Kevin Karplus Publications

(Last Update: 10:28 PDT 13 April 2017 )


This page has pointers to essentially all 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 some of the papers that were not findable on the web have not been scanned yet.

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. Kevin Karplus and 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. Jenny L. Draper, Lori M. Hansen, David L. Bernick, Samar Abedrabbo, Jason G. Underwood, Nguyet Kong, Bihua C. Huang, Allison M. Weis, Bart C. Weimer, Arnoud H. M. van Vliet, Nader Pourmand, Jay V. Solnick, Kevin Karplus, Karen M. Ottemann
    Fallacy of the Unique Genome: Sequence Diversity within Single Helicobacter pylori Strains
    mBio 8(1):e02321-16, 21 February 2017.
    doi: 10.1128/mBio.02321-16
  2. Jacob Schrieber and Kevin Karplus
    Analysis of Nanopore Data using Hidden Markov Models
    Bioinformatics, 31(12):1897&ndash:1903, 2015. preprint URL: http://bioinformatics.oxfordjournals.org/content/31/12/1897 doi: 10.1093/bioinformatics/btv046
  3. Jacob Schreiber, Zachary L. Wescoe, Robin Abu-Shumays, John T. Vivian, Baldandorj Baatar, Kevin Karplus, and Mark Akeson
    Error Rates for Nanopore Discrimination Among Cytosine, Methylcytosine, and Hydroxymethylcytosine Along Individual DNA Strands
    Proceedings of the National Academy of Sciences of the United States of America , 2013 Oct 28.
    url: http://www.pnas.org/content/early/2013/10/23/1310615110.abstract doi: 10.1073/pnas.1310615110
  4. Gerald M Cherf, Kate R Lieberman, Hytham Rashid, Christopher E Lam, Kevin Karplus, Mark Akeson
    Automated forward and reverse ratcheting of DNA in a nanopore at 5-Å precision
    Nature biotechnology 30(4):344–348, 2012 Feb. 14.
    URL:http://www.nature.com/nbt/journal/v30/n4/full/nbt.2147.html doi:10.1038/nbt.2147
  5. David Bernick, Kevin Karplus, Lauren Lui, Joanna Coker, Julie Murphy, Patricia Chan, Aaron Cozen, and Todd Lowe.
    Complete genome sequence of Pyrobaculum oguniense,
    Standards in Genomic Science 6(3):336–345, 2012.
    URL:http://standardsingenomics.org/index.php/sigen/article/view/sigs.2645906
    doi:10.4056/sigs.2645906
  6. Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H, Remmert M, Söding J, Thompson J, Higgins D.
    Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega.
    Molecular Systems Biology, 7(539), 11 October 2011
    doi:10.1038/msb.2011.75}
  7. Jenny Draper, Kevin Karplus, and Karen M. Ottemann. CZ: A Zinc-binding domain common to cytoplasmic bacterial chemoreceptors. Journal of Bacteriology (193)17:4338-4345, September 2011. doi:10.1128/JB.05140-11
  8. Josue Samayoa, Fitnat Yildiz, and Kevin Karplus
    Identification of Prokaryotic Small Proteins using a Comparative Genomic Approach.
    Bioinformatics, 27 (13): 1765-1771, 2011.
    doi:10.1093/bioinformatics/btr275
  9. Martin Madera, Ryan Calmus, Grant Thiltgen, Kevin Karplus, and Julian Gough.
    Improving protein secondary structure prediction using a simple k-mer model.
    Bioinformatics, 26(5):596–602, March 2010.
    doi:10.1093/bioinformatics/btq020
  10. Elmar Krieger and Keehyoung Joo and Jinwoo Lee and Jooyoung Lee and Srivatsan Raman and James Thompson and Mike Tyka and David Baker and Kevin Karplus.
    Improving physical realism, stereochemistry and side-chain accuracy in homology modeling: four approaches that performed well in CASP8.
    Proteins: Structure, Function, and Bioinformatics, 77(S9):114–122, 12 August 2009. CASP8 special issue. doi:10.1002/prot.22570
  11. John G. Archie, Martin Paluszewski, and Kevin Karplus. Applying Undertaker to Quality Assessment. Proteins: Structure, Function, and Bioinformatics, 77(S9):191–195, 12 August 2009. CASP8 special issue. doi:10.1002/prot.22508
  12. Kevin Karplus. SAM-T08: HMM-based Protein Structure Prediction. Nucleic Acids Research 37(Suppl.2):W492-E497, 2009, Web Server Issue. doi:10.1093/nar/gkp403
  13. Firas Khatib, Carol A. Rohl, and Kevin Karplus. Pokefind: a novel topological filter for use with protein structure prediction. Bioinformatics 2009 25(12):i281-i288;
    doi:10.1093/bioinformatics/btp198
  14. John Archie and Kevin Karplus. Applying Undertaker Cost Functions to Model Quality Assessment. Proteins: Structure, Function, and Bioinformatics75(3):550-555, 2009.
