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

Gene tree discordance of wild and cultivated Asian rice deciphered by genome-wide sequence comparison

(2011) Ching-chia Yang et al.   GENE

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

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

(2011) Ziwen He et al.   PLoS Genetics

Massive gene losses in Asian cultivated rice unveiled by comparative genome analysis

(2010) Hiroaki Sakai et al.   BMC 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

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

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

Evolutionary History of GS3 , a Gene Conferring Grain Length in Rice

(2009) Noriko Takano-Kai et al.   GENETICS

Comparative sequence analysis ofMONOCULM1-orthologous regions in 14Oryzagenomes

(2009) Fei Lu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The origin and evolution of fragrance in rice (Oryza sativa L.)

(2009) M. J. Kovach et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Species Trees from Highly Incongruent Gene Trees in Rice

(2009) Karen A. Cranston et al.   SYSTEMATIC BIOLOGY

Gene tree discordance, phylogenetic inference and the multispecies coalescent

(2009) James H. Degnan et al.   TRENDS IN ECOLOGY & EVOLUTION

Collection and Comparative Analysis of 1888 Full-length cDNAs from Wild Rice Oryza rufipogon Griff. W1943

(2008) T. Lu et al.   DNA RESEARCH

Nonindependent Domestication of the Two Rice Subspecies, Oryza sativa ssp. indica and ssp. japonica , Demonstrated by Multilocus Microsatellites

(2008) Li-zhi Gao et al.   GENETICS

Control of a key transition from prostrate to erect growth in rice domestication

(2008) Lubin Tan et al.   NATURE GENETICS

Genetic control of rice plant architecture under domestication

(2008) Jian Jin et al.   NATURE GENETICS

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

The evolving story of rice evolution

(2008) Duncan A. Vaughan et al.   PLANT SCIENCE

Analysis of 142 genes resolves the rapid diversification of the rice genus

(2008) Xin-Hui Zou et al.   GENOME BIOLOGY