Publications

Table of Contents

Books |Journal Articles | Refereed Articles in Books | Refereed Articles in Proceedings

Books

  1. Boolean Functions and Models of Computation, by P. Clote and E. Kranakis, 615 pages, Springer-Verlag, 2003, ISBN: 3-540-59436-1 (hardcover).
  2. Computational Molecular Biology: An Introduction, P. Clote and R. Backofen, John Wiley & Sons, Ltd., 286 pages, ISBN 0-471-87251-2 (hardback), ISBN 0-471-87252-0 (paperback) August 2000.

    Japanese translation of Computational Molecular Biology: An Introduction, P. Clote and R. Backofen (2005).

  3. Computer Science Logic, by P. Clote and H. Schwichtenberg (Eds.), 14th International Workshop, CSL 2000, Springer Lecture Notes in Computer Science 1862, ISBN 3-540-67895-6, August 2000.
  4. Arithmetic, Proof Theory and Computational Complexity, Oxford University Press, eds. P. Clote and J. Krajicek (1993).
  5. Feasible Mathematics II, Birkhäuser Inc (1995), eds. P. Clote and J. Remmel.
  6. Research monograph translation, Theory of Relations, by R. Fraissé, North Holland (1986), 397 pages, from French into English.

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Journal Articles

  1. Predicting transmembrane β-barrel and inter-strand residue interactions from sequence, J. Waldispuhl, B. Berger, P. Clote, J.-M. Steyaert, Proteins: Structure, Function and Bioinformatics, to appear.
  2. transFold: a Web Server for Predicting Transmembrane beta-barrels and Inter-strand Residue Interactions from Sequence, J. Waldispühl, B. Berger, P. Clote, J.-M. Steyaert, Nucleic Acids Res., Web Server Issue (2006), in press.
  3. DiANNA 1.1: An extension of the DiANNA web server for ternary cysteine classification, F. Ferre, P. Clote, Nucleic Acids Res., Web Server Issue, in press.
  4. BTW: A web server for Boltzmann time warping of gene expression time series, F. Ferre, P. Clote, Nucleic Acids Res., Web Server Issue, in press.
  5. Symmetric time warping, Boltzmann pair probabilities and functional genomics , P. Clote, J. Straubhaar, Journal of Mathematical Biology, in press.
  6. transFold: A Web Server for Predicting the Structure and Residue Contacts of Transmembrane β-Barrels, J. Waldispühl, B. Berger, P. Clote, J.-M. Steyaert, Nucleic Acids Res., Web Server Issue, in press.
  7. An efficient algorithm to compute the landscape of locally optimal RNA secondary structures with respect to the Nussinov-Jacobson energy model, P. Clote, Journal of Computational Biology 12(1) 2005 83--101.
  8. Solving the Fisher-Wright and coalescence problems with a discrete Markov chain analysis, S.R. Buss and P. Clote, Advances in Applied Probability, 36(3), 1175-1197 (2004).
  9. Structural RNA has lower folding energy than random RNA of the same dinucleotide frequency, P. Clote, F. Ferre, E. Kranakis, D. Krizanc, RNA RNA, 11(5):578-591 (2005).
  10. Asymptotic expected number of base pairs in optimal secondary structure for random RNA using the Nussinov-Jacobson energy model, P. Clote, E. Kranakis, D. Krizanc and L. Stacho, to appear Discrete Applied Mathematics, special issue in Bioinformatics (eds S. Istrail and P. Pevzner).
  11. Disulfide connectivity prediction using secondary structure information and diresidue frequencies", F. Ferre and P. Clote, Bioinformatics 21(10):2336-2346 (2005).
  12. On realizing shapes in the theory of RNA neutral networks, P. Clote, L. Gasieniec, R. Kolpakov, E. Kranakis, D. Krizanc, J. Theoretical Biology 236(2): 216-227.
  13. RNALOSS: A web server for RNA locally optimal secondary structures, P. Clote, Nucleic Acids Res., 33(Web Server issue):W600-604 (2005).
  14. DiANNA: a web server for disulfide connectivity prediction, F. Ferre, P. Clote, Nucleic Acids Research, Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W230-2.
  15. "Reverse mathematics of some topics from algorithmic graph theory", with J. Hirst, Fundamenta Mathematica 157(1), 1-13 (1998).
  16. "Nondeterministic stack register machines", Theoretical Computer Science 178 (June 1997) 37-76.
  17. "Note on monotonic complexity of 2-REF" , Information Processing Letters 57, 117-123 (1996).
  18. "Cutting planes, connectivity and threshold logic", joint with S. Buss, Archive for Mathematical Logic 35, 33-62 (1995).
  19. "Cutting plane and Frege proofs", Information and Computation, 121(1) 103-122 (1995).
  20. "ALOGTIME and a conjecture of S.A. Cook", in proceedings of IEEE Logic in Computer Science (LICS), Philadelphia PA, June 1990, journal version in Annals of Mathematics and Artificial Intelligence 6 (1992) 57-106.
  21. "Bounded arithmetic for NC, ALOGTIME, L and NL", joint with G. Takeuti, Annals of Pure and Applied Logic 56 73-117 (1992).
  22. "A time-space hierarchy between P and PSPACE", Mathematical Systems Theory 25 77-92 (1992).
  23. "On some formalized consistency statements in arithmetic", joint with P. Hájek and J. Paris, Archive for Mathematical Logic 30(4) 201-221 (1991).
  24. "Boolean functions, invariance groups, and parallel complexity", joint with E. Kranakis, SIAM J. Comput. 20 (3) 553-590 (1991), extended abstract appeared in the Proceedings of Structure in Complexity Theory, Fourth Annual IEEE sponsored conference (1989), 55-65.
  25. "The metamathematics of scattered linear orderings", Archive for Mathematical Logic 29 9-20 (1989).
  26. "A note on the MacDowell-Specker Theorem", Fundamenta Mathematicae 127 (1986), 163-170.
  27. "Members of PI01 classes", with D. Cenzer, R. Smith, R. Soare, S. Wainer, Annals of Pure and Applied Logic 31 (1986), 145-161.
  28. "On the finite containment problem for Petri nets", Theoretical Computer Science 43 (1986), 99-105.
  29. "A generalization of the limit lemma and clopen games", Journal of Symbolic Logic 51 (1986), 273-291.
  30. "Sharp bounds on ordinal comparison maps", Archiv für Mathematische Logik und Grundlagenforschung 25 (1985), 99-107.
  31. "On recursive trees with a unique infinite branch", Proceedings of the American Mathematical Society 93 (1985), 335-342.
  32. "A recursion theoretic analysis of the clopen Ramsey theorem", Journal of Symbolic Logic 49 (1984), 376-400.
  33. "Two further combinatorial theorems equivalent to the 1-consistency of Peano arithmetic", with K. McAloon, Journal of Symbolic Logic 48 (1983), 1090-1104.

