The Fox Project: a language-structured approach to networking software. - Jeremy Buhler (XRDS, 1995)

Efficient large-scale sequence comparison by locality-sensitive hashing. - Jeremy Buhler (Bioinform., 2001)

Search algorithms for biosequences using random projection. - Jeremy Buhler (2001)

Finding Motifs Using Random Projections. - Jeremy Buhler; Martin Tompa (J. Comput. Biol., 2002)

Detecting protein sequence conservation via metric embeddings. - Eran Halperin; Jeremy Buhler; Richard M. Karp; Robert Krauthgamer; Ben Westover (ISMB (Supplement of Bioinformatics), 2003)

Selecting Degenerate Multiplex PCR Primers. - Richard Souvenir; Jeremy Buhler; Gary D. Stormo; Weixiong Zhang (WABI, 2003)

Provably Sensitive Indexing Strategies for Biosequence Similarity Search. - Jeremy Buhler (J. Comput. Biol., 2003)

Biosequence Similarity Search on the Mercury System. - Praveen Krishnamurthy; Jeremy Buhler; Roger D. Chamberlain; Mark A. Franklin; Kwame Gyang; Joseph M. Lancaster (ASAP, 2004)

Design of a High-Throughput Assay for Alternative Splicing Using Polymerase Colonies. - Jeremy Buhler; Richard Souvenir; Weixiong Zhang; Rob Mitra (Pacific Symposium on Biocomputing, 2004)

Toward a Phylogenetically Aware Algorithm for Fast DNA Similarity Search. - Jeremy Buhler; Rachel Nordgren (Comparative Genomics, 2004)

Exploiting Coarse-Grained Parallelism to Accelerate Protein Motif Finding with a Network Processor. - Ben Wun; Jeremy Buhler; Patrick Crowley (IEEE PACT, 2005)

Operon prediction without a training set. - Benjamin P. Westover; Jeremy D. Buhler; Justin L. Sonnenburg; Jeffrey I. Gordon (Bioinform., 2005)

Designing Multiple Simultaneous Seeds for DNA Similarity Search. - Yanni Sun; Jeremy Buhler (J. Comput. Biol., 2005)

Designing seeds for similarity search in genomic DNA. - Jeremy Buhler; Uri Keich; Yanni Sun (J. Comput. Syst. Sci., 2005)

Scalable Softcore Vector Processor for Biosequence Applications. - Arpith C. Jacob; Brandon Harris; Jeremy Buhler; Roger D. Chamberlain; Young H. Cho (FCCM, 2006)

Accelerator design for protein sequence HMM search. - Rahul P. Maddimsetty; Jeremy Buhler; Roger D. Chamberlain; Mark A. Franklin; Brandon Harris (ICS, 2006)

RNA Secondary Structure Prediction Via Energy Density Minimization. - Can Alkan; Emre Karakoç; Süleyman Cenk Sahinalp; Peter J. Unrau; H. Alexander Ebhardt; Kaizhong Zhang; Jeremy Buhler (RECOMB, 2006)

Choosing the best heuristic for seeded alignment of DNA sequences. - Yanni Sun; Jeremy Buhler (BMC Bioinform., 2006)

FPGA-accelerated seed generation in Mercury BLASTP. - Arpith C. Jacob; Joseph M. Lancaster; Jeremy Buhler; Roger D. Chamberlain (FCCM, 2007)

A Banded Smith-Waterman FPGA Accelerator for Mercury BLASTP. - Brandon Harris; Arpith C. Jacob; Joseph M. Lancaster; Jeremy Buhler; Roger D. Chamberlain (FPL, 2007)

Preliminary results in accelerating profile HMM search on FPGAs. - Arpith C. Jacob; Joseph M. Lancaster; Jeremy D. Buhler; Roger D. Chamberlain (IPDPS, 2007)

Application development on hybrid systems. - Roger D. Chamberlain; Mark A. Franklin; Eric J. Tyson; Jeremy Buhler; Saurabh Gayen; Patrick Crowley; James H. Buckley (SC, 2007)

Designing patterns for profile HMM search. - Yanni Sun; Jeremy Buhler (Bioinform., 2007)

Biosequence Similarity Search on the Mercury System. - Praveen Krishnamurthy; Jeremy Buhler; Roger D. Chamberlain; Mark A. Franklin; Kwame Gyang; Arpith C. Jacob; Joseph M. Lancaster (J. VLSI Signal Process., 2007)

