Jeremy Buhler

Int. J. High Perform. Comput. Appl., 2017

MERCATOR: A GPGPU Framework for Irregular Streaming Applications.

[BibT_eX]

[DOI]

Stephen V. Cole

Proceedings of the 2017 International Conference on High Performance Computing & Simulation, 2017

2014

WOODSTOCC: Extracting Latent Parallelism from a DNA Sequence Aligner on a GPU.

[BibT_eX]

[DOI]

Stephen V. Cole

Jacob R. Gardner

Proceedings of the IEEE 13th International Symposium on Parallel and Distributed Computing, 2014

Orchestrating safe streaming computations with precise control.

[BibT_eX]

[DOI]

Proceedings of the 20th IEEE International Conference on Parallel and Distributed Systems, 2014

Improving performance of streaming applications with filtering and control messages.

[BibT_eX]

[DOI]

Peng Li

Proceedings of the International Conference on Parallel Architectures and Compilation, 2014

2013

Adding data parallelism to streaming pipelines for throughput optimization.

[BibT_eX]

[DOI]

Proceedings of the 20th Annual International Conference on High Performance Computing, 2013

2012

Designing Filters for Fast-Known NcRNA Identification.

[BibT_eX]

[DOI]

Cheng Yuan

IEEE ACM Trans. Comput. Biol. Bioinform., 2012

Fast, Sensitive Discovery of Conserved Genome-Wide Motifs.

[BibT_eX]

[DOI]

Nnamdi E. Ihuegbu

Gary D. Stormo

J. Comput. Biol., 2012

PhyLAT: a phylogenetic local alignment tool.

[BibT_eX]

[DOI]

Hongtao Sun

Bioinform., 2012

Efficient deadlock avoidance for streaming computation with filtering.

[BibT_eX]

[DOI]

Proceedings of the 17th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, 2012

2011

Bloom Filter Performance on Graphics Engines.

[BibT_eX]

[DOI]

Proceedings of the International Conference on Parallel Processing, 2011

TimeTrial: A low-impact performance profiler for streaming data applications.

[BibT_eX]

[DOI]

Proceedings of the 22nd IEEE International Conference on Application-specific Systems, 2011

2010

Auto-Pipe: Streaming Applications on Architecturally Diverse Systems.

[BibT_eX]

[DOI]

Computer, 2010

Deadlock avoidance for streaming computations with filtering.

[BibT_eX]

[DOI]

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.

[BibT_eX]

[DOI]

Proceedings of the 2010 ACM Symposium on Applied Computing (SAC), 2010

Design space exploration of throughput-optimized arrays from recurrence abstractions (abstract only).

[BibT_eX]

[DOI]

Proceedings of the ACM/SIGDA 18th International Symposium on Field Programmable Gate Arrays, 2010

Rapid RNA Folding: Analysis and Acceleration of the Zuker Recurrence.

[BibT_eX]

[DOI]

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.

[BibT_eX]

[DOI]

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.

[BibT_eX]

[DOI]

Proceedings of the 21st IEEE International Conference on Application-specific Systems Architectures and Processors, 2010

Design of throughput-optimized arrays from recurrence abstractions.

[BibT_eX]

[DOI]

Proceedings of the 21st IEEE International Conference on Application-specific Systems Architectures and Processors, 2010

2009

Designing Patterns and Profiles for Faster HMM Search.

[BibT_eX]

[DOI]

IEEE ACM Trans. Comput. Biol. Bioinform., 2009

Acceleration of ungapped extension in Mercury BLAST.

[BibT_eX]

[DOI]

Joseph M. Lancaster

Microprocess. Microsystems, 2009

Efficient runtime performance monitoring of FPGA-based applications.

[BibT_eX]

[DOI]

Joseph M. Lancaster

Proceedings of the Annual IEEE International SoC Conference, SoCC 2009, 2009

Optimal runtime reconfiguration strategies for systolic arrays.

[BibT_eX]

[DOI]

Proceedings of the 19th International Conference on Field Programmable Logic and Applications, 2009

2008

Mercury BLASTP: Accelerating Protein Sequence Alignment.

[BibT_eX]

[DOI]

ACM Trans. Reconfigurable Technol. Syst., 2008

Accelerating Nussinov RNA secondary structure prediction with systolic arrays on FPGAs.

