Kevin Karplus Publications

(Last Update: 11:23 PDT 17 August 2008 )

This page will eventually have pointers to most of Kevin Karplus's publications (at least the academic ones, not necessarily letters to the editors and other minor publications). The listing is fairly complete at the moment, but pointers (URLs) have not yet been added to online copies of the papers.

Preprints of some of these papers can be found in this directory.

Patents

  1. 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.
  2. with Alexander R. Strong. 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, Canadian Patent 1,215,869, 30 December 1986, and Japanese Patent 6-139341, 1996.

Refereed Journal Articles

  1. Sol Katzman, Christian Barrett, Grant Thiltgen, Rachel Karchin, and Kevin Karplus
    Predict-2nd: a tool for generalized protein local structure prediction
    Bioinformatics
    accepted for publication.
    preprint Supplementary material
  2. George Shackelford and Kevin Karplus. Contact Prediction using Mutual Information and Neural Nets. Proteins: Structure, Function, and Bioinformatics, 69(S8):159-164, 2007. (CASP7 sepcial issue).
    doi:10.1002/prot.21791 Preprint
  3. Jiunn C. N. Fong, Kevin Karplus, Gary K. Schoolnik, and Fitnat H. Yildiz. Identification and Characterization of RbmA, a Novel Protein Required for the Development of Rugose Colony Morphology and Biofilm Structure in Vibrio cholera. Journal of Bacteriology, 188(3):1049-1059. Feb 2006. doi:10.1128/JB.188.3.1049-1059.2006
  4. Oscar Hur and Kevin Karplus. Methods of translating NMR proton distances into their corresponding heavy atom distances for protein structure prediction with limited experimental data. Protein Engineering, Design and Selection 18(12):597-605, Dec 2005. doi:10.1093/protein/gzi068 Abstract PDF
  5. Kevin Karplus, Sol Katzman, George Shackleford, Martina Koeva, Jenny Draper, Bret Barnes, Marcia Soriano, and Richard Hughey. SAM-T04: what's new in protein-structure prediction for CASP6. Proteins: Structure, Function, and Bioinformatics, 2005. 61(S7):135-142. doi:doi:10.1002/prot.20730 Pre-publication copy
  6. Kevin Karplus, Rachel Karchin, George Shackleford, and Richard Hughey. Calibrating E-values for hidden Markov models with reverse-sequence null models. Bioinformatics, 2005. 21(22):4107-4115; doi:10.1093/bioinformatics/bti629 UCSC preprint PDF version
  7. Andrea Di Blas, David Dahle, Mark Diekhans, Leslie Grate, Jeffrey Hirschberg, Kevin Karplus, Hansjorg Keller, Mark Kendrick, Francsisco J. Mesa-Martinez, David Pease, Eric Rice, Angela Schmid, Don Speck, and Richard Hughey. The UCSC Kestrel Parallel Processor. IEEE Transactions on Parallel and Distributed Systems, 16(1):80-92, January 2005. The official abstract PDF of article (Note: I believe that Angela's last name is wrong in the IEEE version of the paper---it should be Schmid, not Schultz.)
  8. 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(14):2312--2314, April 2004. abstract and pointer to PDF
  9. 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. doi:10.1002/prot.20008
  10. 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):491-496, 15 October 2003. doi:10.1002/prot.10540 PDF of preprint
  11. 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. doi:10.1002/prot.10369
  12. Richard Hughey and Kevin Karplus. Bioinformatics: A new field in engineering education. Journal of Engineering Education 92(1):101--104, 2003.
  13. 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. abstract and pointer to pdf doe:10.1002/prot.10198
  14. Melissa Cline, Richard Hughey, and Kevin Karplus. Predicting reliable regions in protein sequence alignments. Bioinformatics, 18:306--324, 2002. abstract and pointer to pdf
  15. R. Karchin, K. Karplus, and D Haussler. Classifying g-protein coupled receptors with support vector machines. Bioinformatics, 18:147--159, 2002. Abstract and pointer to PDF
  16. 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, 313:903--919, 2001.
  17. 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. abstract and pointer to pdf
  18. 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. doi:10.1002/prot.10021 preprint
  19. J.E. Cleaver, K. Karplus, M. Kashani-Sabet, and C. Limoli. Nucleotide excision repair, ``a legacy of creativity''. Mutation Research, 485(1):23--36, 25 February 2001.
  20. 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. abstract and pointer to PDF
  21. 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, Suppl. 3(1):121--125, 1999. abstract and pointer to pdf PDF on UCSC server
  22. 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, Suppl. 3(1):209--217, 1999. abstract and pointer to pdf
  23. Kevin Karplus, Christian Barrett, and Richard Hughey. Hidden Markov models for detecting remote protein homologies. Bioinformatics, 14(10):846--856, 1998. abstract and pointer to pdf
  24. 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.
  25. J.D. Hirschberg, D. Dahle, K. Karplus, D. Speck, and R. Hughey. Kestrel: A programmable array for sequence analysis. Journal of VLSI Signal Processing, 1997, 19:115--126, 1998.
  26. 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. abstract and pointer to pdf prepublication version of paper (PDF)
  27. Christian Barrett, Richard Hughey, and Kevin Karplus. Scoring hidden Markov models. CABIOS, 13(2):191-199, 1997. preprint
  28. 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), 1996. preprint version
  29. Philipp Bucher, Kevin Karplus, Nicolas Moeri, and Kay Hoffman, ``A Flexible Motif Search Technique based on Generalized Profiles'', Computers and Chemistry, Volume 20, Number 1, pps. 3--24, January 1996.
  30. with Habib Krit. A systolic decoder for the PDSC-73 error-correcting code. Discrete Applied Math, 33(1--2), August 1991.
  31. with Pak K. Chan. 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.
  32. with Susan Hertz and Jim Kadin. The Delta rule development system for speech synthesis from text. Proceedings of the IEEE, 73(11):1589--1601, November 1985.
  33. with 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.
  34. with 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.
  35. A proof of the isomorphism of wxyz-transformals and 2×2 integer matrices under multiplication. Computers and Mathematics with Applications, 7(5):425--430, 1981.

