jbuhler AT wustl DOT edu
https://www.cse.washu.edu/~jbuhler/
Voicemail
314-935-6129
Postal Address
Department of Computer Science and Engineering
MSC 1045-213-1010J
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.
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 (March 1999). 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.
S. Timcheck and J. Buhler. "Interruptible nodes: Reducing queueing costs in irregular streaming dataflow applications on wide-SIMD architectures." Int'l J. Parallel Programming 51:43-60, 2023.
S Timcheck and J Buhler. "Reducing Queuing Impact in Streaming Applications with Irregular Dataflow." Parallel Computing 109:102863, March 2022.
D Lopatto, AG Rosenwald, RC Burgess, CS Key, et al. "Student Attitudes Contribute the the Effectiveness of a Genomics CURE." J. Microbiology and Biology Education e00208-21, 2022.
Z Hughes, J Buckley, L Bergstrom, W Binns, J Buhler, W Chen, M Cherry, S Funk, D Hooper, J Mitchell, G De Nolfo, S Al Nussirat, S Profumo, B Rauch, D Stern, G Varner, S Wakely, and A Zink. "Report of 2019 APTLite balloon flight." Bulletin of the American Astronomical Society 52(3), 2020.
D Lopatto, AG Rosenwald, JR DiAngelo, AT Hark, et al. "Facilitating growth through frustration: using genomics research in a course-based undergraduate research experience: formative frustration is an element of CUREs." Journal of Microbiology and Biology Education 21:1, 2020.
J Buckley, L Bergstrom, B Binns, J Buhler, W Chen, M Cherry, S Funk, D Hooper, J Mitchell, G de Nolfo, S al Nussirat, S Profumo, B Rauch, D Stern, G Varner, S Wakely, and A Zink. "The Advanced Particle-astrophysics Telescope (APT)." Bulletin of the American Astronomical Society 51(7):78, 2019.
W Leung, CD Shaffer, EJ Chen, TJ Quisenberry, et al. "Retrotransposons are the major contributors to the expansion of the Drosophila ananassae Muller F element." Genes, Genomes, and Genetics 7(8):2439-2460, 2017.
P Li, J Beard, and J Buhler. "Deadlock-free buffer configuration for streaming computing." Int'l J. High Performance Computing Applications 31(5):441-450, 2017.
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.
D. Wang, Y. Htet, J. Buhler, F. Markovic, and M. Sudvarg. "Suborbital and orbital real-time localization of gamma-ray bursts via utility-guided coordination." Proc. 2026 IEEE/ACM Int'l Conf. Embedded Software (EMSOFT), October 2026.
D. Wang, M. Sudvarg, F. Markovic, J. Buhler, S. Baruah, and G. Kehne. "Probabilistic response-time-aware search for transient astrophysical phenomena." Proc. 46th IEEE Real-Time Systems Symposium (RTSS), December 2025.
Y. Htet, M. Sudvarg, H. Yang, J. Buhler, R. Chamberlain, and J. Buckley. "Modeling and optimizing real-time telescope interaction for multi-wavelength observation of gamma-ray bursts." Proc. Wkshp. Int'l Conf. High Performance Computing, Networking, Storage, and Analysis (SC Workshops), 2161-2168, November 2025. Presented at Sixth Combined Workshop on Interactive and Urgent High-Performance Computing (WIUHPC), St. Louis, MO, USA.
L. Blair, J. Buhler, K. El Maghraoui, C. D. Carothers, N. Wang, and J. Murray. "Scaled FP32 and Quantization-aware Training of PatchTST for Efficient Time Series Forecasting." Proc. ACM KDD MILETS Wkshp, Toronto, ON, Canada, August 2025.
M. Sudvarg, L. Huang, B. Yang, B. Bal, R. Chamberlain, J. Buhler, L. Di Venere, D. Serini, J. Buckley, and the APT Collaboration. "FPGA-Based Data Processing using High-Level Synthesis on the Antarctic Demonstrator for the Advanced Particle-astrophysics Telescope (ADAPT)." Proc. 39th Int'l Cosmic Ray Conference PoS(ICRC2025), vol. 501, 852:1-9, July 2025.
Y. Htet, M. Sudvarg, H. Yang, J. Buhler, R. Chamberlain, W. Chen, J. Buckley, and the APT Collaboration. "Performance Modeling and Improvements on the GRB Source Localization Streaming Pipeline Aboard the Antarctic Demonstrator for the Advanced Particle-Astrophysics Telescope (ADAPT)." Proc. 39th Int'l Cosmic Ray Conference PoS(ICRC2025), vol. 501, 679:1-9, July 2025.
J. Buhler and M. Sudvarg. "Real-time Likelihood Map Generation to Localize Short-duration Gamma-ray Transients." Proc. 39th Int'l Cosmic Ray Conference PoS(ICRC2025), volume 501, 587:1-9, July 2025.
