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

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

De novo assembly and genotyping of variants using colored de Bruijn graphs

(2012) Zamin Iqbal et al.   NATURE GENETICS

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

(2012) Yuval Benjamini et al.   NUCLEIC ACIDS RESEARCH

Efficient algorithms for tandem copy number variation reconstruction in repeat-rich regions

(2011) D. He et al.   BIOINFORMATICS

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

(2011) Jarupon Fah Sathirapongsasuti 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

Detecting structural variations in the human genome using next generation sequencing

(2011) R. Xi et al.   Briefings in Functional Genomics

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

Mapping copy number variation by population-scale genome sequencing

(2011) Ryan E. Mills et al.   NATURE

Discovery and genotyping of genome structural polymorphism by sequencing on a population scale

(2011) Robert E Handsaker et al.   NATURE GENETICS

Genome structural variation discovery and genotyping

(2011) Can Alkan et al.   NATURE REVIEWS GENETICS

Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries

(2011) Daniel Aird et al.   GENOME BIOLOGY

SVDetect: a tool to identify genomic structural variations from paired-end and mate-pair sequencing data

(2010) Bruno Zeitouni et al.   BIOINFORMATICS

Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome

(2010) A. R. Quinlan et al.   GENOME RESEARCH

Assembly of large genomes using second-generation sequencing

(2010) M. C. Schatz et al.   GENOME RESEARCH

Detecting copy number variation with mated short reads

(2010) P. Medvedev et al.   GENOME RESEARCH

A window into third-generation sequencing

(2010) E. E. Schadt et al.   HUMAN MOLECULAR GENETICS

Diversity of Human Copy Number Variation and Multicopy Genes

(2010) Peter H. Sudmant et al.   SCIENCE

Inversion variants in the human genome: role in disease and genome architecture

(2010) Lars Feuk   Genome Medicine

Towards a comprehensive structural variation map of an individual human genome

(2010) Andy W Pang et al.   GENOME BIOLOGY

A Computer Simulator for Assessing Different Challenges and Strategies of de Novo Sequence Assembly

(2010) Bjarne Knudsen et al.   Genes

Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads

(2009) K. Ye et al.   BIOINFORMATICS

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

(2009) Chao Xie et al.   BMC BIOINFORMATICS

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

(2009) S. Yoon et al.   GENOME RESEARCH

Combinatorial algorithms for structural variation detection in high-throughput sequenced genomes

(2009) F. Hormozdiari et al.   GENOME RESEARCH

Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding

(2009) K. J. McKernan et al.   GENOME RESEARCH

ABySS: A parallel assembler for short read sequence data

(2009) J. T. Simpson et al.   GENOME RESEARCH

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

(2009) R. Li et al.   GENOME RESEARCH

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

(2009) Donald F. Conrad et al.   NATURE

Mapping duplicated sequences

(2009) Derek Y Chiang et al.   NATURE BIOTECHNOLOGY

Personalized copy number and segmental duplication maps using next-generation sequencing

(2009) Can Alkan et al.   NATURE GENETICS

Computational methods for discovering structural variation with next-generation sequencing

(2009) Paul Medvedev et al.   NATURE METHODS

BreakDancer: an algorithm for high-resolution mapping of genomic structural variation

(2009) Ken Chen et al.   NATURE METHODS

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS 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

Evaluation of next generation sequencing platforms for population targeted sequencing studies

(2009) Olivier Harismendy et al.   GENOME BIOLOGY

Mapping short DNA sequencing reads and calling variants using mapping quality scores

(2008) H. Li et al.   GENOME RESEARCH

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

The diploid genome sequence of an Asian individual

(2008) Jun Wang et al.   NATURE

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