Refereed Conference Articles

  1. 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. (presented by Richard Hughey)
  2. 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 Proceedings of the 17th IEEE Conference on Advanced Research in VLSI, September 1997.
  3. Jeffrey D. Hirschberg, Richard Hughey, Kevin Karplus, and Don Speck. Kestrel: A programmable array for sequence analysis. In Proceedings of the IEEE International Conference on Application-Specific Array Processors, pages 25--34, Los Alamitos, CA, July 1996.
  4. Kevin Karplus. ``Regularizers for Estimating Distributions of Amino Acids from Small Samples'', in ISMB-95 proceedings, Cambridge, England, July 1995. PDF
  5. Kevin Karplus. Xtmap: a generate-and-test mapper for table-lookup gate arrays. In Compcon 1993, pages 391--399, 22--26 Feb 1993.
  6. Kevin Karplus. ITEM: an if-then-else minimizer for logic synthesis. In EuroASIC92, pages 2--7, Paris, 1--5 June 1992. Invited talk.
  7. Xmap: a technology mapper for table-lookup field-programmable gate arrays. In ACM IEEE 28th Design Automation Conference Proceedings, pages 240--243, San Francisco, CA, 17--21 June 1991.
  8. Amap: a technology mapper for selector-based field-programmable gate arrays. In ACM IEEE 28th Design Automation Conference Proceedings, pages 244--247, San Francisco, CA, 17--21 June 1991.
  9. with Søren Søe. Logic minimization using two-column rectangle replacement. In ACM IEEE 28th Design Automation Conference Proceedings, pages 470--473, San Francisco, CA, 17--21 June 1991.
  10. with 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.
  11. with Pak K. Chan. Computing signal delay in general RC networks by tree/link partitioning. In ACM IEEE 26th Design Automation Conference Proceedings, pages 485--490, Las Vegas, NV, June 1989.
  12. 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.
  13. 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.
  14. with 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.
  15. with Gary Haggard. Finding minimal perfect hash functions. In 1986 ACM Fourteenth Annual Computer Science Conference, Cincinnati, OH, 4--6 February 1986.
  16. with Alexandru Nicolau. Efficient hardware for multi-way jumps and pre-fetches. In Micro18: the 18th Annual Microprogramming Workshop, pages 11--18, Monterey, CA, December 1985. To be reprinted in Selected Reprints on Microprogramming and Firmware Engineering.
  17. with Alexandru Nicolau. Rope: a statically scheduled supercomputer architecture. In Second SIAM Conference on Parallel Processing for Scientific Computing, Norfolk, Va, 18--21 November 1985.
  18. 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.
  19. with Alexandru Nicolau. ROPE: a statically scheduled supercomputer architecture. In First International Conference on Supercomputing Systems, St. Petersburg, FL, December 1985.
  20. with Susan Hertz and Jim Kadin. The Delta system for synthesis rules. In 107th Meeting of the Acoustical Society of America, Norfolk, Virginia, 6--10 May 1984.
  21. with Danny Dolev, Alan Siegel, Alex Strong, and Jeff Ullman. Optimal wiring between rectangles. In Conference Proceedings of the 13th Annual ACM Symposium on Theory of Computing, pages 312--317, Milwaukee, WI, 11--13 May 1981.

