4.8 Article

The genome sequence of African rice (Oryza glaberrima) and evidence for independent domestication

Related references

Note: Only part of the references are listed.
Article Evolutionary Biology

POPBAM: Tools for Evolutionary Analysis of Short Read Sequence Alignments

Daniel Garrigan

EVOLUTIONARY BIOINFORMATICS (2013)

Article Biochemistry & Molecular Biology

SweeD: Likelihood-Based Detection of Selective Sweeps in Thousands of Genomes

Pavlos Pavlidis et al.

MOLECULAR BIOLOGY AND EVOLUTION (2013)

Review Genetics & Heredity

Evolution of crop species: genetics of domestication and diversification

Rachel S. Meyer et al.

NATURE REVIEWS GENETICS (2013)

Article Multidisciplinary Sciences

Whole-genome sequencing of Oryza brachyantha reveals mechanisms underlying Oryza genome evolution

Jinfeng Chen et al.

NATURE COMMUNICATIONS (2013)

Article Biochemical Research Methods

rehh: an R package to detect footprints of selection in genome-wide SNP data from haplotype structure

Mathieu Gautier et al.

BIOINFORMATICS (2012)

Article Multidisciplinary Sciences

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

Xuehui Huang et al.

NATURE (2012)

Article Genetics & Heredity

Parallel domestication of the Shattering1 genes in cereals

Zhongwei Lin et al.

NATURE GENETICS (2012)

Article Biochemistry & Molecular Biology

The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools

Philippe Lamesch et al.

NUCLEIC ACIDS RESEARCH (2012)

Article Biochemical Research Methods

The variant call format and VCFtools

Petr Danecek et al.

BIOINFORMATICS (2011)

Article Biotechnology & Applied Microbiology

Full-length transcriptome assembly from RNA-Seq data without a reference genome

Manfred G. Grabherr et al.

NATURE BIOTECHNOLOGY (2011)

Letter Biotechnology & Applied Microbiology

Integrative genomics viewer

James T. Robinson et al.

NATURE BIOTECHNOLOGY (2011)

Article Multidisciplinary Sciences

Molecular evidence for a single evolutionary origin of domesticated rice

Jeanmaire Molina et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)

Article Biochemical Research Methods

Fast and accurate long-read alignment with Burrows-Wheeler transform

Heng Li et al.

BIOINFORMATICS (2010)

Article Biochemical Research Methods

BEDTools: a flexible suite of utilities for comparing genomic features

Aaron R. Quinlan et al.

BIOINFORMATICS (2010)

Article Biochemistry & Molecular Biology

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

Aaron McKenna et al.

GENOME RESEARCH (2010)

Article Multidisciplinary Sciences

Genome sequencing and analysis of the model grass Brachypodium distachyon

John P. Vogel et al.

NATURE (2010)

Review Multidisciplinary Sciences

Food Security: The Challenge of Feeding 9 Billion People

H. Charles J. Godfray et al.

SCIENCE (2010)

Article Biochemistry & Molecular Biology

High-throughput genotyping by whole-genome resequencing

Xuehui Huang et al.

GENOME RESEARCH (2009)

Article Biochemistry & Molecular Biology

Fast model-based estimation of ancestry in unrelated individuals

David H. Alexander et al.

GENOME RESEARCH (2009)

Article Multidisciplinary Sciences

The Sorghum bicolor genome and the diversification of grasses

Andrew H. Paterson et al.

NATURE (2009)

Article Genetics & Heredity

Natural variation at the DEP1 locus enhances grain yield in rice

Xianzhong Huang et al.

NATURE GENETICS (2009)

Article Multidisciplinary Sciences

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

Michael J. Kovach et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)

Article Agronomy

De Novo Next Generation Sequencing of Plant Genomes

Steve Rounsley et al.

Article Biotechnology & Applied Microbiology

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

Ben Langmead et al.

GENOME BIOLOGY (2009)

Article Agronomy

Map-based cloning of the ERECT PANICLE 3 gene in rice

Rihua Piao et al.

THEORETICAL AND APPLIED GENETICS (2009)

Article Biochemistry & Molecular Biology

Dynamic Evolution of Oryza Genomes Is Revealed by Comparative Genomic Analysis of a Genus-Wide Vertical Data Set

Jetty S. S. Ammiraju et al.