M. Sudvarg, Y. Htet, R. D. Chamberlain, J. D. Buhler, and J. H. Buckley. "Call for Collaboration: Contributing to Multi-Messenger Astrophysics." Proc. 19th Wkshp. Operating Systems Platforms for Embedded Real-Time Applications (OSPERT), 63-67, July 2025.
M. Sudvarg, D. Wang, J. Buhler, and C. Gill. "Subtask-level elastic scheduling." Proc. 45th Real-Time Systems Symposium, 2024.
Y. Htet, M. Sudvarg, D. Butzel, J. Buhler, R.D. Chamberlain, and J. Buckley. "Machine learning aboard the ADAPT gamma-ray telescope." Proc. 5th Wkshp. Artificial Intelligence and Machine Learning for Scientific Applications (at SC 2024), 2024.
M. Sudvarg, A. Li, D. Wang, S. Baruah, J. Buhler, C. Gill, N. Zhang, and P. Ekberg. "Elastic scheduling for harmonic task systems." Proc. 30th IEEE Real-Time and Embedded Technology and Applications Symp. 334-347, 2024.
M. Sudvarg, Y. Htet, S. Baruah, J. Buhler, R.D. Chamberlain, C. Gill, and J. Buckley. "Adaptive execution for real-time observations of astrophysical transients." Proc 13th Int'l Real-Time Scheduling Open Problems Seminar, 2024.
M. Sudvarg, C. Zhao, Y. Htet, M. Konst, T. Lang, N. Song, R.D. Chamberlain, J. Buhler, and J. Buckley. "HLS taking flight: toward using high-level synthesis techniques in a space-borne instrument." Proc. 21st ACM Int'l Conf. Computing Frontiers 115-125, 2024.
M. Sudvarg, C. Gill, and J. Buhler. "Subtask-level elasticity for federated scheduling of parallel tasks." Proc. Wkshp. Optimization for Embedded and Real-time Systems (OPERA), Dec. 2023.
Y. Htet, M. Sudvarg, J. Buhler, R.D. Chamberlain, and J.H. Buckley. "Localization of gamma-ray bursts in a balloon-borne telescope." Proc. Wkshp. Int'l Conf. High Performance Computing, Network, and Storage Analysis, 395-398, 2023.
M. Sudvarg, J. Buhler, R.D. Chamberlain, C. Gill, J. Buckley, and W. Chen. "Parameterized workload adaptation for fork-join tasks with dynamic workloads and deadlines." Proc. 29th IEEE Int'l Conf. Embedded and Real-Time Computing Systems and Applications (RTCSA) 232-242, 2023.
Y. Htet, M. Sudvarg, J. Buhler, R. Chamberlain, W. Chen, and J. Buckley for the APT collaboration. "Prompt and accurate GRB source localization aboard the Advanced Particle Astrophysics Telescope (APT) and its Antarctic Demonstrator (ADAPT)." 38th Int'l Cosmic Ray Conference (PoS) 956, 2023.
M. Sudvarg, Y. Htet, R. Chamberlain, J. Buhler, B. Bal, C. Altomare, D. Serini, M.N. Mazziotta, L. Di Venere, W. Chen, and J. Buckley for the APT collaboration. "Front-end computational modeling and design for the Antarctic Demonstrator for the Advanced Particle-astrophysics Telescope." 38th Int'l Cosmic Ray Conference (PoS) 764, 2023.
M. Sudvarg, J. Buhler, R.D. Chamberlain, C.D. Gill, and J. Buckley. "Work in Progress: Real-Time GRB Localization for the Advanced Particle-astrophysics Telescope." Proc. 15th Wkshp. Operating Systems Platforms for Embedded Real-Time Applications (OSPERT), 57-61, July 2022.
J. Wheelock, W. Kanu, M. Sudvarg, Z. Xiao, J. Buhler, R.D. Chamberlain, and J. Buckley. "Supporting multi-messenger astrophysics with fast gamma-ray burst localization." Proc. SC21 Wkshp. on HPC for Urgent Decision Making, 21-28, 2021.
C. Faber, T. Plano, S. Kodali, Z. Xiao, A. Dwaraki, J. Buhler, R.D. Chamberlain, and A.M. Cabrera. "Platform-agnostic streaming data application performance models." Proc. SC21 Wkshp. on Redefining Scalability for Diversely Heterogeneous Architectures, 17-26, 2021.
J. Buhler, T. Lavastida, K. Lu, and B. Moseley. "A scalable algorithm for all-substrings weighted longest common subsequence", 27th Int'l European Conf. Parallel and Distributed Computing 368-384, 2021.
