Extensive sequence divergence between the reference genomes of two eliteindicarice varieties Zhenshan 97 and Minghui 63

Genome puzzle master (GPM): an integrated pipeline for building and editing pseudomolecules from fragmented sequences

(2016) Jianwei Zhang et al.   BIOINFORMATICS

Building two indica rice reference genomes with PacBio long-read and Illumina paired-end sequencing data

(2016) Jianwei Zhang et al.   Scientific Data

Differential expression of GS5 regulates grain size in rice

(2015) Chunjue Xu et al.   JOURNAL OF EXPERIMENTAL BOTANY

Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection

(2015) Weibo Xie et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomic analysis of hybrid rice varieties reveals numerous superior alleles that contribute to heterosis

(2015) Xuehui Huang et al.   Nature Communications

Automatic discovery of cell types and microcircuitry from neural connectomics

(2015) Eric Jonas et al.   eLife

Repbase Update, a database of repetitive elements in eukaryotic genomes

(2015) Weidong Bao et al.   Mobile DNA

Global Genomic Diversity ofOryza sativaVarieties Revealed by Comparative Physical Mapping

(2014) Xiaoming Wang et al.   GENETICS

RNA-Seq Alignment to Individualized Genomes Improves Transcript Abundance Estimates in Multiparent Populations

(2014) Steven C. Munger et al.   GENETICS

The InterPro protein families database: the classification resource after 15 years

(2014) Alex Mitchell et al.   NUCLEIC ACIDS RESEARCH

Understanding Reproductive Isolation Based on the Rice Model

(2013) Yidan Ouyang et al.   Annual Review of Plant Biology

Heterosis in elite hybrid rice: speculation on the genetic and biochemical mechanisms

(2013) Stephen A Goff et al.   CURRENT OPINION IN PLANT BIOLOGY

WebAUGUSTUS--a web service for training AUGUSTUS and predicting genes in eukaryotes

(2013) K. J. Hoff et al.   NUCLEIC ACIDS RESEARCH

P-MITE: a database for plant miniature inverted-repeat transposable elements

(2013) Jiongjiong Chen et al.   NUCLEIC ACIDS RESEARCH

miRBase: annotating high confidence microRNAs using deep sequencing data

(2013) Ana Kozomara et al.   NUCLEIC ACIDS RESEARCH

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

A gene ontology inferred from molecular networks

(2012) Janusz Dutkowski et al.   NATURE BIOTECHNOLOGY

MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity

(2012) Y. Wang et al.   NUCLEIC ACIDS RESEARCH

Genetic composition of yield heterosis in an elite rice hybrid

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

genBlastG: using BLAST searches to build homologous gene models

(2011) Rong She et al.   BIOINFORMATICS

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Sequence-based physical mapping of complex genomes by whole genome profiling

(2011) J. van Oeveren et al.   GENOME RESEARCH

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Natural variation in GS5 plays an important role in regulating grain size and yield in rice

(2011) Yibo Li et al.   NATURE GENETICS

The UniProt-GO Annotation database in 2011

(2011) E. C. Dimmer et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database

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

HMMER web server: interactive sequence similarity searching

(2011) R. D. Finn et al.   NUCLEIC ACIDS RESEARCH

A paralog of the MtN3/saliva family recessively confers race-specific resistance to Xanthomonas oryzae in rice

(2011) QINSONG LIU et al.   PLANT CELL AND ENVIRONMENT

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

(2010) Xuehui Huang et al.   NATURE GENETICS

Rfam: Wikipedia, clans and the "decimal" release

(2010) P. P. Gardner et al.   NUCLEIC ACIDS RESEARCH

GenBank

(2010) D. A. Benson et al.   NUCLEIC ACIDS RESEARCH

Evidence and evolutionary analysis of ancient whole-genome duplication in barley predating the divergence from rice

(2009) Thomas Thiel et al.   BMC EVOLUTIONARY BIOLOGY

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

(2009) K. Mochida et al.   PLANT PHYSIOLOGY

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

RICD: A rice indica cDNA database resource for rice functional genomics

(2008) Tingting Lu et al.   BMC PLANT BIOLOGY

Natural variation in Ghd7 is an important regulator of heading date and yield potential in rice

(2008) Weiya Xue et al.   NATURE GENETICS

Assessing the gene space in draft genomes

(2008) Genis Parra et al.   NUCLEIC ACIDS RESEARCH

PlantDB – a versatile database for managing plant research

(2008) Vivien Exner et al.   Plant Methods

Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments

(2008) Brian J Haas et al.   GENOME BIOLOGY