Book chapters

  1. 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. pre-publication draft

Tech reports and other unrefereed articles

  1. 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
  2. Christian Barrett, Richard Hughey, and Kevin Karplus. Scoring hidden Markov models. In Proceedings 4th International Conference on Intelligent Systems for Molecular Biology, poster only, St. Louis, MO, June 1996. AAAI.
  3. Kevin Karplus. ``Regularizers for Estimating Distributions of Amino Acids from Small Samples,'' Technical Report UCSC-CRL-95-11, Computer Engineering, University of California, Santa Cruz, CA 95064, March 1995, URL ftp://ftp.cse.ucsc.edu/pub/tr/ucsc-crl-95-11.ps.Z.
  4. Kevin Karplus. Using Markov models and hidden Markov models to find repetitive extragenic palindromic sequences in Escherichia coli. Technical Report UCSC-CRL-94-24, Board of Studies in Computer Engineering, University of California, Santa Cruz, CA 95064, July 1994.
  5. 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.
  6. Kevin Karplus. Using the ucsc-report LaTeX style file for UCSC technical reports. Technical Report UCSC-CRL-92-47, Board of Studies in Computer Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, October 1992. Replaces and extends UCSC-CRL-87-10 and UCSC-CRL-90-25.
  7. Using if-then-else DAGs to do technology mapping for field-programmable gate arrays. Technical Report UCSC-CRL-90-43, Board of Studies in Computer Engineering, University of California at Santa Cruz, Santa Cruz, CA 95064, September 1990.
  8. with Pak Chan, Wayne Dai, Joel Ferguson, Daniel Helman, and Martine Schlag. VLSI and CAD education at UC Santa Cruz. In 2nd Annual VLSI Education Conference and Exposition, Santa Clara, CA, July 19--21 1989.
  9. Using if-then-else DAGs for multi-level logic minimization. Technical Report UCSC-CRL-88-29, Board of Studies in Computer Engineering, University of California at Santa Cruz, Santa Cruz, CA 95064, December 1988.
  10. Representing Boolean functions with If-Then-Else DAGs. Technical Report UCSC-CRL-88-28, Board of Studies in Computer Engineering, University of California at Santa Cruz, Santa Cruz, CA 95064, December 1988.
  11. with Pak Chan. Computing signal delay in general RC networks by tree/link partitioning. Technical Report UCSC-CRL-88-05, Board of Studies in Computer Engineering, University of California at Santa Cruz, Santa Cruz, CA 95064, September 1988.
  12. with T. V. Verghese. Sizing cMOS gates along a critical path---a tutorial. Technical Report UCSC-CRL-87-30, Board of Studies in Computer Engineering, University of California at Santa Cruz, Santa Cruz, CA 95064, December 1987. Slightly revised May 1989.
  13. Using the ucsc-report LaTeX style file for UCSC technical reports. Technical Report UCSC-CRL-87-10, Board of Studies in Computer Engineering, University of California at Santa Cruz, Santa Cruz, CA 95064, August 1987.
  14. c-util utility package for c. Technical Report UCSC-CRL-87-9, Board of Studies in Computer Engineering, University of California at Santa Cruz, Santa Cruz, CA 95064, July 1987.
  15. A formal model for MOS clocking disciplines. Technical Report TR 84-632, Department of Computer Science, Cornell University, Ithaca, NY 14853, August 1984.
  16. with Gary Haggard. Finding minimal perfect hash functions. Technical Report TR 84-637, Department of Computer Science, Cornell University, Ithaca, NY 14853, August 1984.
  17. 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.
  18. with Danny Dolev, Alan Siegel, Alex Strong, and Jeff Ullman. Optimal algorithms for structural assembly. VLSI Design, 3(2):38--42, March/April 1982.

