sbs_papers.bib

@article{mblastn,
  author = {Praveen Krishnamurthy and Jeremy Buhler and Roger Chamberlain and
  Mark Franklin and Kwame Gyang and Arpith Jacob and Joseph Lancaster},
  title = {Biosequence Similarity Search on the \emph{Mercury} System},
  journal = {Journal of VLSI Signal Processing},
  volume = 49,
  number = 1,
  month = oct,
  pages = {101--121},
  year = 2007,
  doi = {http://dx.doi.org/10.1007/s11265-007-0087-0}
}
@article{lbc09a,
  author = {J. Lancaster and J. Buhler and R. D. Chamberlain},
  title = {Acceleration of Ungapped Extension in {Mercury BLAST}},
  journal = {Journal of Microprocessors and Microsystems},
  volume = 33,
  number = 4,
  pages = {281--289},
  month = jun,
  year = 2009,
  doi = {http://dx.doi.org/10.1016/j.micpro.2009.02.007}
}
@inproceedings{bljc07,
  author = {Jeremy D. Buhler and Joseph M. Lancaster and Arpith C. Jacob and
 Roger D. Chamberlain},
  title = {Mercury {BLASTN}: Faster {DNA} Sequence Comparison Using
a Streaming Hardware Architecture},
  booktitle = {Proc.\ Reconfigurable Systems Summer Institute},
  month = jul,
  year = 2007,
  eprint = {bljc07.pdf}
}
@article{jlbhc08,
  author = {Jacob, Arpith and Lancaster, Joseph and Buhler, Jeremy and
  Harris, Brandon and Chamberlain, Roger D.},
  title = {Mercury {BLASTP}: Accelerating Protein Sequence Alignment},
  journal = {ACM Trans. Reconfigurable Technol. Syst.},
  volume = {1},
  number = {2},
  year = {2008},
  month = jun,
  issn = {1936-7406},
  pages = {1--44},
  doi = {http://doi.acm.org/10.1145/1371579.1371581},
  publisher = {ACM},
  address = {New York, NY, USA}
}
@article{cft10,
  author = {Roger D. Chamberlain and Mark A. Franklin and Eric J. Tyson and
 James H. Buckley and Jeremy Buhler and Greg Galloway and Saurabh Gayen and
 Michael Hall and E.F. Berkley Shands and Naveen Singla},
  title = {{Auto-Pipe}: Streaming Applications on Architecturally Diverse Systems},
  journal = {Computer},
  volume = 43,
  number = 3,
  pages = {42--49},
  month = mar,
  year = 2010,
  doi = {http://doi.ieeecomputersociety.org/10.1109/MC.2010.62}
}
@inproceedings{hjlbc07,
  author = {Brandon Harris and Arpith C. Jacob and Joseph M. Lancaster and
 Jeremy Buhler and Roger D. Chamberlain},
  title = {A Banded {Smith-Waterman} {FPGA} Accelerator for {Mercury} {BLASTP}},
  booktitle = {Proc.\ 17th Int'l Conf. on Field Programmable Logic
 and Applications (FPL)},
  month = aug,
  year = 2007,
  eprint = {hjlbc07.pdf},
  doi = {http://dx.doi.org/10.1109/FPL.2007.4380764}
}
@inproceedings{jlbc07b,
  author = {Arpith Jacob and Joseph Lancaster and Jeremy Buhler and
 Roger D. Chamberlain},
  title = {{FPGA}-accelerated seed generation in {Mercury} {BLASTP}},
  booktitle = {Proc.\ 15th IEEE Symposium on Field-Programmable Custom
 Computing Machines},
  month = apr,
  year = 2007,
  eprint = {jlbc07b.pdf},
  doi = {http://dx.doi.org/10.1109/FCCM.2007.11}
}
@article{tbfc08,
  author = {Eric J. Tyson and James Buckley and Mark A. Franklin and
 Roger D. Chamberlain},
  title = {Acceleration of atmospheric {Cherenkov} telescope signal processing
 to real-time speed with the {Auto-Pipe} design system},
  journal = {Nuclear Inst. and Methods in Physics Research A},
  volume = 585,
  number = 2,
  pages = {474--479},
  month = oct,
  year = 2008,
  doi = {http://dx.doi.org/10.1016/j.nima.2008.06.047}
}
@inproceedings{shsc08,
  author = {Naveen Singla and Michael Hall and Berkley Shands and
 Roger D. Chamberlain},
  title = {Financial {Monte Carlo} Simulation on Architecturally Diverse Systems},
  booktitle = {Proc.\  Workshop on High Performance Computational Finance},
  month = nov,
  year = 2008,
  eprint = {shsc08.pdf},
  doi = {http://dx.doi.org/10.1109/WHPCF.2008.4745401}
}
@inproceedings{lbc09b,
  author = {Joseph M. Lancaster and Jeremy D. Buhler and Roger D. Chamberlain},
  title = {Efficient Runtime Performance Monitoring of {FPGA}-based Applications},
  booktitle = {Proc.\  22nd IEEE Int'l System-on-Chip Conf.},
  month = sep,
  year = 2009,
  pages = {23--28},
  eprint = {lbc09b.pdf},
  doi = {http://dx.doi.org/10.1109/SOCCON.2009.5398106}
}
@inproceedings{lsbc11,
  author = {Joseph M. Lancaster and E. F. Berkley Shands and Jeremy D. Buhler
 and Roger D. Chamberlain},
  title = {{TimeTrial}: A Low-Impact Performance Profiler for Streaming Data
 Applications},
  booktitle = {Proc.\ IEEE Int'l Conf.\ on
  Application-specific Systems, Architectures and Processors},
  year = 2011,
  month = sep,
  eprint = {lsbc11.pdf},
  doi = {http://dx.doi.org/10.1109/ASAP.2011.6043238}
}
@inproceedings{csw04,
  author = {Roger Chamberlain and Berkley Shands and Jason White},
  title = {Achieving Real Data Throughput for an {FPGA} Co-Processor
  on Commodity Server Platforms},
  booktitle = {Proc.\  1st Workshop on Building Block Engine Architectures
  for Computers and Networks},
  year = 2004,
  month = oct,
  eprint = {csw04.pdf}
}
@inproceedings{cs05,
  author = {Roger D. Chamberlain and Berkley Shands},
  title = {Streaming Data from Disk Store to Application},
  booktitle = {Proc.\  3rd Int'l Workshop on Storage Network
  Architecture and Parallel I/Os},
  pages = {17--23},
  year = 2005,
  month = sep,
  eprint = {cs05.pdf}
}
@mastersthesis{JustinThesis,
  author = {Justin Bedings},
  title = {{Software and Hardware Acceleration of the Genomic Motif Finding Tool PhyloNet}},
  school = {Dept. of Computer Science and Engineering, Washington University in St. Louis},
  month = aug,
  year = 2008,
  eprint = {phylonet_thesis.pdf}
}
@inproceedings{cfbc06,
  author = {Patrick Crowley and Mark A. Franklin and Jeremy Buhler and
 Roger D. Chamberlain},
  title = {Impact of {CMP} Design on High-Performance Embedded Computing},
  booktitle = {Proc.\  10th High Performance Embedded Computing Workshop},
  month = sep,
  year = 2006,
  eprint = {cfbc06.pdf}
}
@inproceedings{bc06,
  author = {Michela Becchi and Patrick Crowley},
  title = {Dynamic thread assignment on heterogeneous multiprocessor
architectures},
  booktitle = {Proc.\  ACM Int'l Conf. on Computing Frontiers},
  pages = {29--40},
  month = may,
  year = 2006,
  doi = {http://dx.doi.org/10.1145/1128022.1128029}
}
@inproceedings{bfc07,
  author = {Michela Becchi and Mark A. Franklin and Patrick Crowley},
  title = {Performance/area efficiency in chip multiprocessors with micro-caches},
  booktitle = {Proc.\  ACM Int'l Conf. on Computing Frontiers},
  pages = {247--258},
  month = may,
  year = 2007,
  doi = {http://dx.doi.org/10.1145/1242531.1242567}
}
@inproceedings{bc07,
  author = {Michela Becchi and Patrick Crowley},
  title = {An improved algorithm to accelerate regular expression evaluation},
  booktitle = {Proc.\  ACM/IEEE Symp. on Architectures for Networking and
Communications Systems},
  pages = {145--154},
  month = dec,
  year = 2007,
  doi = {http://dx.doi.org/10.1145/1323548.1323573}
}
@inproceedings{bc08,
  author = {Michela Becchi and Patrick Crowley},
  title = {Efficient Regular Expression Evaluation: Theory to Practice},
  booktitle = {Proc.\  ACM/IEEE Symp. on Architectures for Networking and
Communications Systems},
  pages = {50--59},
  month = nov,
  year = 2008,
  doi = {http://dx.doi.org/10.1145/1477942.1477950}
}
@inproceedings{bfc08,
  author = {Michela Becchi and Mark A. Franklin and Patrick Crowley},
  title = {A workload for evaluating deep packet inspection architectures},
  booktitle = {Proc.\  IEEE Int'l Symp. on Workload Characterization},
  pages = {79--89},
  month = sep,
  year = 2008,
  doi = {http://dx.doi.org/10.1109/IISWC.2008.4636093}
}
@inproceedings{cbfb10,
  author = {Roger D. Chamberlain and Jeremy Buhler and Mark Franklin and James H. Buckley},
  title = {Application-guided Tool Development for
Architecturally Diverse Computation},
  booktitle = {Proc.\  Symp. on Applied Computing},
  pages = {496--501},
  month = mar,
  year = 2010,
  eprint = {cbfb10.pdf},
  doi = {http://dx.doi.org/10.1145/1774088.1774191}
}
@inproceedings{cf07,
  author = {Roger D. Chamberlain and Mark A. Franklin},
  title = {Automatic Deployment of Streaming Applications on
 Hybrid Architectures},
  booktitle = {Proc.\  11th High Performance Embedded Computing Workshop},
  month = sep,
  year = 2007,
  eprint = {cf07.pdf}
}
@inproceedings{cfi06,
  author = {Roger D. Chamberlain and Mark A. Franklin and Ronald S. Indeck},
  title = {Exploiting Reconfigurability for Text Search},
  booktitle = {Proc.\  10th High Performance Embedded Computing Workshop},
  month = sep,
  year = 2006,
  eprint = {cfi06.pdf}
}
@inproceedings{cs07a,
  author = {Roger D. Chamberlain and Berkley Shands},
  title = {Performance of Direct Attached Disk Subsystems},
  booktitle = {Proc.\  11th High Performance Embedded Computing Workshop},
  month = sep,
  year = 2007,
  eprint = {cs07a.pdf}
}
@inproceedings{cs07b,
  author = {Roger D. Chamberlain and Berkley Shands},
  title = {Direct-Attached Disk Subsystem Performance Assessment},
  booktitle = {Proc.\  4th Int'l Workshop on Storage Network Architecture and
 Parallel I/Os},
  month = sep,
  year = 2007,
  eprint = {cs07b.pdf}
}
@inproceedings{gftc08,
  author = {Saurabh Gayen and Mark A. Franklin and Eric J. Tyson and
 Roger D. Chamberlain},
  title = {Simulation of Streaming Applications on Multicore Systems},
  booktitle = {Proc.\  3rd Workshop on Software Tools for MultiCore Systems},
  month = apr,
  year = 2008,
  eprint = {gftc08.pdf}
}
@inproceedings{ctgfbcb07,
  author = {Roger D. Chamberlain and Eric J. Tyson and Saurabh Gayen and
 Mark A. Franklin and Jeremy Buhler and Patrick Crowley and James Buckley},
  title = {Application Development on Hybrid Systems},
  booktitle = {Proc.\  ACM/IEEE Conf. on Supercomputing},
  month = nov,
  year = 2007,
  eprint = {ctgfbcb07.pdf},
  doi = {http://dx.doi.org/10.1145/1362622.1362690}
}
@inproceedings{fchsw04,
  author = {Mark A. Franklin and Roger D. Chamberlain and Michael Henrichs and
Berkley Shands and Jason White},
  title = {An architecture for fast processing of large unstructured data sets},
  booktitle = {Proc.\  IEEE 22nd Int'l Conf. on Computer Design},
  month = oct,
  year = {2004},
  pages = {280--287},
  eprint = {fchsw04.pdf},
  doi = {http://dx.doi.org/10.1109/ICCD.2004.1347934}
}
@inproceedings{fccbb05,
  author = {Mark A. Franklin and Patrick Crowley and
  Roger D. Chamberlain and Jeremy Buhler and James H. Buckley},
  title = {Application Development for Hybrid Pipelined Systems},
  booktitle = {Proc.\  9th High Performance Embedded Computing Workshop},
  year = 2005,
  month = sep,
  eprint = {fccbb05.pdf}
}
@inproceedings{kbcfgl04,
  author = {Praveen Krishnamurthy and Jeremy Buhler and Roger Chamberlain
  and Mark Franklin and Kwame Gyang and Joseph Lancaster},
  title = {Biosequence Similarity Search on the {Mercury} System},
  booktitle = {Proc.\  the IEEE 15th Int'l Conf. on
  Application-Specific Systems, Architectures and Processors},
  pages = {365--375},
  year = 2004,
  month = sep,
  eprint = {kbcfgl04.pdf}
}
@inproceedings{mbcfh06,
  author = {Rahul P. Maddimsetty and Jeremy Buhler and Roger D. Chamberlain
          and Mark A. Franklin and Brandon Harris},
  title = {Accelerator Design for Protein Sequence {HMM} Search},
  booktitle = {Proc.\  20th ACM Int'l Conf. on Supercomputing},
  month = jun,
  year = 2006,
  eprint = {mbcfh06.pdf},
  doi = {http://dx.doi.org/10.1145/1183401.1183442}
}
@inproceedings{ftbcm06,
  author = {Mark A. Franklin and Eric J. Tyson and James Buckley and
Patrick Crowley and John Maschmeyer},
  booktitle = {Proc.\  Int'l Parallel and Distributed Processing Symp.},
  title = {Auto-Pipe and the {X} Language: A Pipeline Design Tool
and Description Language},
  month = apr,
  year = {2006},
  eprint = {ftbcm06.pdf},
  doi = {http://dx.doi.org/10.1109/IPDPS.2006.1639353}
}
@mastersthesis{sg08,
  author = {Saurabh Gayen},
  title = {{X-Sim} and {X-Eval}: Tools for Simulation and Analysis of
Heterogeneous Pipelined Architectures},
  school = {Dept. of Computer Science and Engineering,
Washington University in St. Louis},
  month = may,
  year = 2008,
  eprint = {sg08.pdf}
}
@inproceedings{gtfcc06,
  author = {Saurabh Gayen and Eric J. Tyson and Mark A. Franklin and
 Roger D. Chamberlain and Patrick Crowley},
  title = {{X-Sim}: A Federated Heterogeneous Simulation Environment},
  booktitle = {Proc.\  10th High Performance Embedded Computing Workshop},
  month = sep,
  year = 2006,
  eprint = {gtfcc06.pdf}
}
@inproceedings{gtfc07,
  author = {Saurabh Gayen and Eric J. Tyson and Mark A. Franklin and
 Roger D. Chamberlain},
  title = {A Federated Simulation Environment for Hybrid Systems},
  booktitle = {Proc.\  21st Int'l Workshop on Principles of Advanced and
Distributed Simulation},
  month = jun,
  year = 2007,
  eprint = {gtfc07.pdf}
}
@phdthesis{praveen,
  author = {Praveen Krishnamurthy},
  title = {Performance Evaluation for Hybrid Architectures},
  school = {Dept. of Computer Science and Engineering, Washington University
in St. Louis},
  month = dec,
  year = 2006,
  eprint = {krishnamurthy-dsc.pdf}
}
@inproceedings{kc08,
  author = {Praveen Krishnamurthy and Roger D. Chamberlain},
  title = {Analytic Performance Models for Bounded Queueing Systems},
  booktitle = {Proc.\  Workshop on Advances of Parallel and Distributed
 Computing Models},
  month = apr,
  year = 2008,
  eprint = {kc08.pdf}
}
@mastersthesis{rpm06,
  author = {Rahul P. Maddimsetty},
  title = {Acceleration of Profile-{HMM} Search for Protein Sequences in Reconfigurable Hardware},
  school = {Dept. of Computer Science and Engineering,
Washington University in St. Louis},
  month = may,
  year = 2006,
  eprint = {507_maddimsetty-thesis-acceleration-of-profile-hmm-search.pdf}
}
@inproceedings{sc06,
  author = {Gary Stiehr and Roger D. Chamberlain},
  title = {Improving Cluster Utilization through Intelligent Processor Sharing},
  booktitle = {Proc.\  2nd Workshop on System Management Tools for Large-Scale Parallel Systems},
  year = 2006,
  month = apr,
  eprint = {sc06.pdf}
}
@mastersthesis{ejt06,
  author = {Eric J. Tyson},
  title = {{Auto-Pipe} and the {X} Language: A Toolset and Language for the
Simulation, Analysis, and Synthesis of Heterogeneous Pipelined Architectures},
  school = {Dept. of Computer Science and Engineering,
Washington University in St. Louis},
  month = aug,
  year = 2006,
  eprint = {538_thesis.pdf}
}
@article{clc08,
  author = {Roger D. Chamberlain and Joseph Lancaster and Ron Cytron},
  title = {Visions for Application Development on Hybrid Computing Systems},
  journal = {Parallel Computing},
  volume = 34,
  number = {4--5},
  pages = {201--216},
  month = may,
  year = 2008,
  doi = {http://dx.doi.org/10.1016/j.parco.2008.03.001}
}
@inproceedings{lcc08,
  author = {Joseph Lancaster and Ron Cytron and Roger D. Chamberlain},
  title = {Understanding the Performance of Streaming Applications
 Deployed on Hybrid Systems},
  booktitle = {Proc.\  Next Generation Software Workshop},
  month = apr,
  year = 2008,
  eprint = {lcc08.pdf},
  doi = {http://dx.doi.org/10.1109/IPDPS.2008.4536381}
}
@inproceedings{lc10,
  author = {Joseph M. Lancaster and Roger D. Chamberlain},
  title = {Crossing Timezones in the {TimeTrial} Performance Monitor},
  booktitle = {Proc.\  Symposium on Application Accelerators
in High Performance Computing},
  month = jul,
  year = 2010,
  eprint = {lc10.pdf}
}
@inproceedings{pcc10,
  author = {Shobana Padmanabhan and Yixin Chen and Roger D. Chamberlain},
  title = {Design-space Optimization for Automatic Acceleration of
Streaming Applications},
  booktitle = {Proc.\  Symposium on Application Accelerators
in High Performance Computing},
  month = jul,
  year = 2010,
  eprint = {pcc10.pdf},
  doi = {http://doi.ieeecomputersociety.org/10.1109/ICPADS.2012.95}
}
@inproceedings{labc10,
  author = {Peng Li and Kunal Agrawal and Jeremy Buhler and Roger D. Chamberlain},
  title = {Deadlock Avoidance for Streaming Computation with Filtering},
  booktitle = {Proc.\  22nd ACM Symposium on Parallelism in Algorithms and
Architectures},
  month = jun,
  year = 2010,
  pages = {243--252},
  eprint = {labc10.pdf}
}
@inproceedings{labcl10,
  author = {Peng Li and Kunal Agrawal and Jeremy Buhler and Roger D. Chamberlain
and Joseph M. Lancaster},
  title = {Deadlock-avoidance for Streaming Applications
with Split-Join Structure: Two Case Studies},
  booktitle = {Proc.\  21st IEEE Int'l Conf.\ 
Application-specific Systems, Architectures and Processors},
  month = jul,
  year = 2010,
  pages = {333--336},
  eprint = {labcl10.pdf},
  doi = {http://dx.doi.org/10.1109/ASAP.2010.5540957}
}
@inproceedings{lwc11,
  author = {Joseph M. Lancaster and Joseph G. Wingbermuehle and Roger D. Chamberlain},
  title = {Asking for Performance: Exploiting Developer Intuition to Guide Instrumentation with {TimeTrial}},
  booktitle = {Proc.\  13th Int'l Conf.\  High Performance Computing and Communications},
  month = sep,
  year = 2011,
  doi = {http://dx.doi.org/10.1109/HPCC.2011.49},
  eprint = {lwc11.pdf}
}
@inproceedings{pcc11,
  author = {Shobana Padmanabhan and Yixin Chen and Roger D. Chamberlain},
  title = {Optimal Design-space Exploration of Streaming Applications},
  booktitle = {Proc.\  IEEE Int'l Conf.\  Application-specific Systems,
Architectures and Processors},
  month = sep,
  year = 2011,
  pages = {227--230},
  doi = {http://dx.doi.org/10.1109/ASAP.2011.6043274},
  eprint = {pcc11.pdf}
}
@inproceedings{lwbc11,
  author = {Joseph M. Lancaster and Joseph G. Wingbermuehle and Jonathan C. Beard and Roger D. Chamberlain},
  title = {Crossing Boundaries in {TimeTrial}: Monitoring Communications Across
Architecturally Diverse Computing Platforms},
  booktitle = {Proc.\  9th IEEE/IFIP Int'l Conf.\  Embedded
and Ubiquitous Computing},
  month = oct,
  year = 2011,
  doi = {http://dx.doi.org/10.1109/EUC.2011.26},
  eprint = {lwbc11.pdf}
}
@phdthesis{lancaster11,
  author = {Joseph M. Lancaster},
  title = {Low-Impact Profiling of Streaming, Hetergeneous Applications},
  school = {Dept. of Computer Science and Engineering, Washington University
in St. Louis},
  month = aug,
  year = 2011
}
@inproceedings{Jac10b,
  author = {A. Jacob and J. Buhler and R. Chamberlain},
  title = {Design of throughput-optimized arrays from recurrence abstractions},
  booktitle = {Proc.\ of 21st IEEE Int'l Conf.\ Application-specific Systems, Architectures and Processors},
  pages = {133--40},
  year = 2010
}
@inproceedings{Jac10a,
  author = {A. Jacob and J. Buhler and R. Chamberlain},
  title = {Rapid {RNA} Folding: Analysis and Acceleration of the {Z}uker
          Recurrence},
  booktitle = {Proc.\ of 18th IEEE Int'l Symposium
              on Field-Programmable Custom Computing Machines (FCCM)},
  pages = {87--94},
  year = 2010
}
@phdthesis{Jac10thesis,
  author = {A. Jacob},
  title = {Parallelization of Dynamic Programming Recurrences in
          Computational Biology},
  school = {washington University},
  address = {St.\ Louis, MO},
  year = 2010
}
@inproceedings{Jac07,
  author = {A. Jacob and J. Lancaster and J. Buhler and R. Chamberlain},
  title = {Preliminary results in accelerating profile {HMM} search on {FPGA}s},
  booktitle = {Proc.\ 6th IEEE Int'l Workshop on High Performance Computational
              Biology},
  month = mar,
  year = 2007
}
@inproceedings{devore02,
  author = {Michael D. DeVore and Roger D. Chamberlain and George L. Engel and
Joseph A. O'Sullivan and Mark A. Franklin},
  title = {Tradeoffs Between Quality of Results and Resource Consumption
in a Recognition System},
  booktitle = {Proc. of IEEE Int'l Conf. on Application-specific Systems,
Architectures and Processors},
  month = jul,
  year = 2002,
  pages = {391-402}
}
@inproceedings{dlfbc10,
  author = {Rahav Dor and Joseph M. Lancaster and Mark A. Franklin and
Jeremy Buhler and Roger D. Chamberlain},
  title = {Using Queuing Theory to Model Streaming Applications},
  booktitle = {Proc. of 2010 Symposium on Application Accelerators in High
Performance Computing},
  month = jul,
  year = 2010
}
@inproceedings{mcbf11,
  author = {Lin Ma and Roger D. Chamberlain and Jeremy D. Buhler
 and Mark A. Franklin},
  title = {Bloom Filter Performance on Graphics Engines},
  booktitle = {Proc. of 40th International Conference on Parallel Processing},
  month = sep,
  year = 2011,
  pages = {522-531},
  eprint = {mcbf11.pdf},
  doi = {http://dx.doi.org/10.1109/ICPP.2011.27}
}
@inproceedings{cf93,
  author = {Roger D. Chamberlain and Mark A. Franklin},
  title = {Performance Effects of Synchronization in Parallel Processors},
  booktitle = {Proc. of 5th Symp. on Parallel and Distributed Processing},
  month = dec,
  year = 1993,
  pages = {611-616}
}
@inproceedings{wcc12,
  author = {Joseph G. Wingbermuehle and Roger D. Chamberlain and Ron K. Cytron},
  title = {{ScalaPipe}: A Streaming Application Generator},
  booktitle = {Proc. Symp.\ on Application Accelerators in
High-Performance Computing},
  month = jul,
  year = 2012,
  eprint = {wcc12.pdf},
  doi = {http://dx.doi.org/10.1109/FCCM.2012.54}
}
@inproceedings{mc12,
  author = {Lin Ma and Roger D. Chamberlain},
  title = {A Performance Model for Memory Bandwidth Constrained Applications on Graphics Engines},
  booktitle = {Proc.\ 23rd IEEE Int'l Conf.\ on Application-specific Systems, Architectures and Processors},
  month = jul,
  year = 2012,
  pages = {24-31},
  eprint = {mc12.pdf},
  doi = {http://dx.doi.org/10.1109/ASAP.2012.19}
}
@inproceedings{balc12,
  author = {Jeremy D. Buhler and Kunal Agrawal and Peng Li and Roger D. Chamberlain},
  title = {Efficient Deadlock Avoidance for Streaming Computation with Filtering},
  booktitle = {Proc.\ 17th ACM SIGPLAN Symp.\ on Principles and Practice of Parallel Programming},
  month = feb,
  year = 2012,
  pages = {235-246},
  eprint = {balc11.pdf},
  doi = {http://dx.doi.org/10.1145/2145816.2145846}
}
@inproceedings{pcc12,
  author = {Shobana Padmanabhan and Yixin Chen and Roger D. Chamberlain},
  title = {Convexity in Non-convex Optimizations of Streaming Applications},
  booktitle = {Proc.\ of 18th IEEE Int'l Conf.\ on Parallel and Distributed Systems},
  month = dec,
  year = 2012,
  pages = {668--675},
  eprint = {pcc12.pdf},
  doi = {http://dx.doi.org/10.1109/ICPADS.2012.95}
}
@inproceedings{pcc13,
  author = {Shobana Padmanabhan and Yixin Chen and Roger D. Chamberlain},
  title = {Decomposition Techniques for Optimal Design-Space Exploration
of Streaming Applications},
  booktitle = {Proc.\ of 18th ACM SIGPLAN Symp.\ on Principles and Practice
of Parallel Programming},
  month = feb,
  year = 2013,
  eprint = {pcc13.pdf},
  doi = {http://dx.doi.org.libproxy.wustl.edu/10.1145/2442516.2442547}
}
@inproceedings{mac12,
  author = {Lin Ma and Kunal Agrawal and Roger D. Chamberlain},
  title = {A Memory Access Model for Highly-threaded Many-core Architectures},
  booktitle = {Proc.\ of IEEE 18th International Conference on
	Parallel and Distributed Systems},
  month = dec,
  year = 2012,
  pages = {339-347},
  eprint = {mac12.pdf},
  doi = {http://dx.doi.org/10.1109/ICPADS.2012.54}
}
@article{Wingbermuehle2013615,
  title = {Compiling for power with {S}cala{P}ipe},
  journal = {Journal of Systems Architecture},
  volume = 59,
  number = 8,
  month = sep,
  pages = {615-625},
  year = 2013,
  issn = {1383-7621},
  doi = {http://dx.doi.org/10.1016/j.sysarc.2013.05.021},
  author = {Joseph G. Wingbermuehle and Ron K. Cytron and Roger D. Chamberlain}
}
@inproceedings{bc13,
  author = {Jonathan C. Beard and Roger D. Chamberlain},
  title = {Use of Simple Analytic Performance Models of Streaming Data
Applications Deployed on Diverse Architectures},
  booktitle = {Proc. of Int'l Symp. on Performance Analysis of Systems
and Software},
  month = apr,
  year = 2013,
  pages = {138-139},
  eprint = {bc13.pdf},
  url = {Posters/ISPASS_2013.pdf},
  doi = {http://dx.doi.org/10.1109/ISPASS.2013.6557162}
}
@inproceedings{bc13b,
  author = {Jonathan C. Beard and Roger D. Chamberlain},
  title = {Analysis of a Simple Approach to Modeling Performance for Streaming Data Applications},
  booktitle = {Proc. of IEEE Int'l Symposium on Modeling, Analysis and Simulation of Computer and Telecommunication Systems},
  month = aug,
  year = 2013,
  pages = {345-349},
  eprint = {bc13b.pdf},
  url = {Presentations/MASCOTS_2013.pdf},
  doi = {http://dx.doi.org/10.1109/MASCOTS.2013.49}
}
@inproceedings{nc99,
  author = {Bradley L. Noble and Roger D. Chamberlain},
  title = {Performance Model for Speculative Simulation Using Predictive Optimism},
  booktitle = {Proc.\ of Hawaii International Conference on System Sciences},
  volume = {8},
  month = jan,
  year = {1999},
  eprint = {nc99.pdf},
  doi = {http://dx.doi.org/10.1109/HICSS.1999.773081}
}
@inproceedings{hgc11,
  author = {Michael J. Hall and Viktor Gruev and Roger D. Chamberlain},
  title = {Noise Analysis of a Current-Mode Read Circuit for Sensing Magnetic
Tunnel Junction Resistance},
  booktitle = {Proc.\ of IEEE International Symposium on Circuits and Systems},
  month = may,
  year = 2011,
  pages = {1816-1819},
  eprint = {hgc11.pdf},
  doi = {http://dx.doi.org/10.1109/ISCAS.2011.5937938}
}
@article{buhler2007mercury,
  title = {Mercury BLASTN: Faster DNA sequence comparison using a streaming hardware architecture},
  author = {Buhler, Jeremy D and Lancaster, Joseph M and Jacob, Arpith C and Chamberlain, Roger D and others},
  journal = {Proc. of Reconfigurable Systems Summer Institute},
  year = {2007},
  eprint = {mercuryblastn.pdf}
}
@article{wcc13,
  author = {Joseph G. Wingbermuehle and Ron K. Cytron and Roger D. Chamberlain},
  journal = {Computer Architecture Letters},
  title = {Optimization of Application-Specific Memories},
  year = {2013},
  month = apr,
  keywords = {B Hardware;B.3 Memory Structures;B.3.2 Design Styles;B.3.3 Performance Analysis and Design Aids;B.3.3.b Simulation;C Computer Systems Organization;C.1 Processor Architectures;C.1.5 Micro-architecture implementation considerations;C.1.5.e Memory hierarchy},
  doi = {http://dx.doi.org/10.1109/L-CA.2013.7},
  issn = {1556-6056}
}
@inproceedings{pcc13b,
  title = {Unchaining in Design-space Optimization of Streaming Applications},
  author = {Padmanabhan, Shobana and Chen, Yixin and Chamberlain, Roger D.},
  booktitle = {Proc.\ of Workshop on Data-Flow Execution Models for Extreme Scale Computing},
  month = sep,
  year = 2013,
  eprint = {pcc13b.pdf}
}
@inproceedings{mswim13,
  title = {Assessing the Appropriateness of using Markov Decision Processes for RF Spectrum Management},
  author = {Meier, John and Karaus, Benjamin and Sistla, Sreeharsha and Tidwell, Terry and Chamberlain, Roger D and Gill, Christopher},
  booktitle = {Proceedings of the 16th ACM international conference on Modeling, analysis \& simulation of wireless and mobile systems},
  pages = {41--48},
  year = 2013,
  month = nov,
  organization = {ACM},
  eprint = {mswim13.pdf}
}
@article{Ma2014202,
  author = {Ma,Lin and Agrawal,Kunal and Chamberlain,Roger D.},
  title = {A memory access model for highly-threaded many-core architectures},
  journal = {Future Generation Computer Systems},
  volume = {30},
  number = {0},
  pages = {202 - 215},
  year = {2014},
  month = jan,
  issn = {0167-739X},
  doi = {http://dx.doi.org/10.1016/j.future.2013.06.020}
}
@inproceedings{ma2014analysis,
  title = {Analysis of Classic Algorithms on GPUs},
  author = {Ma, Lin and Agrawal, K and Chamberlain, RD},
  booktitle = {Proc. of the 12th ACM/IEEE Int’l Conf. on High Performance Computing and Simulation (HPCS)},
  year = {2014},
  month = jul,
  eprint = {mca14b.pdf},
  pages = {65--73}
}
@incollection{bc14a,
  year = {2014},
  month = sep,
  isbn = {978-3-319-10884-1},
  booktitle = {Computer Performance Engineering},
  volume = {8721},
  series = {Lecture Notes in Computer Science},
  editor = {Horv\'{a}th, A. and Wolter, K.},
  doi = {http://dx.doi.org/10.1007/978-3-319-10885-8_6},
  title = {Use of a {Levy} Distribution for Modeling Best Case Execution Time Variation},
  publisher = {Springer International Publishing},
  author = {Beard, Jonathan C. and Chamberlain, Roger D.},
  pages = {74-88},
  eprint = {bc14a.pdf}
}
@inproceedings{hc14b,
  author = {Hall, M.J. and Chamberlain, R.D.},
  booktitle = {Application-specific Systems, Architectures and Processors (ASAP), 2014 IEEE 25th International Conference on},
  title = {Performance modeling of virtualized custom logic computations},
  year = {2014},
  month = {June},
  pages = {72--73},
  eprint = {hc14b.pdf},
  doi = {10.1109/ASAP.2014.6868635}
}
@inproceedings{mca14a,
  author = {Lin Ma and Chamberlain, R.D. and Agrawal, K.},
  booktitle = {Application-specific Systems, Architectures and Processors (ASAP), 2014 IEEE 25th International Conference on},
  title = {Performance modeling for highly-threaded many-core GPUs},
  year = {2014},
  month = {June},
  pages = {84--91},
  eprint = {mca14a.pdf},
  doi = {10.1109/ASAP.2014.6868641}
}
@inproceedings{wcc14,
  author = {Wingbermuehle, Joseph G. and Cytron, Ron K. and Chamberlain, Roger D.},
  title = {Superoptimization of Memory Subsystems},
  booktitle = {Proceedings of the 2014 SIGPLAN/SIGBED Conference on Languages, Compilers and Tools for Embedded Systems},
  series = {LCTES '14},
  year = {2014},
  eprint = {wcc14.pdf},
  isbn = {978-1-4503-2877-7},
  location = {Edinburgh, United Kingdom},
  pages = {145--154},
  numpages = {10},
  doi = {10.1145/2597809.2597816},
  acmid = {2597816},
  publisher = {ACM},
  address = {New York, NY, USA}
}
@inproceedings{hc14a,
  title = {Performance modeling of virtualized custom logic computations},
  author = {Hall, Michael J and Chamberlain, Roger D},
  title = {Proceedings of the 24th edition of the great lakes symposium on VLSI},
  pages = {89--90},
  year = {2014},
  eprint = {hc14a.pdf},
  organization = {ACM}
}
@inproceedings{labc14,
  author = {Peng Li and Kunal Agrawal and Jeremy Buhler and Roger D. Chamberlain},
