Correcting for cancer genome size and tumour cell content enables better estimation of copy number alterations from next-generation sequence data

Control-free calling of copy number alterations in deep-sequencing data using GC-content normalization

(2010) Valentina Boeva et al.   BIOINFORMATICS

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

(2010) Sergii Ivakhno et al.   BIOINFORMATICS

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

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

DNA copy number, including telomeres and mitochondria, assayed using next-generation sequencing

(2010) John C Castle et al.   BMC GENOMICS

Using next-generation sequencing for high resolution multiplex analysis of copy number variation from nanogram quantities of DNA from formalin-fixed paraffin-embedded specimens

(2010) Henry M. Wood et al.   NUCLEIC ACIDS RESEARCH

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

PICNIC: an algorithm to predict absolute allelic copy number variation with microarray cancer data

(2009) C. D. Greenman et al.   BIOSTATISTICS

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

(2009) Chao Xie et al.   BMC BIOINFORMATICS

CGHnormaliter: an iterative strategy to enhance normalization of array CGH data with imbalanced aberrations

(2009) Bart PP van Houte et al.   BMC GENOMICS

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

(2009) S. Yoon et al.   GENOME RESEARCH

A comprehensive catalogue of somatic mutations from a human cancer genome

(2009) Erin D. Pleasance et al.   NATURE

A probe-density-based analysis method for array CGH data: simulation, normalization and centralization

(2008) Hung-I Harry Chen et al.   BIOINFORMATICS

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

(2008) Derek Y Chiang et al.   NATURE METHODS