    doi:10.1002/prot.22288
    preprint supplementary material
  15. Martin Paluszewski and Kevin Karplus. Model Quality Assessment using Distance Constraints from Alignments. Proteins: Structure, Function, and Bioinformatics 75(3):540-549, 2009.
    doi:10.1002/prot.22262
    preprint
  16. Sol Katzman, Christian Barrett, Grant Thiltgen, Rachel Karchin, and Kevin Karplus. Predict-2nd: a tool for generalized protein local structure prediction. Bioinformatics 2008 24: 2453-2459
    Free Reprint:http://bioinformatics.oxfordjournals.org/cgi/reprint/btn438?
    doi:10.1093/bioinformatics/btn438 Supplementary material
  17. George Shackelford and Kevin Karplus. Contact Prediction using Mutual Information and Neural Nets. Proteins: Structure, Function, and Bioinformatics, 69(S8):159-164, 2007. (CASP7 special issue).
    doi:10.1002/prot.21791 Preprint
  18. 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 reprint
  19. 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 reprint
  20. Kevin Karplus, Sol Katzman, George Shackelford, 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:10.1002/prot.20730 reprint Draft copy
  21. Kevin Karplus, Rachel Karchin, George Shackelford, 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
  22. 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 reprint (Note: I believe that Angela's last name is wrong in the IEEE version of the paper—it should be Schmid, not Schultz.)
  23. 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. doi:10.1093/bioinformatics/bth223 abstract and pointer to free pdf reprint
  24. 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 reprint
  25. 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 preprint
  26. 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 reprint
  27. Richard Hughey and Kevin Karplus. Bioinformatics: A new field in engineering education. Journal of Engineering Education 92(1):101–104, 2003. scanned copy of conference version—text should be identical
  28. 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. doe:10.1002/prot.10198 abstract and pointer to pdf reprint
  29. Melissa Cline, Richard Hughey, and Kevin Karplus. Predicting reliable regions in protein sequence alignments. Bioinformatics, 18:306–324, 2002. abstract and pointer to free pdf reprint
  30. 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 free pdf reprint
  31. 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. doi:10.1006/jmbi.2001.5080 reprint
  32. 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 preprint
  33. 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
  34. 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. doi:10.1016/S0921-8777(00)00073-2 reprint
  35. 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 free pdf reprint
  36. 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 preprint
  37. 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.
    doi:10.1002/(SICI)1097-0134(1999)37:3+<209::AID-PROT27>3.0.CO;2-Y
    abstract and pointer to pdf reprint
  38. 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 free pdf reprint
  39. 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. doi:10.1006/jmbi.2001.5080 reprint
  40. 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. official site reprint
  41. 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 longer tech-report version of paper (UCSC-CRL-97-13)
  42. Christian Barrett, Richard Hughey, and Kevin Karplus. Scoring hidden Markov models. CABIOS, 13(2):191-199, 1997. preprint
  43. 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
  44. 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. scanned copy
  45. Kevin Karplus and Habib Krit. A semi-systolic decoder for the PDSC-73 error-correcting code. Discrete Applied Math, 33(1–2), August 1991. scanned copy
  46. 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. scanned copy
  47. Susan Hertz, Jim Kadin, and Kevin Karplus. The Delta rule development system for speech synthesis from text. Proceedings of the IEEE, 73(11):1589–1601, November 1985. scanned copy
  48. 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. scanned copy
  49. 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. scanned copy
  50. 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. scanned copy

