

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

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

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

Large and linked in scientific publishing

(2012) Laurie Goodman et al.   GigaScience

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

Gene Space Dynamics During the Evolution of Aegilops tauschii, Brachypodium distachyon, Oryza sativa, and Sorghum bicolor Genomes

(2011) A. N. Massa et al.   MOLECULAR BIOLOGY AND EVOLUTION

Targeted Identification of Short Interspersed Nuclear Element Families Shows Their Widespread Existence and Extreme Heterogeneity in Plant Genomes

(2011) Torsten Wenke et al.   PLANT CELL

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

Assembly of large genomes using second-generation sequencing

(2010) M. C. Schatz et al.   GENOME RESEARCH

Genome sequencing and analysis of the model grass Brachypodium distachyon

(2010) John P. Vogel et al.   NATURE

MITE-Hunter: a program for discovering miniature inverted-repeat transposable elements from genomic sequences

(2010) Y. Han et al.   NUCLEIC ACIDS RESEARCH

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

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

(2009) K. Mochida et al.   PLANT PHYSIOLOGY

Genome comparisons reveal a dominant mechanism of chromosome number reduction in grasses and accelerated genome evolution in Triticeae

(2009) M. C. Luo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The B73 Maize Genome: Complexity, Diversity, and Dynamics

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

Exceptional Diversity, Non-Random Distribution, and Rapid Evolution of Retroelements in the B73 Maize Genome

(2009) Regina S. Baucom et al.   PLoS Genetics

Univariate Distribution Relationships

(2008) Lawrence M Leemis et al.   AMERICAN STATISTICIAN

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

(2008) David Ellinghaus et al.   BMC BIOINFORMATICS