jbuhler AT cse DOT wustl DOT edu
314-935-6180 (phone)
314-935-7302 (fax)
http://www.cse.wustl.edu/~jbuhler/
Postal Address
Department of Computer Science
Campus Box 1045
Washington University
One Brookings Drive
St. Louis, MO 63130-4899
I am an associate professor in the Computer Science and Engineering Department of Washington University in St. Louis, MO. I have secondary appointments in the Genetics Department of the Division of Biological and Biomedical Sciences (DBBS) and in the Biology Department in the School of Arts and Sciences. I work in the field of computational biology, designing algorithms for use by researchers in molecular biology and genetics. This work involves frequent collaboration with working biologists to identify important problems and engineer practical solutions using the results of my algorithms research.
My primary research interests lie in developing algorithms to analyze massive or otherwise intractable biosequence data sets produced by molecular biologists. I have applied randomized and probabilistic strategies to efficiently automate large-scale tasks in genome annotation, such as discovering repeats in genomic sequence, comparing very long orthologous sequences, and finding subtle sequence motifs.
Presently, my focus is on improved alignment methods, both for classic BLAST-like seeded similarity search and for extensions in which the query and/or database consists of multiple alignments. I am also interested in how to modify the designs of similarity search algorithms for maximum performance on specialized hardware, such as FPGAs and network processors.
Ph.D. in Computer Science from University of Washington, Seattle, WA (August 2001). Thesis: Search Algorithms for Biosequences Using Random Projection. Advisor: Martin Tompa.
M.S. in Computer Science from University of Washington, Seattle, WA (October 1998). Qualifying exam topic: "Improved Techniques for Finding Spots on DNA Microarrays." Advisors: Richard Karp (CS), David Haynor (Radiology).
B.A. in Computer Science from Rice University, Houston, TX (May 1996). Advisor: Alejandro Schäffer.
J. Lancaster, J. Buhler, and R. Chamberlain. "Acceleration of ungapped extension in Mercury BLAST." Microprocessors and Microsystems 33:281-9, 2009.
Y. Sun and J. Buhler. "Designing patterns and profile for faster HMM search." IEEE Transactions on Computational Biology and Bioinformatics 6(2):232-243, 2009. (Appeared electronically as article 2008.14, 2008.)
D. Lopatto, C. Alvarez, D. Barnard, C. Chandrasekaran, H.-M. Chung, C. Du, T. Eckdahl, A. L. Goodman, C. Hauser, C. J. Jones, O. R. Kopp, G. A. Kuleck, G. McNeil, R. Morris, J. L. Myka, A. Nagengast, P. J. Overvoorde, J. L. Poet, K. Reed, G. Regisford, D. Revie, A. Rosenwald, K. Saville, M. Shaw, G. R. Skuse, C. Smith, M. Smith, M. Spratt, J. Stamm, J. S. Thompson, B. A. Wilson, C. Witkowski, J. Youngblom, W. Leung, C. D. Shaffer, J. Buhler, E. Mardis, and S. C. R. Elgin. "Genomics Education Partnership." Science 322:684-5, 2008.
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.
P. Krishnamurthy, J. Buhler, R. Chamberlain, M. Franklin, K. Gyang, and J. Lancaster. "Biosequence similarity search on the Mercury system." Journal of VLSI Signal Processing, 49:101-121, 2007.
Y. Sun and J. Buhler. "Choosing the best heuristic for seeded alignment of DNA sequences." BMC Bioinformatics 7:133, 2006.
E. Slawson, C. Shaffer, C. Malone, W. Leung, E. Kellmann and R. Shevchek, C. Craig, Seth Bloom, J. Bogenpohl II, J. Dee, E. Morimoto, J. Myoung, A. Nett, F. Ozsolak, M. Tittiger, A. Zeug, M-L. Pardue, J. Buhler, E. Mardis, and S. Elgin. "Comparison of dot chromosome sequences from D. melanogaster and D. virilis reveals an enrichment of DNA transposon sequences in heterochromatic domains." Genome Biology 7(2):15, 2006.
Y. Sun and J. Buhler. "Designing multiple simultaneous seeds for DNA similarity search." Journal of Computational Biology 12:847-861, 2005.
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.
