Curriculum Vitae for Jeremy Buhler

Contact Information

jbuhler AT wustl DOT edu
314-935-6180 (phone)
314-935-7302 (fax)
http://www.cse.wustl.edu/~jbuhler/

Postal Address
Department of Computer Science and Engineering
Campus Box 1045
Washington University
One Brookings Drive
St. Louis, MO 63130-4899

I am a 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.

Research Interests

My primary research interests lie in analysis of massive or otherwise intractable biosequence data sets produced by molecular biologists. My group takes two major approaches to these problems. First, we apply various algorithmic strategies -- including randomized, probabilistic, and approximation algorithms -- 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.

Second, we study how to best implement these computations on modern computing architectures such as field-programmable gate arrays (FPGAs) and GPUs. The latter research raises numerous interesting theoretical and engineering problems in mapping and scheduling of parallel computations and the in design of programming frameworks to support streaming and modular computation.

Professional Preparation

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.

Academic Appointments

Publications

Refereed Journals

P Li, J Beard, and J Buhler. "Deadlock-free buffer configuration for streaming compu-ting." Int'l J. High Performance Computing Applications, rapid pub online 12/2016.

SCR Elgin, C Hauser, TM Holzen, C Jones, A Kleinschmit, J Leatherman, et al. "The GEP: crowd-sourcing big data analysis with undergraduates." Trends in Genetics 33(2):81-85, 2017.

W. Leung, C.D. Shaffer, L.K. Reed, S.T. Smith, et al. "Drosophila Muller F elements maintain a distinct set of genomic properties over 40 million years of evolution." Genes, Genomes, and Genetics 5(5):719-740, 2015.

D. Lopatto, C. Hauser, C.J. Jones, D. Paetkau, et al. "A central support system can facilitate implementation and sustainability of a classroom-based undergraduate research experience (CURE) in genomics." CBE Life Science Education 13(4):711-723, 2014.

C.D. Shaffer, C.J. Alvarez, A.E. Bednarski, D. Dunbar, et al. "A course-based research experience: how benefits change with increased investments in instructional time." CBE Life Sciences Education 13:111-130, 2014.

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.

W. Leung, C. Shaffer, T. Cordonnier, J. Wong, et al. "Evolution of a Distinct Genomic Domain in Drosophila: Comparative Analysis of the Dot Chromosome in Drosophila melanogaster and Drosophila virilis." Genetics 185:1519-34, 2010.

C.D. Shaffer, C. Alvarez, C. Bailey, D. Barnard, et al. "The Genomics Education Partnership: Successful Integration of Research into Laboratory Classes at a Diverse Group of Undergraduate Institutions." CBE Life Sciences Education 9(1):55-69, 2010.

R. Chamberlain, M. Franklin, E. Tyson, J. Buckley, J. Buhler, G. Galloway, S. Gayen, M. Hall, B. Shands, and N. Singla. "Auto-Pipe: Streaming Applications on Architecturally Diverse Systems." IEEE Computer 43:42-49, 2010.

R. Sowell, Y. Chen, J. Buhler, S.A. Goldman, C. Grimm, and K.J. Goldman. "Experiences with active learning in CS 3." Journal of Computing Sciences in Colleges 25(5):173-179, 2010.

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/ACM 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, et al. "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, A. Jacob, 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, et al. "Comparison of dot chromosome sequences from D. melanogaster and D. virilis reveals an enrichment of DNA transposon sequences in heterochromatic domains." Genome Biology 7:15, 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.

Refereed Conferences

S. Cole and J. Buhler. "The function-centric model: supporting SIMD execution of streaming computations." 5th Workshop on Data-flow Execution Models for Extreme Scale Computing, San Francisco, CA, 2015.

P. Li, J. Beard, and J. Buhler. "Deadlock-free buffer configuration for stream computing." 2015 Int'l Workshop on Programming Models and Applications for Multicores and Manycores 164-169, San Francisco, CA, 2015.

P. Li, K. Agrawal, J. Buhler, and R.D. Chamberlain. "Orchestrating safe streaming computations with precise control." Proc 4th Int'l Workshop on Extreme Scale Computing Application Enablement - Modeling and Tools 1017-1022, Hsinchu, Taiwan, 2014.

S. Cole, J. Gardner, and J. Buhler. "WOODSTOCC: Extracting Latent Parallelism from a DNA Sequence Aligner on a GPU." Proc 13th IEEE Int'l Symp. on Parallel and Distributed Computing 197-204, Marseilles, France, 2014.

P. Li, K. Agrawal, J. Buhler, and R.D. Chamberlain. "Adding Data Parallism to Streaming Pipelines for Throughput Optimization." Proc. 20th IEEE Int'l Conf. High Performance Computing 20-29, Bangalore, India, 2013.

P. Li and J. Buhler. "Polyhedral constraints for bounded-memory execution of synchronized filtering data flow." 2013 Workshop on Data Flow Execution Models for Extreme-Scale Computing 29-37, Edinburgh, Scotland, 2013.

J. Buhler, K. Agrawal, P. Li, and R. D. Chamberlain. "Efficient Deadlock Avoidance for Streaming Computation with Filtering." Proc. 17th ACM SIGPLAN Symp. Principles and Practice of Parallel Programming (PPoPP) 235-246, New Orleans, LA, 2012.

J. Lancaster, E.F. Berkley Shands, J.D. Buhler, and R.D. Chamberlain. "TimeTrial: a low-impact performance profile for streaming data applications." Proc. 2011 IEEE Int'l. Conf. Application-Specific Systems, Architectures, and Processors (ASAP) 69-76, Santa Monica, CA, 2011.

L. Ma, R.D. Chamberlain, J.D. Buhler, and M.A. Franklin. "Bloom filter performance on graphics engines." Proc. 2011 Int.l. Conf. Parallel Processing (ICPP) 522-531, Taipei, 2011.

N. Ganesan, R.D. Chamberlain, J. Buhler, and M. Taufer. "Rolling partial prefix-sums to speedup evaluation of uniform and affine recurrence equations." Modeling and Simulation for Defense Systems and Applications VI (Proc. SPIE Defense, Security, and Sensing 2011) v8060, 806003 - 806003-8, 2011.

N. Ganesan, R. Chamberlain, J. Buhler, and M. Taufer. "Accelerating HMMER on GPUs by implementing hybrid data and task parallelism." Proc ACM Intl. Conf on Bioinformatics and Computationa Biology (BCB) 418-421, Niagra Falls, NY, 2010.

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.

P. Li, K. Agrawal, J. Buhler, and R. Chamberlain. "Deadlock Avoidance for Streaming Computation with Filtering." Proc. 22nd ACM Symposium on Parallelism in Algorithms and Architectures (SPAA) 243-252, Santorini, Greece, 2010.

A. Jacob, J. Buhler, and R. Chamberlain. "Rapid RNA Folding: Analysis and Acceleration of the Zuker Recurrence." Proc. 18th IEEE Ann. Intl. Symposium on Field-Programmable Custom Computing Machines (FCCM) 87-94, Charlotte, NC, 2010.

R. Chamberlain, J. Buhler, M. Franklin, and J. Buckley. "Application-guided Tool Development for Architecturally Diverse Computation." Proc. Symp. on Applied Computing (SAC) 496-501, Sierre, Switzerland, 2010.

J. Lancaster, J. Buhler, and R. Chamberlain. "Efficient runtime performance monitoring of FPGA-based applications." Proc. 22nd Intl. System-on-a-Chip Conf. (SoCC) 23-28, Belfast, Northern Ireland, 2009.

A. Jacob, J. Buhler, and R. Chamberlain. "Optimal runtime reconfiguration strategies for systolic arrays." Proc. 19th Intl. Conf. Field Programmable Logic and Applications (FPL) 162-167, Prague, Czech Republic, 2009.

Y. Sun and J. Buhler. "Designing secondary structure profiles for fast ncRNA identification." Proc. 2008 Conf. Computational Systems Bioinformatics (CSB), Stanford, CA, 2008.

A. Jacob, J. Buhler, and R. Chamberlain. "Accelerating Nussinov RNA secondary structure prediction with systolic arrays on FPGAs." Proc. 2008 Intl. Conf. Application-Specific Systems, Architectures, and Processors (ASAP) 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," Proc. 2007 Supercomputing Conf. (SC), 2007.

B. Harris, A. Jacob, J. Lancaster, J. Buhler, and R. Chamberlain. "A banded Smith-Waterman FPGA accelerator for Mercury BLASTP." Proc. 2007 Intl. Conf. Field Programmable Logic and Applications (FPL) 765-769, 2007.

J. Buhler, J. Lancaster, A. Jacob, and R. Chamberlain. "Mercury BLASTN: fast streaming DNA sequence comparison." Proc. 2007 Reconfigurable Systems Summer Institute (RSSI), 2007.

A. Jacob, J. Lancaster, J. Buhler, and R. Chamberlain. "FPGA-accelerated seed generation in Mercury BLASTP." Proc. 15th IEEE Symp. on Field-Programmable Custom Computing Machines (FCCM) 95-106, 2007.

A. Jacob, J. Lancaster, J. Buhler, and R. Chamberlain. "Preliminary results in accelerating profile HMM search on FPGAs." Proc. 6th IEEE Intl. Workshop on High Performance Computational Biology (HICOMB), 2007.

Y. Sun and J. Buhler. "Designing patterns for profile HMM search." Proc. 5th European Conf. Computational Biology (ECCB), 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 Intl. Conf. Supercomputing (ICS) 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." Proc. 10th Ann. Intl. Conf. Computational Molecular Biology (RECOMB) 130-142, 2006.

J. Lancaster, J. Buhler, and R. Chamberlain. "Acceleration of ungapped extension in Mercury BLAST." Proc. 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." Proc. 14th Intl. Conf. Parallel Architectures and Compilation Techniques (PACT) 173-184, 2005.

J. Buhler and R. Nordgren. "Toward a phylogenetically aware algorithm for fast DNA similarity search." Proc. 2nd RECOMB Satellite Conf. 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." Proc. IEEE 15th Intl. Conf. Application-Specific Systems, Architectures and Processors (ASAP) 365-75, 2004.

Y. Sun and J. Buhler. "Designing multiple simultaneous seeds for DNA similarity search." Proc. 8th Ann. Intl. Conf. Computational Molecular Biology (RECOMB) 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 Symp. on Biocomputing (PSB) 5-16, 2004.

R. Souvenir, J. Buhler, G. Stormo, and W. Zhang. "Selecting degenerate multiplex PCR primers." Algorithms in Bioinformatics, 3rd Intl. Workshop (WABI) 512-526, 2003.

E. Halperin, J. Buhler, R. Karp, R. Krauthgamer, and B. Westover. "Detecting protein sequence conservation via metric embeddings." Proc. 11th Intl. Conf. Intelligent Systems for Molecular Biology (ISMB) 122-129, Brisbane, Australia, 2003.

J. Buhler, U. Keich, and Y. Sun. "Designing seeds for similarity search in genomic DNA." Proc. 7th Ann. Intl. Conf. Computational Molecular Biology (RECOMB) 67-75, Berlin, Germany, April 2003.

J. Buhler. "Provably sensitive indexing strategies for biosequence similarity search." Proc. 6th Ann. Intl. Conf. Computational Molecular Biology (RECOMB) 90-99, Washington, D.C., 2002.

J. Buhler and M. Tompa. "Finding motifs using random projections." In Proc. 5th Ann. Intl. Conf. Computational Molecular Biology (RECOMB) 69-76, Montreal, Canada, 2001.

Other Publications

P. Li and J. Buhler. "Improving performance of streaming applications with filtering and control messages." Poster at PACT 2014 Student Research Competition, Edmonton, Alberta, Canada 2014.

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.

Patents

U.S. 9,547,680, "Method and Apparatus for Performing Similarity Searching." Issued January 17, 2017.

U.S. 8,515,682, "Method and Apparatus for Performing Similarity Searching." Issued August 20, 2013.

U.S. 7,917,299, "Method and Apparatus for Performing Similarity Searching on a Data Stream with Respect to a Query String." Issued March 29, 2011.

Research Support

Current Support

NSF CNS-1500173: "EAGER: Rapid, Efficient Implementation of Irregular Applications on SIMD Many-Core Platforms", PI Jeremy Buhler, 8/2015-7/2017.

This grant supports modeling, analysis, and development of infrastructure for implementing modular, streaming dataflow applications with filtering or other irregular semantics on GPUs and other SIMD multiprocessors. Target apps include those from high-throughput biological sequence analysis.

NSF IUSE-1431407: "Effective Implementation of a Classroom Undergraduate Research Experience (CURE): Testing, Optimizing, and Extending a Bioinformatics Project", PI Sarah CR Elgin (WU Biology), 09/01/2014-08/31/2017

This grant supports the Genomics Education Partnership, run by Dr. Elgin and described below. My role in the project is to help with curriculum development for college students from a variety of institutions (over 90) around the U.S., in particular developing new materials on motif finding and other advanced annotation topics.

Completed Support

NSF CNS-1205498: "CI-P: a Flexible Platform for Accelerating Biological Sequence Analysis", PI Jeremy Buhler, 7/2012-6/2014.

This grant supported the construction of development and deployment infrastructure for rapidly building accelerators for computational biology problems.

NSF CNS-0905368, "CSR: Medium: Architecturally Diverse Systems for Streaming Applications", PI Mark Franklin, 9/2009-8/2013.

