CLImAT: accurate detection of copy number alteration and loss of heterozygosity in impure and aneuploid tumor samples using whole-genome sequencing data

Comparative Studies of Copy Number Variation Detection Methods for Next-Generation Sequencing Technologies

(2013) Junbo Duan et al.   PLoS One

Virmid: accurate detection of somatic mutations with sample impurity inference

(2013) Sangwoo Kim et al.   GENOME BIOLOGY

Patchwork: allele-specific copy number analysis of whole-genome sequenced tumor tissue

(2013) Markus Mayrhofer et al.   GENOME BIOLOGY

THetA: inferring intra-tumor heterogeneity from high-throughput DNA sequencing data

(2013) Layla Oesper et al.   GENOME BIOLOGY

Integrative analysis of genome-wide loss of heterozygosity and monoallelic expression at nucleotide resolution reveals disrupted pathways in triple-negative breast cancer

(2012) G. Ha et al.   GENOME RESEARCH

Absolute quantification of somatic DNA alterations in human cancer

(2012) Scott L Carter et al.   NATURE BIOTECHNOLOGY

Exome sequencing-based copy-number variation and loss of heterozygosity detection: ExomeCNV

(2011) Jarupon Fah Sathirapongsasuti 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

Control-FREEC: a tool for assessing copy number and allelic content using next-generation sequencing data

(2011) Valentina Boeva et al.   BIOINFORMATICS

The telomerase inhibitor PinX1 is a major haploinsufficient tumor suppressor essential for chromosome stability in mice

(2011) Xiao Zhen Zhou et al.   JOURNAL OF CLINICAL INVESTIGATION

GPHMM: an integrated hidden Markov model for identification of copy number alteration and loss of heterozygosity in complex tumor samples using whole genome SNP arrays

(2011) Ao Li et al.   NUCLEIC ACIDS RESEARCH

Copy number variation detection in whole-genome sequencing data using the Bayesian information criterion

(2011) R. Xi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2010) Valentina Boeva et al.   BIOINFORMATICS

SNVMix: predicting single nucleotide variants from next-generation sequencing of tumors

(2010) Rodrigo Goya et al.   BIOINFORMATICS

Signatures of mutation and selection in the cancer genome

(2010) Graham R. Bignell 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

High-risk neuroblastoma tumors with 11q-deletion display a poor prognostic, chromosome instability phenotype with later onset

(2010) H. Caren et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

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

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

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Next-Generation DNA Sequencing Methods

(2008) Elaine R. Mardis   Annual Review of Genomics and Human Genetics

Experimental Design and Data Analysis for Array Comparative Genomic Hybridization

(2008) Peter J. Park   CANCER INVESTIGATION

Applications of next-generation sequencing technologies in functional genomics

(2008) Olena Morozova et al.   GENOMICS