Recent talks (not complete)

20 July 2007
Better than chance: the importance of null models a keynote of 3DSig (Satellite conference of ISMB/ECCB07), Vienna, Austria.
26 May 2006
Protein structure prediction: not just optimization Insititute of Pure and Applied Mathematics (UCLA)
1 May 2006
Origami with strings: protein folding by computer CASP 6.5 @ Columbia University
25 March 2006
Origami with strings: protein folding by computer UCSD Bioinformatics Symposium
6 March 2006
Origami with strings: protein folding by computer (CHEM 200B, Tony Fink)
22 Aug 2005
Summer bridge program, informal talk with engineering students
12 July 2005
Annual CBSE Summer Workshop on Genome Research, UCSC)
11 June 2005
Introduction to protein-structure prediction (UCSC, for "SUPERB" REU program)
15 Apr 2005
Origami with strings: protein folding by computer (Univ Minnesota)
25 Feb 2005
recruiting talk (Univ Puerto Rico)
23 Feb 2005
Origami with strings: protein folding by computer (Univ Puerto Rico)
22-25 Feb 2005
course on protein structure prediction (Univ Puerto Rico) [two lectures plus 3-hour lab]
6 Dec 2004
SAM-T04: what's new for CASP6? (CASP6, Gaeta, Italy)
21 Oct 2004
Protein structure prediction (BME 280B)
16 Oct 2004
Preview Day, UCSC--staffed the Bioinformatics table.
14 Oct 2004
Tips on technical writing (in CMPS/CMPE/BME 200)
22 Sept 2004
Grad Advising day, welcome and advising speech
21 Sept 2004
Undergrad Advising day, welcome and advising speech
21 Feb 2004
Origami with strings: predicting how proteins fold Odyssey (Johns Hopkins Ceter for Talented Youth) UCSC.
19 Oct 2003
Preview Day, UCSC--staffed the Bioinformatics table.
24 June 2003, ...
Summer orientation
14 Apr 2003
Unifying secondary-structure, fold-recognition, and new-fold methods for protein structure prediction Genome Therapeutics
14 Apr 2003
A protocol for evaluating local structure alphabets MIT
6 Dec 2002
Unifying secondary-structure, fold-recognition, and new-fold methods for protein structure prediction Second Biennial UCSC-QB3 Bioinformatics Symposium
5 Dec 2002
Unifying secondary-structure, fold-recognition, and new-fold methods for protein structure prediction Stanford (Jeff Ullman retirement seminar)
4 Dec 2002
Fragfinder and Undertaker: new-fold methods for protein structure prediction CASP5, Asilomar, Pacific Grove CA
26 Nov 2002
A protocol for evaluating the usefulness of protein local structure alphabets Max-Planck Institute, Saarbruecken, Germany
25 Nov 2002
Estimating statistical significance with the reverse-sequence null models: Why it works and why it fails. Max-Planck Institute, Saarbruecken, Germany
20 Nov 2002
Unifying secondary-structure, fold-recognition, and new-fold methods for protein structure prediction Dagstuhl seminar 02471 Schloss Dagstuhl Germany
1 Oct 2002
"What is bioinformatics?" Information Systems Management Club UCSC
17 July 2002
"Protein Structure Prediction" COSMOS summer program UCSC
20 May 2002
"Protein Structure Prediction (Fold Recognition) using Hidden Markov Models" Reading and Research in Computational Biology Seattle, Washington
23 April 2002
"Using hidden Markov models to recognize protein folds" Journal Club, David Baker's group Seattle, Washington
26 Jan 2002
Fold Recognition using Hidden Markov Models and Secondary Structure DOE workshop.
4 Oct 2001
Getting the most out of hidden Markov models Molecular Modeling Workshop 2001 Canberra, Australia
2 Oct 2001
Using hidden Markov models to recognize protein folds Combio 2001 Canberra, Australia
26 July 2001
"Bioinformatics BS at the University of California, Santa Cruz" Workshop on Education in Bioinformatics 2001 Copenhagen, Denmark
12 July 2001
"Using Hidden Markov Models and Secondary Structure Prediction to Predict Tertiary Structure of Proteins" Centre for Molecular and Biomolecular Informatics University of Nijmegen, Netherlands
6 April 2001
"Using Hidden Markov Models and Secondary Structure Prediction to Predict Tertiary Structure of Proteins" Oregon State, Corvallis
9 March 2001
Estimating Statistical Significance for Reverse-sequence Null Models DIMACS workshop Rutgers
9 Oct 2000
"Protein Structure Prediction and Remote Homology using Hidden Markov Models" University of Michigan, Pfizer (Ann Arbor)
11,12,13,14 Sept 2000
"Predicting the 3D Structure of Proteins from just their Amino-Acid Sequences" mini-course for new Regents' Scholars
7 Sept 2000
"Getting the most out of hidden Markov models" Neomorphic
22 July 2000
Open lab demos for COSMOS program.
6 May 2000
Odyssey 2000 lab demos
3 Feb 2000
"Notes for Science Teachers from a Science Fair Judge" Long Marine Lab for County Office of Education seminar series on science fair.
6 August 1999
ISMB99 4-hour tutorial. ``Getting the most out of hidden {Markov} models'' with Melissa Cline and Christian Barrett.
17 May 1999
Bike Week Santa Cruz Living Without A Car
27 Jan 1999
ACM student chapter SAM-T98: Predicting the structure of proteins using hidden Markov models
Dec 1998 CASP3
Predicting the Secondary Structure of Proteins Using Neural Nets
4 Dec 1998
Invited talk Newton Institute Cambridge, England SAM-T98: Predicting the structure of proteins using hidden Markov models
15 Oct 1998
Invited talk San Jose State University (Math/CS colloquium) SAM-T98: Predicting the structure of proteins using hidden Markov models
Missing 6 years from this list (92-97)---here is an attempt to recreate the missing portion of the list:
May? 1997
Ecole Polytechnique Federale de Laussane one-day class Stochastic Modeling Techniques: Understanding and using hidden Markov models
July 1996
ISMB 96 St. Louis, double-length tutorial Stochastic Modeling Techniques: Understanding and using hidden Markov models
July 1995
ISMB 95 Cambridge, England Regularizers for estimating distributions of amino acids from small samples.