This was the continuation of the SBS ITR described below. My role was to explore the use of architecturally diverse systems for computational biology applications, particularly in the area of metagenomics and high-throughput DNA sequencing.

NIH/NGHRI R42 HG003225, "STTR: Fast Biosequence Annotation via Reconfigurable Hardware," 9/2004-8/2011.

The major goal of this project was to develop a high-performance, cost-effective engine for accelerating BLAST and BLAST-like similarity search using reconfigurable FPGA logic. This STTR was held in collaboration with BECS Technology, Inc. of Olivette, Missouri.

NSF ITR-427794, "ITR: Storage-Based Supercomputing for Scientific Applications," 9/1/2004-8/31/2009, PI Mark Franklin.

The major goal of this project was 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.

NSF DBI-0237902, "CAREER: New Technologies for Biosequence Comparison," PI Buhler, 7/2003-6/2009.

The primary purpose of this grant was 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.

HHMI 52005790, "Genomics Education Partnership", PI Sarah Elgin (WU Biology), 6/2005-6/2010.

This project was an initiative to expand BIO4342, a course on genome sequencing and annotation, to a group of more than 60 universities. Participating institutions cooperate in carrying out distributed finishing and annotation of genomic DNA for research purposes. I developed materials for the GEP on using BLAST for annotation. I participated in thrice-yearly workshops to teach use of GEP materials to new participants in the program.

NIH/NCRR P41-RR0954, "Washington University Center for Biomedical and Bioorganic Mass Spectrometry", PIs Michael Gross and Reid Townsend, 8/2006-8/2008.

This grant funded a center that, among other things, supported work in high-throughput protein mass spectrometry. I and a student were 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," 7/2004-6/2006, PI Michael Brent.

The goal of this contract was 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.

Teaching

Course Master

CSE 584, Algorithms for Biosequence Comparison

CSE 591, Introduction to Graduate Study in CSE

CSE 7800 / BIO 5496, Computational Molecular Biology Journal Club (with Barak Cohen)

CSE 241, Algorithms and Data Structures

CSE 441/541, Advanced Algorithms

CSE 547, Introduction to Formal Languages and Automata

Guest Teaching

CSE 587, Algorithms for Computational Biology (for Michael Brent)

BIO 4342, Research Explorations in Genetics (for Sarah Elgin)

CSE 565, Acceleration of Algorithms in Reconfigurable Logic (for Roger Chamberlain)

Students Currently Advised

Doctoral Student: Stephen Cole

serving on doctoral committees for students in Genetics and Computational Biology programs, Division of Biological and Biomedical Sciences.

Graduates (with Placements)

Ph.D.

Hongtao Sun, Google

Peng Li, Amazon

Arpith Jacob, Advanced Compiler Technologies Group, IBM Research

Yanni Sun, Michigan State University CSE (tenured)

Postdocs

Narayan Ganesan, Stevens College

Professional Activities

Program committees: (comp bio) ISMB, RECOMB, ECCB, CPM, PSB, IEEE CSB, IEEE BIBM, ISBRA, ACM BCB; (computer engineering) ASAP (program co-chair 2009), SAAHPC (track chair, bioinformatics, 2011; special session chair, bioinformatics, 2012)

Journals: Bioinformatics, BMC Bioinformatics, IEEE/ACM Transactions on Computational Biology and Bioinformatics, Genome Research, Journal of Computational Biology, Nucleic Acids Research

Grant Reviewing: on NIH GGG, IMST, GCAT, BDMA; NSF BIO/DBI; NSF CISE/IIS

Departmental and University Service

Search Committee for Director of Biomedical Informatics, School of Medicine, 2015-16

Search Committee, Computational Biology, Biology Department, 2015-2016.

Search Committee for Dean of Graduate School, 2013

Alternate, Faculty Senate Academic Freedom & Tenure Hearing Committee, 2013-2016

Interim Department Chair, Computer Science and Engineering, 2011-2013

Doctoral Program Director, Computer Science and Engineering, 2003-2011

CSE Leadership Committee, 2008-2011

Speaker for Engineering Faculty Assembly, 2010-2011

Advisory Committee to Engineering Faculty Assembly, 2009-2010

Graduate Council Teaching and Professional Development Committee, 2008-2010

Awards and Honors

2014 Department Chair's Award for Outstanding Teaching

RECOMB 2013 "Test of Time" Award for the 2001 paper "Finding Motifs Using Random Projections", with Martin Tompa

Best paper award, ASAP 2010

Best paper award, FCCM 2010

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)


Jeremy Buhler (jbuhler AT wustl DOT edu)
Last Update: 1/24/2017