Whole Genome Sequencing of Elite Rice Cultivars as a Comprehensive Information Resource for Marker Assisted Selection

An integrated framework for discovery and genotyping of genomic variants from high-throughput sequencing experiments

(2014) Jorge Duitama et al.   NUCLEIC ACIDS RESEARCH

Genome-Wide DNA Polymorphisms in Seven Rice Cultivars of Temperate and Tropical Japonica Groups

(2014) Yuko Arai-Kichise et al.   PLoS One

Genome Wide Association Mapping of Grain Arsenic, Copper, Molybdenum and Zinc in Rice (Oryza sativa L.) Grown at Four International Field Sites

(2014) Gareth J. Norton et al.   PLoS One

Harvesting the Promising Fruits of Genomics: Applying Genome Sequencing Technologies to Crop Breeding

(2014) Rajeev K. Varshney et al.   PLOS BIOLOGY

The 3,000 rice genomes project

(2014)   GigaScience

Genome-wide copy number variations in Oryza sativa L.

(2013) Ping Yu et al.   BMC GENOMICS

Gramene 2013: comparative plant genomics resources

(2013) Marcela K. Monaco 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

Comparative Studies of Copy Number Variation Detection Methods for Next-Generation Sequencing Technologies

(2013) Junbo Duan et al.   PLoS One

Functional divergence of gene duplicates through ectopic recombination

(2012) Joaquin F Christiaens et al.   EMBO REPORTS

Phylogeography of Asian wild rice,Oryza rufipogon: a genome-wide view

(2012) PU HUANG et al.   MOLECULAR ECOLOGY

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

(2012) Xuehui Huang et al.   NATURE

Genome sequencing reveals agronomically important loci in rice using MutMap

(2012) Akira Abe et al.   NATURE BIOTECHNOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

dbVar and DGVa: public archives for genomic structural variation

(2012) Ilkka Lappalainen et al.   NUCLEIC ACIDS RESEARCH

Independent Domestication of Asian Rice Followed by Gene Flow from japonica to indica

(2011) C.-c. Yang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Long-Range and Targeted Ectopic Recombination between the Two Homeologous Chromosomes 11 and 12 in Oryza Species

(2011) J. Jacquemin et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2011) Xun Xu et al.   NATURE BIOTECHNOLOGY

Levels and Patterns of Nucleotide Variation in Domestication QTL Regions on Rice Chromosome 3 Suggest Lineage-Specific Selection

(2011) Xianfa Xie et al.   PLoS One

Molecular evidence for a single evolutionary origin of domesticated rice

(2011) J. Molina et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identification of candidate genes in rice for resistance to sheath blight disease by whole genome sequencing

(2011) James Silva et al.   THEORETICAL AND APPLIED GENETICS

Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa

(2011) Keyan Zhao et al.   Nature Communications

Two Evolutionary Histories in the Genome of Rice: the Roles of Domestication Genes

(2011) Ziwen He et al.   PLoS Genetics

Genetic Architecture of Aluminum Tolerance in Rice (Oryza sativa) Determined through Genome-Wide Association Analysis and QTL Mapping

(2011) Adam N. Famoso et al.   PLoS Genetics

Flapjack--graphical genotype visualization

(2010) I. Milne et al.   BIOINFORMATICS

Polymorphism in the GBSS gene affects amylose content in US and European rice germplasm

(2010) Macaire Dobo et al.   JOURNAL OF CEREAL SCIENCE

Gain of deleterious function causes an autoimmune response and Bateson–Dobzhansky–Muller incompatibility in rice

(2010) Eiji Yamamoto et al.   MOLECULAR GENETICS AND GENOMICS

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

(2010) Xuehui Huang et al.   NATURE GENETICS

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

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Personalized copy number and segmental duplication maps using next-generation sequencing

(2009) Can Alkan et al.   NATURE GENETICS

A ricetryptophan deficient dwarfmutant,tdd1,contains a reduced level of indole acetic acid and develops abnormal flowers and organless embryos

(2009) Takashi Sazuka et al.   PLANT JOURNAL

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

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

(2009) S. Fukuoka et al.   SCIENCE