[BibT_eX]

[DOI]

Proceedings of the 19th IEEE International Conference on Application-Specific Systems, 2008

2007

Biosequence Similarity Search on the <i>Mercury</i> System.

[BibT_eX]

[DOI]

Praveen Krishnamurthy

J. VLSI Signal Process., 2007

Designing patterns for profile HMM search.

[BibT_eX]

[DOI]

Bioinform., 2007

Application development on hybrid systems.

[BibT_eX]

[DOI]

Proceedings of the ACM/IEEE Conference on High Performance Networking and Computing, 2007

Preliminary results in accelerating profile HMM search on FPGAs.

[BibT_eX]

[DOI]

Proceedings of the 21th International Parallel and Distributed Processing Symposium (IPDPS 2007), 2007

A Banded Smith-Waterman FPGA Accelerator for Mercury BLASTP.

[BibT_eX]

[DOI]

Proceedings of the FPL 2007, 2007

FPGA-accelerated seed generation in Mercury BLASTP.

[BibT_eX]

[DOI]

Proceedings of the IEEE Symposium on Field-Programmable Custom Computing Machines, 2007

2006

Choosing the best heuristic for seeded alignment of DNA sequences.

[BibT_eX]

[DOI]

BMC Bioinform., 2006

RNA Secondary Structure Prediction Via Energy Density Minimization.

[BibT_eX]

[DOI]

Can Alkan

Emre Karakoç

Süleyman Cenk Sahinalp

Proceedings of the Research in Computational Molecular Biology, 2006

Accelerator design for protein sequence HMM search.

[BibT_eX]

[DOI]

Proceedings of the 20th Annual International Conference on Supercomputing, 2006

Scalable Softcore Vector Processor for Biosequence Applications.

[BibT_eX]

[DOI]

Proceedings of the 14th IEEE Symposium on Field-Programmable Custom Computing Machines (FCCM 2006), 2006

2005

Designing seeds for similarity search in genomic DNA.

[BibT_eX]

[DOI]

Uri Keich

J. Comput. Syst. Sci., 2005

Designing Multiple Simultaneous Seeds for DNA Similarity Search.

[BibT_eX]

[DOI]

J. Comput. Biol., 2005

Operon prediction without a training set.

[BibT_eX]

[DOI]

Bioinform., 2005

Exploiting Coarse-Grained Parallelism to Accelerate Protein Motif Finding with a Network Processor.

[BibT_eX]

[DOI]

Ben Wun

Patrick Crowley

Proceedings of the 14th International Conference on Parallel Architectures and Compilation Techniques (PACT 2005), 2005

2004

Toward a Phylogenetically Aware Algorithm for Fast DNA Similarity Search.

[BibT_eX]

[DOI]

Rachel Nordgren

Proceedings of the Comparative Genomics, 2004

Design of a High-Throughput Assay for Alternative Splicing Using Polymerase Colonies.

[BibT_eX]

[DOI]

Proceedings of the Biocomputing 2004, 2004

Biosequence Similarity Search on the Mercury System.

[BibT_eX]

[DOI]

Praveen Krishnamurthy

Proceedings of the 15th IEEE International Conference on Application-Specific Systems, 2004

2003

Provably Sensitive Indexing Strategies for Biosequence Similarity Search.

[BibT_eX]

[DOI]

J. Comput. Biol., 2003

Selecting Degenerate Multiplex PCR Primers.

[BibT_eX]

[DOI]

Proceedings of the Algorithms in Bioinformatics, Third International Workshop, 2003

Detecting protein sequence conservation via metric embeddings.

[BibT_eX]

[DOI]

Proceedings of the Eleventh International Conference on Intelligent Systems for Molecular Biology, June 29, 2003

2002

Finding Motifs Using Random Projections.

[BibT_eX]

[DOI]

Martin Tompa

J. Comput. Biol., 2002

2001

Search algorithms for biosequences using random projection.

[BibT_eX]

[DOI]

PhD thesis, 2001

Efficient large-scale sequence comparison by locality-sensitive hashing.

[BibT_eX]

[DOI]

Bioinform., 2001

1995

The Fox Project: a language-structured approach to networking software.

[BibT_eX]

[DOI]