Genome sequencing and analysis of the model grass Brachypodium distachyon.

Phytozome: a comparative platform for green plant genomics. Nucleic Acids Res (2011) 11.32

A physical, genetic and functional sequence assembly of the barley genome. Nature (2012) 7.25

Analysis of the bread wheat genome using whole-genome shotgun sequencing. Nature (2012) 5.67

Construction and application for QTL analysis of a Restriction Site Associated DNA (RAD) linkage map in barley. BMC Genomics (2011) 3.42

Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation. Nature (2013) 3.40

Evolution and functional diversification of MIRNA genes. Plant Cell (2011) 3.07

Unlocking the barley genome by chromosomal and comparative genomics. Plant Cell (2011) 3.03

Draft genome of the wheat A-genome progenitor Triticum urartu. Nature (2013) 2.86

Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential. Nat Biotechnol (2012) 2.82

Crop genomics: advances and applications. Nat Rev Genet (2011) 2.72

MicroRNAs as master regulators of the plant NB-LRR defense gene family via the production of phased, trans-acting siRNAs. Genes Dev (2011) 2.66

The genome of the extremophile crucifer Thellungiella parvula. Nat Genet (2011) 2.33

A microRNA superfamily regulates nucleotide binding site-leucine-rich repeats and other mRNAs. Plant Cell (2012) 2.32

Comprehensive sequence analysis of 24,783 barley full-length cDNAs derived from 12 clone libraries. Plant Physiol (2011) 2.04

Comparative genomics of flowering time pathways using Brachypodium distachyon as a model for the temperate grasses. PLoS One (2010) 2.04

Frequent gene movement and pseudogene evolution is common to the large and complex genomes of wheat, barley, and their relatives. Plant Cell (2011) 1.98

Dissecting plant genomes with the PLAZA comparative genomics platform. Plant Physiol (2011) 1.98

Genome-wide distribution and organization of microsatellites in plants: an insight into marker development in Brachypodium. PLoS One (2011) 1.96

Brachypodium as a model for the grasses: today and the future. Plant Physiol (2011) 1.93

Combining SNP discovery from next-generation sequencing data with bulked segregant analysis (BSA) to fine-map genes in polyploid wheat. BMC Plant Biol (2012) 1.88

Setaria viridis: a model for C4 photosynthesis. Plant Cell (2010) 1.72

A 4-gigabase physical map unlocks the structure and evolution of the complex genome of Aegilops tauschii, the wheat D-genome progenitor. Proc Natl Acad Sci U S A (2013) 1.70

Phased, secondary, small interfering RNAs in posttranscriptional regulatory networks. Plant Cell (2013) 1.69

Ancestral grass karyotype reconstruction unravels new mechanisms of genome shuffling as a source of plant evolution. Genome Res (2010) 1.55

Transcriptome sequencing of lentil based on second-generation technology permits large-scale unigene assembly and SSR marker discovery. BMC Genomics (2011) 1.54

Genes identified by visible mutant phenotypes show increased bias toward one of two subgenomes of maize. PLoS One (2011) 1.52

Alternative splicing expands the repertoire of dominant JAZ repressors of jasmonate signaling. Plant J (2010) 1.51

The first draft of the pigeonpea genome sequence. J Plant Biochem Biotechnol (2011) 1.48

Selection patterns on restorer-like genes reveal a conflict between nuclear and mitochondrial genomes throughout angiosperm evolution. Proc Natl Acad Sci U S A (2011) 1.44

Rice pollen hybrid incompatibility caused by reciprocal gene loss of duplicated genes. Proc Natl Acad Sci U S A (2010) 1.43

Theobroma cacao L. pathogenesis-related gene tandem array members show diverse expression dynamics in response to pathogen colonization. BMC Genomics (2016) 1.43

De Novo Transcriptome Analysis for Kentucky Bluegrass Dwarf Mutants Induced by Space Mutation. PLoS One (2016) 1.43

Whole genome comparisons of Fragaria, Prunus and Malus reveal different modes of evolution between Rosaceous subfamilies. BMC Genomics (2012) 1.43

The relationship of recombination rate, genome structure, and patterns of molecular evolution across angiosperms. BMC Evol Biol (2015) 1.41

Transcriptome sequencing of field pea and faba bean for discovery and validation of SSR genetic markers. BMC Genomics (2012) 1.41

