Short read alignment with populations of genomes

Extensive compensatory cis-trans regulation in the evolution of mouse gene expression

(2012) A. Goncalves et al.   GENOME RESEARCH

Compressive genomics

(2012) Po-Ru Loh et al.   NATURE BIOTECHNOLOGY

Automated forward and reverse ratcheting of DNA in a nanopore at 5-Å precision

(2012) Gerald M Cherf et al.   NATURE BIOTECHNOLOGY

Efficient storage of high throughput DNA sequencing data using reference-based compression

(2011) M. Hsi-Yang Fritz et al.   GENOME RESEARCH

Mouse genomic variation and its effect on phenotypes and gene regulation

(2011) Thomas M. Keane et al.   NATURE

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

(2011) Robert E Handsaker 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

Personal genome sequencing: current approaches and challenges

(2010) M. Snyder et al.   GENES & DEVELOPMENT

Two Efficient Algorithms for Linear Time Suffix Array Construction

(2010) Ge Nong et al.   IEEE TRANSACTIONS ON COMPUTERS

The mutation spectrum revealed by paired genome sequences from a lung cancer patient

(2010) William Lee et al.   NATURE

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

Accurate SNP and mutation detection by targeted custom microarray-based genomic enrichment of short-fragment sequencing libraries

(2010) Michal Mokry et al.   NUCLEIC ACIDS RESEARCH

Analysis of Genetic Inheritance in a Family Quartet by Whole-Genome Sequencing

(2010) J. C. Roach et al.   SCIENCE

The case for cloud computing in genome informatics

(2010) Lincoln D Stein   GENOME BIOLOGY

Towards a comprehensive structural variation map of an individual human genome

(2010) Andy W Pang et al.   GENOME BIOLOGY

VarScan: variant detection in massively parallel sequencing of individual and pooled samples

(2009) Daniel C. Koboldt et al.   BIOINFORMATICS

SOAP2: an improved ultrafast tool for short read alignment

(2009) R. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Exome sequencing identifies the cause of a mendelian disorder

(2009) Sarah B Ng et al.   NATURE GENETICS

SHRiMP: Accurate Mapping of Short Color-space Reads

(2009) Stephen M. Rumble et al.   PLoS Computational Biology

Simultaneous alignment of short reads against multiple genomes

(2009) Korbinian Schneeberger et al.   GENOME BIOLOGY

Searching for SNPs with cloud computing

(2009) Ben Langmead et al.   GENOME BIOLOGY

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

(2009) Ben Langmead et al.   GENOME BIOLOGY