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    Refereed Articles in Books

  34. Applications of RNA minimum free energy computations, in Wiley Encyclopedia of Bioinformatics, ed. S. Subramaniam (2005).
  35. "Computation models and function algebras" , Handbook of Computability Theory, ed. E.R. Griffor, Elsevier Science B.V. (1999). pp. 589-681.
  36. "On PHP, st-connectivity and odd charged graphs", with A. Setzer, Proof Complexity and Feasible Arithmetics, 93-118, DIMACS Series in Discrete Mathematics and Theoretical Computer Science, Vol 39, eds. Paul W. Beame and Samuel R. Buss, 1998.
  37. "Computation models and function algebras (extended abstract}", in Logic and Computational Complexity, Springer Lecture Notes in Computer Science 960, ed. D. Leivant, 98--130 (1995).
  38. "First order bounded arithmetic and small boolean circuit complexity classes", joint with G. Takeuti, in Feasible Mathematics II, eds. P. Clote and J. Remmel, Birkhäuser Inc. (1995).
  39. "Polynomial size Frege proofs of certain combinatorial principles", Arithmetic, Proof Theory and Computational Complexity, Oxford University Press, eds. P. Clote and J. Krajicek (1993).
  40. "Sequential, machine independent characterizations of the parallel complexity classes ALOGTIME, ACk, NCk and NC, in Feasible Mathematics, eds. S. Buss and P. Scott, Birkhäuser, 49-70 (1990).
  41. "Théorème de Cantor-Bendixson", Séminaire Général de Logique, Publications Mathématiques de l'Université Paris VII 27 (1983-84), 73-88, ISSN 0073-8301.

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    Publications in Computer Science Professional Publications

  42. "Aktuelles Schlagwort Bioinformatik", Rolf Backofen, Francois Bry, Peter Clote, Hans-Peter Kriegel, Thomas Seidl and Klaus Schulz, Informatik Spektrum, Okt. 1999 (in German).


