DNA copy number analysis of fresh and formalin-fixed specimens by shallow whole-genome sequencing with identification and exclusion of problematic regions in the genome assembly

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

(2014) Zhenhua Yu et al.   BIOINFORMATICS

Coverage Bias and Sensitivity of Variant Calling for Four Whole-genome Sequencing Technologies

(2013) Nora Rieber et al.   PLoS One

Change-point model on nonhomogeneous Poisson processes with application in copy number profiling by next-generation DNA sequencing

(2012) Jeremy J. Shen et al.   Annals of Applied Statistics

Statistical challenges associated with detecting copy number variations with next-generation sequencing

(2012) Shu Mei Teo et al.   BIOINFORMATICS

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

An integrated map of genetic variation from 1,092 human genomes

(2012)   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

ENCODE Data in the UCSC Genome Browser: year 5 update

(2012) Kate R. Rosenbloom et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2013

(2012) Paul Flicek et al.   NUCLEIC ACIDS RESEARCH

Summarizing and correcting the GC content bias in high-throughput sequencing

(2012) Yuval Benjamini et al.   NUCLEIC ACIDS RESEARCH

Genetics and pharmacogenomics of diffuse gliomas

(2012) H.F. van Thuijl et al.   PHARMACOLOGY & THERAPEUTICS

Fast Computation and Applications of Genome Mappability

(2012) Thomas Derrien et al.   PLoS One

Detection limits of DNA copy number alterations in heterogeneous cell populations

(2012) Oscar Krijgsman et al.   CELLULAR ONCOLOGY

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

Chipster: user-friendly analysis software for microarray and other high-throughput data

(2011) M Aleksi Kallio et al.   BMC GENOMICS

Hallmarks of Cancer: The Next Generation

(2011) Douglas Hanahan et al.   CELL

Two Distinct Routes to Oral Cancer Differing in Genome Instability and Risk for Cervical Node Metastasis

(2011) A. Bhattacharya et al.   CLINICAL CANCER RESEARCH

CGH arrays compared for DNA isolated from formalin-fixed, paraffin-embedded material

(2011) Oscar Krijgsman et al.   GENES CHROMOSOMES & CANCER

Genomic aberrations in pediatric diffuse intrinsic pontine gliomas

(2011) K. E. Warren et al.   NEURO-ONCOLOGY

ReadDepth: A Parallel R Package for Detecting Copy Number Alterations from Short Sequencing Reads

(2011) Christopher A. Miller et al.   PLoS One

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

Preprocessing and downstream analysis of microarray DNA copy number profiles

(2010) M. A. van de Wiel et al.   BRIEFINGS IN BIOINFORMATICS

The European Nucleotide Archive

(2010) R. Leinonen et al.   NUCLEIC ACIDS RESEARCH

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

Smoothing waves in array CGH tumor profiles

(2009) Mark A. van de Wiel 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

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

(2009) R. Li et al.   GENOME RESEARCH

Random DNA fragmentation allows detection of single-copy, single-exon alterations of copy number by oligonucleotide array CGH in clinical FFPE samples

(2009) Galen Hostetter et al.   NUCLEIC ACIDS RESEARCH

The Fine-Scale and Complex Architecture of Human Copy-Number Variation

(2008) George H. Perry et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Enhanced detection of clinically relevant genomic imbalances using a targeted plus whole genome oligonucleotide microarray

(2008) Erin L Baldwin et al.   GENETICS IN MEDICINE

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

(2008) Derek Y Chiang et al.   NATURE METHODS