Interests
Short-read sequencing technologies produce a huge volume of data. Many of the researchers interested in analyzing that data do not have large computing budgets. I am interested in building short-read analysis software that runs on common workstations.
Ben Langmead, Mihai Pop, Steven Salzberg and I recently released Bowtie, an ultrafast short read mapping program. Bowtie can map around 25 million reads to the human genome per CPU hour. Bowtie is meant to be used with whole-genome resequencing projects as well as new short-read applications like RNA-Seq, ChIP-Seq, and others.
My current research focus is improving Bowtie and building tools on top of it to help analyze RNA-Seq and ChIP-Seq datasets.
Publications
High-throughput bioinformatics
Langmead, B., Trapnell, C., Pop, M., and Salzberg, S. L., Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. (submitted)
Trapnell, C., Schatz, M.C., Optimizing Data Intensive GPGPU Computations for DNA Sequence Alignment. (submitted)
Schatz, M.C., Trapnell, C., Delcher, A.L., Varshney, A. (2007) High-throughput sequence alignment using Graphics Processing Units. BMC Bioinformatics 8:474 [view]
Genomics
Steven L. Salzberg et al., Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A, BMC Genomics 9:204 (2008) [view]
Former interests - Artificial Immune Systems
B. C. Trapnell, Jr., A Peer-to-Peer Blacklisting Strategy Inspired by Leukocyte-Endothelium Interaction, In Proc. of the Fourth International Conference on Artificial Immune Systems, (ICARIS-05), Springer LNCS 3627, pages 339-352, 2005 [view]
M. Neal, B. C. Trapnell, Jr., Go Dutch: Exploiting Interactions in the Immune System, in In Silico Immunology, J Timmis and D Flower, 313-330, 2007 [view]
Presentations
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High-throughput sequence alignment using Graphics Processing Units, CBCB Seminar, 9/20/2007
High-throughput sequence alignment using Graphics Processing Units, Poster in 15th Annual Microbial Genomes Conference, 2007
- Co-presented with Michael Schatz
Cole Trapnell Is a PhD student at the University of Maryland, College Park, in the Department of Computer Science.