Detection of genomic variations and DNA polymorphisms and impact on analysis of meiotic recombination and genetic mapping

Massive genomic variation and strong selection in Arabidopsis thaliana lines from Sweden

(2013) Quan Long et al.   NATURE GENETICS

The genomic landscape of meiotic crossovers and gene conversions in Arabidopsis thaliana

(2013) Erik Wijnker et al.   eLife

Performance comparison of benchtop high-throughput sequencing platforms

(2012) Nicholas J Loman et al.   NATURE BIOTECHNOLOGY

The UCSC Genome Browser database: extensions and updates 2013

(2012) Laurence R. Meyer et al.   NUCLEIC ACIDS RESEARCH

Great majority of recombination events in Arabidopsis are gene conversion events

(2012) S. Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Deep Genome-Wide Measurement of Meiotic Gene Conversion Using Tetrad Analysis in Arabidopsis thaliana

(2012) Yujin Sun et al.   PLoS Genetics

Analysis of Arabidopsis genome-wide variations before and after meiosis and meiotic recombination by resequencing Landsberg erecta and all four products of a single meiosis

(2011) P. Lu et al.   GENOME RESEARCH

Mapping copy number variation by population-scale genome sequencing

(2011) Ryan E. Mills et al.   NATURE

Whole-genome sequencing of multiple Arabidopsis thaliana populations

(2011) Jun Cao et al.   NATURE GENETICS

inGAP-sv: a novel scheme to identify and visualize structural variation from paired end mapping data

(2011) Ji Qi et al.   NUCLEIC ACIDS RESEARCH

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

(2011) Philippe Lamesch et al.   NUCLEIC ACIDS RESEARCH

Reference-guided assembly of four diverse Arabidopsis thaliana genomes

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

Enhanced structural variant and breakpoint detection using SVMerge by integration of multiple detection methods and local assembly

(2011) Kim Wong et al.   GENOME BIOLOGY

Structural Variation in the Human Genome and its Role in Disease

(2010) Paweł Stankiewicz et al.   Annual Review of Medicine

Detection and characterization of novel sequence insertions using paired-end next-generation sequencing

(2010) Iman Hajirasouliha et al.   BIOINFORMATICS

SVDetect: a tool to identify genomic structural variations from paired-end and mate-pair sequencing data

(2010) Bruno Zeitouni et al.   BIOINFORMATICS

SLOPE: a quick and accurate method for locating non-SNP structural variation from targeted next-generation sequence data

(2010) H. J. Abel et al.   BIOINFORMATICS

The flowering gene SINGLE FLOWER TRUSS drives heterosis for yield in tomato

(2010) Uri Krieger et al.   NATURE GENETICS

Genome-wide association studies of 14 agronomic traits in rice landraces

(2010) Xuehui Huang et al.   NATURE GENETICS

inGAP: an integrated next-generation genome analysis pipeline

(2009) Ji Qi et al.   BIOINFORMATICS

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

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Characterization of meiotic crossovers and gene conversion by whole-genome sequencing in Saccharomyces cerevisiae

(2009) Ji Qi et al.   BMC GENOMICS

Combinatorial algorithms for structural variation detection in high-throughput sequenced genomes

(2009) F. Hormozdiari et al.   GENOME RESEARCH

Bursts of retrotransposition reproduced in Arabidopsis

(2009) Sayuri Tsukahara et al.   NATURE

MoDIL: detecting small indels from clone-end sequencing with mixtures of distributions

(2009) Seunghak Lee et al.   NATURE METHODS

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

(2009) Ken Chen et al.   NATURE METHODS

PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data

(2009) Jan O Korbel et al.   GENOME BIOLOGY

SOAP: short oligonucleotide alignment program

(2008) R. Li et al.   BIOINFORMATICS

Quality scores and SNP detection in sequencing-by-synthesis systems

(2008) W. Brockman et al.   GENOME RESEARCH

Mapping short DNA sequencing reads and calling variants using mapping quality scores

(2008) H. Li et al.   GENOME RESEARCH

Mapping and sequencing of structural variation from eight human genomes

(2008) Jeffrey M. Kidd et al.   NATURE

Natural Selection Shapes Genome-Wide Patterns of Copy-Number Polymorphism in Drosophila melanogaster

(2008) J. J. Emerson et al.   SCIENCE

The functional impact of structural variation in humans

(2008) Matthew E. Hurles et al.   TRENDS IN GENETICS