I am interested high-performance software for modern sequence analysis problems, especially short read alignment and analysis of RNA-seq, ChIP-seq, and bisulfite sequencing data. I previously wrote and released an extremely efficient short read alignment tool called Bowtie. Bowtie was developed in collaboration with Cole Trapnell at University of Maryland and is available for download from http://bowtie-bio.sf.net. More recently, I wrote a tool called Crossbow that exploits Bowtie in a Cloud Computing context to align and call SNPs from whole-human resequencing datasets in a few hours. Crossbow was developed in collaboration with Michael C. Schatz at University of Maryland and is available for download from http://bowtie-bio.sf.net/crossbow.

sequence alignment, alignment, short read, short read mapping, high performance, cloud computing, parallel computing

Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 10:R25.

Langmead B, Schatz M, Lin J, Pop M, Salzberg SL. Searching for SNPs with cloud computing. Genome Biology In press.