J.L. Sonnenburg, J. Xu, D.D. Leip, C-H. Chien, B.P. Westover, J. Weatherford, J.D. Buhler, and J.I. Gordon. "Glycan foraging in vivo by an intestine-adapted bacterial symbiont." Science 307:1955-1959, 2005.
B. Westover, J. Buhler, J. Sonnenburg, and J. Gordon. "Operon prediction without a training set." Bioinformatics 21(7):880-888, 2005.
J. Buhler. "Provably sensitive indexing strategies for biosequence similarity search." Journal of Computational Biology 10(3/4):399-418, 2003.
J. Buhler and M. Tompa. "Finding motifs using random projections." Journal of Computational Biology 9(2):225-242, 2002.
J. Buhler. "Efficient large-scale sequence comparison by locality-sensitive hashing." Bioinformatics 17:419-428, 2001.
T. Ideker, V. Thorsson, J.A. Ranish, R. Christmas, J. Buhler, R. Bumgarner, R. Aebersold, and L. Hood. "Integrated genomic and proteomic analysis of a systematically perturbed metabolic network." Science 292:929-934, 2001.
J. Buhler, D. Owerbach, A.A. Schäffer, M. Kimmel, and K.H. Gabbay. "Linkage analysis in type I diabetes mellitus using CASPAR, a software and statistical program for conditional analysis of polygenic diseases." Human Heredity 47:211-222, 1997.
A. Jacob, J. Buhler, and R. Chamberlain. "Optimal runtime reconfiguration strategies for systolic arrays." Proceedings of the 19th International Conference on Field Programmable Logic and Applications, Prague, 2009, to appear.
Y. Sun and J. Buhler. "Designing secondary structure profiles for fast ncRNA identification." Proceedings of the 2008 Conference on Computational Systems Bioinformatics (CSB08), Stanford, CA, 2008.
A. Jacob, J. Buhler, and R. Chamberlain. "Accelerating Nussinov RNA secondary structure prediction with systolic arrays on FPGAs." Proceedings of the 2008 International Conference on Application-Specific Systems, Architectures, and Processors (ASAP 2008), 191-196, Leuven, Belgium 2008.
R. Chamberlain, E. Tyson, S. Gayen, M. Franklin, J. Buhler, P. Crowley, and J. Buckley. "Application Development on Hybrid Systems," Proceedings of the 2007 Supercomputing Conference (SC07), 2007.
B. Harris, A. Jacob, J. Lancaster, J. Buhler, and R. Chamberlain. "A banded Smith-Waterman FPGA accelerator for Mercury BLASTP." Proceedings of the 2007 International Conference on Field Programmable Logic and Applications (FPL07), 765-769, 2007.
J. Buhler, J. Lancaster, A. Jacob, and R. Chamberlain. "Mercury BLASTN: fast streaming DNA sequence comparison." Proceedings of the 2007 Reconfigurable Systems Summer Institute (RSSI07), 2007.
A. Jacob, J. Lancaster, J. Buhler, and R. Chamberlain. "FPGA-accelerated seed generation in Mercury BLASTP." Proceedings of the 15th IEEE Symposium on Field-Programmable Custom Computing Machines (FCCM07) 95-106, 2007.
A. Jacob, J. Lancaster, J. Buhler, and R. Chamberlain. "Preliminary results in accelerating profile HMM search on FPGAs." Proceedings of the 6th IEEE International Workshop on High Performance Computational Biology (HICOMB07), 2007.
Y. Sun and J. Buhler. "Designing patterns for profile HMM search." Proceedings of the 5th European Conference on Computational Biology (ECCB06), published as Bioinformatics 23:e36-43, 2007.
R. P. Maddimsetty, J. Buhler, R. Chamberlain, M. Franklin, and B. Harris. "Accelerator design for protein sequence HMM search." Proceedings of the 20th ACM International Conference on Supercomputing (ICS06) 288-296, 2006.
C. Alkan, E. Karakoc, S.C. Sahinalp, P. Unrau, H. Ebhardt, K. Zhang, and J. Buhler. "RNA secondary structure prediction via energy density minimization." Proceedings of the Tenth Annual International Conference on Computational Molecular Biology (RECOMB06) 130-142, 2006.
J. Lancaster, J. Buhler, and R. Chamberlain. "Acceleration of ungapped extension in Mercury BLAST." Proceedings of the 7th Workshop on Media and Streaming Processors 50-57, 2005.