Patching gaps in plant genomes results in gene movement and erosion of colinearity. Genome Res (2010) 1.36

Genome-wide analysis of syntenic gene deletion in the grasses. Genome Biol Evol (2012) 1.36

From RNA-seq to large-scale genotyping - genomics resources for rye (Secale cereale L.). BMC Plant Biol (2011) 1.35

Genomics and bioinformatics resources for crop improvement. Plant Cell Physiol (2010) 1.33

Next-generation sequencing of the Chrysanthemum nankingense (Asteraceae) transcriptome permits large-scale unigene assembly and SSR marker discovery. PLoS One (2013) 1.29

Engineering of a synthetic electron conduit in living cells. Proc Natl Acad Sci U S A (2010) 1.29

Regulation of FLOWERING LOCUS T by a microRNA in Brachypodium distachyon. Plant Cell (2013) 1.28

Advances in omics and bioinformatics tools for systems analyses of plant functions. Plant Cell Physiol (2011) 1.28

Gene body methylation is conserved between plant orthologs and is of evolutionary consequence. Proc Natl Acad Sci U S A (2013) 1.28

Genetic dissection of the biotic stress response using a genome-scale gene network for rice. Proc Natl Acad Sci U S A (2011) 1.27

Supersplat--spliced RNA-seq alignment. Bioinformatics (2010) 1.27

Back to the sea twice: identifying candidate plant genes for molecular evolution to marine life. BMC Evol Biol (2011) 1.25

Global profiling of rice and poplar transcriptomes highlights key conserved circadian-controlled pathways and cis-regulatory modules. PLoS One (2011) 1.25

Plant immune responses against viruses: how does a virus cause disease? Plant Cell (2013) 1.24

Analysis of plant diversity with retrotransposon-based molecular markers. Heredity (Edinb) (2010) 1.24

Seventy million years of concerted evolution of a homoeologous chromosome pair, in parallel, in major Poaceae lineages. Plant Cell (2011) 1.23

Whole-genome sequencing of Oryza brachyantha reveals mechanisms underlying Oryza genome evolution. Nat Commun (2013) 1.22

The WRKY transcription factor family in Brachypodium distachyon. BMC Genomics (2012) 1.20

Sequencing of 6.7 Mb of the melon genome using a BAC pooling strategy. BMC Plant Biol (2010) 1.20

Generation and characterization of the Western Regional Research Center Brachypodium T-DNA insertional mutant collection. PLoS One (2012) 1.19

Comparative analysis of syntenic genes in grass genomes reveals accelerated rates of gene structure and coding sequence evolution in polyploid wheat. Plant Physiol (2012) 1.19

Genome-wide analysis of alternative splicing landscapes modulated during plant-virus interactions in Brachypodium distachyon. Plant Cell (2015) 1.19

Genome-wide screening and functional analysis identify a large number of long noncoding RNAs involved in the sexual reproduction of rice. Genome Biol (2014) 1.18

An integrative approach to the identification of Arabidopsis and rice genes involved in xylan and secondary wall development. PLoS One (2010) 1.17

Investigation of terpene diversification across multiple sequenced plant genomes. Proc Natl Acad Sci U S A (2014) 1.16

Molecular characterization of 60 isolated wheat MYB genes and analysis of their expression during abiotic stress. J Exp Bot (2011) 1.15

Gene space dynamics during the evolution of Aegilops tauschii, Brachypodium distachyon, Oryza sativa, and Sorghum bicolor genomes. Mol Biol Evol (2011) 1.14

CYP701A8: a rice ent-kaurene oxidase paralog diverted to more specialized diterpenoid metabolism. Plant Physiol (2012) 1.14

Interaction of photoperiod and vernalization determines flowering time of Brachypodium distachyon. Plant Physiol (2013) 1.13

Expression, splicing, and evolution of the myosin gene family in plants. Plant Physiol (2011) 1.13

Analysis of expressed sequence tags generated from full-length enriched cDNA libraries of melon. BMC Genomics (2011) 1.13

Wheat grain development is characterized by remarkable trehalose 6-phosphate accumulation pregrain filling: tissue distribution and relationship to SNF1-related protein kinase1 activity. Plant Physiol (2011) 1.12

Disruption of signaling in a fungal-grass symbiosis leads to pathogenesis. Plant Physiol (2010) 1.12

Sequencing of chloroplast genomes from wheat, barley, rye and their relatives provides a detailed insight into the evolution of the Triticeae tribe. PLoS One (2014) 1.11