    Refereed Articles in Proceedings

  43. "Performance comparison of generalized PSSM in signal peptide cleavage site and disulfide bond recognition", BIBE'03 (2003).
  44. "Algorithmic approach to quantifying the hydrophobic force contribution in protein folding" (journal version), with R. Backofen and S. Will, PSB'00 (Pacific Symposium on Biocomputing), ed. Russ Altman, Honolulu, Jan 2000.
  45. "Algorithmic approach to quantifying the hydrophobic force contribution in protein folding", with R. Backofen and S. Will, GCB'99 (German Conference on Bioinformatics), Oct 4-6, 1999, Hannover Germany.
  46. "Protein folding, the Levinthal paradox and rapidly mixing Markov chains", Automata, Languages and Programming, 26th International Colloquium, ICALP'99, Prague (July 1999), Springer Lecture Notes in Computer Science 1644, 240-249 .
  47. "How optimal is the genetic code?", with S. Schönauer, Computer Science and Biology, Proceedings of the German Conference on Bioinformatics (GCB'97), pp. 65-67, eds. D. Frishman and H.W. Mewes, Sep 21-24, 1997.
  48. "Evolution as a computational engine", with R. Backofen, Computer Science Logic, Aug 25-29, 1997, Springer Lecture Notes in Computer Science 14114, pp. 35--55, Denmark (1997).
  49. "A safe recursion scheme for exponential time", Logical Foundations of Computer Science (LFCS'97), Fourth International Symposium, Yaroslavl (Russia), 4-15 July 1997, Springer Lecture Notes in Computer Science 1234, pp. 44-52 eds. S. Adian and A. Nerode (1997).
  50. "A note on the relation between polynomial time functionals and Constable's class K" , Computer Science Logic, Springer Lecture Notes in Computer Science 1092, ed. Hans Kleine-Büning, 145-160 (1996).
  51. "Parallel computable higher type functionals", joint with B. Kapron and A. Ignjatovic, Thirty-Fourth IEEE Symposium on Foundations of Computer Science, Nov 3-5, 1993.
  52. "The metamathematics of Fraissé's order type conjecture", Proceedings of Recursion Theory Week, ed. K. Ambos-Spies, G. Müller, and G.E. Sacks, Springer Lecture Notes in Mathematics 1432, pp. 41-56, (1991).
  53. "A smash-based hierarchy between P and PSPACE", Logic and Computation, Contemporary Mathematics 106, American Mathematical Society, 85-100 (1990), ed. W. Sieg.
  54. "Exponential time and bounded arithmetic", with G. Takeuti, Springer Lecture Notes in Computer Science 223, Structure in Complexity Theory, (1986), 125-143.
  55. "Ultrafilters on definable sets in arithmetic", Logic Colloquium '84, (1986), ed. J.B. Paris, A.J. Wilkie, and G.M.Wilmers, 37-58.
  56. "Partition relations in arithmetic", Springer Lecture Notes in Mathematics 1130, Methods in Mathematical Logic, (1985), ed. C. A. DiPrisco, 32-68.
  57. "Applications of the low basis theorem in arithmetic", Springer Lecture Notes in Mathematics 1141,Recursion Theory Week, Proceedings Oberwolfach 1984, ed. H.D. Ebbinghaus, G.H. Müller, G. E. Sacks (1985), 65-88.
  58. "A note on the leftmost infinite branch of a recursive tree", in Open Days in Model Theory and Set Theory, ed. W. Guzicki, Z. Marek, A. Pelc, C. Rauszer, (1984), 93-102, published by University of Leeds (England).
  59. "A note on decidable model theory", Model Theory and Arithmetic, Springer Lecture Notes in Mathematics 890 (1981), 134-142.
  60. "Anti-basis theorems and their relation to independence results in Peano arithmetic", Model Theory and Arithmetic, Springer Lecture Notes in Mathematics 890 (1981), 115-133.
  61. "Weak partition relations, finite games and independence results in Peano arithmetic", Model Theory of Algebra and Arithmetic, Springer Lecture Notes in Mathematics 834, (1980), 92-107.

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    Unpublished tech reports

  62. "Vax Pascal and Hypercard implementation of an assembler for a parallel random access machine", joint with A. Lai, Technical Report BCCS-91-9, 22 October 1991, 61 pages. Unpublished technical report for simulation programs for parallel SIMD-type machines.
  63. "Translator from a fragment of parallel Pascal into sequential Pascal", joint with J. Peng, Technical Report BCCS-91-19, 26 November 1991, 132 pages. Unpublished technical report for translation program (using yacc, lex) to translate programs written in a version of parallel Pascal into sequential programs, suitable for illustrating parallel algorithms in an environment without access to a SIMD-type machine.


Reviews

Book review of Subrecursion: Functions and Hierarchies for Advances in Mathematics 58 (1985), 205-207.
Review of "Countable algebra and set existence axioms" for Journal of Symbolic Logic 52 (1), (1987), 286-288 and of "Fragments of arithmetic" for Journal of Symbolic Logic.
Book review of Modèles nonstandard en arithmétique et en théorie des ensembles (J.-P. Ressayre and A.J. Wilkie) for Journal of Symbolic Logic.
Book review of Bounded arithmetic, propositional logic and complexity theory . Krajicek) for Journal of Symbolic Logic (1999).
Book reviewer for Springer-Verlag and Zentralblatt für Mathematik.

Regular reviewer for Zentralblatt für Mathematik and Mathematical Reviews.


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clote@cs.bc.edu, Nov-12-1999