B. Wun, J. Buhler, and P. Crowley. "Exploiting coarse-grained parallelism to accelerate protein motif finding with a network processor." Proceedings of the Fourteenth International Conference on Parallel Architectures and Compilation Techniques (PACT 2005), 173-184, 2005.
J. Buhler and R. Nordgren. "Toward a phylogenetically aware algorithm for fast DNA similarity search." Proceedings of the Second RECOMB Satellite Conference on Comparative Genomics, Bertinoro, Italy, 15-22, 2004.
P. Krishnamurthy, J. Buhler, R. Chamberlain, M. Franklin, K. Gyang, and J. Lancaster. "Biosequence similarity search on the Mercury system." Proceedings of the IEEE 15th International Conference on Application-Specific Systems, Architectures and Processors (ASAP04), 365-75, 2004.
Y. Sun and J. Buhler. "Designing multiple simultaneous seeds for DNA similarity search." Proceedings of the Eighth Annual International Conference on Computational Molecular Biology (RECOMB04), 76-84, 2004.
J. Buhler, R. Souvenir, W. Zhang, and R. Mitra. "Design of a high-throughput assay for alternative splicing using polymerase colonies." Pacific Symposium on Biocomputing 2004, 5-16, 2004.
R. Souvenir, J. Buhler, G. Stormo, and W. Zhang. "Selecting degenerate multiplex PCR primers." Algorithms in Bioinformatics, Third International Workshop (WABI 2003) 512-526, 2003.
E. Halperin, J. Buhler, R. Karp, R. Krauthgamer, and B. Westover. "Detecting protein sequence conservation via metric embeddings." Proceedings of the Eleventh International Conference on Intelligent Systems for Molecular Biology (ISMB 2003) 122-129, Brisbane, Australia, 2003.
J. Buhler, U. Keich, and Y. Sun. "Designing seeds for similarity search in genomic DNA." Proceedings of the Seventh Annual International Conference on Computational Molecular Biology (RECOMB03) 67-75, Berlin, Germany, April 2003.
J. Buhler. "Provably sensitive indexing strategies for biosequence similarity search." Proceedings of the Sixth Annual International Conference on Computational Molecular Biology (RECOMB02) 90-99, Washington, D.C., 2002.
J. Buhler and M. Tompa. "Finding motifs using random projections." In Proceedings of the Fifth Annual International Conference on Computational Molecular Biology (RECOMB01) 69-76, Montreal, Canada, 2001.
R. Souvenir, J. Buhler, G. Stormo, and W. Zhang. "An iterative method for selecting degenerate multiplex PCR primers." In Methods in Molecular Biology 402: PCR Primer Design, ed. A Yuryev, 245-267, Humana Press, Totowa, 2008.
J. Buhler, T. Ideker, and D. Haynor. "Dapple: improved techniques for finding spots on DNA microarrays." UWCSE Tech Report UWTR 2000-08-05, Department of Computer Science and Engineering, University of Washington, Seattle, WA, August 2000. Also presented as a poster at ISMB 2000.
NSF DBI-0237902, "CAREER: New Technologies for Biosequence Comparison," 7/2003-6/2008.
The primary purpose of this grant is to develop seed design technology for improving the speed and sensitivity of BLAST-like alignment algorithms, and to pursue other technologies for next-generation genome alignment.
NIH/NGHRI R42 HG003225, "STTR: Fast Biosequence Annotation via Reconfigurable Hardware," 9/30/2004-8/29/2010.
The major goal of this project is to develop a high-performance, cost-effective engine for accelerating BLAST and BLAST-like similarity search using reconfigurable FPGA logic. This STTR is held in collaboration with BECS Technology, Inc. of Olivette, Missouri.
NSF ITR-427794, "ITR: Storage-Based Supercomputing for Scientific Applications," 9/1/2004-8/31/2008, PI Mark Franklin.
The major goal of this project is to create a development platform for exploiting streaming computation and specialized hardware to solve data-intensive problems in scientific computing. Includes acceleration of high-cost similarity search problems in bioinformatics.
NIH/NCRR P41-RR0954, "Washington University Center for Biomedical and Bioorganic Mass Spectrometry", PIs Michael Gross and Reid Townsend.
This grant funds a center that, among other things, supports work in high-throughput protein mass spectrometry. I am supported for research and development of improved methods for identifying proteins from peptide mass spectra using whole-proteome and whole-genome databases.
