Prospects of pan-genomics in barley

Core Hunter 3: flexible core subset selection

(2018) Herman De Beukelaer et al.   BMC BIOINFORMATICS

Small RNA-based prediction of hybrid performance in maize

(2018) Felix Seifert et al.   BMC GENOMICS

Pan-genome analysis highlights the extent of genomic variation in cultivated and wild rice

(2018) Qiang Zhao et al.   NATURE GENETICS

Targeted resequencing reveals genomic signatures of barley domestication

(2018) Artem Pankin et al.   NEW PHYTOLOGIST

MUMmer4: A fast and versatile genome alignment system

(2018) Guillaume Marçais et al.   PLoS Computational Biology

Genomic variation in 3,010 diverse accessions of Asian cultivated rice

(2018) Wensheng Wang et al.   NATURE

Discovery of multi-megabase polymorphic inversions by chromosome conformation capture sequencing in large-genome plant species

(2018) Axel Himmelbach et al.   PLANT JOURNAL

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

(2018) et al.   SCIENCE

Genebank genomics highlights the diversity of a global barley collection

(2018) Sara G. Milner et al.   NATURE GENETICS

Direct determination of diploid genome sequences

(2017) Neil I. Weisenfeld et al.   GENOME RESEARCH

A chromosome conformation capture ordered sequence of the barley genome

(2017) Martin Mascher et al.   NATURE

Characterization of Rph24: A Gene Conferring Adult Plant Resistance to Puccinia hordei in Barley

(2017) Laura A. Ziems et al.   PHYTOPATHOLOGY

Assembly and analysis of a qingke reference genome demonstrate its close genetic relation to modern cultivated barley

(2017) Fei Dai et al.   PLANT BIOTECHNOLOGY JOURNAL

The pangenome of hexaploid bread wheat

(2017) Juan D. Montenegro et al.   PLANT JOURNAL

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

(2017) Eva Bauer et al.   PLANT JOURNAL

Wild emmer genome architecture and diversity elucidate wheat evolution and domestication

(2017) Raz Avni et al.   SCIENCE

Extensive gene content variation in the Brachypodium distachyon pan-genome correlates with population structure

(2017) Sean P. Gordon et al.   Nature Communications

Development and Evaluation of a Barley 50k iSelect SNP Array

(2017) Micha M. Bayer et al.   Frontiers in Plant Science

The first near-complete assembly of the hexaploid bread wheat genome, Triticum aestivum

(2017) Aleksey V Zimin et al.   GigaScience

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

(2017) Sebastian Beier et al.   Scientific Data

Chromosome-scale shotgun assembly using an in vitro method for long-range linkage

(2016) Nicholas H. Putnam et al.   GENOME RESEARCH

Exome sequencing of geographically diverse barley landraces and wild relatives gives insights into environmental adaptation

(2016) Joanne Russell et al.   NATURE GENETICS

novoBreak: local assembly for breakpoint detection in cancer genomes

(2016) Zechen Chong et al.   NATURE METHODS

Multiplex sequencing of bacterial artificial chromosomes for assembling complex plant genomes

(2016) Sebastian Beier et al.   PLANT BIOTECHNOLOGY JOURNAL

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

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

Evolution of the Grain Dispersal System in Barley

(2015) Mohammad Pourkheirandish et al.   CELL

Structure and Function of the Bacterial Root Microbiota in Wild and Domesticated Barley

(2015) Davide Bulgarelli et al.   Cell Host & Microbe

Bulbosum to Go: A Toolbox to Utilize Hordeum vulgare / bulbosum Introgressions for Breeding and Beyond

(2015) Neele Wendler et al.   Molecular Plant

Barley: a translational model for adaptation to climate change

(2015) Ian K. Dawson 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

High-resolution genetic mapping of maize pan-genome sequence anchors

(2015) Fei Lu et al.   Nature Communications

GBIS: the information system of the German Genebank

(2015) Markus Oppermann et al.   Database-The Journal of Biological Databases and Curation

ANGSD: Analysis of Next Generation Sequencing Data

(2014) Thorfinn Sand Korneliussen et al.   BMC BIOINFORMATICS

An evaluation of genotyping by sequencing (GBS) to map the Breviaristatum-e (ari-e) locus in cultivated barley

