The repetitive DNA landscape in Avena (Poaceae): chromosome and genome evolution defined by major repeat classes in whole-genome sequence reads

Oat evolution revealed in the maternal lineages of 25 Avena species

(2018) Yong-Bi Fu   Scientific Reports

OUP accepted manuscript

(2018)   ANNALS OF BOTANY

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

(2018) et al.   SCIENCE

Replicative and non-replicative mechanisms in the formation of clustered CNVs are indicated by whole genome characterization

(2018) Lusine Nazaryan-Petersen et al.   PLoS Genetics

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

(2017) Ming-Cheng Luo et al.   NATURE

Convergent adaptive evolution in marginal environments: unloading transposable elements as a common strategy among mangrove genomes

(2017) Haomin Lyu et al.   NEW PHYTOLOGIST

Successive evolutionary steps drove Pooideae grasses from tropical to temperate regions

(2017) Jinshun Zhong et al.   NEW PHYTOLOGIST

Diverse genome organization following 13 independent mesopolyploid events in Brassicaceae contrasts with convergent patterns of gene retention

(2017) Terezie Mandáková et al.   PLANT JOURNAL

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

(2017) Eva Bauer et al.   PLANT JOURNAL

Genome-wide chromatin mapping with size resolution reveals a dynamic sub-nucleosomal landscape in Arabidopsis

(2017) Daniel Antony Pass et al.   PLoS Genetics

The repetitive landscape of the 5100 Mbp barley genome

(2017) Thomas Wicker et al.   Mobile DNA

Revisiting ancestral polyploidy in plants

(2017) Colin Ruprecht et al.   Science Advances

Unraveling the evolutionary dynamics of ancient and recent polyploidization events in Avena (Poaceae)

(2017) Qing Liu et al.   Scientific Reports

Impact and insights from ancient repetitive elements in plant genomes

(2016) Florian Maumus et al.   CURRENT OPINION IN PLANT BIOLOGY

Genome size variation in the genus Avena

(2016) Honghai Yan et al.   GENOME

Reconstruction of ancestral chromosome architecture and gene repertoire reveals principles of genome evolution in a model yeast genus

(2016) Nikolaos Vakirlis et al.   GENOME RESEARCH

Repetitive sequence analysis and karyotyping reveals centromere-associated DNA sequences in radish (Raphanus sativus L.)

(2015) Qunyan He et al.   BMC PLANT BIOLOGY

Repetitive DNA in eukaryotic genomes

(2015) Maria Assunta Biscotti et al.   CHROMOSOME RESEARCH

The Contributions of Transposable Elements to the Structure, Function, and Evolution of Plant Genomes

(2014) Jeffrey L. Bennetzen et al.   Annual Review of Plant Biology

Differential genome evolution and speciation of Coix lacryma-jobi L. and Coix aquatica Roxb. hybrid guangxi revealed by repetitive sequence analysis and fine karyotyping

(2014) Zexi Cai et al.   BMC GENOMICS

RNA-directed DNA methylation: an epigenetic pathway of increasing complexity

(2014) Marjori A. Matzke et al.   NATURE REVIEWS GENETICS

Ecological and evolutionary significance of genomic GC content diversity in monocots

(2014) Petr Šmarda et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RepeatExplorer: a Galaxy-based web server for genome-wide characterization of eukaryotic repetitive elements from next-generation sequence reads

(2013) P. Novak et al.   BIOINFORMATICS

SNP Discovery and Chromosome Anchoring Provide the First Physically-Anchored Hexaploid Oat Map and Reveal Synteny with Model Species

(2013) Rebekah E. Oliver et al.   PLoS One

Nucleosomes and centromeric DNA packaging

(2013) J. S. Heslop-Harrison et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse et al.   BIOINFORMATICS

The tomato genome sequence provides insights into fleshy fruit evolution

(2012)   NATURE

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

(2011) Guillaume Marçais et al.   BIOINFORMATICS

Next Generation Sequencing Reveals Genome Downsizing in Allotetraploid Nicotiana tabacum, Predominantly through the Elimination of Paternally Derived Repetitive DNAs

(2011) S. Renny-Byfield et al.   MOLECULAR BIOLOGY AND EVOLUTION

The 1.688 Repetitive DNA of Drosophila: Concerted Evolution at Different Genomic Scales and Association with Genes

(2011) Gustavo C. S. Kuhn et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genome sequence and analysis of the tuber crop potato

(2011) Xun Xu et al.   NATURE

Repetitive DNA and next-generation sequencing: computational challenges and solutions

(2011) Todd J. Treangen et al.   NATURE REVIEWS GENETICS

Organisation of the plant genome in chromosomes

(2011) J. S. Pat Heslop-Harrison et al.   PLANT JOURNAL

Repetitive Elements May Comprise Over Two-Thirds of the Human Genome

(2011) A. P. Jason de Koning et al.   PLoS Genetics

Global sequence characterization of rice centromeric satellite based on oligomer frequency analysis in large-scale sequencing data

(2010) J. Macas et al.   BIOINFORMATICS

Graph-based clustering and characterization of repetitive sequences in next-generation sequencing data

(2010) Petr Novák et al.   BMC BIOINFORMATICS

Repetitive part of the banana (Musa acuminata) genome investigated by low-depth 454 sequencing

(2010) Eva Hřibová et al.   BMC PLANT BIOLOGY

Parallelism in Evolution of Highly Repetitive DNAs in Sibling Species

(2010) B. Mravinac et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genome sequencing and analysis of the model grass Brachypodium distachyon

(2010) John P. Vogel et al.   NATURE

A new chromosome nomenclature system for oat (Avena sativa L. and A. byzantina C. Koch) based on FISH analysis of monosomic lines

(2010) M. J. Sanz et al.   THEORETICAL AND APPLIED GENETICS

Mobile DNA and evolution in the 21st century

(2010) James A Shapiro   Mobile DNA

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

The DNA-encoded nucleosome organization of a eukaryotic genome

(2008) Noam Kaplan et al.   NATURE

The CACTA transposonBot1played a major role inBrassicagenome divergence and gene proliferation

(2008) Karine Alix et al.   PLANT JOURNAL