Genome sequencing of rice subspecies and genetic analysis of recombinant lines reveals regional yield- and quality-associated loci

Pan-genome analysis highlights the extent of genomic variation in cultivated and wild rice

(2018) Qiang Zhao et al.   NATURE GENETICS

Deciphering the Environmental Impacts on Rice Quality for Different Rice Cultivated Areas

(2018) Xiukun Li et al.   Rice

Genomic variation in 3,010 diverse accessions of Asian cultivated rice

(2018) Wensheng Wang et al.   NATURE

Canu: scalable and accurate long-read assembly via adaptivek-mer weighting and repeat separation

(2017) Sergey Koren et al.   GENOME RESEARCH

Sequencing and de novo assembly of a near complete indica rice genome

(2017) Huilong Du et al.   Nature Communications

The DENSE AND ERECT PANICLE 1 (DEP1) gene offering the potential in the breeding of high-yielding rice

(2016) Hai Xu et al.   BREEDING SCIENCE

Genomic architecture of heterosis for yield traits in rice

(2016) Xuehui Huang et al.   NATURE

Using intron position conservation for homology-based gene prediction

(2016) Jens Keilwagen et al.   NUCLEIC ACIDS RESEARCH

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

(2016) Jianwei Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phytochromes function as thermosensors in Arabidopsis

(2016) Jae-Hoon Jung et al.   SCIENCE

Breeding high-yield superior quality hybrid super rice by rational design

(2016) Qian Qian et al.   National Science Review

A Robust CRISPR/Cas9 System for Convenient, High-Efficiency Multiplex Genome Editing in Monocot and Dicot Plants

(2015) Xingliang Ma et al.   Molecular Plant

Assembly and diploid architecture of an individual human genome via single-molecule technologies

(2015) Matthew Pendleton et al.   NATURE METHODS

SET DOMAIN GROUP 708, a histone H3 lysine 36-specific methyltransferase, controls flowering time in rice (Oryza sativa )

(2015) Bing Liu et al.   NEW PHYTOLOGIST

Conserved miR164-targeted NAC genes negatively regulate drought resistance in rice

(2014) Yujie Fang et al.   JOURNAL OF EXPERIMENTAL BOTANY

Construction and Analysis of High-Density Linkage Map Using High-Throughput Sequencing Data

(2014) Dongyuan Liu et al.   PLoS One

Infernal 1.1: 100-fold faster RNA homology searches

(2013) E. P. Nawrocki et al.   BIOINFORMATICS

DNA targeting specificity of RNA-guided Cas9 nucleases

(2013) Patrick D Hsu et al.   NATURE BIOTECHNOLOGY

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

(2012) Xuehui Huang et al.   NATURE

The contribution of intersubspecific hybridization to the breeding of super-high-yielding japonica rice in northeast China

(2012) Jian Sun et al.   THEORETICAL AND APPLIED GENETICS

Phytochrome B regulates Heading date 1 (Hd1)-mediated expression of rice florigen Hd3a and critical day length in rice

(2011) Ryo Ishikawa et al.   MOLECULAR GENETICS AND GENOMICS

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

Genome-wide analysis of NAC transcription factor family in rice

(2010) Mohammed Nuruzzaman et al.   GENE

A pair of floral regulators sets critical day length for Hd3a florigen expression in rice

(2010) Hironori Itoh et al.   NATURE GENETICS

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

(2010) Xuehui Huang et al.   NATURE GENETICS

MITE-Hunter: a program for discovering miniature inverted-repeat transposable elements from genomic sequences

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

CDD: a Conserved Domain Database for the functional annotation of proteins

(2010) A. Marchler-Bauer et al.   NUCLEIC ACIDS RESEARCH

DTH8 Suppresses Flowering in Rice, Influencing Plant Height and Yield Potential Simultaneously

(2010) X. Wei et al.   PLANT PHYSIOLOGY

SOAP2: an improved ultrafast tool for short read alignment

(2009) R. Li et al.   BIOINFORMATICS

SNP detection for massively parallel whole-genome resequencing

(2009) R. Li et al.   GENOME RESEARCH

Natural variation at the DEP1 locus enhances grain yield in rice

(2009) Xianzhong Huang et al.   NATURE GENETICS

Reply: A unified classification system for eukaryotic transposable elements should reflect their phylogeny

(2009) Thomas Wicker et al.   NATURE REVIEWS GENETICS

Isolation and initial characterization of GW5, a major QTL associated with rice grain width and weight

(2008) Jianfeng Weng et al.   CELL RESEARCH

genBlastA: Enabling BLAST to identify homologous gene sequences

(2008) R. She et al.   GENOME RESEARCH

Deletion in a gene associated with grain size increased yields during rice domestication

(2008) Ayahiko Shomura et al.   NATURE GENETICS

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

(2008) Brian J Haas et al.   GENOME BIOLOGY