Detecting structural variations in the human genome using next generation sequencing

Structural variation analysis with strobe reads

(2010) A. Ritz et al.   BIOINFORMATICS

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

(2010) Iman Hajirasouliha et al.   BIOINFORMATICS

Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery

(2010) Fereydoun Hormozdiari et al.   BIOINFORMATICS

rSW-seq: Algorithm for detection of copy number alterations in deep sequencing data

(2010) Tae-Min Kim et al.   BMC BIOINFORMATICS

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

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

Global and unbiased detection of splice junctions from RNA-seq data

(2010) Adam Ameur et al.   GENOME BIOLOGY

Copy Number Variation in Human Health, Disease, and Evolution

(2009) Feng Zhang et al.   Annual Review of Genomics and Human Genetics

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

CNV-seq, a new method to detect copy number variation using high-throughput sequencing

(2009) Chao Xie et al.   BMC BIOINFORMATICS

Sensitive and accurate detection of copy number variants using read depth of coverage

(2009) S. Yoon et al.   GENOME RESEARCH

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

(2009) F. Hormozdiari et al.   GENOME RESEARCH

Transcriptome sequencing to detect gene fusions in cancer

(2009) Christopher A. Maher et al.   NATURE

Large, rare chromosomal deletions associated with severe early-onset obesity

(2009) Elena G. Bochukova et al.   NATURE

Autism genome-wide copy number variation reveals ubiquitin and neuronal genes

(2009) Joseph T. Glessner et al.   NATURE

Origins and functional impact of copy number variation in the human genome

(2009) Donald F. Conrad et al.   NATURE

PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls

(2009) Joel Rozowsky et al.   NATURE BIOTECHNOLOGY

Duplications of noncoding elements 5′ of SOX9 are associated with brachydactyly-anonychia

(2009) Ingo Kurth et al.   NATURE GENETICS

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

Chimeric transcript discovery by paired-end transcriptome sequencing

(2009) C. A. Maher et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Contemplating effects of genomic structural variation

(2008) Janet A Buchanan et al.   GENETICS IN MEDICINE

ALLPATHS: De novo assembly of whole-genome shotgun microreads

(2008) J. Butler et al.   GENOME RESEARCH

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

Mapping and sequencing of structural variation from eight human genomes

(2008) Jeffrey M. Kidd et al.   NATURE

Next-generation DNA sequencing

(2008) Jay Shendure et al.   NATURE BIOTECHNOLOGY

Systematic assessment of copy number variant detection via genome-wide SNP genotyping

(2008) Gregory M Cooper et al.   NATURE GENETICS

Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing

(2008) Peter J Campbell et al.   NATURE GENETICS

High-resolution mapping of copy-number alterations with massively parallel sequencing

(2008) Derek Y Chiang et al.   NATURE METHODS

Substantial biases in ultra-short read data sets from high-throughput DNA sequencing

(2008) J. C. Dohm et al.   NUCLEIC ACIDS RESEARCH

Evaluation of Paired-End Sequencing Strategies for Detection of Genome Rearrangements in Cancer

(2008) Ali Bashir et al.   PLoS Computational Biology