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

Geography and end use drive the diversification of worldwide winter rye populations

(2016) Florence Parat et al.   MOLECULAR ECOLOGY

Multiplex sequencing of bacterial artificial chromosomes for assembling complex plant genomes

(2016) Sebastian Beier et al.   PLANT BIOTECHNOLOGY JOURNAL

Model training across multiple breeding cycles significantly improves genomic prediction accuracy in rye (Secale cereale L.)

(2016) Hans-Jürgen Auinger et al.   THEORETICAL AND APPLIED GENETICS

PGP repository: a plant phenomics and genomics data publication infrastructure

(2016) Daniel Arend et al.   Database-The Journal of Biological Databases and Curation

transPLANT Resources for Triticeae Genomic Data

(2016) Manuel Spannagl et al.   Plant Genome

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Combined de novo and genome guided assembly and annotation of the Pinus patula juvenile shoot transcriptome

(2015) Erik A. Visser et al.   BMC GENOMICS

PGSB PlantsDB: updates to the database framework for comparative plant genome research

(2015) Manuel Spannagl et al.   NUCLEIC ACIDS RESEARCH

Understanding and utilizing crop genome diversity via high-resolution genotyping

(2015) Kai Voss-Fels et al.   PLANT BIOTECHNOLOGY JOURNAL

High-density SNP genotyping array for hexaploid wheat and its secondary and tertiary gene pool

(2015) Mark O. Winfield et al.   PLANT BIOTECHNOLOGY JOURNAL

Detection of donor effects in a rye introgression population with genome-wide prediction

(2015) Gregory S. Mahone et al.   PLANT BREEDING

De novo and comparative transcriptome analysis of cultivated and wild spinach

(2015) Chenxi Xu et al.   Scientific Reports

A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome

(2015) Jarrod A Chapman et al.   GENOME BIOLOGY

Chloroplastic and mitochondrial GPX genes play a critical role in rice development

(2014) G. Passaia et al.   BIOLOGIA PLANTARUM

e!DAL - a framework to store, share and publish research data

(2014) Daniel Arend et al.   BMC BIOINFORMATICS

A powerful tool for genome analysis in maize: development and evaluation of the high density 600 k SNP genotyping array

(2014) Sandra Unterseer et al.   BMC GENOMICS

SNPhylo: a pipeline to construct a phylogenetic tree from huge SNP data

(2014) Tae-Ho Lee et al.   BMC GENOMICS

LAILAPS: The Plant Science Search Engine

(2014) Maria Esch et al.   PLANT AND CELL PHYSIOLOGY

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

(2014) et al.   SCIENCE

GC content evolution in coding regions of angiosperm genomes: a unifying hypothesis

(2014) Sylvain Glémin et al.   TRENDS IN GENETICS

Mapping-by-sequencing accelerates forward genetics in barley

(2014) Martin Mascher et al.   GENOME BIOLOGY

A comprehensive evaluation of assembly scaffolding tools

(2014) Martin Hunt et al.   GENOME BIOLOGY

Kmasker - A Tool for in silico Prediction of Single-Copy FISH Probes for the Large-Genome SpeciesHordeum vulgare

(2013) T. Schmutzer et al.   CYTOGENETIC AND GENOME RESEARCH

Performance of winter cereals grown on field-stored soil moisture only

(2013) Siegfried Schittenhelm et al.   EUROPEAN JOURNAL OF AGRONOMY

Robust Identification of Local Adaptation from Allele Frequencies

(2013) T. Gunther et al.   GENETICS

Single nucleotide polymorphism genotyping using Kompetitive Allele Specific PCR (KASP): overview of the technology and its application in crop improvement

(2013) Kassa Semagn et al.   MOLECULAR BREEDING

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

Reticulate Evolution of the Rye Genome

(2013) M. M. Martis et al.   PLANT CELL

Barley whole exome capture: a tool for genomic research in the genusHordeumand beyond

(2013) Martin Mascher et al.   PLANT JOURNAL

Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ)

(2013) Martin Mascher et al.   PLANT JOURNAL

Rapid Genome Mapping in Nanochannel Arrays for Highly Complete and Accurate De Novo Sequence Assembly of the Complex Aegilops tauschii Genome

(2013) Alex R. Hastie et al.   PLoS One

synbreed: a framework for the analysis of genomic prediction data using R

(2012) Valentin Wimmer et al.   BIOINFORMATICS

Genetic architecture of complex agronomic traits examined in two testcross populations of rye (Secale cereale L.)

