Rice Annotation Project Database (RAP-DB): An Integrative and Interactive Database for Rice Genomics

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

(2012) Xuehui Huang et al.   NATURE

Oryzabase: an integrated information resource for rice science

(2011) Yukiko Yamazaki et al.   BREEDING SCIENCE

Retrogenes in Rice (Oryza sativa L. ssp. japonica) Exhibit Correlated Expression with Their Source Genes

(2011) Hiroaki Sakai et al.   Genome Biology and Evolution

Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasm

(2011) Xuehui Huang et al.   NATURE GENETICS

Phytozome: a comparative platform for green plant genomics

(2011) David M. Goodstein et al.   NUCLEIC ACIDS RESEARCH

Reorganizing the protein space at the Universal Protein Resource (UniProt)

(2011)   NUCLEIC ACIDS RESEARCH

The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools

(2011) Philippe Lamesch et al.   NUCLEIC ACIDS RESEARCH

NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy

(2011) K. D. Pruitt et al.   NUCLEIC ACIDS RESEARCH

KEGG for integration and interpretation of large-scale molecular data sets

(2011) M. Kanehisa et al.   NUCLEIC ACIDS RESEARCH

ATTED-II Updates: Condition-Specific Gene Coexpression to Extend Coexpression Analyses and Applications to a Broad Range of Flowering Plants

(2011) T. Obayashi et al.   PLANT AND CELL PHYSIOLOGY

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

(2011) T. Matsumoto et al.   PLANT PHYSIOLOGY

mRNA-Seq Reveals a Comprehensive Transcriptome Profile of Rice under Phosphate Stress

(2011) Youko Oono et al.   Rice

Massive gene losses in Asian cultivated rice unveiled by comparative genome analysis

(2010) Hiroaki Sakai et al.   BMC GENOMICS

Massive parallel sequencing of mRNA in identification of unannotated salinity stress-inducible transcripts in rice (Oryza sativa L.)

(2010) Hiroshi Mizuno et al.   BMC GENOMICS

Fine definition of the pedigree haplotypes of closely related rice cultivars by means of genome-wide discovery of single-nucleotide polymorphisms

(2010) Toshio Yamamoto et al.   BMC GENOMICS

Efficient Plant Gene Identification Based on Interspecies Mapping of Full-Length cDNAs

(2010) N. Amano et al.   DNA RESEARCH

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Genome-wide association studies of 14 agronomic traits in rice landraces

(2010) Xuehui Huang et al.   NATURE GENETICS

Gramene database in 2010: updates and extensions

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

RiceXPro: a platform for monitoring gene expression in japonica rice grown under natural field conditions

(2010) Y. Sato et al.   NUCLEIC ACIDS RESEARCH

miRBase: integrating microRNA annotation and deep-sequencing data

(2010) A. Kozomara et al.   NUCLEIC ACIDS RESEARCH

OryzaExpress: An Integrated Database of Gene Expression Networks and Omics Annotations in Rice

(2010) Kazuki Hamada et al.   PLANT AND CELL PHYSIOLOGY

Genomics and Bioinformatics Resources for Crop Improvement

(2010) K. Mochida et al.   PLANT AND CELL PHYSIOLOGY

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Development of 5006 Full-Length CDNAs in Barley: A Tool for Accessing Cereal Genomics Resources

(2009) K. Sato et al.   DNA RESEARCH

DDBJ launches a new archive database with analytical tools for next-generation sequence data

(2009) Eli Kaminuma et al.   NUCLEIC ACIDS RESEARCH

Highly Diversified Molecular Evolution of Downstream Transcription Start Sites in Rice and Arabidopsis

(2009) T. Tanaka et al.   PLANT PHYSIOLOGY

TriFLDB: A Database of Clustered Full-Length Coding Sequences from Triticeae with Applications to Comparative Grass Genomics

(2009) K. Mochida et al.   PLANT PHYSIOLOGY

Loss of Function of a Proline-Containing Protein Confers Durable Disease Resistance in Rice

(2009) S. Fukuoka et al.   SCIENCE

Sequencing, Mapping, and Analysis of 27,455 Maize Full-Length cDNAs

(2009) Carol Soderlund et al.   PLoS Genetics

Collection and Comparative Analysis of 1888 Full-length cDNAs from Wild Rice Oryza rufipogon Griff. W1943

(2008) T. Lu et al.   DNA RESEARCH

tRNADB-CE: tRNA gene database curated manually by experts

(2008) Takashi Abe et al.   NUCLEIC ACIDS RESEARCH

Insights into corn genes derived from large-scale cDNA sequencing

(2008) Nickolai N. Alexandrov et al.   PLANT MOLECULAR BIOLOGY

Gene Nomenclature System for Rice

(2008) Susan R. McCouch et al.   Rice