PLANT CELL (2008)

Review Biochemistry & Molecular Biology

The evolving story of rice evolution

Duncan A. Vaughan et al.

PLANT SCIENCE (2008)

Review Genetics & Heredity

A unified classification system for eukaryotic transposable elements

Thomas Wicker et al.

NATURE REVIEWS GENETICS (2007)

Review Multidisciplinary Sciences

Strategies for developing green super rice

Qifa Zhang

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)

Review Plant Sciences

The complex history of the domestication of rice

Megan Sweeney et al.

ANNALS OF BOTANY (2007)

Article Genetics & Heredity

PLINK: A tool set for whole-genome association and population-based linkage analyses

Shaun Purcell et al.

AMERICAN JOURNAL OF HUMAN GENETICS (2007)

Article Biotechnology & Applied Microbiology

LTR retrotransposons in rice (Oryza sativa, L.):: recent burst amplifications followed by rapid DNA loss

Clementine Vitte et al.

BMC GENOMICS (2007)

Article Biochemistry & Molecular Biology

LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons

Zhao Xu et al.

NUCLEIC ACIDS RESEARCH (2007)

Article Biochemistry & Molecular Biology

The TIGR plant transcript assemblies database

Kevin L. Childs et al.

NUCLEIC ACIDS RESEARCH (2007)

Article Biochemistry & Molecular Biology

The TIGR Rice Genome Annotation Resource: Improvements and new features

Shu Ouyang et al.

NUCLEIC ACIDS RESEARCH (2007)

Review Biochemistry & Molecular Biology

The molecular genetics of crop domestication

John F. Doebley et al.

Article Genetics & Heredity

Population structure and eigenanalysis

Nick Patterson et al.

PLOS GENETICS (2006)

Article Multidisciplinary Sciences

An SNP caused loss of seed shattering during rice domestication

Saeko Konishi et al.

SCIENCE (2006)

Correction Biochemistry & Molecular Biology

A map of recent positive selection in the human genome (vol 4, pg 154, 2006)

BF Voight et al.

PLOS BIOLOGY (2006)

Article Multidisciplinary Sciences

Rice domestication by reducing shattering

CB Li et al.

SCIENCE (2006)

Article Biochemistry & Molecular Biology

A map of recent positive selection in the human genome

BF Voight et al.

PLOS BIOLOGY (2006)

Article Biochemistry & Molecular Biology

Caught red-handed:: Rc encodes a basic helix-loop-helix protein conditioning red pericarp in rice

MT Sweeney et al.

PLANT CELL (2006)

Article Computer Science, Information Systems

Engineering a software tool for gene structure prediction in higher organisms

G Gremme et al.

INFORMATION AND SOFTWARE TECHNOLOGY (2005)

Article Biochemistry & Molecular Biology

Genomic scans for selective sweeps using SNP data

R Nielsen et al.

GENOME RESEARCH (2005)

Article Multidisciplinary Sciences

The map-based sequence of the rice genome

T Matsumoto et al.

NATURE (2005)

Article Biochemical Research Methods

De novo identification of repeat families in large genomes

AL Price et al.

BIOINFORMATICS (2005)

Article Multidisciplinary Sciences

The effects of artificial selection of the maize genome

SI Wright et al.

SCIENCE (2005)

Article Cell Biology

Repbase update, a database of eukaryotic repetitive elements

J Jurka et al.

CYTOGENETIC AND GENOME RESEARCH (2005)

Article Multidisciplinary Sciences

Rapid recent growth and divergence of rice nuclear genomes

JX Ma et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2004)

Article Biotechnology & Applied Microbiology

Versatile and open software for comparing large genomes

S Kurtz et al.

GENOME BIOLOGY (2004)

Article Multidisciplinary Sciences

Semidwarf (sd-1), green revolution rice, contains a defective gibberellin 20-oxidase gene

W Spielmeyer et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2002)

Article Biochemistry & Molecular Biology

Ab initio gene finding in Drosophila genomic DNA

AA Salamov et al.

GENOME RESEARCH (2000)

Article Biochemistry & Molecular Biology

GeneID in Drosophila

G Parra et al.

GENOME RESEARCH (2000)

Article Biochemistry & Molecular Biology

ProtoMap: automatic classification of protein sequences and hierarchy of protein families

G Yona et al.

NUCLEIC ACIDS RESEARCH (2000)