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},
  pages = {202-215},
  year = {2014},
  month = jan,
  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 = {Proc. of 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}
}
@inproceedings{hc14a,
  title = {Performance modeling of virtualized custom logic computations},
  author = {Hall, Michael J and Chamberlain, Roger D},
  booktitle = {Proc. of 24th ACM Great Lakes Symposium on VLSI},
  pages = {89-90},
  year = {2014},
  eprint = {hc14a.pdf}
}
@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 European 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},
  doi = {10.1109/ICCD.2015.7357087}
}
@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},
  doi = {http://dx.doi.org/10.1109/IoTDI.2015.32}
}
@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}
}
@inproceedings{ccgss17,
  author = {Roger D. Chamberlain and Mike Chambers and Darren Greenwalt and Brett Steinbrueck and Todd Steinbrueck},
  title = {Poster Abstract: Water in the Cloud: Remote Understanding of Water Chemistry},
  booktitle = {Proc. of ACM/IEEE 2nd International Conference on Internet-of-Things Design and Implementation (IoTDI)},
  month = apr,
  year = 2017,
  pages = {353-354},
  doi = {http://dx.doi.org/10.1145/3054977.3057327},
  eprint = {ccgss17.pdf}
}
@article{blc17,
  author = {Jonathan C. Beard and Peng Li and Roger D. Chamberlain},
  title = {{RaftLib}: A {C++} template library for high performance stream parallel processing},
  journal = {Internationall Journal of  High Performance Computing Applications},
  volume = {31},
  number = {5},
  pages = {391-404},
  year = {2017},
  doi = {http://dx.doi.org/10.1177/1094342016672542}
}
@inproceedings{c17,
  author = {Roger D. Chamberlain},
  title = {Assessing User Preferences in Programming Language Design},
  booktitle = {Proc.\  ACM Int'l Symp.\ on New Ideas, New Paradigms, and
Reflections on Programming and Software (Onward!)},
  pages = {18-29},
  month = oct,
  eprint = {c17.pdf},
  doi = {http://dx.doi.org/10.1145/3133850.3133851},
  year = 2017
}
@incollection{ccgss18,
  author = {Roger D. Chamberlain and Mike Chambers and Darren Greenwalt and Brett Steinbrueck and Todd Steinbrueck},
  title = {Devices can be Secure and Easy to Install on the Internet of Things},
  year = {2018},
  booktitle = {Interconnection, Integration, and Interoperability of IoT Systems},
  volume = {8721},
  series = {Lecture Notes in Computer Science},
  editor = {R. Gravina and C.E. Palau and M. Manso and A. Liotta and G. Fortino},
  doi = {http://dx.doi.org/10.1007/978-3-319-61300-0_4},
  publisher = {Springer},
  address = {Cham, Switzerland},
  pages = {59-76}
}
@inproceedings{ipgc18,
  author = {Darko Ivanovich and Samuel B. Powell and Viktor Gruev and Roger D. Chamberlain},
  title = {Polarization Division Multiplexing for Optical Data Communications},
  booktitle = {Proc.\ of SPIE 10538, Optical Interconnects XVIII},
  year = 2018,
  eprint = {ipgc18.pdf},
  doi = {http://dx.doi.org/10.1117/12.2290452}
}
@article{hgc18,
  author = {Michael J. Hall and Viktor Gruev and Roger D. Chamberlain},
  title = {Characterization of a Binary Output Resistance-to-Voltage Read Circuit for Sensing Magnetic Tunnel Junctions},
  journal = {IEEE Sensors Journal},
  volume = 18,
  number = 3,
  pages = {1023-1031},
  month = feb,
  year = 2018,
  doi = {http://dx.doi.org/10.1109/JSEN.2017.2780112}
}
@inproceedings{cew18,
  author = {Roger D. Chamberlain and Chris Edmiston and Don Williams},
  title = {Automated Titration in a Recirculating Water System},
  booktitle = {Proc.\ of 4th International Workshop on Cyber-Physical Systems for Smart Water Networks (CySWater)},
  month = apr,
  year = 2018,
  pages = {12-15},
  doi = {http://dx.doi.org/10.1109/CySWater.2018.00010},
  eprint = {cew18.pdf}
}
@article{lbb17,
  author = {Peng Li and Jonathan C. Beard and Jeremy Buhler},
  title = {Deadlock-free buffer configuration for streaming computing},
  journal = {Internationall Journal of  High Performance Computing Applications},
  volume = {31},
  number = {5},
  pages = {441-450},
  year = {2017},
  doi = {http://dx.doi.org/10.1177/1094342016675679}
}
@inproceedings{cfc+18,
  author = {Cabrera, Anthony M and Faber, Clayton J and Cepeda, Kyle and Derber,
Robert and Epstein, Cooper and Zheng, Jason and Cytron, Ron K and Chamberlain,
Roger D},
  title = {{DIBS}: A Data Integration Benchmark Suite},
  booktitle = {Proc. of ACM/SPEC Int'l Conf. on Performance Engineering Companion},
  pages = {25-28},
  month = apr,
  year = 2018,
  doi = {http://dx.doi.org/10.1145/3185768.3186307},
  eprint = {cfcdezcc18.pdf}
}
@article{mca+18,
  author = {Lin Ma and Roger D. Chamberlain and Kunal Agrawal and Chen Tian and Ziang Hu},
  title = {Analysis of Classic Algorithms on Highly-threaded Many-core Architectures},
  journal = {Future Generation Computer Systems},
  volume = 82,
  pages = {528-543},
  month = may,
  year = 2018,
  doi = {http://dx.doi.org/10.1016/j.future.2017.02.007}
}
@inproceedings{cagm18,
  author = {Roger D. Chamberlain and Chandler Ahrens and Christopher Gill and Scott A. Mitchell},
  title = {Work-in-Progress: Hierarchical Control of a Catoptric Surface},
  booktitle = {Proc. of International Conference on Embedded Software (EMSOFT)},
  month = oct,
  year = 2018,
  doi = {http://dx.doi.org/10.1109/EMSOFT.2018.8537230},
  eprint = {cagm18.pdf}
}
@inproceedings{ccss18,
  author = {Roger D. Chamberlain Ron K. Cytron and Doug Shook and Bill Siever},
  title = {Computers Interacting with the Physical World: A First-Year Course},
  booktitle = {Proc. of Workshop on Embedded and Cyber-Physical Systems Education (WESE)},
  month = oct,
  year = 2018,
  doi = {http://dx.doi.org/10.1007/978-3-030-23703-5_11},
  eprint = {ccss18.pdf}
}
@inproceedings{acmb18,
  author = {Chandler Ahrens and Roger D. Chamberlain and Scott Mitchell and Adam Barnstorff},
  title = {Catoptric Surface},
  booktitle = {Proc. of 38th Conference of Association for Computer Aided Design in Architecture (ACADIA)},
  month = oct,
  year = 2018,
  pages = {216-225},
  url = {http://papers.cumincad.org/cgi-bin/works/Show?acadia18_216},
  eprint = {acmb18.pdf}
}
@inproceedings{fcbmc19,
  author = {Clayton J. Faber and Anthony M. Cabrera and Oronde Booker and Gabe Maayan and Roger D. Chamberlain},
  title = {Data Integration Tasks on Heterogeneous Systems Using {OpenCL}},
  booktitle = {Proc. of 7th International Workshop on OpenCL (IWOCL)},
  month = may,
  year = 2019,
  doi = {http://dx.doi.org/10.1145/3318170.3318187},
  url = {Posters/Faber_et_al_IWOCL19.pdf},
  eprint = {fcbmc19.pdf}
}
@inproceedings{cc19,
  author = {Anthony M. Cabrera and Roger D. Chamberlain},
  title = {Exploring Portability and Performance of {OpenCL} {FPGA} Kernels on {Intel} {HARPv2}},
  booktitle = {Proc. of 7th International Workshop on OpenCL (IWOCL)},
  month = may,
  year = 2019,
  doi = {http://dx.doi.org/10.1145/3318170.3318180},
  eprint = {cc19.pdf},
  note = {Received Best Presentation award.}
}
@inproceedings{ccg+19,
  author = {Roger D. Chamberlain and Mike Chambers and Darren Greenwalt and Maria Scharth and Brett Steinbrueck and Todd Steinbrueck and David Thomas},
  title = {Water in the Cloud: Understanding Water Chemistry via the Internet of Things},
  booktitle = {Proc. of 15th International Conference on Distributed Computing in Sensor Systems (DCOSS)},
  month = may,
  year = 2019,
  pages = {408-415},
  doi = {http://dx.doi.org/10.1109/DCOSS.2019.00084},
  eprint = {ccgssst19.pdf},
  note = {Presented at 1st International Workshop on IoT Applications and Industry 4.0 (IoTI4), Santorini, Greece}
}
@inproceedings{bccrs19,
  author = {Tim Bell and Roger D. Chamberlain and Mike Chambers and Brian Rieck and Todd Steinbrueck},
  title = {Security on the Farm: Safely Communicating with Legacy Agricultural Instrumentation},
  booktitle = {Proc. of 15th International Conference on Distributed Computing in Sensor Systems (DCOSS)},
  month = may,
  year = 2019,
  pages = {192-194},
  doi = {http://dx.doi.org/10.1109/DCOSS.2019.00052},
  eprint = {bccrs19.pdf},
  url = {Posters/Bell_et_al_DCOSS19.pdf}
}
@inproceedings{ccb19,
  author = {Anthony M. Cabrera and Roger D. Chamberlain and Jonathan C. Beard},
  title = {Multi-spectral Reuse Distance: Divining Spatial Information from Temporal Data},
  booktitle = {Proc. of IEEE High Performance Extreme Computing Conference (HPEC)},
  month = sep,
  year = 2019,
  doi = {http://dx.doi.org/10.1109/HPEC.2019.8916398},
  eprint = {ccb19.pdf}
}
@inproceedings{cs20,
  author = {Roger D. Chamberlain and Todd Steinbrueck},
  title = {Demo Abstract: More Than Two Decades of IoT},
  booktitle = {Proc. of ACM/IEEE International Conference on Internet of Things Design and Implementation (IoTDI)},
  month = apr,
  year = 2020,
  doi = {http://dx.doi.org/10.1109/IoTDI49375.2020.00041},
  eprint = {cs20.pdf}
}
@inproceedings{cc20a,
  author = {Anthony M. Cabrera and Roger D. Chamberlain},
  title = {Designing Domain Specific Computing Systems},
  booktitle = {Proc. of IEEE 28th International Symposium on Field-Programmable Custom Computing Machines (FCCM)},
  month = may,
  year = 2020,
  doi = {http://dx.doi.org/10.1109/FCCM48280.2020.00052},
  eprint = {cc20a.pdf}
}
@article{Chamberlain20,
  author = {Roger D. Chamberlain},
  title = {Architecturally Truly Diverse Systems: A Review},
  journal = {Future Generation Computer Systems},
  volume = 110,
  pages = {33-44},
  month = sep,
  year = 2020,
  doi = {http://dx.doi.org/10.1016/j.future.2020.03.061}
}
@inproceedings{wbc05,
  author = {B. Wun and J. Buhler and P. Crowley},
  title = {Exploiting coarse-grained parallelism to accelerate protein motif finding with a network processor},
  booktitle = {Proc. of 14th Int'l Conf. on Parallel Architectures and Compilation Techniques (PACT)},
  pages = {173-184},
  year = 2005,
  doi = {http://dx.doi.org/10.1109/PACT.2005.21}
}
@inproceedings{lb13,
  author = {Peng Li and Jeremy Buhler},
  title = {Polyhedral constraints for bounded-memory execution of synchronized filtering data flow},
  booktitle = {Proc. of  Workshop on Data Flow Execution Models for Extreme-Scale Computing},
  pages = {29-37},
  year = 2013,
  doi = {http://dx.doi.org/10.1109/DFM.2013.11}
}
@inproceedings{cgb14,
  author = {Stephen V. Cole and Jacob R. Gardner and Jeremy D. Buhler},
  title = {{WOODSTOCC}: Extracting Latent Parallelism from a {DNA} Sequence Aligner on a {GPU}},
  booktitle = {Proc. of 13th IEEE Int'l Symp. on Parallel and Distributed Computing},
  pages = {197-204},
  year = 2014,
  doi = {http://dx.doi.org/10.1109/ISPDC.2014.30}
}
@inproceedings{pb20,
  author = {Tom Plano and Jeremy Buhler},
  title = {Scheduling irregular dataflow pipelines on {SIMD} architectures},
  booktitle = {Proc. of 6th Wkshp. on Programming Models for SIMD/Vector Processing},
  month = feb,
  year = 2020,
  doi = {https://doi.org/10.1145/3380479.3380480},
  eprint = {pb20.pdf}
}
@inproceedings{tb20a,
  author = {Stephen Timcheck and Jeremy Buhler},
  title = {Streaming computations with region-based state on {SIMD} architectures},
  booktitle = {Proc. of 13th Int'l Wkshp. on Programmability and Architectures for Heterogeneous Multicores},
  month = jan,
  year = 2020,
  eprint = {tb20a.pdf}
}
@inproceedings{cb17,
  author = {Stephen V. Cole and Jeremy Buhler},
  title = {{MERCATOR}: a {GPGPU} Framework for Irregular Streaming Applications},
  booktitle = {Proc. of 15th Int'l Conf. on High Performance Computing and Simulation (HPCS)},
  pages = {727-736},
  month = jul,
  year = 2017,
  doi = {http://dx.doi.org/10.1109/HPCS.2017.111},
  eprint = {cb17.pdf}
}
@inproceedings{cb15,
  author = {Stephen Cole and Jeremy Buhler},
  title = {The function-centric model: Supporting {SIMD} execution of streaming computations},
  booktitle = {Proc. of 5th Workshop on Data-flow Execution Models for Extreme Scale Computing (DFM)},
  year = 2015,
  eprint = {cb15.pdf}
}
@inproceedings{lbb15,
  author = {Peng Li and Jonathan Beard and Jeremy Buhler},
  title = {Deadlock-free buffer configuration for stream computing},
  booktitle = {Proc. of Int'l Workshop on Programming Models and Applications for Multicores and Manycores (PMAM)},
  pages = {164-169},
  year = 2015,
  doi = {https://doi.org/10.1145/2712386.2712403},
  eprint = {lbb15.pdf}
}
@inproceedings{acmbg19,
  author = {Chandler Ahrens and Roger Chamberlain and Scott Mitchell and Adam Barnstorff and Joshua Gelbard},
  title = {Controlling Daylight Reflectance with Cyber-physical Systems},
  booktitle = {Proc. of 24th International Conference on Computer-Aided Architectural Design Research in Asia (CAADRIA)},
  volume = 1,
  month = apr,
  year = 2019,
  pages = {433-442},
  url = {http://papers.cumincad.org/cgi-bin/works/paper/caadria2019_413},
  eprint = {acmbg19.pdf}
}
@inproceedings{hcg20,
  author = {Steven Harris and Roger D. Chamberlain and Christopher Gill},
  title = {{OpenCL} Performance on the {Intel Heterogeneous Architecture Research Platform}},
  booktitle = {Proc.\ of IEEE High-Performance Extreme Computing Conference (HPEC)},
  month = sep,
  year = 2020,
  eprint = {hcg20.pdf},
  doi = {10.1109/HPEC43674.2020.9286213},
  url = {https://github.com/professorengima/OpenCL-HPEC-2020}
}
@inproceedings{cc20b,
  author = {Anthony M. Cabrera and Roger D. Chamberlain},
  title = {Design and Performance Evaluation of Optimizations for {OpenCL FPGA} Kernels},
  booktitle = {Proc.\ of IEEE High-Performance Extreme Computing Conference (HPEC)},
  month = sep,
  year = 2020,
  eprint = {cc20b.pdf},
  doi = {10.1109/HPEC43674.2020.9286221}
}
@inproceedings{idzgzc20,
  author = {Darko Ivanovich and Amit Deliwala and Chenfeng Zhao and Viktor Gruev and Xuan Zhang and Roger D. Chamberlain},
  title = {Chip-to-chip Optical Data Communications using Polarization Division Multiplexing},
  booktitle = {Proc.\ of IEEE High-Performance Extreme Computing Conference (HPEC)},
  month = sep,
  year = 2020,
  eprint = {idzgzc20.pdf},
  doi = {10.1109/HPEC43674.2020.9286227}
}
@inproceedings{ocees20,
  author = {Bryan Orabutt and Roger Chamberlain and Jonathan Elson and George Engel and Lee Sobotka},
  title = {Applied Optimization on Mixed Mode Systems for Pulse Shape Discrimination},
  booktitle = {Bulletin of the American Physical Society},
  year = 2020,
  month = oct,
  eprint = {Orabutt_et_al_APS20.pdf},
  url = {https://meetings.aps.org/Meeting/DNP20/Session/DN.4}
}
@inproceedings{tb20b,
  author = {Stephen W. Timcheck and Jeremy D. Buhler},
  title = {Reducing Queueing Impact in Irregular Data Streaming Applications},
  booktitle = {Proc.\ of IEEE/ACM 10th Workshop on Irregular Applications: Architectures and Algorithms (IA3)},
  month = nov,
  year = 2020,
  pages = {22--30},
  eprint = {tb20b.pdf},
  doi = {10.1109/IA351965.2020.00009}
}
@article{hoc21,
  author = {Michael J. Hall and Neil E. Olson and Roger D. Chamberlain},
  title = {Utilizing Virtualized Hardware Logic Computations to Benefit Multi-User Performance},
  journal = {Electronics},
  volume = 10,
  number = 6,
  pages = 665,
  month = mar,
  year = 2021,
  doi = {10.3390/electronics10060665}
}
@inproceedings{cyl21,
  author = {Anthony M. Cabrera and Aaron R. Young and Jacob Lambert and Zhili Xiao and Amy An and Seyong Lee and Zheming Jin and Jungwon Kim and Jeremy Buhler and Roger D. Chamberlain and Jeffrey S. Vetter},
  title = {Toward Evaluating High-Level Synthesis Portability and Performance between {Intel} and {Xilinx} {FPGAs}},
  booktitle = {Proc.\ of 9th International Workshop on OpenCL (IWOCL)},
  month = apr,
  year = 2021,
  doi = {10.1145/3456669.3456699},
  eprint = {Cabrera_et_al.pdf},
  note = {Collaborative work with Oak Ridge National Laboratory and Univ. of Oregon.}
}
@inproceedings{dc21,
  author = {Justin Deters and Ron Cytron},
  title = {Performance Counter Design Variation in Rocket Chip via Feature-Oriented Programming},
  booktitle = {Proc.\ of Fifth Workshop on Computer Architecture Research with RISC-V (CARRV)},
  month = jun,
  year = 2021,
  eprint = {dc21.pdf},
  url = {https://carrv.github.io/2021/}
}
@article{zzc21,
  author = {Zhao, Chenfeng and Zhang, Xuan and Chamberlain, Roger D.},
  journal = {IEEE Design \& Test},
  title = {Executing Data Integration Effectively and Efficiently Near the Memory},
  volume = 29,
  number = 2,
  year = {2022},
  month = apr,
  pages = {65-73},
  doi = {10.1109/MDAT.2021.3069957}
}
@inproceedings{haa+21,
  author = {Hughes, Zachary and Alnussirat, Samer  and  Altomare, Corrado  and  Bose, Richard G.  and  Braun, Dana L  and  Buckley, James H.  and  Buhler, Jeremy  and  Burns, Eric  and  Chamberlain, Roger D.  and  Chen, Wenlei  and  Cherry, Michael L.  and  Di Venere, Leonardo  and  Dumonthier, Jeffrey  and  Errando, Manel  and  Funk, Stefan  and  Giordano, Francesco  and  Hoffman, Jonah  and  Huth, Dawson J.  and  Kelly, Patrick L.  and  Krizmanic, John F.  and  Kuwahara, Makiko  and  Licciulli, Francesco  and  Liu, Gang  and  Mazziotta, Mario Nicola  and  Mitchell, John Grant  and  Mitchell, John W.  and  de Nolfo, Georgia A.  and  Paoletti, Riccardo  and  Pillera, Roberta  and  Rauch, Brian Flint  and  Serini, Davide  and  Simburger, Garry E  and  Sudvarg, Marion  and  Suarez, George  and  Tatoli, Teresa  and  Varner, Gary S.  and  Wulf, Eric A.  and  Zink, Adrian  and  Zober, Wolfgang V.},
  title = {{Characterization of a prototype imaging calorimeter for the Advanced Particle-astrophysics Telescope from an Antarctic balloon flight and CERN beam test}},
  doi = {10.22323/1.395.0137},
  booktitle = {Proc.\ of 37th International Cosmic Ray Conference {—} PoS(ICRC2021)},
  month = jul,
  year = 2021,
  volume = {395},
  pages = {137:1-137:9},
  eprint = {ICRC2021_137.pdf}
}
@inproceedings{cba+21,
  author = {Chen, Wenlei and Buckley, James H. and Alnussirat, Samer  and  Altomare, Corrado  and  Bose, Richard G.  and  Braun, Dana L  and  Buhler, Jeremy  and  Burns, Eric  and  Chamberlain, Roger D.  and  Cherry, Michael L.  and  Di Venere, Leonardo  and  Dumonthier, Jeffrey  and  Errando, Manel  and  Funk, Stefan  and  Giordano, Francesco  and  Hoffman, Jonah  and  Hughes, Zachary  and  Huth, Dawson J.  and  Kelly, Patrick L.  and  Krizmanic, John F.  and  Kuwahara, Makiko  and  Licciulli, Francesco  and  Liu, Gang  and  Mazziotta, Mario Nicola  and  Mitchell, John Grant  and  Mitchell, John W.  and  de Nolfo, Georgia A.  and  Paoletti, Riccardo  and  Pillera, Roberta  and  Rauch, Brian Flint  and  Serini, Davide  and  Simburger, Garry E  and  Sudvarg, Marion  and  Suarez, George  and  Tatoli, Teresa  and  Varner, Gary S.  and  Wulf, Eric A.  and  Zink, Adrian  and  Zober, Wolfgang V.},
  title = {{The Advanced Particle-astrophysics Telescope: Simulation of the Instrument Performance for Gamma-Ray Detection}},
  doi = {10.22323/1.395.0590},
  booktitle = {Proc.\ of 37th International Cosmic Ray Conference {—} PoS(ICRC2021)},
  month = jul,
  year = 2021,
  volume = {395},
  pages = {590:1-590:9},
  eprint = {ICRC2021_590.pdf}
}
@inproceedings{baa+21,
  author = {Buckley, James  and  Alnussirat, Samer  and  Altomare, Corrado  and  Bose, Richard G.  and  Braun, Dana L  and  Buckley, James H.  and  Buhler, Jeremy  and  Burns, Eric  and  Chamberlain, Roger D.  and  Chen, Wenlei  and  Cherry, Michael L.  and  Di Venere, Leonardo  and  Dumonthier, Jeffrey  and  Errando, Manel  and  Funk, Stefan  and  Giordano, Francesco  and  Hoffman, Jonah  and  Hughes, Zachary  and  Huth, Dawson J.  and  Kelly, Patrick L.  and  Krizmanic, John F.  and  Kuwahara, Makiko  and  Licciulli, Francesco  and  Liu, Gang  and  Mazziotta, Mario Nicola  and  Mitchell, John Grant  and  Mitchell, John W.  and  de Nolfo, Georgia A.  and  Paoletti, Riccardo  and  Pillera, Roberta  and  Rauch, Brian Flint  and  Serini, Davide  and  Simburger, Garry E  and  Sudvarg, Marion  and  Suarez, George  and  Tatoli, Teresa  and  Varner, Gary S.  and  Wulf, Eric A.  and  Zink, Adrian  and  Zober, Wolfgang V.},
  title = {{The Advanced Particle-astrophysics Telescope (APT) Project Status}},
  doi = {10.22323/1.395.0655},
  booktitle = {Proc.\ of 37th International Cosmic Ray Conference {—} PoS(ICRC2021)},
  month = jul,
  year = 2021,
  volume = {395},
  pages = {655:1--655:9},
  eprint = {ICRC2021_655.pdf}
}
@inproceedings{sbb+21,
  author = {Sudvarg, Marion  and  Buhler, Jeremy  and  Buckley, James H.  and  Chen, Wenlei  and  Hughes, Zachary  and  Ramey, Emily  and  Cherry, Michael L.  and  Alnussirat, Samer  and  Larm, Ryan  and  Chungata, Christofer  and  Altomare, Corrado  and  Bose, Richard G.  and  Braun, Dana L  and  Burns, Eric  and  Chamberlain, Roger D.  and  Di Venere, Leonardo  and  Dumonthier, Jeffrey  and  Errando, Manel  and  Funk, Stefan  and  Giordano, Francesco  and  Hoffman, Jonah  and  Huth, Dawson J.  and  Kelly, Patrick L.  and  Krizmanic, John F.  and  Kuwahara, Makiko  and  Licciulli, Francesco  and  Liu, Gang  and  Mazziotta, Mario Nicola  and  Mitchell, John Grant  and  Mitchell, John W.  and  de Nolfo, Georgia A.  and  Paoletti, Riccardo  and  Pillera, Roberta  and  Rauch, Brian Flint  and  Serini, Davide  and  Simburger, Garry E  and  Suarez, George  and  Tatoli, Teresa  and  Varner, Gary S.  and  Wulf, Eric A.  and  Zink, Adrian  and  Zober, Wolfgang V.},
  title = {{A Fast GRB Source Localization Pipeline for the Advanced Particle-astrophysics Telescope}},
  doi = {10.22323/1.395.0588},
  booktitle = {Proc.\ of 37th International Cosmic Ray Conference {—} PoS(ICRC2021)},
  month = jul,
