Structural variants in 3000 rice genomes

Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza

(2018) Joshua C. Stein et al.   NATURE GENETICS

Genomic variation in 3,010 diverse accessions of Asian cultivated rice

(2018) Wensheng Wang et al.   NATURE

The impact of structural variation on human gene expression

(2017) Colby Chiang et al.   NATURE GENETICS

agriGO v2.0: a GO analysis toolkit for the agricultural community, 2017 update

(2017) Tian Tian et al.   NUCLEIC ACIDS RESEARCH

Translational repression by a miniature inverted-repeat transposable element in the 3′ untranslated region

(2017) Jianqiang Shen et al.   Nature Communications

The sponge microbiome project

(2017) Lucas Moitinho-Silva et al.   GigaScience

Nucleotide patterns aiding in prediction of eukaryotic promoters

(2017) Martin Triska et al.   PLoS One

The impact and origin of copy number variations in the Oryza species

(2016) Zetao Bai et al.   BMC GENOMICS

1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana

(2016) Carlos Alonso-Blanco et al.   CELL

Rice SNP-seek database update: new SNPs, indels, and queries

(2016) Locedie Mansueto et al.   NUCLEIC ACIDS RESEARCH

The effect of transposable elements on phenotypic variation: insights from plants to humans

(2016) Liya Wei et al.   Science China-Life Sciences

Nucleotide diversity analysis highlights functionally important genomic regions

(2016) Tatiana V. Tatarinova et al.   Scientific Reports

MetaSV: an accurate and integrative structural-variant caller for next generation sequencing

(2015) Marghoob Mohiyuddin et al.   BIOINFORMATICS

Multiply to conquer: Copy number variations at Ppd-B1 and Vrn-A1 facilitate global adaptation in wheat

(2015) Tobias Würschum et al.   BMC GENETICS

RiTE database: a resource database for genus-wide rice genomics and evolutionary biology

(2015) Dario Copetti et al.   BMC GENOMICS

A decade of structural variants: description, history and methods to detect structural variation

(2015) Geòrgia Escaramís et al.   Briefings in Functional Genomics

An integrated map of structural variation in 2,504 human genomes

(2015) Peter H. Sudmant et al.   NATURE

Copy number variation at the GL7 locus contributes to grain size diversity in rice

(2015) Yuexing Wang et al.   NATURE GENETICS

Genome-Wide Mapping of Structural Variations Reveals a Copy Number Variant That Determines Reproductive Morphology in Cucumber

(2015) Zhonghua Zhang et al.   PLANT CELL

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

(2015) Jorge Duitama et al.   PLoS One

High-resolution genetic mapping of maize pan-genome sequence anchors

(2015) Fei Lu et al.   Nature Communications

ScanIndel: a hybrid framework for indel detection via gapped alignment, split reads and de novo assembly

(2015) Rendong Yang et al.   Genome Medicine

Transposable Elements Contribute to Activation of Maize Genes in Response to Abiotic Stress

(2015) Irina Makarevitch et al.   PLoS Genetics

GROM-RD: resolving genomic biases to improve read depth detection of copy number variants

(2015) Sean D. Smith et al.   PeerJ

A trehalose-6-phosphate phosphatase enhances anaerobic germination tolerance in rice

(2015) Tobias Kretzschmar et al.   Nature Plants

MindTheGap: integrated detection and assembly of short and long insertions

(2014) G. Rizk et al.   BIOINFORMATICS

Socrates: identification of genomic rearrangements in tumour genomes by re-aligning soft clipped reads

(2014) Jan Schröder et al.   BIOINFORMATICS

mPing: The bursting transposon

(2014) Ken Naito et al.   BREEDING SCIENCE

Structural variations in plant genomes

(2014) R. K. Saxena et al.   Briefings in Functional Genomics

Accurate de novo and transmitted indel detection in exome-capture data using microassembly

