Jeremy Buhler

According to our database1, Jeremy Buhler authored at least 48 papers between 2001 and 2017.

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Bibliography

2017
MERCATOR: A GPGPU Framework for Irregular Streaming Applications.
Proceedings of the 2017 International Conference on High Performance Computing & Simulation, 2017

2015
Deadlock-free buffer configuration for stream computing.
Proceedings of the Sixth International Workshop on Programming Models and Applications for Multicores and Manycores, 2015

2014
WOODSTOCC: Extracting Latent Parallelism from a DNA Sequence Aligner on a GPU.
Proceedings of the IEEE 13th International Symposium on Parallel and Distributed Computing, 2014

Orchestrating safe streaming computations with precise control.
Proceedings of the 20th IEEE International Conference on Parallel and Distributed Systems, 2014

Improving performance of streaming applications with filtering and control messages.
Proceedings of the International Conference on Parallel Architectures and Compilation, 2014

2013
Adding data parallelism to streaming pipelines for throughput optimization.
Proceedings of the 20th Annual International Conference on High Performance Computing, 2013

2012
Designing Filters for Fast-Known NcRNA Identification.
IEEE/ACM Trans. Comput. Biology Bioinform., 2012

Fast, Sensitive Discovery of Conserved Genome-Wide Motifs.
Journal of Computational Biology, 2012

PhyLAT: a phylogenetic local alignment tool.
Bioinformatics, 2012

Efficient deadlock avoidance for streaming computation with filtering.
Proceedings of the 17th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, 2012

2011
Bloom Filter Performance on Graphics Engines.
Proceedings of the International Conference on Parallel Processing, 2011

TimeTrial: A low-impact performance profiler for streaming data applications.
Proceedings of the 22nd IEEE International Conference on Application-specific Systems, 2011

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

Deadlock avoidance for streaming computations with filtering.
Proceedings of the SPAA 2010: Proceedings of the 22nd Annual ACM Symposium on Parallelism in Algorithms and Architectures, 2010

Application-guided tool development for architecturally diverse computation.
Proceedings of the 2010 ACM Symposium on Applied Computing (SAC), 2010

Design space exploration of throughput-optimized arrays from recurrence abstractions (abstract only).
Proceedings of the ACM/SIGDA 18th International Symposium on Field Programmable Gate Arrays, 2010

Rapid RNA Folding: Analysis and Acceleration of the Zuker Recurrence.
Proceedings of the 18th IEEE Annual International Symposium on Field-Programmable Custom Computing Machines, 2010

Accelerating HMMER on GPUs by implementing hybrid data and task parallelism.
Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology, 2010

Deadlock-avoidance for streaming applications with split-join structure: Two case studies.
Proceedings of the 21st IEEE International Conference on Application-specific Systems Architectures and Processors, 2010

Design of throughput-optimized arrays from recurrence abstractions.
Proceedings of the 21st IEEE International Conference on Application-specific Systems Architectures and Processors, 2010

2009
Designing Patterns and Profiles for Faster HMM Search.
IEEE/ACM Trans. Comput. Biology Bioinform., 2009

Acceleration of ungapped extension in Mercury BLAST.
Microprocessors and Microsystems - Embedded Hardware Design, 2009

Efficient runtime performance monitoring of FPGA-based applications.
Proceedings of the Annual IEEE International SoC Conference, SoCC 2009, 2009

Optimal runtime reconfiguration strategies for systolic arrays.
Proceedings of the 19th International Conference on Field Programmable Logic and Applications, 2009

2008
Mercury BLASTP: Accelerating Protein Sequence Alignment.
TRETS, 2008

Accelerating Nussinov RNA secondary structure prediction with systolic arrays on FPGAs.
Proceedings of the 19th IEEE International Conference on Application-Specific Systems, 2008

2007
Biosequence Similarity Search on the Mercury System.
VLSI Signal Processing, 2007

Designing patterns for profile HMM search.
Bioinformatics, 2007

Application development on hybrid systems.
Proceedings of the ACM/IEEE Conference on High Performance Networking and Computing, 2007

Preliminary results in accelerating profile HMM search on FPGAs.
Proceedings of the 21th International Parallel and Distributed Processing Symposium (IPDPS 2007), 2007

A Banded Smith-Waterman FPGA Accelerator for Mercury BLASTP.
Proceedings of the FPL 2007, 2007

FPGA-accelerated seed generation in Mercury BLASTP.
Proceedings of the IEEE Symposium on Field-Programmable Custom Computing Machines, 2007

2006
Choosing the best heuristic for seeded alignment of DNA sequences.
BMC Bioinformatics, 2006

RNA Secondary Structure Prediction Via Energy Density Minimization.
Proceedings of the Research in Computational Molecular Biology, 2006

Accelerator design for protein sequence HMM search.
Proceedings of the 20th Annual International Conference on Supercomputing, 2006

Scalable Softcore Vector Processor for Biosequence Applications.
Proceedings of the 14th IEEE Symposium on Field-Programmable Custom Computing Machines (FCCM 2006), 2006

2005
Operon prediction without a training set.
Bioinformatics, 2005

Exploiting Coarse-Grained Parallelism to Accelerate Protein Motif Finding with a Network Processor.
Proceedings of the 14th International Conference on Parallel Architectures and Compilation Techniques (PACT 2005), 2005

2004
Designing multiple simultaneous seeds for DNA similarity search.
Proceedings of the Eighth Annual International Conference on Computational Molecular Biology, 2004

Toward a Phylogenetically Aware Algorithm for Fast DNA Similarity Search.
Proceedings of the Comparative Genomics, 2004

Design of a High-Throughput Assay for Alternative Splicing Using Polymerase Colonies.
Proceedings of the Biocomputing 2004, 2004

Biosequence Similarity Search on the Mercury System.
Proceedings of the 15th IEEE International Conference on Application-Specific Systems, 2004

2003
Selecting Degenerate Multiplex PCR Primers.
Proceedings of the Algorithms in Bioinformatics, Third International Workshop, 2003

Designing seeds for similarity search in genomic DNA.
Proceedings of the Sventh Annual International Conference on Computational Biology, 2003

Detecting protein sequence conservation via metric embeddings.
Proceedings of the Eleventh International Conference on Intelligent Systems for Molecular Biology, June 29, 2003

2002
Provably sensitive Indexing strategies for biosequence similarity search.
Proceedings of the Sixth Annual International Conference on Computational Biology, 2002

2001
Efficient large-scale sequence comparison by locality-sensitive hashing.
Bioinformatics, 2001

Finding motifs using random projections.
Proceedings of the Fifth Annual International Conference on Computational Biology, 2001


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