Brachypodium distachyon: a new pathosystem to study Fusarium head blight and other Fusarium diseases of wheat. BMC Plant Biol (2011) 1.11

Brachypodium distachyon grain: identification and subcellular localization of storage proteins. J Exp Bot (2010) 1.11

A 3,000-loci transcription map of chromosome 3B unravels the structural and functional features of gene islands in hexaploid wheat. Plant Physiol (2011) 1.10

Endosperm development in Brachypodium distachyon. J Exp Bot (2010) 1.10

XAX1 from glycosyltransferase family 61 mediates xylosyltransfer to rice xylan. Proc Natl Acad Sci U S A (2012) 1.09

The Mediator complex in plants: structure, phylogeny, and expression profiling of representative genes in a dicot (Arabidopsis) and a monocot (rice) during reproduction and abiotic stress. Plant Physiol (2011) 1.09

First survey of the wheat chromosome 5A composition through a next generation sequencing approach. PLoS One (2011) 1.09

Mechanisms of chromosome number evolution in yeast. PLoS Genet (2011) 1.09

De novo assembly and characterization of the Barnyardgrass (Echinochloa crus-galli) transcriptome using next-generation pyrosequencing. PLoS One (2013) 1.08

A comprehensive overview of grain development in Brachypodium distachyon variety Bd21. J Exp Bot (2011) 1.08

A role for SR proteins in plant stress responses. Plant Signal Behav (2011) 1.08

The pineapple genome and the evolution of CAM photosynthesis. Nat Genet (2015) 1.08

RNA-seq in grain unveils fate of neo- and paleopolyploidization events in bread wheat (Triticum aestivum L.). Genome Biol (2011) 1.07

Implementing a rational and consistent nomenclature for serine/arginine-rich protein splicing factors (SR proteins) in plants. Plant Cell (2010) 1.07

An integrated physical, genetic and cytogenetic map of Brachypodium distachyon, a model system for grass research. PLoS One (2010) 1.07

SNP discovery and chromosome anchoring provide the first physically-anchored hexaploid oat map and reveal synteny with model species. PLoS One (2013) 1.07

Global landscape of a co-expressed gene network in barley and its application to gene discovery in Triticeae crops. Plant Cell Physiol (2011) 1.06

Synteny between Brachypodium distachyon and Hordeum vulgare as revealed by FISH. Chromosome Res (2010) 1.06

Integrating cereal genomics to support innovation in the Triticeae. Funct Integr Genomics (2012) 1.06

Widespread natural variation of DNA methylation within angiosperms. Genome Biol (2016) 1.06

Multigenic phylogeny and analysis of tree incongruences in Triticeae (Poaceae). BMC Evol Biol (2011) 1.05

Evolutionary history of tall fescue morphotypes inferred from molecular phylogenetics of the Lolium-Festuca species complex. BMC Evol Biol (2010) 1.05

BambooGDB: a bamboo genome database with functional annotation and an analysis platform. Database (Oxford) (2014) 1.05

Transcriptome-scale homoeolog-specific transcript assemblies of bread wheat. BMC Genomics (2012) 1.05

Genome-wide identification and analysis of MAPK and MAPKK gene families in Brachypodium distachyon. PLoS One (2012) 1.05

Comparative genomic analysis of soybean flowering genes. PLoS One (2012) 1.04

The perennial ryegrass GenomeZipper: targeted use of genome resources for comparative grass genomics. Plant Physiol (2012) 1.04

Dichotomy in the NRT gene families of dicots and grass species. PLoS One (2010) 1.04

Evolution and taxonomic split of the model grass Brachypodium distachyon. Ann Bot (2012) 1.04

Genome dynamics explain the evolution of flowering time CCT domain gene families in the Poaceae. PLoS One (2012) 1.03

The Spirodela polyrhiza genome reveals insights into its neotenous reduction fast growth and aquatic lifestyle. Nat Commun (2014) 1.03

The map-based sequence of the rice genome. Nature (2005) 24.17

The Sorghum bicolor genome and the diversification of grasses. Nature (2009) 14.62

A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana. Genes Dev (2006) 11.71

Cereal genome evolution. Grasses, line up and form a circle. Curr Biol (1995) 8.33

Genome-wide analysis of NBS-LRR-encoding genes in Arabidopsis. Plant Cell (2003) 7.66

Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics. Proc Natl Acad Sci U S A (2004) 6.66

Rapid recent growth and divergence of rice nuclear genomes. Proc Natl Acad Sci U S A (2004) 5.35

Evolutionary history of the grasses. Plant Physiol (2001) 5.22

Pack-MULE transposable elements mediate gene evolution in plants. Nature (2004) 5.13

Gene duplication and exon shuffling by helitron-like transposons generate intraspecies diversity in maize. Nat Genet (2005) 4.47

The Rice Annotation Project Database (RAP-DB): 2008 update. Nucleic Acids Res (2007) 4.23

LTR_STRUC: a novel search and identification program for LTR retrotransposons. Bioinformatics (2003) 4.04

Do Plants Have a One-Way Ticket to Genomic Obesity? Plant Cell (1997) 3.86

Physical and genetic structure of the maize genome reflects its complex evolutionary history. PLoS Genet (2007) 3.66

Brachypodium distachyon. A new model system for functional genomics in grasses. Plant Physiol (2001) 3.42

A chromosome bin map of 16,000 expressed sequence tag loci and distribution of genes among the three genomes of polyploid wheat. Genetics (2004) 3.37

Genetics and geography of wild cereal domestication in the near east. Nat Rev Genet (2002) 3.30

Identification and characterization of shared duplications between rice and wheat provide new insight into grass genome evolution. Plant Cell (2008) 3.25

Unique aspects of the grass cell wall. Curr Opin Plant Biol (2008) 2.91

Nuclear DNA amounts in angiosperms: progress, problems and prospects. Ann Bot (2005) 2.57

High-efficiency Agrobacterium-mediated transformation of Brachypodium distachyon inbred line Bd21-3. Plant Cell Rep (2007) 2.47

A 1,000-loci transcript map of the barley genome: new anchoring points for integrative grass genomics. Theor Appl Genet (2007) 2.44

Genome comparisons reveal a dominant mechanism of chromosome number reduction in grasses and accelerated genome evolution in Triticeae. Proc Natl Acad Sci U S A (2009) 2.32

The nuclear genome of Brachypodium distachyon: analysis of BAC end sequences. Funct Integr Genomics (2007) 1.97

Comparison of orthologous loci from small grass genomes Brachypodium and rice: implications for wheat genomics and grass genome annotation. Plant J (2007) 1.96

Agrobacterium-mediated transformation of the temperate grass Brachypodium distachyon (genotype Bd21) for T-DNA insertional mutagenesis. Plant Biotechnol J (2007) 1.82

Genome-wide comparative analysis of copia retrotransposons in Triticeae, rice, and Arabidopsis reveals conserved ancient evolutionary lineages and distinct dynamics of individual copia families. Genome Res (2007) 1.78

EST sequencing and phylogenetic analysis of the model grass Brachypodium distachyon. Theor Appl Genet (2006) 1.77

Construction and characterization of two BAC libraries from Brachypodium distachyon, a new model for grass genomics. Genome (2006) 1.77

Development of SSR markers and analysis of diversity in Turkish populations of Brachypodium distachyon. BMC Plant Biol (2009) 1.51

Applications of ultra-high-throughput sequencing. Methods Mol Biol (2009) 1.51

The billion-ton biofuels vision. Science (2006) 1.50

An SSR-based genetic linkage map of the model grass Brachypodium distachyon. Genome (2010) 1.41

Comparative analyses reveal high levels of conserved colinearity between the finger millet and rice genomes. Theor Appl Genet (2007) 1.36

A BAC-based physical map of Brachypodium distachyon and its comparative analysis with rice and wheat. BMC Genomics (2009) 1.30

Molecular, morphological, and cytological analysis of diverse Brachypodium distachyon inbred lines. Genome (2009) 1.28

Variability, recombination, and mosaic evolution of the barley BARE-1 retrotransposon. J Mol Evol (2005) 1.20

Sixty million years in evolution of soft grain trait in grasses: emergence of the softness locus in the common ancestor of Pooideae and Ehrhartoideae, after their divergence from Panicoideae. Mol Biol Evol (2009) 1.18

A recommendation for naming transcription factor proteins in the grasses. Plant Physiol (2009) 1.17

Analysis of intraspecies diversity in wheat and barley genomes identifies breakpoints of ancient haplotypes and provides insight into the structure of diploid and hexaploid triticeae gene pools. Plant Physiol (2008) 1.11