Analysis of deletion breakpoints from 1,092 humans reveals details of mutation mechanisms

TIGRA: A targeted iterative graph routing assembler for breakpoint assembly

(2013) K. Chen et al.   GENOME RESEARCH

Replicative mechanisms for CNV formation are error prone

(2013) Claudia M B Carvalho et al.   NATURE GENETICS

Organization of the Mitotic Chromosome

(2013) N. Naumova et al.   SCIENCE

Comment on “Genomic Hypomethylation in the Human Germline Associates with Selective Structural Mutability in the Human Genome”

(2013) Corey T. Watson et al.   PLoS Genetics

Differential Relationship of DNA Replication Timing to Different Forms of Human Mutation and Variation

(2012) Amnon Koren et al.   AMERICAN JOURNAL OF HUMAN GENETICS

DELLY: structural variant discovery by integrated paired-end and split-read analysis

(2012) T. Rausch et al.   BIOINFORMATICS

BreakFusion: targeted assembly-based identification of gene fusions in whole transcriptome paired-end sequencing data

(2012) K. Chen et al.   BIOINFORMATICS

TrxG and PcG Proteins but Not Methylated Histones Remain Associated with DNA through Replication

(2012) Svetlana Petruk et al.   CELL

Personal Omics Profiling Reveals Dynamic Molecular and Medical Phenotypes

(2012) Rui Chen et al.   CELL

Mechanisms of Formation of Structural Variation in a Fully Sequenced Human Genome

(2012) Andy Wing Chun Pang et al.   HUMAN MUTATION

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

Detecting and annotating genetic variations using the HugeSeq pipeline

(2012) Hugo Y K Lam et al.   NATURE BIOTECHNOLOGY

Iterative correction of Hi-C data reveals hallmarks of chromosome organization

(2012) Maxim Imakaev et al.   NATURE METHODS

Extrachromosomal MicroDNAs and Chromosomal Microdeletions in Normal Tissues

(2012) Y. Shibata et al.   SCIENCE

Landscape of Somatic Retrotransposition in Human Cancers

(2012) E. Lee et al.   SCIENCE

The NIH Roadmap Epigenomics Program data resource

(2012) Lisa Helbling Chadwick   Epigenomics

Genomic Hypomethylation in the Human Germline Associates with Selective Structural Mutability in the Human Genome

(2012) Jian Li et al.   PLoS Genetics

AGE: defining breakpoints of genomic structural variants at single-nucleotide resolution, through optimal alignments with gap excision

(2011) Alexej Abyzov et al.   BIOINFORMATICS

Sperm Methylation Profiles Reveal Features of Epigenetic Inheritance and Evolution in Primates

(2011) Antoine Molaro et al.   CELL

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

Extensive genomic and transcriptional diversity identified through massively parallel DNA and RNA sequencing of eighteen Korean individuals

(2011) Young Seok Ju et al.   NATURE GENETICS

Structural Variation in the Human Genome and its Role in Disease

(2010) Paweł Stankiewicz et al.   Annual Review of Medicine

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

A Human Genome Structural Variation Sequencing Resource Reveals Insights into Mutational Mechanisms

(2010) Jeffrey M. Kidd et al.   CELL

Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls

(2010)   NATURE

Functional impact of global rare copy number variation in autism spectrum disorders

(2010) Dalila Pinto et al.   NATURE

Mutation spectrum revealed by breakpoint sequencing of human germline CNVs

(2010) Donald F Conrad et al.   NATURE GENETICS

Towards a comprehensive structural variation map of an individual human genome

(2010) Andy W Pang et al.   GENOME BIOLOGY

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

Duplication hotspots, rare genomic disorders, and common disease

(2009) Heather C Mefford et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Extrachromosomal Circular DNA in Eukaryotes: Possible Involvement in the Plasticity of Tandem Repeats

(2009) S. Cohen et al.   CYTOGENETIC AND GENOME RESEARCH

HapMap methylation-associated SNPs, markers of germline DNA methylation, positively correlate with regional levels of human meiotic recombination

(2009) M. I. Sigurdsson et al.   GENOME RESEARCH

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

(2009) Donald F. Conrad et al.   NATURE

Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library

(2009) Hugo Y K Lam et al.   NATURE BIOTECHNOLOGY

Microduplications of 16p11.2 are associated with schizophrenia

(2009) Shane E McCarthy et al.   NATURE GENETICS

The DNA replication FoSTeS/MMBIR mechanism can generate genomic, genic and exonic complex rearrangements in humans

(2009) Feng Zhang et al.   NATURE GENETICS

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

(2009) Ken Chen et al.   NATURE METHODS

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

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

(2008) Steven A McCarroll et al.   NATURE GENETICS