AbsCN-seq: a statistical method to estimate tumor purity, ploidy and absolute copy numbers from next-generation sequencing data

The Exomes of the NCI-60 Panel: A Genomic Resource for Cancer Biology and Systems Pharmacology

(2013) O. D. Abaan et al.   CANCER RESEARCH

PurityEst: estimating purity of human tumor samples using next-generation sequencing data

(2012) X. Su et al.   BIOINFORMATICS

VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing

(2012) D. C. Koboldt et al.   GENOME RESEARCH

Sequence analysis of mutations and translocations across breast cancer subtypes

(2012) Shantanu Banerji et al.   NATURE

Absolute quantification of somatic DNA alterations in human cancer

(2012) Scott L Carter et al.   NATURE BIOTECHNOLOGY

Immune Surveillance from Chromosomal Chaos?

(2012) M. Zanetti et al.   SCIENCE

BACOM: in silico detection of genomic deletion types and correction of normal cell contamination in copy number data

(2011) Guoqiang Yu et al.   BIOINFORMATICS

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

(2011) Arief Gusnanto et al.   BIOINFORMATICS

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

Low-coverage sequencing: Implications for design of complex trait association studies

(2011) Y. Li et al.   GENOME RESEARCH

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

TumorBoost: Normalization of allele-specific tumor copy numbers from a single pair of tumor-normal genotyping microarrays

(2010) Henrik Bengtsson et al.   BMC BIOINFORMATICS

The landscape of somatic copy-number alteration across human cancers

(2010) Rameen Beroukhim et al.   NATURE

Allele-specific copy number analysis of tumors

(2010) P. Van Loo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Sequence Alignment/Map format and SAMtools

(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

Genomic copy number determination in cancer cells from single nucleotide polymorphism microarrays based on quantitative genotyping corrected for aneuploidy

(2009) E. F. Attiyeh et al.   GENOME RESEARCH

Comprehensive genomic characterization defines human glioblastoma genes and core pathways

(2008) Roger McLendon et al.   NATURE