Accelerating Nussinov RNA secondary structure prediction with systolic arrays on FPGAs. - Arpith C. Jacob; Jeremy Buhler; Roger D. Chamberlain (ASAP, 2008)

Mercury BLASTP: Accelerating Protein Sequence Alignment. - Arpith C. Jacob; Joseph M. Lancaster; Jeremy Buhler; Brandon Harris; Roger D. Chamberlain (ACM Trans. Reconfigurable Technol. Syst., 2008)

Optimal runtime reconfiguration strategies for systolic arrays. - Arpith C. Jacob; Jeremy D. Buhler; Roger D. Chamberlain (FPL, 2009)

Efficient runtime performance monitoring of FPGA-based applications. - Joseph M. Lancaster; Jeremy D. Buhler; Roger D. Chamberlain (SoCC, 2009)

Acceleration of ungapped extension in Mercury BLAST. - Joseph M. Lancaster; Jeremy Buhler; Roger D. Chamberlain (Microprocess. Microsystems, 2009)

Designing Patterns and Profiles for Faster HMM Search. - Yanni Sun; Jeremy Buhler (IEEE ACM Trans. Comput. Biol. Bioinform., 2009)

Design of throughput-optimized arrays from recurrence abstractions. - Arpith C. Jacob; Jeremy D. Buhler; Roger D. Chamberlain (ASAP, 2010)

Deadlock-avoidance for streaming applications with split-join structure: Two case studies. - Peng Li; Kunal Agrawal 001; Jeremy Buhler; Roger D. Chamberlain; Joseph M. Lancaster (ASAP, 2010)

Accelerating HMMER on GPUs by implementing hybrid data and task parallelism. - Narayan Ganesan; Roger D. Chamberlain; Jeremy Buhler; Michela Taufer (BCB, 2010)

Rapid RNA Folding: Analysis and Acceleration of the Zuker Recurrence. - Arpith C. Jacob; Jeremy D. Buhler; Roger D. Chamberlain (FCCM, 2010)

Design space exploration of throughput-optimized arrays from recurrence abstractions (abstract only). - Arpith C. Jacob; Jeremy D. Buhler; Roger D. Chamberlain (FPGA, 2010)

Application-guided tool development for architecturally diverse computation. - Roger D. Chamberlain; Jeremy Buhler; Mark A. Franklin; James H. Buckley (SAC, 2010)

Deadlock avoidance for streaming computations with filtering. - Peng Li; Kunal Agrawal 001; Jeremy Buhler; Roger D. Chamberlain (SPAA, 2010)

Auto-Pipe: Streaming Applications on Architecturally Diverse Systems. - 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 (Computer, 2010)

Experiences with active learning in CS 3. - Ross T. Sowell; Yixin Chen; Jeremy Buhler; Sally A. Goldman; Cindy Grimm; Kenneth J. Goldman (J. Comput. Sci. Coll., 2010)

TimeTrial: A low-impact performance profiler for streaming data applications. - Joseph M. Lancaster; E. F. Berkley Shands; Jeremy D. Buhler; Roger D. Chamberlain (ASAP, 2011)

Bloom Filter Performance on Graphics Engines. - Lin Ma 007; Roger D. Chamberlain; Jeremy D. Buhler; Mark A. Franklin (ICPP, 2011)

Efficient deadlock avoidance for streaming computation with filtering. - Jeremy D. Buhler; Kunal Agrawal 001; Peng Li; Roger D. Chamberlain (PPoPP, 2012)

PhyLAT: a phylogenetic local alignment tool. - Hongtao Sun; Jeremy D. Buhler (Bioinform., 2012)

Fast, Sensitive Discovery of Conserved Genome-Wide Motifs. - Nnamdi E. Ihuegbu; Gary D. Stormo; Jeremy Buhler (J. Comput. Biol., 2012)

Designing Filters for Fast-Known NcRNA Identification. - Yanni Sun; Jeremy Buhler; Cheng Yuan 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2012)

Adding data parallelism to streaming pipelines for throughput optimization. - Peng Li; Kunal Agrawal 001; Jeremy Buhler; Roger D. Chamberlain (HiPC, 2013)

Improving performance of streaming applications with filtering and control messages. - Peng Li; Jeremy Buhler (PACT, 2014)

Orchestrating safe streaming computations with precise control. - Peng Li; Kunal Agrawal 001; Jeremy Buhler; Roger D. Chamberlain (ICPADS, 2014)

WOODSTOCC: Extracting Latent Parallelism from a DNA Sequence Aligner on a GPU. - Stephen V. Cole; Jacob R. Gardner; Jeremy D. Buhler (ISPDC, 2014)