M. Sudvarg, J. Buhler, J. Buckley, W. Chen, Z. Hughes, E. Ramey, M. Cherry, S. Alnussirat, R. Larm, and C. Berruz Chungata on behalf of the ADAPT collaboration. "A fast GRB source localization pipeline for the Advanced Particle-astrophysics telescope." 37th Int'l Cosmic Ray Conference (PoS), 395:588, 2021.
W. Chen, J. Buckley, S. Alnussirat, C. Altomare, R. Bose, D. Braun, J. Buhler, et al. on behalf of the ADAPT collaboration. "The Advanced Particle-astrophysics Telescope: simulation of the instrument performance for gamma-ray detection". 37th Int'l Cosmic Ray Conference (PoS), 395:590, 2021.
T. Plano and J. Buhler. "Enabling real-time irregular data-flow pipelines on SIMD devices." Proc. 50th Int'l Conference Parallel Processing Wkshps, 9:1-8, 2021.
A.M. Cabrera, A.R. Young, J. Lambert, Z. Xiao, A. An, S. Lee, Z. Jin, J. Kim, J.D. Buhler, R.D. Chamberlain, and J.S. Vetter. "Toward evaluating high-level synthesis portability and performance between Intel and Xilinx FPGAs." Proc. Int'l Wkshp. on OpenCL (IWOCL) 7, 2021.
S. Timcheck and J. Buhler. "Reducing queueing impact in irregular data streaming applications." 10th Wkshp. on Irregular Applications: Architectures and Algorithms (IA3), 22-30, Nov 2020.
T. Plano and J. Buhler. "Scheduling irregular dataflow pipelines on SIMD architectures." 6th Wkshp. on Programming Models for SIMD/Vector Processing, 1-9, San Diego, CA, Feb 2020.
S. Timcheck and J. Buhler. "Streaming computations with region-based state on SIMD architectures." 13th Int'l Wkshp. on Programmability and Architectures for Heterogeneous Multicores, 1, Bologna, Italy, Jan 2020.
S. Cole and J. Buhler. "MERCATOR: a GPGPU Framework for Irregular Streaming Applications." 15th Int'l Conf. on High Performance Computing and Simulation 727-736, Genoa, Italy, July 2017.
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.
D. Wang, M. Sudvarg, J. Buhler, F. Markovic, and J. Buckley. "Strategies to Plan Time-Critical Optical Follow-Up of Transient Astrophysical Events." AAS/High Energy Astrophysics Division, 57(5), 302-04, 2025.
Y. Htet, M. Sudvarg, A. Butzel, J. Buhler, R. Chamberlain, J. Buckley, and the APT Collaboration. "Neural Network Extensions for the GRB Localization Pipeline on the ADAPT Gamma-Ray Telescope." AAS/High Energy Astrophysics Division 57(5), 111-25, 2025.
J. Shin, M. Sudvarg, J. Buhler, J. Buckley, and the APT Collaboration. "Accelerating Compton Imaging of Astrophysical Sources in Python." AAS/High Energy Astrophysics Division 21 (2024): 105-27.
L. Blair, K. El Maghraoui, N. Wang, P-Y. Chen, J. Murray, J. Buhler, and C.D. Carothers. "Low-bit quantization of Patch Time Series Transformer (PatchTST) Model." IBM/IEEE CAS/EDS AI Compute Symposium, Nov. 2023.
D. Wang, J. Zhang, J. Buhler, and J. Wang. Real-time analysis of aerosol size distributions with the Fast Integrated Mobility Spectrometer (FIMS)." 41st Conf. American Association for Aerosol Research (AAAR), Oct. 2023.
Y. Htet, M. Sudvarg, J. Buhler, R. Chamberlain, and J. Buckley on behalf of the APT Collaboration. "Prompt, accurate localization of gamma-ray bursts in the Advanced Particle-astrophysics Telescope." 20th Divisional Meeting of the High Energy Astrophysics Division (HEAD), American Astronomical Society, Mar. 2023.
M. Sudvarg, M. Konst, T. Lang, D. Pacheco-Garcia, R. Chamberlain, and J. Buhler on behalf of the APT Collaboration. "Design of front-end signal processing for the Advanced Particle-astrophysics Telescope." 20th Divisional Meeting of the High Energy Astrophysics Division (HEAD), American Astronomical Society, Mar. 2023.
D. Wang, Y. Htet, M. Sudvarg, R. Chamberlain, J. Buhler, and J. Buckley. “Coordinat-ing instruments for multi-messenger astrophysics.” Proc. 22nd ACM Int’l Conf. Computing Frontiers, Workshops and Special Sessions 213-218, May 2025.
J.H. Buckley, J. Buhler, and R.D. Chamberlain. "The Advanced Particle-astrophysics Telescope (APT): computation in space." Proc. 21st ACM Int'l Conf. Computing Frontiers, Workshops and Special Sessions 122-7, 2024.
