PeSV-Fisher: Identification of Somatic and Non-Somatic Structural Variants Using Next Generation Sequencing Data

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

(2012) T. Rausch et al.   BIOINFORMATICS

The Life History of 21 Breast Cancers

(2012) Serena Nik-Zainal et al.   CELL

Detectable clonal mosaicism and its relationship to aging and cancer

(2012) Kevin B Jacobs et al.   NATURE GENETICS

The GEM mapper: fast, accurate and versatile alignment by filtration

(2012) Santiago Marco-Sola et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

An integrative probabilistic model for identification of structural variation in sequencing data

(2012) Suzanne S Sindi et al.   GENOME BIOLOGY

Massive Genomic Rearrangement Acquired in a Single Catastrophic Event during Cancer Development

(2011) Philip J. Stephens et al.   CELL

Chromosome Catastrophes Involve Replication Mechanisms Generating Complex Genomic Rearrangements

(2011) Pengfei Liu et al.   CELL

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

Chromothripsis as a mechanism driving complex de novo structural rearrangements in the germline†

(2011) Wigard P. Kloosterman et al.   HUMAN MOLECULAR GENETICS

Mapping copy number variation by population-scale genome sequencing

(2011) Ryan E. Mills et al.   NATURE

Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia

(2011) Xose S. Puente et al.   NATURE

CREST maps somatic structural variation in cancer genomes with base-pair resolution

(2011) Jianmin Wang et al.   NATURE METHODS

Genome structural variation discovery and genotyping

(2011) Can Alkan et al.   NATURE REVIEWS 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

A Comprehensive Map of Mobile Element Insertion Polymorphisms in Humans

(2011) Chip Stewart et al.   PLoS Genetics

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

(2011) Kim Wong et al.   GENOME BIOLOGY

Chromothripsis is a common mechanism driving genomic rearrangements in primary and metastatic colorectal cancer

(2011) Wigard P Kloosterman 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

Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery

(2010) Fereydoun Hormozdiari et al.   BIOINFORMATICS

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

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

Detecting copy number variation with mated short reads

(2010) P. Medvedev et al.   GENOME RESEARCH

International network of cancer genome projects

(2010) Thomas J. Hudson (Chairperson) et al.   NATURE

Diversity of Human Copy Number Variation and Multicopy Genes

(2010) Peter H. Sudmant et al.   SCIENCE

Copy Number Variation in Human Health, Disease, and Evolution

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

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

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   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

De novo assembly of human genomes with massively parallel short read sequencing

(2009) R. Li et al.   GENOME RESEARCH

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

(2009) Donald F. Conrad et al.   NATURE

Personalized copy number and segmental duplication maps using next-generation sequencing

(2009) Can Alkan et al.   NATURE GENETICS

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

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

Sparse representation and Bayesian detection of genome copy number alterations from microarray data

(2008) Roger Pique-Regi et al.   BIOINFORMATICS

SOAP: short oligonucleotide alignment program

(2008) R. Li et al.   BIOINFORMATICS

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