(2014) Giuseppe Narzisi et al.   NATURE METHODS

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

(2014) Jorge Duitama et al.   NUCLEIC ACIDS RESEARCH

SNP-Seek database of SNPs derived from 3000 rice genomes

(2014) Nickolai Alexandrov et al.   NUCLEIC ACIDS RESEARCH

LUMPY: a probabilistic framework for structural variant discovery

(2014) Ryan M Layer et al.   GENOME BIOLOGY

The 3,000 rice genomes project

(2014)   GigaScience

Computational tools for copy number variation (CNV) detection using next-generation sequencing data: features and perspectives

(2013) Min Zhao et al.   BMC BIOINFORMATICS

Comparison of class 2 transposable elements at superfamily resolution reveals conserved and distinct features in cereal grass genomes

(2013) Yujun Han et al.   BMC GENOMICS

Diverse Mechanisms of Somatic Structural Variations in Human Cancer Genomes

(2013) Lixing Yang et al.   CELL

Copy number polymorphism in plant genomes

(2013) Agnieszka Żmieńko et al.   THEORETICAL AND APPLIED GENETICS

DELLY: structural variant discovery by integrated paired-end and split-read analysis

(2012) T. Rausch et al.   BIOINFORMATICS

Control of grain size, shape and quality by OsSPL16 in rice

(2012) Shaokui Wang et al.   NATURE GENETICS

Genome-wide efficient mixed-model analysis for association studies

(2012) Xiang Zhou et al.   NATURE GENETICS

Structural variation: the genome's hidden architecture

(2012) Monya Baker   NATURE METHODS

A tandem segmental duplication (TSD) in green revolution gene Rht-D1b region underlies plant height variation

(2012) Yiyuan Li et al.   NEW PHYTOLOGIST

Structural Variants in the Soybean Genome Localize to Clusters of Biotic Stress-Response Genes

(2012) L. K. McHale et al.   PLANT PHYSIOLOGY

Copy Number Variation of Multiple Genes at Rhg1 Mediates Nematode Resistance in Soybean

(2012) D. E. Cook et al.   SCIENCE

Crops that feed the world 7: Rice

(2012) Papa Abdoulaye Seck et al.   Food Security

CNVnator: An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing

(2011) A. Abyzov et al.   GENOME RESEARCH

Miniature Inverted-Repeat Transposable Elements (MITEs) Have Been Accumulated through Amplification Bursts and Play Important Roles in Gene Expression and Species Diversity in Oryza sativa

(2011) C. Lu 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

Genome structural variation discovery and genotyping

(2011) Can Alkan et al.   NATURE REVIEWS GENETICS

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

(2010) Heng Li et al.   BIOINFORMATICS

Copy Number Variation Shapes Genome Diversity in Arabidopsis Over Immediate Family Generational Scales

(2010) Seth DeBolt   Genome Biology and Evolution

Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome

(2010) A. R. Quinlan et al.   GENOME RESEARCH

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

(2010) A. McKenna et al.   GENOME RESEARCH

Pervasive gene content variation and copy number variation in maize and its undomesticated progenitor

(2010) R. A. Swanson-Wagner et al.   GENOME RESEARCH

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

Q-TARO: QTL Annotation Rice Online Database

(2010) Jun-ichi Yonemaru et al.   Rice

A geometric approach for classification and comparison of structural variants

(2009) S. Sindi et al.   BIOINFORMATICS

Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads

(2009) K. Ye et al.   BIOINFORMATICS

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

(2009) Noriko Takano-Kai et al.   GENETICS

Unexpected consequences of a sudden and massive transposon amplification on rice gene expression

(2009) Ken Naito et al.   NATURE

Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library

(2009) Hugo Y K Lam et al.   NATURE BIOTECHNOLOGY

Computational methods for discovering structural variation with next-generation sequencing

(2009) Paul Medvedev et al.   NATURE METHODS

BreakDancer: an algorithm for high-resolution mapping of genomic structural variation

(2009) Ken Chen et al.   NATURE METHODS

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH

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

(2008) Ayahiko Shomura et al.   NATURE GENETICS