Y. Htet, M. Sudvarg, J. Buhler, R. Chamberlain, J. Buckley, and the APT collaboration. "A Computational Pipeline for Prompt Gamma-Ray Burst Localization Aboard APT and ADAPT." AAS/High Energy Astrophysics Division 21 (2024): 105-30.
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.
U.S. 10,957,423, "Method and Apparatus for Performing Similarity Searching." Issued March 23, 2021.
U.S. 10,580,518, "Method and Apparatus for Performing Similarity Searching." Issued March 3, 2020.
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.
NASA 80NSSC26K0764: "Development of enhanced detectors for the Antarctic Demonstrator for the Advanced Particle-Astrophysics Telescope (ADAPT2)", PI James Buckley, 5/2026-4/2028
This grant funds the ADAPT Consortium, which is designing and testing a next-generation gamma-ray observatory. This grant continues development of a successor to the ADAPT demonstrator instrument described for NASA 80NSSC21K1741. I continue to lead development of real-time algorithms to localize and characterize gamma-ray bursts that run on low-power, flight-qualified hardware.
NASA 80NSSC21K1741: "Antarctic Demonstration of the Advanced Particle-Astrophysics Telescope", PI James Buckley, 8/2021-7/2026
This grant funds the ADAPT Consortium, which is designing and testing a next-generation gamma-ray observatory. The eventual instrument will be space-based, but the demonstration device constructed by this project will be tested through a high-altitude balloon flight. My role on the project is co-lead for analysis, including development of both algorithms to localize energetic gamma-ray bursts in the sky and infrastructure to deploy these algorithms on low-power hardware in a way that meets strict computational throughput and latency constraints dictated by the application.
Washington U. CSE/EECE seed grant: "Adding Real-Time Detection Capabilities to an Aerosol Sampling Instrument", PI Jeremy Buhler, 1/2023-2/2024
This seed grant funds initial exploration of how to add real-time data analysis to the Fast Integrated Mobility Spectrometer, an airborne instrument developed by the Jian Wang lab in Wash U.'s EECE Department to characterize atmospheric aerosol density and particle size distribution. We are rebuilding the existing analysis pipeline to support accurate, fully automated characterization of atmospheric aerorsols with a sampling rate of at least 10 Hz using low-power hardware that could support future deployment on small, unmanned aircraft.
NSF CNS-1763503: "CSR: Medium: Performant Architecturally Diverse Systems via Aspect-oriented Programming", PI Roger Chamberlain, 9/2018-8/2023
This grant supports development of tools for high-level specification, implementation, and tuning of efficient parallel algorithms across diverse platforms, including multicores, GPUs, and FPGAs. Ongoing work on parallelizing streaming computation, including the MERCATOR system, is part of this project.
NSF CNS-1500173: "EAGER: Rapid, Efficient Implementation of Irregular Applications on SIMD Many-Core Platforms", PI Jeremy Buhler, 8/2015-7/2018.
This grant supported modeling, analysis, and development of the MERCATOR system 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 supported the Genomics Education Partnership (still ongoing), run by Dr. Elgin and described below. My role in the project was 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.
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.
CSE 247, Algorithms and Data Structures
CSE 347/3407, Analysis of Algorithms
CSE 541T, Advanced Algorithms
CSE 447T/547T/4470, Introduction to Formal Languages and Automata
CSE 584A/5804, Algorithms for Biosequence Comparison
CSE 591, Introduction to Graduate Study in CSE
CSE 7800 / BIO 5496, Computational Molecular Biology Journal Club (with Gary Stormo)
CSE 7900, Seminar on Parallel Computing (with Roger Chamberlain)
CSE 587A, 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)
Doctoral Students: Ye Htet
serving on doctoral committees for students in CSE and in Division of Biological and Biomedical Sciences.
Stephen Timcheck
Steve Cole, senior lecturer, Wash U. CSE
Hongtao Sun, Google
Peng Li, Amazon
Arpith Jacob, Google
Yanni Sun, City University of Hong Kong (tenured)
Narayan Ganesan, Stevens College
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: NIH GGG, IMST, GCAT, BDMA; NSF BIO/DBI; NSF CISE/IIS
University Committe for Program Assessment (representing the McKelvey School of Engineering), 2024-present
CSE Masters Program and Admissions Director, 2019-2023
University Security and Privacy Governance Committee, 2018-present
CSE Leadership Committee, 2008-2011, 2018-2020
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
Speaker for Engineering Faculty Assembly, 2010-2011
Advisory Committee to Engineering Faculty Assembly, 2009-2010
Graduate Council Teaching and Professional Development Committee, 2008-2010
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)