MERCATOR: A GPGPU Framework for Irregular Streaming Applications. - Stephen V. Cole; Jeremy Buhler (HPCS, 2017)

Deadlock-free buffer configuration for stream computing. - Peng Li; Jonathan C. Beard; Jeremy D. Buhler (Int. J. High Perform. Comput. Appl., 2017)

Scheduling Irregular Dataflow Pipelines on SIMD Architectures. - Tom Plano; Jeremy Buhler (WPMVP@PPoPP, 2020)

Reducing Queuing Impact in Irregular Data Streaming Applications. - Stephen W. Timcheck; Jeremy D. Buhler (IA3@SC, 2020)

Streaming Computations with Region-Based State on SIMD Architectures. - Stephen Timcheck; Jeremy Buhler (CoRR, 2020)

A Scalable Approximation Algorithm for Weighted Longest Common Subsequence. - Jeremy Buhler; Thomas Lavastida; Kefu Lu; Benjamin Moseley (Euro-Par, 2021)

Enabling Real-Time Irregular Data-Flow Pipelines on SIMD Devices. - Tom Plano; Jeremy Buhler (ICPP Workshops, 2021)

Toward Evaluating High-Level Synthesis Portability and Performance between Intel and Xilinx FPGAs. - Anthony M. Cabrera; Aaron R. Young; Jacob Lambert 002; Zhili Xiao; Amy An; Seyong Lee; Zheming Jin; Jungwon Kim; Jeremy Buhler; Roger D. Chamberlain; Jeffrey S. Vetter (IWOCL, 2021)

Platform Agnostic Streaming Data Application Performance Models. - Clayton J. Faber; Tom Plano; Samatha Kodali; Zhili Xiao; Abhishek Dwaraki; Jeremy D. Buhler; Roger D. Chamberlain; Anthony M. Cabrera (RSDHA@SC, 2021)

Supporting Multi-messenger Astrophysics with Fast Gamma-ray Burst Localization. - Jacob Wheelock; William Kanu; Marion Sudvarg; Zhili Xiao; Jeremy D. Buhler; Roger D. Chamberlain; James H. Buckley (UrgentHPC@SC, 2021)

Reducing queuing impact in streaming applications with irregular dataflow. - Stephen Timcheck; Jeremy Buhler (Parallel Comput., 2022)

Parameterized Workload Adaptation for Fork-Join Tasks with Dynamic Workloads and Deadlines. - Marion Sudvarg; Jeremy Buhler; Roger D. Chamberlain; Christopher D. Gill; James H. Buckley; Wenlei Chen (RTCSA, 2023)

Localization of Gamma-ray Bursts in a Balloon-Borne Telescope. - Ye Htet; Marion Sudvarg; Jeremy Buhler; Roger D. Chamberlain; James H. Buckley (SC Workshops, 2023)

Interruptible Nodes: Reducing Queueing Costs in Irregular Streaming Dataflow Applications on Wide-SIMD Architectures. - Stephen Timcheck; Jeremy Buhler (Int. J. Parallel Program., 2023)

The Advanced Particle-astrophysics Telescope (APT): Computation in Space. - James H. Buckley; Jeremy Buhler; Roger D. Chamberlain (CF (Companion), 2024)

HLS Taking Flight: Toward Using High-Level Synthesis Techniques in a Space-Borne Instrument. - Marion Sudvarg; Chenfeng Zhao; Ye Htet; Meagan Konst; Thomas Lang; Nick Song; Roger D. Chamberlain; Jeremy Buhler; James H. Buckley (CF, 2024)

Elastic Scheduling for Harmonic Task Systems. - Marion Sudvarg; Ao Li 006; Daisy Wang; Sanjoy K. Baruah; Jeremy Buhler; Chris Gill 001; Ning Zhang 017; Pontus Ekberg (RTAS, 2024)

Subtask-Level Elastic Scheduling. - Marion Sudvarg; Daisy Wang; Jeremy Buhler; Chris Gill 001 (RTSS, 2024)

Machine Learning Aboard the ADAPT Gamma-Ray Telescope. - Ye Htet; Marion Sudvarg; Andrew Butzel; Jeremy D. Buhler; Roger D. Chamberlain; James H. Buckley (SC Workshops, 2024)

Coordinating Instruments for Multi-Messenger Astrophysics: Invited Paper. - Daisy Wang; Ye Htet; Marion Sudvarg; Roger D. Chamberlain; Jeremy Buhler; James H. Buckley (CF (Companion), 2025)