VNTRseek—a computational tool to detect tandem repeat variants in high-throughput sequencing data

HighSSR: high-throughput SSR characterization and locus development from next-gen sequencing data

(2012) Alexander Churbanov et al.   BIOINFORMATICS

Population-scale analysis of human microsatellites reveals novel sources of exonic variation

(2012) L.J. McIver et al.   GENE

lobSTR: A short tandem repeat profiler for personal genomes

(2012) Melissa Gymrek et al.   GENOME RESEARCH

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

(2012)   NATURE

A direct characterization of human mutation based on microsatellites

(2012) James X Sun et al.   NATURE GENETICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Accurate human microsatellite genotypes from high-throughput resequencing data using informed error profiles

(2012) Gareth Highnam et al.   NUCLEIC ACIDS RESEARCH

Analysis of Microsatellite Variation in Drosophila melanogaster with Population-Scale Genome Sequencing

(2012) John W. Fondon et al.   PLoS One

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

(2011) D. He et al.   BIOINFORMATICS

ART: a next-generation sequencing read simulator

(2011) Weichun Huang et al.   BIOINFORMATICS

Evaluation of microsatellite variation in the 1000 Genomes Project pilot studies is indicative of the quality and utility of the raw data and alignments

(2011) L.J. McIver et al.   GENOMICS

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Detection and characterization of novel sequence insertions using paired-end next-generation sequencing

(2010) Iman Hajirasouliha et al.   BIOINFORMATICS

Repeat elements and the Arabidopsis DNA methylation landscape

(2010) F K Teixeira et al.   HEREDITY

Small insertions and deletions (INDELs) in human genomes

(2010) J. M. Mullaney et al.   HUMAN MOLECULAR GENETICS

Complete Khoisan and Bantu genomes from southern Africa

(2010) Stephan C. Schuster et al.   NATURE

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

QDD: a user-friendly program to select microsatellite markers and design primers from large sequencing projects

(2009) Emese Meglécz 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

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Accurate, Large-Scale Genotyping of 5HTTLPR and Flanking Single Nucleotide Polymorphisms in an Association Study of Depression, Anxiety, and Personality Measures

(2009) Naomi R. Wray et al.   BIOLOGICAL PSYCHIATRY

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

(2009) Chao Xie et al.   BMC BIOINFORMATICS

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

(2009) F. Hormozdiari et al.   GENOME RESEARCH

MoDIL: detecting small indels from clone-end sequencing with mixtures of distributions

(2009) Seunghak Lee et al.   NATURE METHODS

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

(2009) Ken Chen et al.   NATURE METHODS

Unstable Tandem Repeats in Promoters Confer Transcriptional Evolvability

(2009) M. D. Vinces et al.   SCIENCE

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

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Association Between the Stin2 VNTR Polymorphism of the Serotonin Transporter Gene and Treatment Outcome in Alcohol-Dependent Patients

(2008) G. Florez et al.   ALCOHOL AND ALCOHOLISM

All hits all the time: parameter-free calculation of spaced seed sensitivity

(2008) D. Y.F. Mak et al.   BIOINFORMATICS

The complete genome of an individual by massively parallel DNA sequencing

(2008) David A. Wheeler et al.   NATURE

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

(2008) Derek Y Chiang et al.   NATURE METHODS

A genome-wide view of the spectrum of spontaneous mutations in yeast

(2008) M. Lynch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA