Washington University in St. Louis


Jeremy Buhler

In 2001, Professor Buhler joined the faculty at Washington University in St. Louis. He currently has secondary appointments in the Genetics Department of the Division of Biological and Biomedical Sciences (DBBS) and in the Biology Department in the College of Arts & Sciences.
Professor Buhler's primary research interests lie in the field of computational biology and bioinformatics. The development of high-throughput experimental methods in molecular biology has led to a proliferation of raw data, including numerous species' genomes and measurements of gene and protein activity in living cells. The challenge of computational biology is to efficiently extract meaning from this raw data, and in particular to generate and test new hypotheses about how the diverse network of biological processes is organized so as to make life possible.

Professor Buhler's research group focuses on developing algorithms and tools to efficiently search and annotate large databases of DNA and protein sequences. Widely used annotation software such as BLAST relies on heuristic methods to make large-scale comparison of biosequences computationally feasible. These heuristics can be improved by applying ideas from probabilistic, randomized, and approximation algorithms, resulting in faster and more sensitive annotation tools. Similar ideas can greatly accelerate more recently developed annotation tools that use probabilistic sequence models; such tools are more computationally intensive than pairwise sequence comparison and so benefit more from algorithmic improvements.

A second approach to speeding up biosequence annotation is to design special-purpose computers that can execute annotations algorithms faster. This strategy has become attractive with the advent of fast, reasonably priced reconfigurable computing hardware such as field-programmable gate arrays (FPGAs). Professor Buhler's group has accelerated several well-known annotation algorithms using FPGA hardware. His interests include generalizing the methods used in these accelerators to allow rapid, economical porting of a wide variety of annotation tools to reconfigurable computing platforms.
Selected Publications
H. Sun and J. D. Buhler. "PhyLAT: a phylogenetic local alignment tool." Bioinformatics 28(10):1336-1344, 2012.
N. Ihuegbu, G. Stormo, and J. Buhler. "Fast, sensitive discovery of conserved genome-wide motifs." Journal of Computational Biology 19(2):139-147, 2012.
Y. Sun, J. Buhler, and C. Yuan. "Designing filters for fast known nCRNA identification." IEEE/ACM Transactions on Computational Biology and Bioinformatics 9(3):774-787, 2012.
A. Jacob, J. Buhler, and R. Chamberlain. "Design of throughput-optimized arrays from recurrence abstractions." Proc. 21st IEEE Intl. Conf. Application-specific Systems, Architectures and Processors (ASAP) 133-140, Rennes, France, 2010.
A. Jacob, J. Lancaster, J. Buhler, B. Harris, and R.D. Chamberlain. "Mercury BLASTP: Accelerating Protein Sequence Alignment." ACM Transactions on Reconfigurable Technology and Systems 1(2):1-44, 2008.
J. Buhler, U. Keich, and Y. Sun. "Designing seeds for similarity search in genomic DNA." Journal of Computing and Systems Science 70:342-363, 2005.
Selected Research
"STTR: Fast Biosequence Annotation via Reconfigurable Hardware," 9/2004-8/2011.
"CSR: Medium: Architecturally Diverse Systems for Streaming Applications", PI Mark Franklin, 9/2009-9/2012.
"ITR: Storage-Based Supercomputing for Scientific Applications," PI Mark Franklin, 9/1/2004-8/31/2009.    

NSF CAREER: "New Technologies for Biosequence Comparison," PI Buhler, 7/2003-6/2009.

"Genomics Education Partnership", PI Sarah Elgin (WUSTL Biology), 6/2005-6/2010.

Contact Jeremy Buhler
Address 1 Brookings Drive
Campus Box 1045
City/St/Zip St. Louis, MO 63130
Jolley Hall, Room 506
Phone (314) 935-6180
Fax (314) 935-7302
Email jbuhler@wustl.edu
Other Appt. Genetics & Biology

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PhD, University of Washington, 2001
MS, University of Washington, 1998
BA, Rice University, 1996
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