Triticeae Resources in Ensembl Plants

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

Activities at the Universal Protein Resource (UniProt)

(2014)   NUCLEIC ACIDS RESEARCH

Characterization of polyploid wheat genomic diversity using a high-density 90 000 single nucleotide polymorphism array

(2014) Shichen Wang et al.   PLANT BIOTECHNOLOGY JOURNAL

De Novo Transcriptome Assembly and Analyses of Gene Expression during Photomorphogenesis in Diploid Wheat Triticum monococcum

(2014) Samuel E. Fox et al.   PLoS One

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

(2014) et al.   SCIENCE

Structural and functional partitioning of bread wheat chromosome 3B

(2014) F. Choulet et al.   SCIENCE

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

Gramene 2013: comparative plant genomics resources

(2013) Marcela K. Monaco et al.   NUCLEIC ACIDS RESEARCH

Ensembl Genomes 2013: scaling up access to genome-wide data

(2013) Paul Julian Kersey et al.   NUCLEIC ACIDS RESEARCH

Expression Atlas update—a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments

(2013) Robert Petryszak et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2014

(2013) Paul Flicek et al.   NUCLEIC ACIDS RESEARCH

ATTED-II in 2014: Evaluation of Gene Coexpression in Agriculturally Important Plants

(2013) Takeshi Obayashi et al.   PLANT AND CELL PHYSIOLOGY

HapRice, an SNP Haplotype Database and a Web Tool for Rice

(2013) Jun-ichi Yonemaru et al.   PLANT AND CELL PHYSIOLOGY

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

(2013) Martin Mascher et al.   PLANT JOURNAL

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

CerealsDB 2.0: an integrated resource for plant breeders and scientists

(2012) Paul A Wilkinson et al.   BMC BIOINFORMATICS

Discovery of High-Confidence Single Nucleotide Polymorphisms from Large-Scale De Novo Analysis of Leaf Transcripts of Aegilops tauschii, A Wild Wheat Progenitor

(2012) J. C. M. Iehisa et al.   DNA RESEARCH

Flow cytometric chromosome sorting in plants: The next generation

(2012) Jan Vrána et al.   METHODS

Analysis of the bread wheat genome using whole-genome shotgun sequencing

(2012) Rachel Brenchley et al.   NATURE

ArrayExpress update—trends in database growth and links to data analysis tools

(2012) Gabriella Rustici et al.   NUCLEIC ACIDS RESEARCH

The Plant Ontology as a Tool for Comparative Plant Anatomy and Genomic Analyses

(2012) Laurel Cooper et al.   PLANT AND CELL PHYSIOLOGY

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

Resolving the Ortholog Conjecture: Orthologs Tend to Be Weakly, but Significantly, More Similar in Function than Paralogs

(2012) Adrian M. Altenhoff et al.   PLoS Computational Biology

WheatGenome.info: An Integrated Database and Portal for Wheat Genome Information

(2011) K. Lai et al.   PLANT AND CELL PHYSIOLOGY

Transcript-specific, single-nucleotide polymorphism discovery and linkage analysis in hexaploid bread wheat (Triticum aestivum L.)

(2011) Alexandra M. Allen et al.   PLANT BIOTECHNOLOGY JOURNAL

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

(2011) T. Matsumoto et al.   PLANT PHYSIOLOGY

BioMart: driving a paradigm change in biological data management

(2011) A. Kasprzyk   Database-The Journal of Biological Databases and Curation

An Improved Consensus Linkage Map of Barley Based on Flow-Sorted Chromosomes and Single Nucleotide Polymorphism Markers

(2011) María Muñoz-Amatriaín et al.   Plant Genome

Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor

(2010) William McLaren et al.   BIOINFORMATICS

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

(2010) T. D. Wu et al.   BIOINFORMATICS

Homoeolog-specific transcriptional bias in allopolyploid wheat

(2010) Alina R Akhunova et al.   BMC GENOMICS

The European Nucleotide Archive

(2010) R. Leinonen et al.   NUCLEIC ACIDS RESEARCH

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

The B73 Maize Genome: Complexity, Diversity, and Dynamics

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

EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates

(2008) A. J. Vilella et al.   GENOME RESEARCH