  title = {Orchestrating Safe Streaming Computations with Precise Control},
  booktitle = {Proc. of International Workshop on Extreme Scale Computing Application Enablement - Modeling and Tools (ESCAPE)},
  month = dec,
  year = 2014,
  eprint = {labc14.pdf}
}
@inproceedings{blc15,
  author = {Jonathan C. Beard and Peng Li and Roger D. Chamberlain},
  title = {{RaftLib}: A {C++} Template Library for High Performance Stream Parallel Processing},
  booktitle = {Proc. of 6th International Workshop on Programming Models and Applications for Multicores and Manycores (PMAM)},
  month = feb,
  year = 2015,
  pages = {96-105},
  eprint = {blc15.pdf}
}
@inproceedings{bec15a,
  author = {Jonathan C. Beard and Cooper Epstein and Roger D. Chamberlain},
  title = {Automated Reliability Classification of Queueing Models for Streaming
Computation},
  booktitle = {Proc. of 6th ACM/SPEC International Conference on Performance Engineering (ICPE)},
  month = feb,
  year = 2015,
  pages = {325-328},
  eprint = {bec15a.pdf}
}
@inproceedings{wcc15a,
  author = {Joseph G. Wingbermuehle and Ron K. Cytron and Roger D. Chamberlain},
  title = {Superoptimized Memory Subsystems for Streaming Applications},
  booktitle = {Proc. of ACM/SIGDA International Symposium on Field-Programmable Gate Arrays (FPGA)},
  month = feb,
  year = 2015,
  pages = {126-135},
  eprint = {wcc15a.pdf}
}
@incollection{wcc15b,
  author = {Joseph G. Wingbermuehle and Ron K. Cytron and Roger D. Chamberlain},
  title = {Superoptimizing Memory Subsystems for Multiple Objectives},
  booktitle = {Proc. of 4th International Workshop on On-chip Memory Hierarchies and Interconnects (OMHI)},
  series = {Lecture Notes in Computer Science},
  volume = {9523},
  month = aug,
  year = 2015,
  pages = {352-363},
  eprint = {wcc15b.pdf}
}
@inproceedings{bc15,
  author = {Jonathan C. Beard and Roger D. Chamberlain},
  title = {Run Time Approximation of Non-blocking Service Rates for Streaming Systems},
  booktitle = {Proc. of IEEE 17th International Conference on High Performance Computing and Communications (HPCC)},
  month = aug,
  year = 2015,
  pages = {792-797},
  eprint = {bc15.pdf}
}
@incollection{bec15b,
  author = {Jonathan C. Beard and Cooper Epstein and Roger D. Chamberlain},
  title = {Online Automated Reliability Classification of Queueing Models for
Streaming Processing Using Support Vector Machines},
  booktitle = {Proc.of 21st International Conference on Parallel and Distributed Computing (Euro-Par)},
  series = {Lecture Notes in Computer Science},
  vol = 9233,
  month = aug,
  year = 2015,
  pages = {82-93},
  eprint = {bec15b.pdf}
}
@inproceedings{hc15,
  author = {Michael J. Hall and Roger D. Chamberlain},
  title = {Using {M/G/1} Queueing Models with Vacations to Analyze
Virtualized Logic Computations},
  booktitle = {Proc. of 33rd IEEE International Conference on Computer Design (ICCD)},
  month = oct,
  year = 2015,
  pages = {86-93},
  eprint = {hc15.pdf}
}
@inproceedings{ccgss16,
  author = {Roger D. Chamberlain and Mike Chambers and Darren Greenwalt and Brett Steinbrueck and Todd Steinbrueck},
  title = {Layered Security and Ease of Installation for Devices on the Internet of Things},
  booktitle = {Proc. of IEEE 1st International Conference on Internet-of-Things Design and Implementation (IoTDI)},
  month = apr,
  year = 2016,
  pages = {297-300},
  note = {Presented at 1st International Workshop on Interoperability, Integration, and Interconnection of Internet of Things (I4T), Berlin, Germany},
  eprint = {ccgss16.pdf}
}
@inproceedings{mgc16,
  author = {John Meier and Christopher Gill and Roger D. Chamberlain},
  title = {Combining Admission and Modulation Decisions for Wireless Embedded Systems},
  booktitle = {Proc. of 19th IEEE International Symposium on Real-Time Computing (ISORC)},
  month = may,
  year = 2016,
  eprint = {mgc16.pdf},
  doi = {http://doi.ieeecomputersociety.org/10.1109/ISORC.2016.19}
}
@techreport{mercatormanual,
  author = {Stephen V. Cole and Jeremy Buhler},
  title = {{MERCATOR (Mapping EnumeRATOR for CUDA) User's Manual}},
  number = {WUCSE-2016-003},
  institution = {Dept. of Computer Science and Engineering, Washington University in St. Louis},
  month = jul,
  year = 2016,
  eprint = {MercatorManual.pdf}
}