(2012) Thomas Miedaner et al.   BMC GENOMICS

Population structure and linkage disequilibrium in elite barley breeding germplasm from the United States

(2012) Hao Zhou et al.   Journal of Zhejiang University-SCIENCE B

Comparative analysis of genome composition in Triticeae reveals strong variation in transposable element dynamics and nucleotide diversity

(2012) Christopher P. Middleton et al.   PLANT JOURNAL

Identification of novel transcripts in annotated genomes using RNA-Seq

(2011) A. Roberts et al.   BIOINFORMATICS

Improving SNP discovery by base alignment quality

(2011) H. Li   BIOINFORMATICS

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Population- and genome-specific patterns of linkage disequilibrium and SNP variation in spring and winter wheat (Triticum aestivum L.)

(2011) Shiaoman Chao et al.   BMC GENOMICS

From RNA-seq to large-scale genotyping - genomics resources for rye (Secale cereale L.)

(2011) Grit Haseneyer et al.   BMC PLANT BIOLOGY

High levels of nucleotide diversity and fast decline of linkage disequilibrium in rye (Secale cereale L.) genes involved in frost response

(2011) Yongle Li et al.   BMC PLANT BIOLOGY

Unlocking the Barley Genome by Chromosomal and Comparative Genomics

(2011) Klaus F.X. Mayer et al.   PLANT CELL

Comprehensive Sequence Analysis of 24,783 Barley Full-Length cDNAs Derived from 12 Clone Libraries

(2011) T. Matsumoto et al.   PLANT PHYSIOLOGY

Scaffolding pre-assembled contigs using SSPACE

(2010) Marten Boetzer et al.   BIOINFORMATICS

Fast and SNP-tolerant detection of complex variants and splicing in short reads

(2010) T. D. Wu 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

Genetic architecture of plant height in winter rye introgression libraries

(2010) T. Miedaner et al.   PLANT BREEDING

Q-TARO: QTL Annotation Rice Online Database

(2010) Jun-ichi Yonemaru et al.   Rice

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

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

Rye introgression lines as source of alleles for pollen-fertility restoration in Pampa CMS

(2009) K. C. Falke et al.   PLANT BREEDING

Identification of genomic regions carrying QTL for agronomic and quality traits in rye (Secale cereale) introgression libraries

(2009) K. C. Falke et al.   PLANT BREEDING

A whole-genome snapshot of 454 sequences exposes the composition of the barley genome and provides evidence for parallel evolution of genome size in wheat and barley

(2009) Thomas Wicker et al.   PLANT JOURNAL

Short panicle1encodes a putative PTR family transporter and determines rice panicle size

(2009) Shengben Li et al.   PLANT JOURNAL

Genetic Properties of the Maize Nested Association Mapping Population

(2009) M. D. McMullen et al.   SCIENCE

LOSITAN: A workbench to detect molecular adaptation based on a Fst-outlier method

(2008) Tiago Antao et al.   BMC BIOINFORMATICS

A first survey of the rye (Secale cereale) genome composition through BAC end sequencing of the short arm of chromosome 1R

(2008) Jan Bartoš et al.   BMC PLANT BIOLOGY

Neocentric activity in chromosome 5R of rye revealed by haploidy

(2008) ROLF SCHLEGEL   HEREDITAS

High-throughput functional annotation and data mining with the Blast2GO suite

(2008) S. Gotz et al.   NUCLEIC ACIDS RESEARCH

DCW11, Down-Regulated Gene 11 in CW-Type Cytoplasmic Male Sterile Rice, Encoding Mitochondrial Protein Phosphatase 2C is Related to Cytoplasmic Male Sterility

(2008) S. Fujii et al.   PLANT AND CELL PHYSIOLOGY