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Books and Theses
- 2001
[b1]Jeremy Buhler:
Search algorithms for biosequences using random projection. University of Washington, USA, 2001
Journal Articles
- 2023
- [j21]Stephen Timcheck, Jeremy Buhler
:
Interruptible Nodes: Reducing Queueing Costs in Irregular Streaming Dataflow Applications on Wide-SIMD Architectures. Int. J. Parallel Program. 51(1): 43-60 (2023) - 2022
- [j20]Stephen Timcheck, Jeremy Buhler:
Reducing queuing impact in streaming applications with irregular dataflow. Parallel Comput. 109: 102863 (2022) - 2017
- [j19]Peng Li, Jonathan C. Beard, Jeremy D. Buhler:
Deadlock-free buffer configuration for stream computing. Int. J. High Perform. Comput. Appl. 31(5): 441-450 (2017) - 2012
- [j18]Hongtao Sun, Jeremy D. Buhler:
PhyLAT: a phylogenetic local alignment tool. Bioinform. 28(10): 1336-1344 (2012) - [j17]Nnamdi E. Ihuegbu, Gary D. Stormo, Jeremy Buhler:
Fast, Sensitive Discovery of Conserved Genome-Wide Motifs. J. Comput. Biol. 19(2): 139-147 (2012) - [j16]Yanni Sun, Jeremy Buhler, Cheng Yuan:
Designing Filters for Fast-Known NcRNA Identification. IEEE ACM Trans. Comput. Biol. Bioinform. 9(3): 774-787 (2012) - 2010
- [j15]Roger D. Chamberlain, Mark A. Franklin, Eric J. Tyson, James H. Buckley, Jeremy Buhler, Greg Galloway, Saurabh Gayen, Michael J. Hall, E. F. Berkley Shands, Naveen Singla:
Auto-Pipe: Streaming Applications on Architecturally Diverse Systems. Computer 43(3): 42-49 (2010) - [j14]Ross T. Sowell, Yixin Chen, Jeremy Buhler, Sally A. Goldman, Cindy Grimm, Kenneth J. Goldman:
Experiences with active learning in CS 3. J. Comput. Sci. Coll. 25(5): 173-179 (2010) - 2009
- [j13]Joseph M. Lancaster, Jeremy Buhler, Roger D. Chamberlain:
Acceleration of ungapped extension in Mercury BLAST. Microprocess. Microsystems 33(4): 281-289 (2009) - [j12]Yanni Sun, Jeremy Buhler:
Designing Patterns and Profiles for Faster HMM Search. IEEE ACM Trans. Comput. Biol. Bioinform. 6(2): 232-243 (2009) - 2008
- [j11]Arpith C. Jacob, Joseph M. Lancaster, Jeremy Buhler, Brandon Harris, Roger D. Chamberlain:
Mercury BLASTP: Accelerating Protein Sequence Alignment. ACM Trans. Reconfigurable Technol. Syst. 1(2): 9:1-9:44 (2008) - 2007
- [j10]Yanni Sun, Jeremy Buhler:
Designing patterns for profile HMM search. Bioinform. 23(2): 42-43 (2007) - [j9]Praveen Krishnamurthy, Jeremy Buhler, Roger D. Chamberlain, Mark A. Franklin, Kwame Gyang, Arpith C. Jacob, Joseph M. Lancaster:
Biosequence Similarity Search on the Mercury System. J. VLSI Signal Process. 49(1): 101-121 (2007) - 2006
- [j8]Yanni Sun, Jeremy Buhler:
Choosing the best heuristic for seeded alignment of DNA sequences. BMC Bioinform. 7: 133 (2006) - 2005
- [j7]Benjamin P. Westover, Jeremy D. Buhler, Justin L. Sonnenburg, Jeffrey I. Gordon:
Operon prediction without a training set. Bioinform. 21(7): 880-888 (2005) - [j6]Yanni Sun, Jeremy Buhler:
Designing Multiple Simultaneous Seeds for DNA Similarity Search. J. Comput. Biol. 12(6): 847-861 (2005) - [j5]Jeremy Buhler, Uri Keich, Yanni Sun:
Designing seeds for similarity search in genomic DNA. J. Comput. Syst. Sci. 70(3): 342-363 (2005) - 2003
