Construction of Pseudomolecule Sequences of the aus Rice Cultivar Kasalath for Comparative Genomics of Asian Cultivated Rice

TASUKE: a web-based visualization program for large-scale resequencing data

(2013) M. Kumagai et al.   BIOINFORMATICS

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

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

A BAC physical map ofausrice cultivar ‘Kasalath’, and the map-based genomic sequence of ‘Kasalath’ chromosome 1

(2013) Hiroyuki Kanamori et al.   PLANT JOURNAL

The advantages and limitations of trait analysis with GWAS: a review

(2013) Arthur Korte et al.   Plant Methods

Dissecting yield-associated loci in super hybrid rice by resequencing recombinant inbred lines and improving parental genome sequences

(2013) Z.-Y. Gao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Resequencing rice genomes: an emerging new era of rice genomics

(2013) Xuehui Huang et al.   TRENDS IN GENETICS

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

(2013) Daehwan Kim et al.   GENOME BIOLOGY

The protein kinase Pstol1 from traditional rice confers tolerance of phosphorus deficiency

(2012) Rico Gamuyao et al.   NATURE

Genome sequencing reveals agronomically important loci in rice using MutMap

(2012) Akira Abe et al.   NATURE BIOTECHNOLOGY

Efficient de novo assembly of large genomes using compressed data structures

(2011) J. T. Simpson et al.   GENOME RESEARCH

The impact of next-generation sequencing on genomics

(2011) Jun Zhang et al.   Journal of Genetics and Genomics

Dynamic Intra-Japonica Subspecies Variation and Resource Application

(2011) Haiyan Lin et al.   Molecular Plant

Multiple reference genomes and transcriptomes for Arabidopsis thaliana

(2011) Xiangchao Gan et al.   NATURE

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

Artificial selection for a green revolution gene during japonica rice domestication

(2011) K. Asano et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

(2010) A. McKenna et al.   GENOME RESEARCH

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Limitations of next-generation genome sequence assembly

(2010) Can Alkan et al.   NATURE METHODS

Rice structural variation: a comparative analysis of structural variation between rice and three of its closest relatives in the genus Oryza

(2010) Bonnie L. Hurwitz et al.   PLANT JOURNAL

Molecular cloning of Sdr4, a regulator involved in seed dormancy and domestication of rice

(2010) K. Sugimoto et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mapping 49 quantitative trait loci at high resolution through sequencing-based genotyping of rice recombinant inbred lines

(2010) Lu Wang et al.   THEORETICAL AND APPLIED GENETICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

The ethylene response factors SNORKEL1 and SNORKEL2 allow rice to adapt to deep water

(2009) Yoko Hattori et al.   NATURE

Comparative analysis of complete orthologous centromeres from two subspecies of rice reveals rapid variation of centromere organization and structure

(2009) Jianzhong Wu et al.   PLANT JOURNAL

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

(2008) Ayahiko Shomura et al.   NATURE GENETICS

Genome-Wide Analysis of Transposon Insertion Polymorphisms Reveals Intraspecific Variation in Cultivated Rice

(2008) X. Huang et al.   PLANT PHYSIOLOGY