A unified approach for allele frequency estimation, SNP detection and association studies based on pooled sequencing data using EM algorithms

1000 Genomes-based imputation identifies novel and refined associations for the Wellcome Trust Case Control Consortium phase 1 Data

(2012) Jie Huang et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

Evolution and Functional Impact of Rare Coding Variation from Deep Sequencing of Human Exomes

(2012) J. A. Tennessen et al.   SCIENCE

An Abundance of Rare Functional Variants in 202 Drug Target Genes Sequenced in 14,002 People

(2012) M. R. Nelson et al.   SCIENCE

vipR: variant identification in pooled DNA using R

(2011) A. Altmann et al.   BIOINFORMATICS

On optimal pooling designs to identify rare variants through massive resequencing

(2011) Joon Sang Lee et al.   GENETIC EPIDEMIOLOGY

Next generation sequencing of pooled samples reveals new SNRNP200 mutations associated with retinitis pigmentosa

(2011) Paola Benaglio et al.   HUMAN MUTATION

Deep resequencing of GWAS loci identifies independent rare variants associated with inflammatory bowel disease

(2011) Manuel A Rivas et al.   NATURE GENETICS

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

(2011) Mark A DePristo et al.   NATURE GENETICS

SNVer: a statistical tool for variant calling in analysis of pooled or individual next-generation sequencing data

(2011) Zhi Wei et al.   NUCLEIC ACIDS RESEARCH

Genome-Wide Association Analysis of Autoantibody Positivity in Type 1 Diabetes Cases

(2011) Vincent Plagnol et al.   PLoS Genetics

A statistical method for the detection of variants from next-generation resequencing of DNA pools

(2010) V. Bansal   BIOINFORMATICS

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

(2010) Heng Li et al.   BIOINFORMATICS

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

(2010) Su Yeon Kim et al.   GENETIC EPIDEMIOLOGY

Resequencing of pooled DNA for detecting disease associations with rare variants

(2010) Tao Wang et al.   GENETIC EPIDEMIOLOGY

Common SNPs explain a large proportion of the heritability for human height

(2010) Jian Yang et al.   NATURE GENETICS

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

(2010) K. Wang et al.   NUCLEIC ACIDS RESEARCH

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Deep sequencing to reveal new variants in pooled DNA samples

(2009) Astrid A. Out et al.   HUMAN MUTATION

Finding the missing heritability of complex diseases

(2009) Teri A. Manolio et al.   NATURE

Genome-wide association study and meta-analysis find that over 40 loci affect risk of type 1 diabetes

(2009) Jeffrey C Barrett et al.   NATURE GENETICS

Sense from sequence reads: methods for alignment and assembly

(2009) Paul Flicek et al.   NATURE METHODS

Quantification of rare allelic variants from pooled genomic DNA

(2009) Todd E Druley et al.   NATURE METHODS

Rare Variants of IFIH1, a Gene Implicated in Antiviral Responses, Protect Against Type 1 Diabetes

(2009) S. Nejentsev et al.   SCIENCE

Meta-analysis of genome-wide association study data identifies additional type 1 diabetes risk loci

(2008) Jason D Cooper et al.   NATURE GENETICS

Pyrobayes: an improved base caller for SNP discovery in pyrosequences

(2008) Aaron R Quinlan et al.   NATURE METHODS

Whole-genome sequencing and variant discovery in C. elegans

(2008) LaDeana W Hillier et al.   NATURE METHODS