Refereed Conference Articles

  1. Rasmus Fonseca, Pawel Winter, and Kevin Karplus. Protein Packing Quality Using Delaunay Complexes. In Eighth International Symposium on Voronoi Diagrams in Science and Engineering, Qingdao, China, June 28th - 30th, 2011. pdf Presented by Rasmus Fonseca.
  2. 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) scanned copy
  3. 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. scanned copy
  4. 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. scanned copy
  5. Kevin Karplus. ``Evaluating Regularizers for Estimating Distributions of Amino Acids from Small Samples'', in ISMB-95 proceedings, Cambridge, England, July 1995. pdf
  6. Kevin Karplus. Xtmap: a generate-and-test mapper for table-lookup gate arrays. In Compcon 1993, pages 391–399, 22–26 Feb 1993. IEEE site scanned copy preprint
  7. Kevin Karplus. ITEM: an if-then-else minimizer for logic synthesis. In EuroASIC92, pages 2–7, Paris, 1–5 June 1992. Invited talk. scanned copy preprint (backwards) revised tables for EuroASIC paper
  8. Kevin Karplus. 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. doi:10.1145/127601.127672 scanned copy
  9. Kevin Karplus. 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. doi:A href="http://dx.doi.org/10.1145/127601.127673">10.1145/127601.127673 scanned copy
  10. Søren Søe and Kevin Karplus. 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. doi:10.1145/127601.127714 scanned copy
  11. 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. scanned copy of journal version
  12. Pak K. Chan and Kevin Karplus. 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. doi:10.1145/74382.74463 (doi is only for citation information—ACM has not scanned the article) IEEE record for article scanned copy
  13. 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. scanned copy
  14. 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. scanned copy
  15. 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. copy not available.
  16. Gary Haggard and Kevin Karplus. Finding minimal perfect hash functions. In 1986 ACM Fourteenth Annual Computer Science Conference, Cincinnati, OH, 4–6 February 1986. doi:10.1145/5600.5899 scanned copy
  17. Kevin Karplus and 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. doi:10.1145/18927.18908 scanned copy doi:10.1145/18906.18908 Also published in ACM SIGMicro Newsletter 16(4):11-18, 1985.
  18. 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. scanned preprint
  19. 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. scanned copy
  20. Alexandru Nicolau and Kevin Karplus. ROPE: a statically scheduled supercomputer architecture. In First International Conference on Supercomputing Systems, St. Petersburg, FL, December 1985. scanned preprint
  21. Susan Hertz, Jim Kadin, and Kevin Karplus. The Delta system for synthesis rules. In 107th Meeting of the Acoustical Society of America, Norfolk, Virginia, 6–10 May 1984. doi:10.1121/1.2021520 (text never published)
  22. Danny Dolev, Kevin Karplus, 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. doi:10.1145/800076.802484 scanned copy

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 pdf
  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. copy not available.
  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, pdf
  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. pdf
  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. copy not available.
  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. pdf
  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. scanned copy Original, without pictures, backwards
  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. copy not available.
  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. scanned copy Original, without pictures, backwards
  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. scanned copy Original, without pictures, backwards
  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. copy not available.
  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. copy not available.
  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. copy not available.
  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. copy not available.
  15. Kevin Karplus and Alexandru Nicolau. ROPE: A New Twist in Computer Architecture. Technical Report 87-885. Department of Computer Science, Cornell University, Ithaca, NY 14853, November 1987. scanned copy
  16. A formal model for MOS clocking disciplines. Technical Report TR 84-632, Department of Computer Science, Cornell University, Ithaca, NY 14853, August 1984. scanned copy
  17. 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. scanned copy
  18. 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. copy not available.
  19. 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. scanned copy (Note: this article is a reprint of the refereed paper in ACM/STOC 1981, Optimal wiring between rectangles.)

Recent talks (not complete)

6 Nov 2014
Segmentation and HMMs for nanopore data BME 280B Seminar series.
14 Nov 2013
Segmenting Nanopore Traces BME 280B Seminar series.
15 Sept 2011
Bioinformatics Methods 16th International Conference on Image Anlysis and Processing (ICIAP 2011). Invited Talk.
13 Sept 2011
Better than Chance: the importance of null modelsFirst International Workshop on Pattern Recognition in Proteomics, Structural Biology and Bioinformatics (PR PS BB 2011). Invited Talk.
1 Aug 2011
Bioinformatics Methods for COSMOS.
20 Nov 2009
Tech Writing Quick Review
9 Nov 2009
Better than Chance: the importance of null models in BME 205.
1 Oct 2009
What the Karplus lab does Presentation about the research in my lab for departmental research seminar (BME 280B)
22 July 2009
Tutorial on protein structure prediction (2 hours for COSMOS)
28 May 2009
Origami with strings: protein folding by computer (Guest lecture in BME 110 for Todd Lowe)
8 May 2009
Better than chance: the importance of null models in bioinformatics University College Dublin (Dublin, Ireland)
Dec 2008
three short talks at CASP8: Two using Tweaking structures: working on the fiddly bits One based on poster Is there any point to human prediction?
28 Oct 2008
Model Quality Assessment: Guessing how good protein structure predictions are Department seminar.
7 July 2008, 11 July 2008, 14 July 2008, 6 August 2008
What the Karplus lab does presentation of research for NSF-REU students, COSMOS students, MBRS/MARC/CAMP students, and incoming freshmen.
2 Oct 2007
Origami with strings: protein folding by computer Department seminar.
21 Sept 2007
Better than chance: the importance of null models in bioinformatics Invited talk, Ensenda, Mexico
20 July 2007
Better than chance: the importance of null models a keynote of 3DSig (Satellite conference of ISMB/ECCB07), Vienna, Austria.
25 Jan 2007
Origami with strings: protein folding by computer UC Merced
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 slides poster 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


baskin-icon
SoE home
sketch of Kevin Karplus by Abe
Kevin Karplus's home page
BME-slug-icon
Biomolecular Engineering Department
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

Locations of visitors to pages with this footer (started 3 Nov 2008)