  year = 2021,
  volume = {395},
  pages = {588:1--588:9},
  eprint = {ICRC2021_588.pdf}
}
@inproceedings{oce+21,
  author = {Bryan Orabutt and Roger D. Chamberlain and Jonathan Elson and George Engel and Franck Delaunay and Lee G. Sobotka},
  title = {Design of Mixed-mode Systems for Pulse-shape Discrimination},
  booktitle = {Proc.\ of IEEE 64th International Midwest Symposium on Circuits and Systems (MWSCAS)},
  month = aug,
  year = 2021,
  eprint = {oceeds21.pdf},
  pages = {990-994},
  doi = {10.1109/MWSCAS47672.2021.9531905}
}
@article{bbb+19,
  journal = {Bulletin of the American Astronomical Society},
  number = {7},
  title = {{The Advanced Particle-astrophysics Telescope (APT)}},
  url = {https://baas.aas.org/pub/2020n7i078},
  volume = {51},
  author = {Buckley, James and Bergstrom, Lars and Binns, Bob and Buhler, Jeremy and Chen, Wenlei and Cherry, Michael and Funk, Stefan and Hooper, Dan and Mitchell, John and Nolfo, Georgia De and Nussirat, Samer Al and Profumo, Stefano and Rauch, Brian and Stern, Daniel and Varner, Garry and Wakely, Scott and Zink, Adrian},
  year = {2019},
  month = sep
}
@article{hbb+20,
  journal = {Bulletin of the American Astronomical Society},
  number = {3},
  title = {Report of 2019 {APTlite} balloon flight},
  url = {https://baas.aas.org/pub/aas236-142p04-hughes},
  volume = {52},
  author = {Hughes, Z. and Buckley, J. and Bergström, L. and Binns, W. and Buhler, J. and Chen, W. and Cherry, M. and Funk, S. and Hooper, D. and Mitchell, J. and Nolfo, G. De and Nussirat, S. Al and Profumo, S. and Rauch, B. and Stern, D. and Varner, G. and Wakely, S. and Zink, A.},
  year = {2020},
  month = jun,
  note = {Poster link: https://aas236-aas.ipostersessions.com/?s=32-A8-2A-D4-AD-EB-6E-39-65-5C-09-9C-49-24-61-AB}
}
@inproceedings{pb21,
  author = {Tom Plano and Jeremy Buhler},
  title = {Enabling Real-Time Irregular Data-Flow Pipelines on {SIMD} Devices},
  booktitle = {Proc.\ of 50th International Conference on Parallel Processing Workshops},
  year = 2021,
  month = aug,
  pages = {9:1--9:8},
  eprint = {pb21.pdf},
  doi = {10.1145/3458744.3473367}
}
@incollection{bllm21,
  author = {Jeremy Buhler and Thomas Lavastida and Kefu Lu and Benjamin Moseley},
  title = {A Scalable Approximation Algorithm for Weighted Longest Common Subsequence},
  booktitle = {Proc.of 27st International European Conference on Parallel and Distributed Computing (Euro-Par)},
  series = {Lecture Notes in Computer Science},
  vol = 12820,
  month = aug,
  year = 2021,
  pages = {368-384},
  doi = {10.1007/978-3-030-85665-6_23},
  eprint = {bllm21.pdf}
}
@inproceedings{hc17,
  author = {Michael J. Hall and Roger D. Chamberlain},
  title = {Virtualization of Deeply Pipelined Magnetologic},
  booktitle = {Proc. of IEEE Conf.\ on Rebooting Computing},
  month = nov,
  year = 2017,
  url = {Posters/icrc_poster_42x36.pdf}
}
@inproceedings{xcc21,
  author = {Zhili Xiao and Roger D. Chamberlain and Anthony M. Cabrera},
  title = {{HLS} Portability from {Intel} to {Xilinx}: A Case Study},
  booktitle = {Proc.\ of IEEE High-Performance Extreme Computing Conference (HPEC)},
  month = sep,
  year = 2021,
  doi = {10.1109/HPEC49654.2021.9622785},
  eprint = {xcc21.pdf}
}
@inproceedings{swbbc21,
  author = {Marion Sudvarg and Jacob Wheelock and Jeremy D. Buhler and James H. Buckley and Wenlei Chen},
  title = {Parallel {GRB} Source Localization Pipelines for the Advanced Particle-Astrophysics Telescope},
  booktitle = {Proc. of IEEE/ACM International Conference for High Performance Computing, Networking, Storage, and Analysis (SC)},
  month = nov,
  year = 2021,
  eprint = {swbbc21.pdf},
  url = {Posters/Sudvarg_et_al_SC21.pdf}
}
@inproceedings{fpk+21,
  author = {Clayton J. Faber and Tom Plano and Samatha Kodali and Zhili Xiao and Abhishek Dwaraki and Jeremy D. Buhler and Roger D. Chamberlain and Anthony M. Cabrera},
  title = {Platform Agnostic Streaming Data Application Performance Models},
  booktitle = {Proc. of IEEE/ACM Workshop on Redefining Scalability for Diversely Heterogeneous Architectures (RSDHA)},
  month = nov,
  year = 2021,
  doi = {10.1109/RSDHA54838.2021.00008},
  eprint = {fpkxdbcc21.pdf}
}
@inproceedings{wks+21,
  author = {Jacob Wheelock and William Kanu and Marion Sudvarg and Zhili Xiao and Jeremy D. Buhler and Roger D. Chamberlain and James H. Buckley},
  title = {Supporting Multi-messenger Astrophysics with Fast Gamma-ray Burst Localization},
  booktitle = {Proc. of IEEE/ACM HPC for Urgent Decision Making Workshop (UrgentHPC)},
  month = nov,
  year = 2021,
  doi = {10.1109/UrgentHPC54802.2021.00008},
  eprint = {wksxbcb21.pdf}
}
@article{tb21,
  author = {Stephen Timcheck and Jeremy Buhler},
  title = {Reducing queuing impact in streaming applications with irregular dataflow},
  journal = {Parallel Computing},
  volume = 109,
  month = mar,
  year = 2022,
  pages = {102863},
  doi = {10.1016/j.parco.2021.102863}
}
@inproceedings{bscr22,
  author = {Tim Bell and Todd Steinbrueck and Roger D. Chamberlain and Brian Rieck},
  title = {IoT Benefits for Livestock Farmers},
  booktitle = {Proc. of 18th International Conference on Distributed Computing in Sensor Systems (DCOSS)},
  month = may,
  year = 2022,
  pages = {159-166},
  doi = {10.1109/DCOSS4816.2022.00038},
  eprint = {bscr22.pdf},
  note = {Presented at 4th International Workshop on IoT Applications and Industry 4.0 (IoTI4), Marina del Rey, CA, USA}
}
@inproceedings{sbcgb22,
  author = {Marion Sudvarg and Jeremy Buhler and Roger Chamberlain and Chris Gill and James Buckley},
  title = {{Work in Progress: Real-Time GRB Localization for the Advanced Particle-astrophysics Telescope}},
  booktitle = {Proc. of 15th Workshop on Operating Systems Platforms for Embedded Real-Time Applications (OSPERT)},
  month = jul,
  year = 2022,
  pages = {57-61},
  eprint = {sbcgb22.pdf}
}
@inproceedings{sg22,
  author = {Marion Sudvarg and Chris Gill},
  title = {Analysis of Federated Scheduling for Integer-Valued Workloads},
  booktitle = {Proc. of 30th International Conference and Real-Time Networks and Systems (RTNS)},
  month = jun,
  year = 2022,
  pages = {12-23},
  eprint = {sg22.pdf},
  doi = {10.1145/3534879.3534892}
}
@inproceedings{zcz22,
  author = {Chenfeng Zhao and Roger D. Chamberlain and Xuan Zhang},
  title = {Graph Partitioning for Near Memory Processing},
  booktitle = {In-Memory Architectures and Computing Applications Workshop (iMACAW)},
  month = jul,
  year = 2022,
  eprint = {zcz22.pdf},
  url = {Posters/Zhao_et_al_iMACAW22.pdf}
}
@article{sgb21,
  author = {Sudvarg, Marion and Gill, Chris and Baruah, Sanjoy},
  title = {Linear-time admission control for elastic scheduling},
  journal = {Real-Time Systems},
  year = {2021},
  month = oct,
  volume = {57},
  number = {4},
  pages = {485-490},
  doi = {10.1007/s11241-021-09373-4}
}
@inproceedings{Det21,
  author = {Justin Deters},
  title = {Novel Hardware Design Variation through Feature-Oriented Programming},
  booktitle = {Programming Language Design and Implementation (PLDI) Student Research Competition},
  month = jun,
  year = 2021,
  eprintx = {PLDI_SRC_2021.pdf},
  url = {Posters/PLDI_SRC_2021_Poster.pdf}
}