Information Commons for Rice (IC4R)

Genome-Wide Disruption of Gene Expression in Allopolyploids but Not Hybrids of Rice Subspecies

(2014) Chunming Xu et al.   MOLECULAR BIOLOGY AND EVOLUTION

RiceVarMap: a comprehensive database of rice genomic variations

(2014) Hu Zhao et al.   NUCLEIC ACIDS RESEARCH

Araport: the Arabidopsis Information Portal

(2014) Vivek Krishnakumar et al.   NUCLEIC ACIDS RESEARCH

PLAZA 3.0: an access point for plant comparative genomics

(2014) Sebastian Proost et al.   NUCLEIC ACIDS RESEARCH

SNP-Seek database of SNPs derived from 3000 rice genomes

(2014) Nickolai Alexandrov et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2015

(2014) Fiona Cunningham et al.   NUCLEIC ACIDS RESEARCH

UniProt: a hub for protein information

(2014)   NUCLEIC ACIDS RESEARCH

dbPPT: a comprehensive database of protein phosphorylation in plants

(2014) Han Cheng et al.   Database-The Journal of Biological Databases and Curation

The 3,000 rice genomes project

(2014)   GigaScience

AuthorReward: increasing community curation in biological knowledge wikis through automated authorship quantification

(2013) Lin Dai et al.   BIOINFORMATICS

BioJS: an open source JavaScript framework for biological data visualization

(2013) J. Gomez et al.   BIOINFORMATICS

EKPD: a hierarchical database of eukaryotic protein kinases and protein phosphatases

(2013) Yongbo Wang et al.   NUCLEIC ACIDS RESEARCH

RiceWiki: a wiki-based database for community curation of rice genes

(2013) Zhang Zhang et al.   NUCLEIC ACIDS RESEARCH

Manually curated database of rice proteins

(2013) Pratibha Gour et al.   NUCLEIC ACIDS RESEARCH

Gramene 2013: comparative plant genomics resources

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

eggNOG v4.0: nested orthology inference across 3686 organisms

(2013) Sean Powell et al.   NUCLEIC ACIDS RESEARCH

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

(2013) Hiroaki Sakai et al.   PLANT AND CELL PHYSIOLOGY

Spatio-Temporal Transcript Profiling of Rice Roots and Shoots in Response to Phosphate Starvation and Recovery

(2013) D. Secco et al.   PLANT CELL

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

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

(2012) Xuehui Huang et al.   NATURE

Differential analysis of gene regulation at transcript resolution with RNA-seq

(2012) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

UUCD: a family-based database of ubiquitin and ubiquitin-like conjugation

(2012) Tianshun Gao et al.   NUCLEIC ACIDS RESEARCH

NGS QC Toolkit: A Toolkit for Quality Control of Next Generation Sequencing Data

(2012) Ravi K. Patel et al.   PLoS One

Transcriptome and methylome interactions in rice hybrids

(2012) Ramakrishna K. Chodavarapu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2011) Xun Xu et al.   NATURE BIOTECHNOLOGY

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

The sequence read archive: explosive growth of sequencing data

(2011) Y. Kodama et al.   NUCLEIC ACIDS RESEARCH

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

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

(2010) Xuehui Huang et al.   NATURE GENETICS

GreenPhylDB v2.0: comparative and functional genomics in plants

(2010) Mathieu Rouard 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

The Sequence Read Archive

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

Q-TARO: QTL Annotation Rice Online Database

(2010) Jun-ichi Yonemaru et al.   Rice

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

JBrowse: A next-generation genome browser

(2009) M. E. Skinner et al.   GENOME RESEARCH

InParanoid 7: new algorithms and tools for eukaryotic orthology analysis

(2009) G. Ostlund et al.   NUCLEIC ACIDS RESEARCH

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

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