(2014) Hui Liu et al.   BMC GENOMICS

Evolutionary History of Wild Barley (Hordeum vulgare subsp. spontaneum) Analyzed Using Multilocus Sequence Data and Paleodistribution Modeling

(2014) Sabine S. Jakob et al.   Genome Biology and Evolution

Epigenetics in health and disease: heralding the EWAS era

(2014) Therese M Murphy et al.   LANCET

DNA methylation and body-mass index: a genome-wide analysis

(2014) Katherine J Dick et al.   LANCET

De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits

(2014) Ying-hui Li et al.   NATURE BIOTECHNOLOGY

Insights into the Maize Pan-Genome and Pan-Transcriptome

(2014) C. N. Hirsch et al.   PLANT CELL

The USDA Barley Core Collection: Genetic Diversity, Population Structure, and Potential for Genome-Wide Association Studies

(2014) María Muñoz-Amatriaín et al.   PLoS One

Structural and functional partitioning of bread wheat chromosome 3B

(2014) F. Choulet et al.   SCIENCE

Extensive Error in the Number of Genes Inferred from Draft Genome Assemblies

(2014) James F. Denton et al.   PLoS Computational Biology

High-throughput genome scaffolding from in vivo DNA interaction frequency

(2013) Noam Kaplan et al.   NATURE BIOTECHNOLOGY

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

(2013) Joshua N Burton et al.   NATURE BIOTECHNOLOGY

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

Copy number variation detection and genotyping from exome sequence data

(2012) N. Krumm et al.   GENOME RESEARCH

The global plant council: Increasing the impact of plant research to meet global challenges

(2012) Wilhelm Gruissem et al.   JOURNAL OF PLANT BIOLOGY

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

(2012)   NATURE

A map of rice genome variation reveals the origin of cultivated rice

(2012) Xuehui Huang et al.   NATURE

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

(2012) Ernest T Lam et al.   NATURE BIOTECHNOLOGY

Natural variation in a homolog of Antirrhinum CENTRORADIALIS contributed to spring growth habit and environmental adaptation in cultivated barley

(2012) Jordi Comadran et al.   NATURE GENETICS

Genomic and metabolic prediction of complex heterotic traits in hybrid maize

(2012) Christian Riedelsheimer et al.   NATURE GENETICS

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

Quality of core collections for effective utilisation of genetic resources review, discussion and interpretation

(2012) T. L. Odong et al.   THEORETICAL AND APPLIED GENETICS

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

(2012) Ruibang Luo et al.   GigaScience

Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes

(2011) Xun Xu et al.   NATURE BIOTECHNOLOGY

Epigenome-wide association studies for common human diseases

(2011) Vardhman K. Rakyan et al.   NATURE REVIEWS GENETICS

Analysis of >1000 single nucleotide polymorphisms in geographically matched samples of landrace and wild barley indicates secondary contact and chromosome-level differences in diversity around domestication genes

(2011) Joanne Russell et al.   NEW PHYTOLOGIST

Brachypodium as a Model for the Grasses: Today and the Future

(2011) Jelena Brkljacic et al.   PLANT PHYSIOLOGY

A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species

(2011) Robert J. Elshire et al.   PLoS One

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

Promoters of the Barley Germin-Like GER4 Gene Cluster Enable Strong Transgene Expression in Response to Pathogen Attack

(2010) A. Himmelbach et al.   PLANT CELL

High-quality draft assemblies of mammalian genomes from massively parallel sequence data

(2010) S. Gnerre et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CBF gene copy number variation at Frost Resistance-2 is associated with levels of freezing tolerance in temperate-climate cereals

(2010) Andrea K. Knox et al.   THEORETICAL AND APPLIED GENETICS

Correcting for ascertainment bias in the inference of population structure

(2009) Gilles Guillot et al.   BIOINFORMATICS

Characterization of six human disease-associated inversion polymorphisms

(2009) Francesca Antonacci et al.   HUMAN MOLECULAR GENETICS

Strong correlation of wild barley (Hordeum spontaneum) population structure with temperature and precipitation variation

(2009) S. HÜBNER et al.   MOLECULAR ECOLOGY

The Sorghum bicolor genome and the diversification of grasses

(2009) Andrew H. Paterson et al.   NATURE

The International Barley Sequencing Consortium--At the Threshold of Efficient Access to the Barley Genome

(2009) D. Schulte 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

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS