Kevin Karplus's publications

This web page is for most of Kevin Karplus's publications in academic journals and archived conferences. A few technical reports and patents have also been tossed in.

OBSOLETE
See papers/paper-list.html for a more up-to-date listing.

• Kevin Karplus, Rachel Karchin, George Shackleford, and Richard Hughey.
  Calibrating E-values for hidden Markov models with reverse-sequence null models.
  Bioinformatics, 2004.
  accepted, final version not to publisher yet.
• T. J. Dolinksy, P. M. J. Burgers, K. Karplus, and N. A. Baker.
  SPrCY: comparison of structural predictions in the Saccharomyces cerevisiae genome.
  Bioinformatics, 20:2312-2314, April 2004.
• Rachel Karchin, Melissa Cline, and Kevin Karplus.
  Evaluation of local structure alphabets based on residue burial.
  Proteins: Structure, Function, and Genetics, 55(3):508-518, 5 March 2004.
  Online: http://www3.interscience.wiley.com/cgi-bin/abstract/107632554/ABSTRACT
• Kevin Karplus, Rachel Karchin, Jenny Draper, Jonathan Casper, Yael Mandel-Gutfreund, Mark Diekhans, and Richard Hughey.
  Combining local-structure, fold-recognition, and new-fold methods for protein structure prediction.
  Proteins: Structure, Function, and Genetics, 53(Suppl. 6, pages=491-496), 15 October 2003.
• Rachel Karchin, Melissa Cline, Yael Mandel-Gutfreund, and Kevin Karplus.
  Hidden Markov models that use predicted local structure for fold recognition: alphabets of backbone geometry.
  Proteins: Structure, Function, and Genetics, 51(4):504-514, June 2003.
• Kevin Karplus.
  Predicting protein structure using SAM, UCSC's hidden Markov model tools.
  In Igor F. Tsigelny, editor, Protein Structure Prediction: Bioinformatic Approach, IUL Biotechnology Series, pages 297-323. International University Line, La Jolla, California, 2002.
• Melissa Cline, Kevin Karplus, Richard Lathrop, Temple Smith, Robert G. Rogers Jr., and David Haussler.
  Information-theoretic dissection of pairwise contact potentials.
  Proteins: Structure, Function, and Genetics, 49(1):7-14, 1 October 2002.
• Melissa Cline, Richard Hughey, and Kevin Karplus.
  Predicting reliable regions in protein sequence alignments.
  Bioinformatics, 18(2):306-314, February 2002.
• R. Karchin, K. Karplus, and D Haussler.
  Classifying g-protein coupled receptors with support vector machines.
  Bioinformatics, 18(1):147-159, January 2002.
• Julian Gough, Kevin Karplus, Richard Hughey, and Cyrus Chothia.
  Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure.
  Journal of Molecular Biology, 313(4):903-919, 2 Nov 2001.
• Richard Hughey and Kevin Karplus.
  Bioinformatics: A new field in engineering education.
  In 31st ASEE/IEEE Frontiers in Education Conference, pages F2B-15-F2B-19, October 2001.
• J.E. Cleaver, K. Karplus, M. Kashani-Sabet, and C. Limoli.
  Nucleotide excision repair, ``a legacy of creativity''.
  Mutation Research/DNA Repair, 485(1):23-36, 25 February 2001.
• Kevin Karplus and Birong Hu.
  Evaluation of protein multiple alignments by SAM-T99 using the BaliBASE multiple alignment test set.
  Bioinformatics, 17:713-720, August 2001.
• Kevin Karplus, Rachel Karchin, Christian Barrett, Spencer Tu, Melissa Cline, Mark Diekhans, Leslie Grate, Jonathan Casper, and Richard Hughey.
  What is the value added by human intervention in protein structure prediction?
  Proteins: Structure, Function, and Genetics, 45(S5):86-91, 2001.
• Chang Zhu, Kevin Karplus, Leslie Grate, and Philip Coffino.
  A homolog of mammalian antizyme is present in fission yeast Schizosaccharomyces pombe but not detected in budding yeast Saccharomyces cerevisiae.
  Bioinformatics, 16(5):478-481, 2000.
• Richard Hughey, Kevin Karplus, and Anders Krogh.
  SAM: Sequence alignment and modeling software system, version 3.
  Technical Report UCSC-CRL-99-11, University of California, Santa Cruz, Computer Engineering, UC Santa Cruz, CA 95064, October 1999.
  Available from http://www.cse.ucsc.edu/research/compbio/sam.html
• Kevin Karplus, Christian Barrett, and Melissa Cline.
  Getting the most out of hidden Markov models.
  In ISMB99 tutorial, Heidelberg, Germany, August 1999.
• Kevin Karplus, Christian Barrett, Melissa Cline, Mark Diekhans, Leslie Grate, and Richard Hughey.
  Predicting protein structure using only sequence information.
  Proteins: Structure, Function, and Genetics, Supplement 3(1):121-125, 1999.
• Daniel Fischer, Christian Barrett, Kevin Bryson, Arne Elofsson, Adam Godzik, David Jones, Kevin Karplus, Lawrence A. Kelley, Robert M. MacCallum, Krzysztof Pawlowski, Burkhard Rost, Leszek Rychlewski, and Michael Sternberg.
  CAFASP-1: Critical assessment of fully automated structure prediction methods.
  Proteins: Structure, Function, and Genetics, Supplement 3(1):209-217, 1999.
• Kevin Karplus, Christian Barrett, and Richard Hughey.
  Hidden Markov models for detecting remote protein homologies.
  Bioinformatics, 14(10):846-856, 1998.
• J. Park, K. Karplus, C. Barrett, R. Hughey, D. Haussler, T. Hubbard, and C. Chothia.
  Sequence comparisons using multiple sequences detect twice as many remote homologues as pairwise methods.
  Journal of Molecular Biology, 284(4):1201-1210, 1998.
  http://www.mrc-lmb.cam.ac.uk/genomes/jong/assess_paper/assess_paperNov.html (Link appears to be obsolete.)
• Melissa Cline and Kevin Karplus.
  On alignment shift and its measures.
  Technical Report UCSC-CRL-97-27, University of California, Santa Cruz, Jack Baskin School of Engineering, UC Santa Cruz, CA 95064, February 1998.
• J. D. Hirschberg, D. Dahle, K. Karplus, D. Speck, and R. Hughey.
  Kestrel: A programmable array for sequence analysis.
  Journal of VLSI Signal Processing, 19:115-126, 1998.
• David M. Dahle, Jeffrey D. Hirschberg, Kevin Karplus, Hansjörg Keller, Eric Rice, Don Speck, Douglas H. Williams, and Richard Hughey.
  Kestrel: Design of an 8-bit SIMD parallel processor.
  In Proc. 17th Conf. on Advanced Research in VLSI, pages 145-162. Institute of Electrical and Electronic Engineers Computer Society, September 1997.
• Christian Barrett, Richard Hughey, and Kevin Karplus.
  Scoring hidden Markov models.
  CABIOS, 13(2):191-199, 1997.
• Jeffrey D. Hirschberg, Richard Hughey, Kevin Karplus, and Don Speck.
  Kestrel: A programmable array for sequence analysis.
  In Proceedings of the International Conference on Application-Specific Array Processors, pages 25-34, Los Alamitos, CA, July 1996. Institute of Electrical and Electronic Engineers Computer Society.
• Kevin Karplus, Kimmen Sjölander, Christian Barrett, Melissa Cline, David Haussler, Richard Hughey, Liisa Holm, and Chris Sander.
  Predicting protein structure using hidden Markov models.
  Proteins: Structure, Function, and Genetics, Suppl. 1:134-139, 1997.
• Kevin Karplus, Kimmen Sjölander, Christian Barrett, Melissa Cline, David Haussler, Richard Hughey, Liisa Holm, and Chris Sander.
  Predicting protein structure using hidden Markov models, the CASP2 contest.
  Technical Report UCSC-CRL-97-13, University of California, Santa Cruz, Computer Science, UC Santa Cruz, CA 95064, November 1997.
• K. Sjölander, K. Karplus, M. P. Brown, R. Hughey, A. Krogh, I. S. Mian, and D. Haussler.
  Dirichlet mixtures: A method for improving detection of weak but significant protein sequence homology.
  Computer Applications in the Biosciences, 12(4):327-345, August 1996.
• Jeffrey Hisrchberg, Richard Hughey, Kevin Karplus, and Don Speck.
  Kestrel: a programmable array for sequence analysis.
  In Application-Specific Array Processors, August 1996.
• Christian Barrett, Richard Hughey, and Kevin Karplus.
  Scoring hidden Markov models.
  In Proceedings, 4th International Conference on Intelligent Systems for Molecular Biology, page poster only, St. Louis, MO, June 1996. AAAI.
• Kevin Karplus, Kimmen Sjölander, Richard Hughey, and Leslie Grate.
  Stochastic modeling techniques: Understanding and using hidden Markov models.
  In Proceedings, 4th International Conference on Intelligent Systems for Molecular Biology, page Tutorial, St. Louis, MO, June 1996.
• Philipp Bucher, Kevin Karplus, Nicolas Moeri, and Kay Hoffman.
  A flexible motif search technique based on generalized profiles.
  Computers and Chemistry, 20(1):3-24, January 1996.
• Kevin Karplus.
  Regularizers for estimating distributions of amino acids from small samples.
  In Proceedings, 3rd International Conference on Intelligent Systems for Molecular Biology, pages 188-196, Cambridge, England, July 1995.
• Kevin Karplus.
  Regularizers for estimating distributions of amino acids from small samples.
  Technical Report UCSC-CRL-95-11, University of California, Santa Cruz, March 1995.
• Kevin Karplus.
  Using Markov models and hidden Markov models to find repetitive extragenic palindromic sequences in Escherichia coli.
  Technical Report UCSC-CRL-94-24, Computer Engineering Department, University of California, Santa Cruz, Santa Cruz, CA 95064, July 1994.
• Robert Levinson and Kevin Karplus.
  Graph isomorphism and experience-based planning.
  In D. Subramaniam, editor, Proceedings of Workshop on Knowledge Compilation and Speed-Up Learning, Amherst, MA, June 1993.
• Søren Søe and Kevin Karplus.
  Iterating variable ordering heuristics to compute small ordered binary decision diagrams.
  In International Workshop on Logic Synthesis, Lake Tahoe, CA, 23-26 May 1993.
• Kevin Karplus.
  Xtmap: a generate-and-test mapper for table-lookup gate arrays.
  In Compcon 1993, pages 391-399, 22-26 Feb 1993.
• Kevin Karplus.
  Using the ucsc-report LaTeX style file for UCSC technical reports.
  Technical Report UCSC-CRL-92-47, Computer Engineering Department, University of California, Santa Cruz, Santa Cruz, CA 95064, October 1992.
  Replaces and extends UCSC-CRL-87-10 and UCSC-CRL-90-25.
• Kevin Karplus.
  A semi-systolic architecture for decoding error-correcting codes.
  United States Patent 5,157,671, 20 October 1992.
  Rights owned by Space Systems/Loral, application filed 29 May 1990.
• Kevin Karplus.
  ITEM: an if-then-else minimizer for logic synthesis.
  In EuroASIC92, pages 2-7, Paris, 1-5 June 1992.
• Søren Søe and Kevin Karplus.
  Logic minimization using two-column rectangle replacement.
  In ACM IEEE 28^{th<\sup> Design Automation Conference Proceedings}, pages 470-473, San Francisco, CA, 17-21 June 1991.
• Kevin Karplus.
  Xmap: a technology mapper for table-lookup field-programmable gate arrays.
  In ACM IEEE 28^th Design Automation Conference Proceedings, pages 240-243, San Francisco, CA, 17-21 June 1991.
• Kevin Karplus.
  Amap: a technology mapper for selector-based field-programmable gate arrays.
  In ACM IEEE 28^th Design Automation Conference Proceedings, pages 244-247, San Francisco, CA, 17-21 June 1991.
• Kevin Karplus and Habib Krit.
  A semi-systolic decoder for the PDSC-73 error-correcting code.
  Discrete Applied Math, 33(1-3):109-28, 7 Nov 1991.
• Kevin Karplus.
  Using if-then-else DAGs to do technology mapping for field-programmable gate arrays.
  Technical Report UCSC-CRL-90-43, Computer Engineering Department, University of California, Santa Cruz, Santa Cruz, CA 95064, September 1990.
• Pak K. Chan and Kevin Karplus.
  Computing signal delay in general RC networks by tree/link partitioning.
  IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems, 9(8):898-902, August 1990.
• Kevin Karplus.
  Using the ucsc-report LaTeX style file for UCSC technical reports.
  Technical Report UCSC-CRL-90-25, Computer Engineering Department, University of California, Santa Cruz, Santa Cruz, CA 95064, July 1990.
  Replaces and extends UCSC-CRL-87-10.
• Kevin Karplus and Habib Krit.
  A systolic decoder for the PDSC-73 error-correcting code.
  In Applied Algebra and Error-Correcting Codes: AAECC 7, Toulouse, France, 26-30 June 1989.
• Pak Chan, Wayne Dai, Joel Ferguson, Daniel Helman, Kevin Karplus, and Martine Schlag.
  VLSI and CAD education at UC Santa Cruz.
  In 2^nd Annual VLSI Education Conference and Exposition, Santa Clara, CA, July 19-21 1989.
• Pak K. Chan and Kevin Karplus.
  Computing signal delay in general RC networks by tree/link partitioning.
  In ACM IEEE 26^th Design Automation Conference Proceedings, pages 485-490, Las Vegas, NV, June 1989.
• Kevin Karplus.
  Using if-then-else DAGs for multi-level logic minimization.
  In Charles L. Seitz, editor, Advanced Research in VLSI: Proceedings of the Decennial Caltech Conference on VLSI, pages 101-118, Pasadena, CA, 20-22 March 1989.
• Kevin Karplus.
  Using if-then-else DAGs for multi-level logic minimization.
  Technical Report UCSC-CRL-88-29, Computer Engineering Department, University of California, Santa Cruz, Santa Cruz, CA 95064, December 1988.
• Kevin Karplus.
  Representing Boolean functions with If-Then-Else DAGs.
  Technical Report UCSC-CRL-88-28, Computer Engineering Department, University of California, Santa Cruz, Santa Cruz, CA 95064, December 1988.
• Pak Chan and Kevin Karplus.
  Computing signal delay in general RC networks by tree/link partitioning.
  Technical Report UCSC-CRL-88-05, Computer Engineering Department, University of California, Santa Cruz, Santa Cruz, CA 95064, September 1988.
• Kevin Karplus and T. V. Verghese.
  Sizing cMOS gates along a critical path--a tutorial.
  Technical Report UCSC-CRL-87-30, Computer Engineering Department, University of California, Santa Cruz, Santa Cruz, CA 95064, December 1987.
  slightly revised May 1989.
• Kevin Karplus.
  c-util utility package for c.
  Technical Report UCSC-CRL-87-9, Computer Engineering Department, University of California, Santa Cruz, Santa Cruz, CA 95064, July 1987.
• Alexander R. Strong and Kevin Karplus.
  Wavetable-modification instrument and method for generating musical sound.
  United States Patent 4,649,783, 17 March 1987.
  Also Australian Patent 570,669, 3 March 1988 and Canadian Patent 1,215,869, 30 December 1986 and Japanese Patent 6-139341, 1996.
• Kevin Karplus.
  Exclusion constraints, a new application of graph algorithms to VLSI design.
  In 4th MIT Conference on Advanced Research in VLSI, pages 123-139, Cambridge, MA, April 7-9 1986.
• Kevin Karplus and Alexandru Nicolau.
  Getting high performance with slow memory.
  In Alan G. Bell, editor, Compcon 86:thirty-first IEEE Computer Society International Conference, pages 248-250, San Francisco, CA, 3-6 March 1986. IEEE Computer Society Press.
• Kevin Karplus and Gary Haggard.
  Finding minimal perfect hash functions.
  In 1986 ACM Fourteenth Annual Computer Science Conference, Cincinnati, OH, 4-6 February 1986.
• Kevin Karplus and Alexandru Nicolau.
  Efficient hardware for multi-way jumps and pre-fetches.
  In Micro18: the 18^th Annual Microprogramming Workshop, pages 11-18, Monterey, CA, December 1985.
  To be reprinted in Selected Reprints on Microprogramming and Firmware Engineering.
• Alexandru Nicolau and Kevin Karplus.
  ROPE: a statically scheduled supercomputer architecture.
  In First International Conference on Supercomputing Systems, St. Petersburg, FL, December 1985.
• Susan Hertz, Kevin Karplus, and Jim Kadin.
  The Delta rule development system for speech synthesis from text.
  Proceedings of the IEEE, 73(11):1589-1601, November 1985.
• Kevin Karplus and Alexandru Nicolau.
  Rope: a statically scheduled supercomputer architecture.
  In Second SIAM Conference on Parallel Processing for Scientific Computing, Norfolk, Va, 18-21 November 1985.
• Kevin Karplus.
  Exclusion constraints for digital MOS switch circuits.
  In IEEE International Conference on Computer-Aided Design ICCAD-85, pages 244-246, Santa Clara, CA, November 1985.
• Kevin Karplus and Alexandru Nicolau.
  A compiler-driven supercomputer.
  Applied Mathematics and Computation, 20(1-2):95-110, September 1986.
  Special issue with proceedings of the Workshop/Conference on Applications of Supercomputers, held at Michigan Technological University, Houghton, MI, 5-9 August 1985.
• Kevin Karplus.
  A formal model for MOS clocking disciplines.
  Technical Report TR 84-632, Department of Computer Science, Cornell University, Ithaca, NY 14853, August 1984.
• Kevin Karplus and Gary Haggard.
  Finding minimal perfect hash functions.
  Technical Report TR 84-637, Department of Computer Science, Cornell University, Ithaca, NY 14853, August 1984.
• Susan Hertz, Kevin Karplus, and Jim Kadin.
  The Delta system for synthesis rules.
  In 107th Meeting of the Acoustical Society of America, Norfolk, Virginia, 6-10 May 1984.
• Kevin Karplus and Alex Strong.
  Digital synthesis of plucked-string and drum timbres.
  Computer Music Journal, 7(2):43-55, Summer 1983.
  Reprinted in The Music Machine edited by Curtis Roads.
• Kevin Karplus.
  Chisel, An Extension to the Programming Language C for VLSI Layout.
  PhD thesis, Stanford University, February 1983.
  Also Stanford CS Technical Report STAN-CS-82-959.
• Danny Dolev, Kevin Karplus, Alan Siegel, Alex Strong, and Jeff Ullman.
  Optimal algorithms for structural assembly.
  VLSI Design, 3(2):38-42, March/April 1982.
• Danny Dolev, Kevin Karplus, Alan Siegel, Alex Strong, and Jeff Ullman.
  Optimal wiring between rectangles.
  In Conference Proceedings of the 13^th Annual ACM Symposium on Theory of Computing, pages 312-317, Milwaukee, WI, 11-13 May 1981.
• Kevin Karplus.
  A proof of the isomorphism of wxyz-transformals and 2x2 integer matrices under multiplication.
  Computers and Mathematics with Applications, 7(5):425-430, 1981.

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