SAIC/NIH Contract 24XS043, "Mammalian Genome Collection Bioinformatics," 7/1/2004-6/30/2006, PI Michael Brent.
The goal of this contract is to provide high-confidence validation of experimentally derived gene sequences from the Mammalian Genome Collection project using a variety of existing and novel computational tools.
CSE 584 / BIO 5504, Algorithms for Biosequence Comparison
CSE 780x / BIO 5746, Graduate Seminar in Computational Biology (with Gary Stormo)
CSE 241, Algorithms and Data Structures
CSE 441/541, Advanced Algorithms
CSE 547, Introduction to Formal Languages and Automata
CSE 587, Algorithms for Computational Biology (for Michael Brent)
BIO 4342, Research Explorations in Genetics (for Sarah Elgin)
Doctoral Students: Arpith Jacob, Hongtao Sun, Yanni Sun, Joe Lancaster (joint w/Roger Chamberlain)
Masters Students: Justin Brown, Joshual Coats
serving on doctoral committees for numerous students in Genetics and Computational Biology programs, Division of Biological and Biomedical Sciences.
Associate member, Washington University Center for Computational Biology
Member of Sequence Analysis Advisory Board, Washington University Genome Sequencing Center
Program committees: Intelligent Systems for Molecular Biology (ISMB), Conference on Combinatorial Pattern Matching (CPM), Pacific Symposium on Biocomputing (PSB), IEEE Computational Systems Bioinformatics Conference (CSB), European Conference on Computational Biology (ECCB)
Reviewer for Bioinformatics, Biotechniques, Genome Research, Journal of Computational Biology, etc.
Served on NIH GGG-J and GCAT study sections
Member, International Society for Computational Biology (ISCB)
Director of Doctoral Study, Department of Computer Science and Engineering
Member, Technology Adoption Committee
Interviewer for applicants to graduate program in computational biology, Division of Biological and Biomedical Sciences
William Chan Memorial Dissertation Award (from University of Washington CSE Dept., 2001)
Fannie and John Hertz Graduate Fellowship (1996-2000)
Summa cum laude, Rice University (1996)
Phi Beta Kappa, Rice University (1996)
Lab Internship and Collaboration with Dr. Jeffrey Gordon, professor and chair of Molecular Biology and Pharmacology, Washington University (2001-present). I initially spent a month in Dr. Gordon's lab during November of 2001 learning basic laboratory protocols for, e.g., sequencing and PCR. Since then, I have informally advised Dr. Gordon's students in work on using multiple closely related genomes to close gaps in incomplete genome assemblies. Our work led to closure of several outstanding gaps in the genome assembly of the gut-living bacterium Bacteroides thetaiotaomicron. Dr. Gordon and I recently shared a CS doctoral student, Ben Westover, who worked on operon finding and other problems of gene regulation in B. theta.
Collaboration with Dr. Sarah Elgin, professor of Biology, Washington University (2002-present). Dr. Elgin is developing a course, BIO4342 "Research Explorations in Genomics," aimed at teaching genome sequencing, assembly, and annotation techniques to advanced undergraduate students. I developed and taught a portion of this course on the use of BLAST and the interpretation of sequence alignments. The course is now (2004) in its second year, with an eventual goal of being "modularized" for use at a large number of universities.
Development of Dapple, a program for quantifying mRNA expression measurements from fluorescent cDNA microarrays. I initially developed Dapple for use by the Hood Laboratory in the UW Department of Molecular Biotechnology (1998), then made further improvements in collaboration with the Microarray Group at the Institute for Systems Biology (1999-present). The Dapple software is freely available at http://www.cse.wustl.edu/~jbuhler/research/dapple/. Collaborators: Trey Ideker (UW Molecular Biotechnology), David Haynor (UW Radiology), Steve Lasky (ISB).
Analysis of genotype data to discover genetic risk factors in juvenile (type I) diabetes, in collaboration with the Molecular Diabetes and Metabolism Group at Baylor College of Medicine, Houston, TX (1995-6). We developed CASPAR, a program to identify high-risk loci for juvenile diabetes using affected sibpair data. Collaborators: Alejandro Schäffer (advisor, Rice University CS), Marek Kimmel (Rice U. Statistics), Kenneth Gabbay and David Owerbach (Baylor).