High Performance Computational Biology Group

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Publications:


2010:

  • Using Queuing Theory to Model Streaming Applications (pdf)
    Rahav Dor, Joseph Lancaster, Mark Franklin, Jeremy Buhler, and Roger Chamberlain
    In Proceedings of the 2010 Symposium on Application Accelerators in High Performance Computing (SAAHPC), July 2010

  • Crossing Timezones in the TimeTrial Performance Monitor (pdf)
    Joseph Lancaster and Roger Chamberlain
    In Proceedings of the 2010 Symposium on Application Accelerators in High Performance Computing (SAAHPC), July 2010

  • Better Languages for More Effective Designing (pdf)
    Roger Chamberlain and Joseph Lancaster
    In Proceedings of the 2010 International Conference on Engineering of Reconfigurable Systems & Algorithms (ERSA), July 2010

  • Design of throughput-optimized arrays from recurrence abstractions (pdf)
    Arpith Jacob, Jeremy Buhler, and Roger Chamberlain
    In Proceedings of the 21st IEEE International Conference on Application-specific Systems, Architectures and Processors, July 2010

  • Deadlock-avoidance for Streaming Applications with Split-Join Structure: Two Case Studies (pdf)
    Peng Li, Kunal Agrawal, Jeremy Buhler, Roger Chamberlain, and Joseph Lancaster
    In Proceedings of the 21st IEEE International Conference on Application-specific Systems, Architectures and Processors, July 2010

  • Deadlock Avoidance for Streaming Computation with Filtering (pdf)
    Peng Li, Kunal Agrawal, Jeremy Buhler, and Roger Chamberlain
    In Proceedings of the 22nd ACM Symposium on Parallelism in Algorithms and Architectures (SPAA), June 2010

  • Rapid RNA Folding: Analysis and Acceleration of the Zuker Recurrence (pdf)
    Arpith Jacob, Jeremy Buhler, and Roger Chamberlain
    In Proceedings of the 18th IEEE Annual International Symposium on Field-Programmable Custom Computing Machines (FCCM), May 2010


    • 2009:

  • Efficient Runtime Performance Monitoring of FPGA-based Applications (pdf)
    Joseph Lancaster, Jeremy Buhler and Roger Chamberlain
    In Proceedings of the 22nd IEEE International System-on-Chip Conference, September 2009

  • Optimal runtime reconfiguration strategies for systolic arrays (pdf)
    Arpith Jacob, Jeremy Buhler and Roger Chamberlain
    In Proceedings of the IEEE Conference on Field Programmable Logic and Applications, September 2009

  • Acceleration of Ungapped Extension in Mercury BLAST (Link)
    Joseph Lancaster, Jeremy Buhler, and Roger D. Chamberlain
    Microprocessors and Microsystems, 33(4):281-289, June 2009


    • 2008:

  • Accelerating Nussinov RNA secondary structure prediction with systolic arrays on FPGAs (pdf)
    Arpith Jacob, Jeremy Buhler and Roger Chamberlain
    In Proceedings of the IEEE International Conference on Application-specific Systems, Architectures and Processors, July 2008

  • Mercury BLASTP: Accelerating Protein Sequence Alignment (Link)
    Arpith Jacob, Joseph Lancaster, Brandon Harris, Jeremy Buhler, and Roger Chamberlain
    ACM Transactions on Reconfigurable Technology and Systems, 1(2):1-44, June 2008

  • Analytic Performance Models for Bounded Queueing Systems (pdf)
    Praveen Krishnamurthy and Roger Chamberlain
    In Proceedings of Workshop on Advances of Parallel and Distributed Computing Models, April 2008


    • 2007:

  • Biosequence Similarity Search on the Mercury System (pdf)
    Praveen Krishnamurthy, Jeremy Buhler, Roger Chamberlain, Mark Franklin, Kwame Gyang, Arpith Jacob, and Joseph Lancaster
    Journal of VLSI Signal Processing, 49(1):101-121, October 2007

  • A Banded Smith-Waterman FPGA Accelerator for Mercury BLASTP (pdf)
    Brandon Harris, Arpith Jacob, Joseph Lancaster, Jeremy Buhler, and Roger Chamberlain
    Poster presentation at the IEEE Conference on Field Programmable Logic and Applications, August 2007

  • Mercury BLASTN: Faster DNA Sequence Comparison using a Streaming Hardware Architecture (pdf)
    Jeremy Buhler, Joseph Lancaster, Arpith Jacob, and Roger Chamberlain
    In Proceedings of Reconfigurable Systems Summer Institute, July 2007

  • FPGA-accelerated seed generation in Mercury BLASTP (pdf)
    Arpith Jacob, Joseph Lancaster, Jeremy Buhler, and Roger Chamberlain
    In Proceedings of the IEEE Symposium on Field-Programmable Custom Computing Machines, April 2007

  • Preliminary Results in Accelerating Profile HMM Search on FPGAs (pdf)
    Arpith Jacob, Joseph Lancaster, Jeremy Buhler, and Roger Chamberlain
    In Proceedings of the IEEE International Workshop on High Performance Computational Biology, March 2007


    • 2005:

  • Acceleration of Ungapped Extension in Mercury BLAST (pdf)
    Joseph Lancaster, Jeremy Buhler, and Roger Chamberlain
    In Proceedings of the 7th Workshop on Media and Streaming Processors, November 2005


    • 2004:

  • Biosequence Similarity Search on the Mercury System (pdf)
    Praveen Krishnamurthy, Jeremy Buhler, Roger Chamberlain, Mark Franklin, Kwame Gyang, and Joseph Lancaster
    In Proceedings of the IEEE Conference on Application-Specific Systems, Architectures and Processors, September 2004

    • Patent Applications:

  • Biosequence Similarity Searching Using FPGA devices, (link)
  • Method and Apparatus for Protein Sequence Alignment Using FPGA devices (link)

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