CODEX: a normalization and copy number variation detection method for whole exome sequencing

Poisson factor models with applications to non-normalized microRNA profiling

(2013) Seonjoo Lee et al.   BIOINFORMATICS

CoNVEX: copy number variation estimation in exome sequencing data using HMM

(2013) Kaushalya C Amarasinghe et al.   BMC BIOINFORMATICS

The genetic landscape of high-risk neuroblastoma

(2013) Trevor J Pugh et al.   NATURE GENETICS

EXCAVATOR: detecting copy number variants from whole-exome sequencing data

(2013) Alberto Magi et al.   GENOME BIOLOGY

Discovery and Statistical Genotyping of Copy-Number Variation from Whole-Exome Sequencing Depth

(2012) Menachem Fromer et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Multiple hypothesis testing adjusted for latent variables, with an application to the AGEMAP gene expression data

(2012) Yunting Sun et al.   Annals of Applied Statistics

An exome sequencing pipeline for identifying and genotyping common CNVs associated with disease with application to psoriasis

(2012) L. J. M. Coin et al.   BIOINFORMATICS

A robust model for read count data in exome sequencing experiments and implications for copy number variant calling

(2012) Vincent Plagnol et al.   BIOINFORMATICS

Copy number variation detection and genotyping from exome sequence data

(2012) N. Krumm et al.   GENOME RESEARCH

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

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

Association of Age at Diagnosis and Genetic Mutations in Patients With Neuroblastoma

(2012) Nai-Kong V. Cheung   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Sequencing of neuroblastoma identifies chromothripsis and defects in neuritogenesis genes

(2012) Jan J. Molenaar et al.   NATURE

De novo mutations revealed by whole-exome sequencing are strongly associated with autism

(2012) Stephan J. Sanders et al.   NATURE

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

(2012) Yuval Benjamini et al.   NUCLEIC ACIDS RESEARCH

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

(2011) Jarupon Fah Sathirapongsasuti et al.   BIOINFORMATICS

CNVnator: An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing

(2011) A. Abyzov et al.   GENOME RESEARCH

Exome sequencing in sporadic autism spectrum disorders identifies severe de novo mutations

(2011) Brian J O'Roak et al.   NATURE GENETICS

Exome sequencing identifies somatic mutations of DNA methyltransferase gene DNMT3A in acute monocytic leukemia

(2011) Xiao-Jing Yan et al.   NATURE GENETICS

Detecting simultaneous changepoints in multiple sequences

(2010) N. R. Zhang et al.   BIOMETRIKA

A Factor Model Approach to Multiple Testing Under Dependence

(2010) Chloé Friguet et al.   JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION

Integrating common and rare genetic variation in diverse human populations

(2010)   NATURE

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

The Sequence Alignment/Map format and SAMtools

(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

High-Dimensional Sparse Factor Modeling: Applications in Gene Expression Genomics

(2009) Carlos M. Carvalho et al.   JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION

Copy number variation at 1q21.1 associated with neuroblastoma

(2009) Sharon J. Diskin et al.   NATURE

Autism genome-wide copy number variation reveals ubiquitin and neuronal genes

(2009) Joseph T. Glessner et al.   NATURE

Origins and functional impact of copy number variation in the human genome

(2009) Donald F. Conrad et al.   NATURE

Exome sequencing identifies the cause of a mendelian disorder

(2009) Sarah B Ng et al.   NATURE GENETICS

PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data

(2009) Jan O Korbel et al.   GENOME BIOLOGY

Mapping and sequencing of structural variation from eight human genomes

(2008) Jeffrey M. Kidd et al.   NATURE

Deletion polymorphism upstream of IRGM associated with altered IRGM expression and Crohn's disease

(2008) Steven A McCarroll et al.   NATURE GENETICS

Integrated detection and population-genetic analysis of SNPs and copy number variation

(2008) Steven A McCarroll et al.   NATURE GENETICS

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

(2008) Derek Y Chiang et al.   NATURE METHODS

A general framework for multiple testing dependence

(2008) J. T. Leek et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA