Ben Langmead

I am a Masters student in the Computer Science Department and Center for Bioinformatics and Computational Biology (CBCB) at the University of Maryland, and will graudate in May 2009. My advisors are Mihai Pop and Steven L. Salzberg.

As a graduate student, I am leveraging my background in high-performance software and hardware into research toward high-performance solutions for modern genome-sequence analysis problems, especially the short read alignment problem. Most recently, I wrote and released an extremely efficient short read aligner, Bowtie, in collaboration with Cole Trapnell, another CBCB graduate student.

I received my B.A. in Computer Science from Columbia University in June 2003. After earning my B.A., I worked full-time for more than 4 years at Reservoir Labs, a small Computer Science R&D consulting firm in New York. While there I worked for a diverse set of clients contributing expertise in high-performance software and compilers. Most significantly, I lead the technical side of an effort funded by Department of Energy to design and create R-Scope, a commercially-viable 10 Gbps network intrusion detection appliance running on a parallel, off-the-shelf network processor called Octeon.

Research

• Bowtie is a short read aligner employing a novel, ultrafast and memory-efficient algorithm based on the Burrows-Wheeler Transform (BWT) and FM Index. A Bowtie index for the human genome fits in a memory footprint of 1.3 gigabytes, allowing it to be queried on a PC with 2 gigabytes of RAM. Bowtie aligns 14.3x coverage worth of Illumina reads from the 1000 Genomes project in 14 hours on a desktop PC with 4 processor cores. Bowtie is work with Cole Trapnell and is freely available open source software: http://bowtie-bio.sf.net.


• Crossbow combines the efficiency of Bowtie with advances in Cloud Computing to enable deep-coverage human resequencing and genotyping in about an hour per individual. Crossbow uses Hadoop and Amazon's EC2 and S3 services to distribute read data across many computers in a CPU-rich cluster. The cluster runs dozens of parallel instances of the Bowtie aligner and SNP caller. Crossbow is work-in-progress.

Completed Courses

• CMSC 631 (Program Analysis and Understanding) Fall 2007
• CMSC 828N (Computational Gene Finding and Genome Assembly) Fall 2007
• CMSC 838F (Language-Based Security) Spring 2008
• CMSC 838P (Algorithms for Biosequence Analysis) Spring 2008
• CMSC 740 (Advanced Computer Graphics) Fall 2008
• LBSC 878A (Introduction to Cloud Computing) Fall 2008
• Master's Thesis Research (6 pts)

Current Courses

• CMSC828E (Scientific Computing on Graphic Processors) Spring 2009
• CMSC858L (Graphs and Networks in Computational Biology) Spring 2009
• Master's Thesis Research (3 pts)