Wham: Identifying Structural Variants of Biological Consequence

RAPTR-SV: a hybrid method for the detection of structural variants

(2015) D. M. Bickhart et al.   BIOINFORMATICS

Large multiallelic copy number variations in humans

(2015) Robert E Handsaker et al.   NATURE GENETICS

Epistatic and Combinatorial Effects of Pigmentary Gene Mutations in the Domestic Pigeon

(2014) Eric T. Domyan et al.   CURRENT BIOLOGY

Duplication of the A17L Locus of Vaccinia Virus Provides an Alternate Route to Rifampin Resistance

(2014) K. J. Erlandson et al.   JOURNAL OF VIROLOGY

Resolving the complexity of the human genome using single-molecule sequencing

(2014) Mark J. P. Chaisson et al.   NATURE

Accurate de novo and transmitted indel detection in exome-capture data using microassembly

(2014) Giuseppe Narzisi et al.   NATURE METHODS

Sequencing depth and coverage: key considerations in genomic analyses

(2014) David Sims et al.   NATURE REVIEWS GENETICS

Adaptive Gene Amplification As an Intermediate Step in the Expansion of Virus Host Range

(2014) Greg Brennan et al.   PLoS Pathogens

LUMPY: a probabilistic framework for structural variant discovery

(2014) Ryan M Layer et al.   GENOME BIOLOGY

MATE-CLEVER: Mendelian-inheritance-aware discovery and genotyping of midsize and long indels

(2013) Tobias Marschall et al.   BIOINFORMATICS

iSVP: an integrated structural variant calling pipeline from high-throughput sequencing data

(2013) Takahiro Mimori et al.   BMC Systems Biology

Domestic pigeons

(2013) Michael D. Shapiro et al.   CURRENT BIOLOGY

Copy number change: evolving views on gene amplification

(2013) Kathryn T Elliott et al.   Future Microbiology

TIGRA: A targeted iterative graph routing assembler for breakpoint assembly

(2013) K. Chen et al.   GENOME RESEARCH

The genomic signature of dog domestication reveals adaptation to a starch-rich diet

(2013) Erik Axelsson et al.   NATURE

Phenotypic impact of genomic structural variation: insights from and for human disease

(2013) Joachim Weischenfeldt et al.   NATURE REVIEWS GENETICS

SoftSearch: Integration of Multiple Sequence Features to Identify Breakpoints of Structural Variations

(2013) Steven N. Hart et al.   PLoS One

SSW Library: An SIMD Smith-Waterman C/C++ Library for Use in Genomic Applications

(2013) Mengyao Zhao et al.   PLoS One

Genomic Diversity and Evolution of the Head Crest in the Rock Pigeon

(2013) M. D. Shapiro et al.   SCIENCE

CLEVER: clique-enumerating variant finder

(2012) Tobias Marschall et al.   BIOINFORMATICS

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

(2012) T. Rausch et al.   BIOINFORMATICS

Poxviruses Deploy Genomic Accordions to Adapt Rapidly against Host Antiviral Defenses

(2012) Nels C. Elde et al.   CELL

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

(2012)   NATURE

forestSV: structural variant discovery through statistical learning

(2012) Jacob J Michaelson et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

dbVar and DGVa: public archives for genomic structural variation

(2012) Ilkka Lappalainen et al.   NUCLEIC ACIDS RESEARCH

An integrative probabilistic model for identification of structural variation in sequencing data

(2012) Suzanne S Sindi et al.   GENOME BIOLOGY

Challenges in studying genomic structural variant formation mechanisms: The short-read dilemma and beyond

(2011) Megumi Onishi-Seebacher et al.   BIOESSAYS

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

A probabilistic disease-gene finder for personal genomes

(2011) M. Yandell et al.   GENOME RESEARCH

Genotype and SNP calling from next-generation sequencing data

(2011) Rasmus Nielsen et al.   NATURE REVIEWS GENETICS

BioStar: An Online Question & Answer Resource for the Bioinformatics Community

(2011) Laurence D. Parnell et al.   PLoS Computational Biology

Enhanced structural variant and breakpoint detection using SVMerge by integration of multiple detection methods and local assembly

(2011) Kim Wong et al.   GENOME BIOLOGY

Variable Tandem Repeats Accelerate Evolution of Coding and Regulatory Sequences

(2010) Rita Gemayel et al.   Annual Review of Genetics

Structural Variation in the Human Genome and its Role in Disease

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

Design of association studies with pooled or un-pooled next-generation sequencing data

(2010) Su Yeon Kim et al.   GENETIC EPIDEMIOLOGY

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

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

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

Towards a comprehensive structural variation map of an individual human genome

(2010) Andy W Pang et al.   GENOME BIOLOGY

Gene Amplification and Adaptive Evolution in Bacteria

(2009) Dan I. Andersson et al.   Annual Review of Genetics

Upcoming challenges for multiple sequence alignment methods in the high-throughput era

(2009) Carsten Kemena et al.   BIOINFORMATICS

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

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

(2009) Ken Chen et al.   NATURE METHODS

Bacterial gene amplification: implications for the evolution of antibiotic resistance

(2009) Linus Sandegren et al.   NATURE REVIEWS MICROBIOLOGY

Adaptive Evolution of Pelvic Reduction in Sticklebacks by Recurrent Deletion of a Pitx1 Enhancer

(2009) Y. F. Chan et al.   SCIENCE

SeqAn An efficient, generic C++ library for sequence analysis

(2008) Andreas Döring et al.   BMC BIOINFORMATICS

Copy number variation and evolution in humans and chimpanzees

(2008) G. H. Perry et al.   GENOME RESEARCH

Mapping and sequencing of structural variation from eight human genomes

(2008) Jeffrey M. Kidd et al.   NATURE