Jeremy Buhler

Publication Activity (10 Years)

Years Active: 1995-2024
Publications (10 Years): 14

Top Topics

Irregularly Shaped

Parallel Processing

Longest Common Subsequence

Top Venues

Publications

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)
James H. Buckley, Jeremy Buhler, Roger D. Chamberlain
The Advanced Particle-astrophysics Telescope (APT): Computation in Space. CF (Companion) (2024)
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)
Stephen Timcheck, Jeremy Buhler
Interruptible Nodes: Reducing Queueing Costs in Irregular Streaming Dataflow Applications on Wide-SIMD Architectures. Int. J. Parallel Program. 51 (1) (2023)
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)
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)
Stephen Timcheck, Jeremy Buhler
Reducing queuing impact in streaming applications with irregular dataflow. Parallel Comput. 109 (2022)
Tom Plano, Jeremy Buhler
Enabling Real-Time Irregular Data-Flow Pipelines on SIMD Devices. ICPP Workshops (2021)
Jeremy Buhler, Thomas Lavastida, Kefu Lu, Benjamin Moseley
A Scalable Approximation Algorithm for Weighted Longest Common Subsequence. Euro-Par (2021)
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)
Stephen Timcheck, Jeremy Buhler
Streaming Computations with Region-Based State on SIMD Architectures. CoRR (2020)
Tom Plano, Jeremy Buhler
Scheduling Irregular Dataflow Pipelines on SIMD Architectures. WPMVP@PPoPP (2020)
Stephen V. Cole, Jeremy Buhler
MERCATOR: A GPGPU Framework for Irregular Streaming Applications. HPCS (2017)
Peng Li, Jonathan C. Beard, Jeremy Buhler
Deadlock-free buffer configuration for stream computing. PMAM@PPoPP (2015)
Peng Li, Kunal Agrawal, Jeremy Buhler, Roger D. Chamberlain
Orchestrating safe streaming computations with precise control. ICPADS (2014)
Peng Li, Jeremy Buhler
Improving performance of streaming applications with filtering and control messages. PACT (2014)
Peng Li, Kunal Agrawal, Jeremy Buhler, Roger D. Chamberlain
Adding data parallelism to streaming pipelines for throughput optimization. HiPC (2013)
Nnamdi E. Ihuegbu, Gary D. Stormo, Jeremy Buhler
Fast, Sensitive Discovery of Conserved Genome-Wide Motifs. J. Comput. Biol. 19 (2) (2012)
Yanni Sun, Jeremy Buhler, Cheng Yuan
Designing Filters for Fast-Known NcRNA Identification. IEEE ACM Trans. Comput. Biol. Bioinform. 9 (3) (2012)
Peng Li, Kunal Agrawal, Jeremy Buhler, Roger D. Chamberlain
Deadlock avoidance for streaming computations with filtering. SPAA (2010)
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)
Narayan Ganesan, Roger D. Chamberlain, Jeremy Buhler, Michela Taufer
Accelerating HMMER on GPUs by implementing hybrid data and task parallelism. BCB (2010)
Roger D. Chamberlain, Jeremy Buhler, Mark A. Franklin, James H. Buckley
Application-guided tool development for architecturally diverse computation. SAC (2010)
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) (2010)
Yanni Sun, Jeremy Buhler
Designing Patterns and Profiles for Faster HMM Search. IEEE ACM Trans. Comput. Biol. Bioinform. 6 (2) (2009)
Joseph M. Lancaster, Jeremy Buhler, Roger D. Chamberlain
Acceleration of ungapped extension in Mercury BLAST. Microprocess. Microsystems 33 (4) (2009)
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) (2008)
Arpith C. Jacob, Jeremy Buhler, Roger D. Chamberlain
Accelerating Nussinov RNA secondary structure prediction with systolic arrays on FPGAs. ASAP (2008)
Praveen Krishnamurthy, Jeremy Buhler, Roger D. Chamberlain, Mark A. Franklin, Kwame Gyang, Arpith C. Jacob, Joseph M. Lancaster
System. J. VLSI Signal Process. 49 (1) (2007)
Yanni Sun, Jeremy Buhler
Designing patterns for profile HMM search. Bioinform. 23 (2) (2007)
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)
Brandon Harris, Arpith C. Jacob, Joseph M. Lancaster, Jeremy Buhler, Roger D. Chamberlain
A Banded Smith-Waterman FPGA Accelerator for Mercury BLASTP. FPL (2007)
Arpith C. Jacob, Joseph M. Lancaster, Jeremy Buhler, Roger D. Chamberlain
FPGA-accelerated seed generation in Mercury BLASTP. FCCM (2007)
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)
Arpith C. Jacob, Brandon Harris, Jeremy Buhler, Roger D. Chamberlain, Young H. Cho
Scalable Softcore Vector Processor for Biosequence Applications. FCCM (2006)
Rahul P. Maddimsetty, Jeremy Buhler, Roger D. Chamberlain, Mark A. Franklin, Brandon Harris
Accelerator design for protein sequence HMM search. ICS (2006)
Yanni Sun, Jeremy Buhler
Choosing the best heuristic for seeded alignment of DNA sequences. BMC Bioinform. 7 (2006)
Jeremy Buhler, Uri Keich, Yanni Sun
Designing seeds for similarity search in genomic DNA. J. Comput. Syst. Sci. 70 (3) (2005)
Ben Wun, Jeremy Buhler, Patrick Crowley
Exploiting Coarse-Grained Parallelism to Accelerate Protein Motif Finding with a Network Processor. IEEE PACT (2005)
Yanni Sun, Jeremy Buhler
Designing Multiple Simultaneous Seeds for DNA Similarity Search. J. Comput. Biol. 12 (6) (2005)
Jeremy Buhler, Rachel Nordgren
Toward a Phylogenetically Aware Algorithm for Fast DNA Similarity Search. Comparative Genomics (2004)
Praveen Krishnamurthy, Jeremy Buhler, Roger D. Chamberlain, Mark A. Franklin, Kwame Gyang, Joseph M. Lancaster
Biosequence Similarity Search on the Mercury System. ASAP (2004)
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)
Yanni Sun, Jeremy Buhler
Designing multiple simultaneous seeds for DNA similarity search. RECOMB (2004)
Jeremy Buhler
Provably Sensitive Indexing Strategies for Biosequence Similarity Search. J. Comput. Biol. 10 (3/4) (2003)
Richard Souvenir, Jeremy Buhler, Gary D. Stormo, Weixiong Zhang
Selecting Degenerate Multiplex PCR Primers. WABI (2003)
Jeremy Buhler, Uri Keich, Yanni Sun
Designing seeds for similarity search in genomic DNA. RECOMB (2003)
Eran Halperin, Jeremy Buhler, Richard M. Karp, Robert Krauthgamer, Ben Westover
Detecting protein sequence conservation via metric embeddings. ISMB (Supplement of Bioinformatics) (2003)
Jeremy Buhler
Provably sensitive Indexing strategies for biosequence similarity search. RECOMB (2002)
Jeremy Buhler, Martin Tompa
Finding Motifs Using Random Projections. J. Comput. Biol. 9 (2) (2002)
Jeremy Buhler, Martin Tompa
Finding motifs using random projections. RECOMB (2001)
Jeremy Buhler
Efficient large-scale sequence comparison by locality-sensitive hashing. Bioinform. 17 (5) (2001)
Jeremy Buhler
The Fox Project: a language-structured approach to networking software. XRDS 2 (1) (1995)