Also given at many other places that summer: Gesellschaft fuer Mathematik und Datenverarbeitung (Bonn) Universitaet Bielefeld (Bielefeld) European Molecular Biology Lab (Heidelberg) CNB (Madrid)

1995
Gesellschaft fuer Mathematik und Datenverarbeitung (Bonn) Simple and hidden Markov models

Also given at Dagstuhl workshop on bioinformatics (near Saarbruecken)

22-26 Feb 1993
Compcon 1993 Xtmap: a Generate-and-Test Mapper for Table-Lookup Gate Arrays
2 June 1992
Euro ASIC '92 (Paris, France) ITEM: If-then-else Minimizer for Logic Synthesis
5 December 1991
Quickturn Systems, Mountain View ITEM: UCSC's multi-level logic minimizer (emphasis on FPGA mapping)
18 Sept 1991
UC Berkeley ITEM: UCSC's multi-level logic minimizer
19 June 1991
Design Automation Conference (San Francisco, CA) Xmap: a technology mapper for table-lookup field-programmable gate arrays
19 June 1991
Design Automation Conference (San Francisco, CA) Amap: a technology mapper for selector-based field-programmable gate arrays
18 April 1991
Actel Corp (Sunnyvale, CA) If-then-else DAGs and technology mapping to Actel cells
21 March 1991
UCSC VLSI Faculty Research Review (Santa Clara, CA) ITEM: UCSC's If-the-else minimizer
31 August 1990
University of Washington (Seattle, WA) Technology mapping for field-programmable gate arrays using if-then-else DAGs
30 March 1990
UCSC VLSI Faculty Research Review (Santa Clara, CA) Multilevel logic minimization using if-then-else DAGs
15 Nov 1989
Dean's Forum at Techmart (Santa Clara, CA) High-speed Error Correction for Reliable Communication
21 July 1989
1989 VLSI Education Conference and Exposition (Santa Clara, CA) VLSI and CAD Education at UC Santa Cruz
27 June 1989
Applied Algebra and Error Correcting Codes, AAECC-7 (Toulouse, France) A Semisystolic Decoder for the PDSC-73 Error-correcting Code
21 March 1989
Advanced Research in VLSI, Caltech Decennial Conference (Pasadena, CA) Multi-level Logic Minimization using If-then-else DAGs
3 Feb 1989
Hewlett-Packard Labs (Palo Alto, CA) Multi-level Logic Minimization using If-then-else DAGs

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Karplus's lab page UCSC Bioinformatics research

Questions about page content should be directed to

Kevin Karplus
Biomolecular Engineering
University of California, Santa Cruz
Santa Cruz, CA 95064
USA
karplus@soe.ucsc.edu
1-831-459-4250
318 Physical Sciences Building