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
- 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 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
- 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
- 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
- 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
- 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
- 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
- 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}
- 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
- 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
-
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
- 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
- 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
- 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
- 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
- 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
- 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
-
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
- 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
- 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
- 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
-
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
-
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
-
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.)
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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)
-
Christian Barrett, Richard Hughey, and Kevin Karplus.
Scoring hidden Markov models. CABIOS, 13(2):191-199, 1997.
preprint
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
- 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.
-
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
-
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
-
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
-
Kevin Karplus. ``Evaluating Regularizers for Estimating Distributions of Amino
Acids from Small Samples'', in ISMB-95 proceedings, Cambridge, England,
July 1995.
pdf
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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.
-
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
-
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.
-
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
-
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
-
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
-
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)
-
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
-
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
-
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
-
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.
-
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
-
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
-
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.
-
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
-
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
-
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.
-
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
-
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
-
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.
-
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.
-
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.
-
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.
- 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
-
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
-
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
-
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.
-
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
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