- [j4]Jeremy Buhler:
Provably Sensitive Indexing Strategies for Biosequence Similarity Search. J. Comput. Biol. 10(3/4): 399-417 (2003) - 2002
- [j3]Jeremy Buhler, Martin Tompa:
Finding Motifs Using Random Projections. J. Comput. Biol. 9(2): 225-242 (2002) - 2001
- [j2]Jeremy Buhler:
Efficient large-scale sequence comparison by locality-sensitive hashing. Bioinform. 17(5): 419-428 (2001) - 1995
- [j1]Jeremy Buhler:
The Fox Project: a language-structured approach to networking software. XRDS 2(1): 12-18 (1995)
Conference and Workshop Papers
- 2025
- [c51]Daisy Wang, Ye Htet, Marion Sudvarg, Roger D. Chamberlain, Jeremy Buhler, James H. Buckley:
Coordinating Instruments for Multi-Messenger Astrophysics: Invited Paper. CF (Companion) 2025: 199-204 - 2024
- [c50]James H. Buckley, Jeremy Buhler, Roger D. Chamberlain:
The Advanced Particle-astrophysics Telescope (APT): Computation in Space. CF (Companion) 2024 - [c49]Marion Sudvarg, Chenfeng Zhao, Ye Htet, Meagan Konst, Thomas Lang, Nick Song, Roger D. Chamberlain, Jeremy Buhler, James H. Buckley:
HLS Taking Flight: Toward Using High-Level Synthesis Techniques in a Space-Borne Instrument. CF 2024 - [c48]Marion Sudvarg, Ao Li, Daisy Wang, Sanjoy K. Baruah, Jeremy Buhler, Chris Gill, Ning Zhang, Pontus Ekberg:
Elastic Scheduling for Harmonic Task Systems. RTAS 2024: 334-347 - [c47]Marion Sudvarg, Daisy Wang, Jeremy Buhler, Chris Gill:
Subtask-Level Elastic Scheduling. RTSS 2024: 388-401 - [c46]Ye Htet, Marion Sudvarg, Andrew Butzel, Jeremy D. Buhler, Roger D. Chamberlain, James H. Buckley:
Machine Learning Aboard the ADAPT Gamma-Ray Telescope. SC Workshops 2024: 4-10 - 2023
- [c45]Marion Sudvarg, Jeremy Buhler, Roger D. Chamberlain, Christopher D. Gill, James H. Buckley, Wenlei Chen:
Parameterized Workload Adaptation for Fork-Join Tasks with Dynamic Workloads and Deadlines. RTCSA 2023: 232-242 - [c44]Ye Htet, Marion Sudvarg, Jeremy Buhler, Roger D. Chamberlain, James H. Buckley:
Localization of Gamma-ray Bursts in a Balloon-Borne Telescope. SC Workshops 2023: 395-398 - 2021
- [c43]Jeremy Buhler, Thomas Lavastida, Kefu Lu, Benjamin Moseley:
A Scalable Approximation Algorithm for Weighted Longest Common Subsequence. Euro-Par 2021: 368-384 - [c42]Tom Plano, Jeremy Buhler:
Enabling Real-Time Irregular Data-Flow Pipelines on SIMD Devices. ICPP Workshops 2021: 9:1-9:8 - [c41]Anthony M. Cabrera, Aaron R. Young, Jacob Lambert, Zhili Xiao, Amy An, Seyong Lee, Zheming Jin, Jungwon Kim, Jeremy Buhler, Roger D. Chamberlain, Jeffrey S. Vetter:
Toward Evaluating High-Level Synthesis Portability and Performance between Intel and Xilinx FPGAs. IWOCL 2021: 7:1-7:9 - [c40]Clayton J. Faber, Tom Plano, Samatha Kodali, Zhili Xiao, Abhishek Dwaraki, Jeremy D. Buhler, Roger D. Chamberlain, Anthony M. Cabrera:
Platform Agnostic Streaming Data Application Performance Models. RSDHA@SC 2021: 17-26 - [c39]Jacob Wheelock, William Kanu, Marion Sudvarg, Zhili Xiao, Jeremy D. Buhler, Roger D. Chamberlain, James H. Buckley:
Supporting Multi-messenger Astrophysics with Fast Gamma-ray Burst Localization. UrgentHPC@SC 2021: 21-28 - 2020
- [c38]Tom Plano, Jeremy Buhler:
Scheduling Irregular Dataflow Pipelines on SIMD Architectures. WPMVP@PPoPP 2020: 1:1-1:9 - [c37]Stephen W. Timcheck, Jeremy D. Buhler:
Reducing Queuing Impact in Irregular Data Streaming Applications. IA3@SC 2020: 22-30 - 2017
- [c36]Stephen V. Cole, Jeremy Buhler:
MERCATOR: A GPGPU Framework for Irregular Streaming Applications. HPCS 2017: 727-736 - 2015
- [c35]Peng Li, Jonathan C. Beard, Jeremy Buhler:
Deadlock-free buffer configuration for stream computing. PMAM@PPoPP 2015: 164-169 - 2014
- [c34]Peng Li, Jeremy Buhler:
Improving performance of streaming applications with filtering and control messages. PACT 2014: 501-502 - [c33]Peng Li, Kunal Agrawal, Jeremy Buhler, Roger D. Chamberlain:
Orchestrating safe streaming computations with precise control. ICPADS 2014: 1017-1022 - [c32]Stephen V. Cole, Jacob R. Gardner, Jeremy D. Buhler:
WOODSTOCC: Extracting Latent Parallelism from a DNA Sequence Aligner on a GPU. ISPDC 2014: 197-204 - 2013
- [c31]Peng Li, Kunal Agrawal, Jeremy Buhler, Roger D. Chamberlain:
Adding data parallelism to streaming pipelines for throughput optimization. HiPC 2013: 20-29 - 2012
- [c30]Jeremy D. Buhler, Kunal Agrawal, Peng Li, Roger D. Chamberlain:
Efficient deadlock avoidance for streaming computation with filtering. PPoPP 2012: 235-246 - 2011
- [c29]Joseph M. Lancaster, E. F. Berkley Shands, Jeremy D. Buhler, Roger D. Chamberlain:
TimeTrial: A low-impact performance profiler for streaming data applications. ASAP 2011: 69-76 - [c28]Lin Ma, Roger D. Chamberlain, Jeremy D. Buhler, Mark A. Franklin:
Bloom Filter Performance on Graphics Engines. ICPP 2011: 522-531 - 2010
- [c27]Arpith C. Jacob, Jeremy D. Buhler, Roger D. Chamberlain:
Design of throughput-optimized arrays from recurrence abstractions. ASAP 2010: 133-140 - [c26]Peng Li, Kunal Agrawal, Jeremy Buhler, Roger D. Chamberlain, Joseph M. Lancaster:
Deadlock-avoidance for streaming applications with split-join structure: Two case studies. ASAP 2010: 333-336 - [c25]Narayan Ganesan, Roger D. Chamberlain, Jeremy Buhler, Michela Taufer:
Accelerating HMMER on GPUs by implementing hybrid data and task parallelism. BCB 2010: 418-421 - [c24]Arpith C. Jacob, Jeremy D. Buhler, Roger D. Chamberlain:
Rapid RNA Folding: Analysis and Acceleration of the Zuker Recurrence. FCCM 2010: 87-94 - [c23]Arpith C. Jacob, Jeremy D. Buhler, Roger D. Chamberlain:
Design space exploration of throughput-optimized arrays from recurrence abstractions (abstract only). FPGA 2010: 286 - [c22]Roger D. Chamberlain, Jeremy Buhler, Mark A. Franklin, James H. Buckley:
Application-guided tool development for architecturally diverse computation. SAC 2010: 496-501 - [c21]Peng Li, Kunal Agrawal, Jeremy Buhler, Roger D. Chamberlain:
Deadlock avoidance for streaming computations with filtering. SPAA 2010: 243-252 - 2009
- [c20]Arpith C. Jacob, Jeremy D. Buhler, Roger D. Chamberlain:
Optimal runtime reconfiguration strategies for systolic arrays. FPL 2009: 162-167 - [c19]Joseph M. Lancaster, Jeremy D. Buhler, Roger D. Chamberlain:
Efficient runtime performance monitoring of FPGA-based applications. SoCC 2009: 23-28 - 2008
- [c18]Arpith C. Jacob, Jeremy Buhler, Roger D. Chamberlain:
Accelerating Nussinov RNA secondary structure prediction with systolic arrays on FPGAs. ASAP 2008: 191-196 - 2007
- [c17]Arpith C. Jacob, Joseph M. Lancaster, Jeremy Buhler, Roger D. Chamberlain:
FPGA-accelerated seed generation in Mercury BLASTP. FCCM 2007: 95-106 - [c16]Brandon Harris, Arpith C. Jacob, Joseph M. Lancaster, Jeremy Buhler, Roger D. Chamberlain:
A Banded Smith-Waterman FPGA Accelerator for Mercury BLASTP. FPL 2007: 765-769 - [c15]Arpith C. Jacob, Joseph M. Lancaster, Jeremy D. Buhler, Roger D. Chamberlain:
Preliminary results in accelerating profile HMM search on FPGAs. IPDPS 2007: 1-8 - [c14]Roger D. Chamberlain, Mark A. Franklin, Eric J. Tyson, Jeremy Buhler, Saurabh Gayen, Patrick Crowley, James H. Buckley:
Application development on hybrid systems. SC 2007: 50 - 2006
- [c13]Arpith C. Jacob, Brandon Harris, Jeremy Buhler, Roger D. Chamberlain, Young H. Cho:
Scalable Softcore Vector Processor for Biosequence Applications. FCCM 2006: 295-296 - [c12]Rahul P. Maddimsetty, Jeremy Buhler, Roger D. Chamberlain, Mark A. Franklin, Brandon Harris:
Accelerator design for protein sequence HMM search. ICS 2006: 288-296 - [c11]Can Alkan, Emre Karakoç, Süleyman Cenk Sahinalp, Peter J. Unrau, H. Alexander Ebhardt, Kaizhong Zhang, Jeremy Buhler:
RNA Secondary Structure Prediction Via Energy Density Minimization. RECOMB 2006: 130-142 - 2005
- [c10]Ben Wun, Jeremy Buhler, Patrick Crowley:
Exploiting Coarse-Grained Parallelism to Accelerate Protein Motif Finding with a Network Processor. IEEE PACT 2005: 173-184 - 2004
- [c9]Praveen Krishnamurthy, Jeremy Buhler, Roger D. Chamberlain, Mark A. Franklin, Kwame Gyang, Joseph M. Lancaster:
Biosequence Similarity Search on the Mercury System. ASAP 2004: 365-375 - [c8]Jeremy Buhler, Richard Souvenir, Weixiong Zhang, Rob Mitra:
Design of a High-Throughput Assay for Alternative Splicing Using Polymerase Colonies. Pacific Symposium on Biocomputing 2004: 5-16 - [c7]Jeremy Buhler, Rachel Nordgren:
Toward a Phylogenetically Aware Algorithm for Fast DNA Similarity Search. Comparative Genomics 2004: 15-29 - [c6]Yanni Sun, Jeremy Buhler:
Designing multiple simultaneous seeds for DNA similarity search. RECOMB 2004: 76-84 - 2003
- [c5]Eran Halperin, Jeremy Buhler, Richard M. Karp, Robert Krauthgamer, Ben Westover:
Detecting protein sequence conservation via metric embeddings. ISMB (Supplement of Bioinformatics) 2003: 122-129 - [c4]Jeremy Buhler, Uri Keich, Yanni Sun:
Designing seeds for similarity search in genomic DNA. RECOMB 2003: 67-75 - [c3]Richard Souvenir, Jeremy Buhler, Gary D. Stormo, Weixiong Zhang:
Selecting Degenerate Multiplex PCR Primers. WABI 2003: 512-526 - 2002
- [c2]Jeremy Buhler:
Provably sensitive Indexing strategies for biosequence similarity search. RECOMB 2002: 90-99 - 2001
- [c1]Jeremy Buhler, Martin Tompa:
Finding motifs using random projections. RECOMB 2001: 69-76
Informal and Other Publications
- 2020
- [i1]Stephen Timcheck, Jeremy Buhler:
Streaming Computations with Region-Based State on SIMD Architectures. CoRR abs/2006.07478 (2020)
Coauthor Index
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