CNAseg—a novel framework for identification of copy number changes in cancer from second-generation sequencing data

The landscape of somatic copy-number alteration across human cancers

(2010) Rameen Beroukhim et al.   NATURE

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

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

A comprehensive catalogue of somatic mutations from a human cancer genome

(2009) Erin D. Pleasance et al.   NATURE

Complex landscapes of somatic rearrangement in human breast cancer genomes

(2009) Philip J. Stephens et al.   NATURE

The cancer genome

(2009) Michael R. Stratton et al.   NATURE

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

(2009) Can Alkan 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

Transcriptome-guided characterization of genomic rearrangements in a breast cancer cell line

(2009) Qi Zhao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A robust framework for detecting structural variations in a genome

(2008) S. Lee et al.   BIOINFORMATICS

A sequence-level map of chromosomal breakpoints in the MCF-7 breast cancer cell line yields insights into the evolution of a cancer genome

(2008) O. A. Hampton et al.   GENOME RESEARCH

Accurate whole human genome sequencing using reversible terminator chemistry

(2008) David R. Bentley et al.   NATURE

Next-generation DNA sequencing

(2008) Jay Shendure et al.   NATURE BIOTECHNOLOGY

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

Whole-genome sequencing and variant discovery in C. elegans

(2008) LaDeana W Hillier 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