Richard Hughey

Jeren Samandari-Rad, Matthew R. Guthaus, Richard Hughey: VAR-TX: A variability-aware SRAM model for predicting the optimum architecture to achieve minimum access-time for yield enhancement in nano-scaled CMOS. ISQED 2012: 506-515

Andrew W. Hill, Andrea Di Blas, Richard Hughey: FPGA-based fine-grain parallel computing (abstract only). FPGA 2011: 283

Richard Hughey, Andrea Di Blas: Finding the Next Computational Model: Experience with the UCSC Kestrel. Signal Processing Systems 53(1-2): 171-186 (2008)

Richard Hughey, Andrea Di Blas: The UCSC Kestrel Application-Unspecific Processor. ASAP 2006: 163-168

Kevin Karplus, Rachel Karchin, George Shackelford, Richard Hughey: Calibrating E-values for hidden Markov models using reverse-sequence null models. Bioinformatics 21(22): 4107-4115 (2005)

Andrea Di Blas, Arun Jagota, Richard Hughey: Optimizing neural networks on SIMD parallel computers. Parallel Computing 31(1): 97-115 (2005)

Andrea Di Blas, David M. Dahle, Mark Diekhans, Leslie Grate, Jeffrey D. Hirschberg, Kevin Karplus, Hansjörg Keller, Mark Kendrick, Francisco J. Mesa-Martinez, David Pease, Eric Rice, Angela Schultz, Don Speck, Richard Hughey: The UCSC Kestrel Parallel Processor. IEEE Trans. Parallel Distrib. Syst. 16(1): 80-92 (2005)

Andrea Di Blas, Arun Jagota, Richard Hughey: A Range-Compaction Heuristic for Graph Coloring. J. Heuristics 9(6): 489-506 (2003)

Eric Rice, Richard Hughey: A New Iterative Structure for Hardware Division: The Parallel Paths Algorithm. IEEE Symposium on Computer Arithmetic 2003: 54-62

Melissa S. Cline, Richard Hughey, Kevin Karplus: Predicting reliable regions in protein sequence alignments. Bioinformatics 18(2): 306-314 (2002)

Andrea Di Blas, Arun Jagota, Richard Hughey: Energy function-based approaches to graph coloring. IEEE Transactions on Neural Networks 13(1): 81-91 (2002)

Thomas E. Ferrin, Bruce A. Foster, Richard Hughey: High Performance Computing for Computational Biology - Session Introduction. Pacific Symposium on Biocomputing 2001: 238-239

Leslie Grate, Mark Diekhans, David M. Dahle, Richard Hughey: Sequence Analysis With the Kestrel SIMD Parallel Processor. Pacific Symposium on Biocomputing 2001: 263-274

Eric Rice, Richard Hughey: Molecular Fingerprinting on the SIMD Parallel Processor Kestrel. Pacific Symposium on Biocomputing 2001: 323-334

Raymond Wheeler, Richard Hughey: Optimizing reduced-space sequence analysis. Bioinformatics 16(12): 1082-1090 (2000)

Andrea Di Blas, Richard Hughey: Explicit SIMD Programming for Asynchronous Applications. ASAP 2000: 258-267

David M. Dahle, Leslie Grate, Eric Rice, Richard Hughey: The UCSC Kestrel General Purpose Parallel Processor. PDPTA 1999: 1243-1249

C. Tarnas, Richard Hughey: Reduced space hidden Markov model training. Bioinformatics 14(5): 401-406 (1998)

Rachel Karchin, Richard Hughey: Weighting hidden Markov models for maximum discrimination. Bioinformatics 14(9): 772-782 (1998)

Kevin Karplus, Christian Barrett, Richard Hughey: Hidden Markov models for detecting remote protein homologies. Bioinformatics 14(10): 846-856 (1998)

Jeffrey D. Hirschberg, David M. Dahle, Kevin Karplus, Don Speck, Richard Hughey: Kestrel: A Programmable Array for Sequence Analysis. VLSI Signal Processing 19(2): 115-126 (1998)

J. Alicia Grice, Richard Hughey, Don Speck: Reduced space sequence alignment. Computer Applications in the Biosciences 13(1): 45-53 (1997)

Christian Barrett, Richard Hughey, Kevin Karplus: Scoring hidden Markov models. Computer Applications in the Biosciences 13(2): 191-199 (1997)

J. Z. Dalgaard, M. J. Moser, Richard Hughey, I. Saira Mian: Statistic Modeling, Phylogenetic Analysis and Strjucture Prediction of a Protein Splicing Domain Common to Infeins and Hedgehog Proteins. Journal of Computational Biology 4(2): 193-214 (1997)

Eric Rice, Richard Hughey: Multiprecision Division on an 8-bit Processor. IEEE Symposium on Computer Arithmetic 1997: 74-81

David M. Dahle, Jeffrey D. Hirschberg, Kevin Karplus, Hansjörg Keller, Eric Rice, Don Speck, Douglas H. Williams, Richard Hughey: Kestrel: Design of an 8-bit SIMD Parallel Processor. ARVLSI 1997: 145-

Richard Hughey, Anders Krogh: Hidden Markov models for sequence analysis: extension and analysis of the basic method. Computer Applications in the Biosciences 12(2): 95-107 (1996)

Kimmen Sjölander, Kevin Karplus, Michael Brown, Richard Hughey, Anders Krogh, I. Saira Mian, David Haussler: Dirichlet mixtures: a method for improved detection of weak but significant protein sequence homology. Computer Applications in the Biosciences 12(4): 327-345 (1996)

Richard Hughey: Parallel hardware for sequence comparison and alignment. Computer Applications in the Biosciences 12(6): 473-479 (1996)

Jeffrey D. Hirschberg, Richard Hughey, Kevin Karplus, Don Speck: Kestrel: A Programmable Array for Sequence Analysis. ASAP 1996: 25-34

Richard Hughey: Parallel Sequence Comparison and Alignment. ASAP 1995: 137-140

J. Alicia Grice, Richard Hughey, Don Speck: Parallel Sequence Alignment in Limited Space. ISMB 1995: 145-153

Yasubumi Sakakibara, Michael Brown, Richard Hughey, I. Saira Mian, Kimmen Sjölander, Rebecca C. Underwood, David Haussler: Recent Methods for RNA Modeling Using Stochastic Context-Free Grammars. CPM 1994: 289-306

Leslie Grate, Mark Herbster, Richard Hughey, David Haussler, I. Saira Mian, Harry Noller: RNA Modeling Using Gibbs Sampling and Stochastic Context Free Grammars. ISMB 1994: 138-146

Richard Hughey: Concurrent Error Detection on Programmable Systolic Arrays. IEEE Trans. Computers 42(6): 752-756 (1993)

Michael Brown, Richard Hughey, Anders Krogh, I. Saira Mian, Kimmen Sjölander, David Haussler: Using Dirichlet Mixture Priors to Derive Hidden Markov Models for Protein Families. ISMB 1993: 47-55

Richard Hughey, Daniel P. Lopresti: B-SYS: A 470-Processor Programmable Systolic Array. ICPP (1) 1991: 580-583

Richard Hughey, Daniel P. Lopresti: A software approach to fault detection on programmable systolic arrays. SPDP 1990: 523-526