Gramene 2016: comparative plant genomics and pathway resources

Nascent Transcription Affected by RNA Polymerase IV in Zea mays

(2015) Karl F. Erhard et al.   GENETICS

Nascent Transcription Affected by RNA Polymerase IV in Zea mays

(2015) Karl F. Erhard et al.   GENETICS

A haplotype map of allohexaploid wheat reveals distinct patterns of selection on homoeologous genomes

(2015) Katherine W Jordan et al.   GENOME BIOLOGY

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

(2015) Jarrod A Chapman et al.   GENOME BIOLOGY

Construction of Pseudomolecule Sequences of the aus Rice Cultivar Kasalath for Comparative Genomics of Asian Cultivated Rice

(2014) H. Sakai et al.   DNA RESEARCH

Ensembl 2015

(2014) Fiona Cunningham et al.   NUCLEIC ACIDS RESEARCH

Exploring genetic variation in the tomato (SolanumsectionLycopersicon) clade by whole-genome sequencing

(2014) et al.   PLANT JOURNAL

Automated Update, Revision, and Quality Control of the Maize Genome Annotations Using MAKER-P Improves the B73 RefGen_v3 Gene Models and Identifies New Genes

(2014) MeiYee Law et al.   PLANT PHYSIOLOGY

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

Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea

(2014) Isobel AP Parkin et al.   GENOME BIOLOGY

The International Oryza Map Alignment Project: development of a genus-wide comparative genomics platform to help solve the 9 billion-people question

(2013) Julie Jacquemin et al.   CURRENT OPINION IN PLANT BIOLOGY

The maize methylome influences mRNA splice sites and reveals widespread paramutation-like switches guided by small RNA

(2013) M. Regulski et al.   GENOME RESEARCH

The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution

(2013) Ignazio Verde et al.   NATURE GENETICS

Gramene 2013: comparative plant genomics resources

(2013) Marcela K. Monaco 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

The Reactome pathway knowledgebase

(2013) David Croft et al.   NUCLEIC ACIDS RESEARCH

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

(2013) Martin Mascher et al.   PLANT JOURNAL

MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations

(2013) M. S. Campbell et al.   PLANT PHYSIOLOGY

Assembly and Validation of the Genome of the Nonmodel Basal Angiosperm Amborella

(2013) S. Chamala et al.   SCIENCE

The Amborella Genome and the Evolution of Flowering Plants

(2013) et al.   SCIENCE

Whole-genome sequencing reveals untapped genetic potential in Africa’s indigenous cereal crop sorghum

(2013) Emma S. Mace et al.   Nature Communications

Maize Metabolic Network Construction and Transcriptome Analysis

(2013) Marcela K. Monaco et al.   Plant Genome

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

(2012) Rachel Brenchley et al.   NATURE

Maize HapMap2 identifies extant variation from a genome in flux

(2012) Jer-Ming Chia et al.   NATURE GENETICS

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

The International Nucleotide Sequence Database Collaboration

(2012) Y. Nakamura 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

Population genomic and genome-wide association studies of agroclimatic traits in sorghum

(2012) G. P. Morris et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Multiple reference genomes and transcriptomes for Arabidopsis thaliana

(2011) Xiangchao Gan et al.   NATURE

Ensembl Genomes: an integrative resource for genome-scale data from non-vertebrate species

(2011) Paul J. Kersey et al.   NUCLEIC ACIDS RESEARCH

Genome-wide patterns of genetic variation in sweet and grain sorghum (Sorghum bicolor)

(2011) Lei-Ying Zheng et al.   GENOME BIOLOGY

Ensembl variation resources

(2010) Yuan Chen et al.   BMC GENOMICS

Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines

(2010) Susanna Atwell et al.   NATURE

Gramene database in 2010: updates and extensions

(2010) K. Youens-Clark et al.   NUCLEIC ACIDS RESEARCH

Rapid Genomic Characterization of the Genus Vitis

(2010) Sean Myles et al.   PLoS One

Genomic Diversity and Introgression in O. sativa Reveal the Impact of Domestication and Breeding on the Rice Genome

(2010) Keyan Zhao et al.   PLoS One

Genomewide SNP variation reveals relationships among landraces and modern varieties of rice

(2009) K. L. McNally et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A First-Generation Haplotype Map of Maize

(2009) M. A. Gore et al.   SCIENCE

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

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