Characterization of genome-wide variations induced by gamma-ray radiation in barley using RNA-Seq

High-resolution melting-based TILLING of γ ray-induced mutations in rice

(2018) Shan Li et al.   Journal of Zhejiang University-SCIENCE B

A chromosome conformation capture ordered sequence of the barley genome

(2017) Martin Mascher et al.   NATURE

MutMapPlus identified novel mutant alleles of a rice starch branching enzyme IIb gene for fine-tuning of cooked rice texture

(2017) Masaru Nakata et al.   PLANT BIOTECHNOLOGY JOURNAL

The Sequences of 1,504 Mutants in the Model Rice Variety Kitaake Facilitate Rapid Functional Genomic Studies

(2017) Guotian Li et al.   PLANT CELL

Construction of a map-based reference genome sequence for barley, Hordeum vulgare L.

(2017) Sebastian Beier et al.   Scientific Data

Frequency and type of inheritable mutations induced by γ rays in rice as revealed by whole genome sequencing

(2016) Shan Li et al.   Journal of Zhejiang University-SCIENCE B

Genome-Wide Sequencing of 41 Rice ( Oryza sativa L.) Mutated Lines Reveals Diverse Mutations Induced by Fast-Neutron Irradiation

(2016) Guotian Li et al.   Molecular Plant

Chalk5 encodes a vacuolar H+-translocating pyrophosphatase influencing grain chalkiness in rice

(2014) Yibo Li et al.   NATURE GENETICS

Sequencing depth and coverage: key considerations in genomic analyses

(2014) David Sims et al.   NATURE REVIEWS GENETICS

Mutation identification by direct comparison of whole-genome sequencing data from mutant and wild-type individuals using k-mers

(2013) Karl J V Nordström et al.   NATURE BIOTECHNOLOGY

MutMap-Gap: whole-genome resequencing of mutant F2 progeny bulk combined withde novoassembly of gap regions identifies the rice blast resistance genePii

(2013) Hiroki Takagi et al.   NEW PHYTOLOGIST

QTL-seq: rapid mapping of quantitative trait loci in rice by whole genome resequencing of DNA from two bulked populations

(2013) Hiroki Takagi et al.   PLANT JOURNAL

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

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

(2012) Pablo Cingolani et al.   FLY

Mutant Resources for the Functional Analysis of the Rice Genome

(2012) Nili Wang et al.   Molecular Plant

Genome sequencing reveals agronomically important loci in rice using MutMap

(2012) Akira Abe et al.   NATURE BIOTECHNOLOGY

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

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

(2011) Yibo Li et al.   NATURE GENETICS

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

d14, a Strigolactone-Insensitive Mutant of Rice, Shows an Accelerated Outgrowth of Tillers

(2009) Tomotsugu Arite et al.   PLANT AND CELL PHYSIOLOGY

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

(2008) Weiya Xue et al.   NATURE GENETICS

RID1, encoding a Cys2/His2-type zinc finger transcription factor, acts as a master switch from vegetative to floral development in rice

(2008) C. Wu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA