2020

  1. Clote P. Are RNA networks scale-free? J Math Biol. 2020 Apr;80(5):1291-1321. doi: 10.1007/s00285-019-01463-z. Epub 2020 Jan 16. A preprint is available on arXiv: here.
  2. Bayegan AH, Clote P. RNAmountAlign: Efficient software for local, global, semiglobal pairwise and multiple RNA sequence/structure alignment. PLoS One. 2020 Jan 24;15(1):e0227177. doi: 10.1371/journal.pone.0227177. arXiv preprint .

2019

  1. Surujon D., Ponty Y. and Clote P. Small-world networks and RNA secondary structures. . J Comput Biol. 2019 Jan;26(1):16-26. doi: 10.1089/cmb.2018.0125.

2018

  1. Clote P, Bayegan AH. RNA folding kinetics using Monte Carlo and Gillespie algorithms. J Math Biol. 2018 Apr;76(5):1195-1227. doi: 10.1007/s00285-017-1169-7. arXiv article ID 1707.03922.

2017

  1. Bayegan AH and Clote P. "An IP algorithm for RNA folding trajectories", Workshop on Algorithms in Bioinformatics (WABI 2017), August 21-23, 2017, Boston, MA. WABI2017 is part of the eighth ACM-BCB 2017 (ACM Conference on Bioinformatics, Computational Biology and Health Informatics). WABI 2017 volume is here: http://drops.dagstuhl.de/portals/extern/index.php?semnr=16042

2016

  1. Bayegan AH, Garcia-Martin JA, and Clote P. New tools to analyze overlapping coding regions. Bayegan AH, Garcia-Martin JA, Clote P. BMC Bioinformatics. 2016 Dec 13;17(1):530.
  2. Garcia-Martin JA, Bayegan AH, Dotu I, and Clote P. RNAdualPF: software to compute the dual partition function with sample applications in molecular evolution theory, with supplementary information. BMC Bioinformatics. 2016 Oct 19;17(1):424.
  3. Garcia-Martin JA, Dotu I, Fernandez-Chamorro J, Lozano G, Ramajo J, Martinez-Salas E, Clote P. RNAiFold2T: Constraint Programming design of thermo-IRES switches. Bioinformatics. 2016 Jun 15;32(12):i360-i368. doi: 10.1093/bioinformatics/btw265.
  4. Javier Fernandez-Chamorro, Gloria Lozano, Juan Antonio Garcia-Martin, Jorge Ramajo, Ivan Dotu, Peter Clote, and Encarna Martinez-Salas. Designing synthetic RNAs to determine the relevance of structural motifs in picornavirus IRES elements. Nature Scientific Reports, 6:24243, DOI: 10.1038/srep24243, 07 April 2016, Link to paper is here.

2015

  1. Garcia-Martin JA, Clote P. RNA Thermodynamic Structural Entropy. PLoS One. 2015 Nov 10;10(11):e0137859. doi: 10.1371/journal.pone.0137859.
  2. Clote P, Bayegan A. Network Properties of the Ensemble of RNA Structures. PLoS One. 2015 Oct 21;10(10):e0139476. doi: 10.1371/journal.pone.0139476.
  3. P. Clote. Abstract: Network properties of the ensemble of RNA structures. 15th International Workshop, WABI 2015, Atlanta, GA, USA, September 10-12, 2015. Eds. Mihai Pop, Hélène Touzet, Eds. Lecture Notes in Bioinformatics, Springer Verlag, pp 3-5, ISBN 978-3-662-48220-9 (2015).
  4. Garcia-Martin JA, Dotu I, Clote P. 1. RNAiFold 2.0 A web server and software to design custom and Rfam-based RNA molecules. Nucleic Acids Research Web Server issue, 2015, doi: 10.1093/nar/gkv460, abstract, full text, pdf.
  5. Clote P. Computational prediction of riboswitches, in the special issue, Computational Methods for Understanding Riboswitches, Methods in Enzymology., Vol 553, Academic Press, 2015, pp. 287-312. ISSN 0076-6879, http://dx.doi.org/10.1016/S0076-6879(14)00064-0.
  6. Senter E, Clote P. Fast, approximate kinetics of RNA folding. J Comp Biol, Vol. 22, No. 2, February 2015: 124-144.
  7. Senter E, Dotu I, Clote P. RNA folding pathways and kinetics using 2D energy landscapes. Senter E, Dotu I, Clote P. J Math Biol. 2015 Jan;70(1-2):173-96. doi: 10.1007/s00285-014-0760-4. Epub 2014 Feb 12.

2014

  1. Dotu I, Garcia-Martin JA, Slinger BL, Mechery V, Meyer MM, Clote P. Complete RNA inverse folding: computational design of functional hammerhead ribozymes. Nucleic Acids Res. 2015 Feb 1;42(18):11752-62. doi: 10.1093/nar/gku740. Epub 2014 Sep 10. Supplementary Information is here and a Web Supplement is available here.. NAR links: abstract, full text, pdf.
  2. Clote P. Expected degree of RNA secondary structure networks. J Comput Chem. 2015 Jan 15;36(2):103-17. doi: 10.1002/jcc.23776. Epub 2014 Nov 7.
  3. Ding Y, Lorenz WA, Dotu I, Senter E, Clote P. Computing the probability of RNA hairpin and multiloop formation. J Comput Biol. 2014 Mar;21(3):201-18. doi: 10.1089/cmb.2013.0148. Epub 2014 Feb 2
  4. Dotu I, Mechery V, Clote P. Energy parameters and novel algorithms for an extended nearest neighbor energy model of RNA. PLoS One. 2014 Feb 21;9(2):e85412. doi: 10.1371/journal.pone.0085412. eCollection 2014.

2013

  1. Dotu I, Lozano G, Clote P, Martinez-Salas E. Using RNA inverse folding to identify IRES-like structural subdomains. RNA Biol. 2013 Dec 1;10(12):1842-52. doi: 10.4161/rna.26994. Epub 2013 Nov 4.
  2. Clote P, Kranakis E, Krizanc D. Asymptotic structural properties of quasi-random saturated structures of RNA. Algorithms Mol Biol. 2013 Oct 25;8(1):24. doi: 10.1186/1748-7188-8-24. Preprint available here.
  3. Clote P, Kranakis E, Krizanc D. Asymptotic number of hairpins of saturated RNA secondary structures. Bull Math Biol. 2013 Dec;75(12):2410-30. doi: 10.1007/s11538-013-9899-1. Epub 2013 Oct 19. Web supplement found here.
  4. Juan Antonio Garcia-Martin, Peter Clote, Ivan Dotu. RNAiFold: A web server for RNA inverse folding and molecular design. Nucleic Acids Research Web Server Issue, 2013, doi: 10.1093/nar/gkt280. Abstract, Full Text, PDF.
  5. E. Senter, S. Sheik, I. Dotu, Y. Ponty, P. Clote. Abstract: Using the Fast Fourier Transform to Accelerate the Computational Search for RNA Conformational Switches. M. Deng et al. (Eds.): RECOMB 2013, LNBI 7821, pp. 264–265, 2013. Springer-Verlag Berlin Heidelberg 2013. Presented at RECOMB 2013, 17th Annual International Conference on Research in Computational Molecular Biology, Beijing, China, April 7-10, 2013.
  6. RNAiFold: A constraint programming algorithm for RNA inverse folding and molecular design. Juan Antonio Garcia-Martin, Peter Clote, Ivan Dotu. J Bioinform Comput Biol 11(2): 1350001, 2013.

2012

  1. Using the Fast Fourier Transform to accelerate the computational search for RNA conformational switches. E. Senter, S. Sheik, I. Dotu, Y. Ponty, P. Clote. Senter E, Sheikh S, Dotu I, Ponty Y, Clote P. PLoS One. 2012;7(12):e50506. doi: 10.1371/journal.pone.0050506. Epub 2012 Dec 19.
  2. E. Fusy and P. Clote. Combinatorics of locally optimal RNA secondary structures. J Math Biol. 2012 Dec 22. [Epub ahead of print]
  3. K. Zarringhalam, M.M. Meyer, I. Dotu, J.H. Chuang, P.Clote. Integrating chemical footprinting data into RNA secondary structure prediction. PLoS One. 2012;7(10):e45160. doi: 10.1371/journal.pone.0045160. Epub 2012 Oct 16.
  4. Clote P, Lou F, Lorenz WA. Maximum expected accuracy structural neighbors of an RNA secondary structure. BMC Bioinformatics. 2012 Apr 12;13 Suppl 5:S6. doi: 10.1186/1471-2105-13-S5-S6.
  5. Clote P, Dobrev S, Dotu I, Kranakis E, Krizanc D, Urrutia J. On the page number of RNA secondary structures with pseudoknots. J Math Biol. 2012 Dec;65(6-7):1337-57. The final publication is available at www.springerlink.com.
  6. P. Clote, Y. Ponty, J.-M. Steyaert. Expected distance between terminal nucleotides of RNA secondary structures. J Math Biol. 2012 Sep;65(3):581-99. The final publication is available at www.springerlink.com.

2011

  1. Feng Lou, Alain Denise and Peter Clote. A new approach to suboptimal pairwise sequence alignment. IASTED conference CompBio 2011, July 11-13, 2011, Cambridge, UK. BibTeX.
  2. P. Bochet, F. Rüheimer, T. Guina, P. Brooks, D. Goodlett, P. Clote, B. Schwikowski. Fragmentation-free LC-MS can identify hundreds of proteins. Proteomics, 2011 Jan;11(1):22-32. Links: preprint, abstract.
  3. Feng Lou and Peter Clote. Maximum expected accurate structural neighbors of an RNA secondary structure. Proceedings of 1st IEEE International Conference on Computational Advances in Bio and medical Sciences (ICCABS), Feb 3-5, 2011, 123-128, Orlando, FL, ISBN 978-1-61284-851-8, doi 10.1109/ICCABS.2011.5729865. BibTeX.
  4. W.A. Lorenz, P. Clote. Computing the partition function for kinetically trapped RNA secondary structures. Public Library of Science One (PLoS ONE), (2011) PLoS ONE 6(1): e16178. doi:10.1371/journal.pone.0016178. Preprint.
  5. Ivan Dotú, Manuel Cebrián, Pascal Van Hentenryck and Peter Clote. On Lattice Protein Structure Prediction Revisited. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 24 Feb. 2011. IEEE computer Society Digital Library. IEEE Computer Society, http://doi.ieeecomputersociety.org/10.1109/TCBB.2011.41

2010

  1. Feng Lou, Peter Clote. Thermodynamics of RNA structures by Wang-Landau sampling. Bioinformatics 2010 Jun 15;26(12):i278-86.
  2. I. Dotú, W.A. Lorenz, P. Van Hentenryck, P. Clote. RNA Structural Segmentation. Pac Symp Biocomput. 2010:57-68. BibTeX, PDF
  3. I. Dotú, W.A. Lorenz, P. Van Hentenryck, P. Clote. Computing folding pathways between RNA secondary structures. Nucleic Acids Res. 2010 Mar 1;38(5):1711-22. PDF

2009

  1. Peter Clote, Evangelos Kranakis, Danny Krizanc, Bruno Salvy. Asymptotics of Canonical and Saturated RNA Secondary Structures. Clote P, Kranakis E, Krizanc D, Salvy B. J Bioinform Comput Biol. 2009 Oct;7(5):869-93. Web supplement is here. BibTeX.
  2. Jerome Waldispühl, Srinivas Devadas, Bonnie Berger, Peter Clote. RNAmutants: A web server to explore the mutational landscape of RNA secondary structures Nucleic Acids Res. 2009 Jul 1;37(Web Server issue):W281-6. Epub 2009 Jun 16. BibTeX.
  3. Peter Clote; Evangelos Kranakis; Danny Krizanc. Asymptotics of Canonical RNA Secondary Structures. 9th IEEE Conference on Bioinformatics and Bioengineering (BIBE 2009). June 22-24, 2009 Taichung, Taiwan, BibTeX.

2008

  1. Jerome Waldispühl, Srinivas Devadas, Bonnie Berger, Peter Clote. Efficient algorithms for probing the RNA mutation landscape. PLoS Comput Biol. 2008 Aug 8;4(8):e1000124. full text, PDF, BibTeX.
  2. Ivan Dotú, Manuel Cebrián, Pascal Van Hentenryck and Peter Clote. Protein Structure Prediction With Large Neighborhood Constraint Programming Search. pp 82-96, Principles and Practice of Constraint Programming, 14th International Conference, CP 2008, Sydney, Australia, September 14-18, 2008, Proceedings Series: Lecture Notes in Computer Science Subseries: Programming and Software Engineering , Vol. 5202 Stuckey, Peter J. (Ed.) 2008, XVII, 648 p., Softcover ISBN: 978-3-540-85957-4 BibTeX
  3. Y. Ponty, R. Istrate, E. Porcelli, P. Clote. LocalMove: Computing on-lattice fits for biopolymers. Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W216-22. abstract, full text, pdf, BibTeX entry
  4. I. Dotú, M. Cebrián, P. Van Hentenryck, P. Clote. A Local Search Approach to Protein Structure Prediciton on the Face Centered Cubic Lattice. Twenty-Third Association for the Advancement of Artificial Intelligence Conference on Artificial Intelligence (AAAI-08), July 13-17, 2008, pp 241-246. BibTeX
  5. W.A. Lorenz, Y. Ponty and P. Clote. Asymptotics of RNA shapes. J Comput Biol. 2008 Jan-Feb;15(1):31-63, BibTeX.
  6. P. Clote. Introduction to special issue on RNA. J Math Biol. 2008 Jan;56(1-2):3-13. PDF, BibTeX.

2007

  1. Modeling ensembles of transmembrane beta-barrel proteins, J. Waldispühl, C.W. O'Donnell, S. Devadas, P. Clote, B. Berger, Proteins. 2007 Nov 14;71(3):1097-1112.
  2. Efficient sampling of RNA secondary structures from the Boltzmann ensemble of low-energy: The boustrophedon method. Ponty Y. J Math Biol. 2007 Oct 12; [Epub ahead of print] PMID: 17932676. J Math Biol.
  3. 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, Discrete Applied Mathematics, special issue in Bioinformatics (eds S. Istrail and P. Pevzner), 157(6-7):759-787 (2007). BibTeX entry
  4. Boltzmann probability of RNA structural neighbors and riboswitch detection. , Eva Freyhult; Vincent Moulton; Peter Clote, Bioinformatics. 2007 Aug 15;23(16):2054-62. Epub 2007 Jun 14.
    Abstract, PDF
  5. DIAL: a web server for the pairwise alignment of two RNA three-dimensional structures using nucleotide, dihedral angle and base-pairing similarities , F. Ferre; Y. Ponty; W. A. Lorenz; Peter Clote Nucleic Acids Res. 2007 Jul 1;35(Web Server issue):W659-68. Epub 2007 Jun 13.
    Abstract , Full Text, PDF, BibTeX entry
  6. RNAbor: A web server for RNA structural neighbors. E. Freyhult, V. Moulton, P. Clote. Nucleic Acids Res. 2007 Jul 1;35(Web Server issue):W305-9. Epub 2007 May 25.
  7. Computing the partition function and sampling for saturated secondary structures of RNA, with respect to the Turner energy model, J. Waldispühl, P. Clote, J Comput Biol 2007 Mar;14(2):190-215.

2006

  1. Combinatorics of saturated secondary structures of RNA, P. Clote, J Comp Biol. 13(9):1640-1657 (2006). BibTeX entry
  2. Predicting transmembrane beta-barrels and interstrand residue interactions from sequence, J. Waldispühl, B. Berger, P. Clote, J.-M. Steyaert, Proteins 65(1):61-74 (2006). BibTeX entry
  3. transFold: a Web Server for predicting the structure and residue contacts of transmembrane beta-barrels, J. Waldispühl, B. Berger, P. Clote, J.-M. Steyaert, Nucleic Acids Res. 34(Web Server Issue):189-193 (2006). BibTeX entry
  4. BTW: A web server for Boltzmann time warping of gene expression time series, F. Ferre, P. Clote, Nucleic Acids Res. 34(Web Server issue):W482-5 (2006). BibTeX entry , full text
  5. DiANNA1.1webServer.pdf DiANNA 1.1: An extension of the DiANNA web server for ternary cysteine classification, F. Ferre, P. Clote, Nucleic Acids Res. 34(Web Server issue):W182-5 (2006). BibTeX entry
  6. Symmetric time warping, Boltzmann pair probabilities and functional genomics , P. Clote, J. Straubhaar, J Math Biol. 53(1):135-61 (2006). BibTeX entry

2005

  1. Energy landscape of k-point mutants of an RNA molecule by P. Clote, J. Waldispuhl, B. Behzadi, J.-M. Steyaert, Bioinformatics, Vol. 21, 4140-4147 (2005). BibTeX entry
  2. 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 (2005). BibTeX entry
  3. 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). BibTeX entry
  4. Disulfide connectivity prediction using secondary structure information and diresidue frequencies, F. Ferre and P. Clote, Bioinformatics 21(10):2336-2346 (2005). BibTeX entry
  5. 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 (2005). BibTeX entry
  6. RNALOSS: A web server for RNA locally optimal secondary structures, P. Clote, Nucleic Acids Res., 33(Web Server issue):W600-604 (2005). BibTeX entry
  7. 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):W230-232 (2005) BibTeX entry
  8. Applications of RNA minimum free energy computations, P. Clote, Wiley Encyclopedia of Bioinformatics, pp 3617-3622 (2005). Volume editor: S. Subramaniam ISBN-13 978-0-470-84974-3.

Books


  1. Genetics, Genomics, Proteomics and Bioinformatics Section editor of Bioinformatics, Modern Programming Paradigms in Biology, in the 8-volume encyclopedia entitled Genetics, Genomics, Proteomics and Bioinformatics (2005), ISBN-13 978-0-470-84974-3.

  2. Computational Molecular Biology: An Introduction , P. Clote and R. Backofen, Japanese translation (2005), 272 pages, ISBN 4-320-05615-9.


  3. Boolean Functions and Computation Models, P. Clote and E. Kranakis, Springer-Verlag, 601 pages (2002), ISBN 3-540-59436-1. BibTeX entry


  4. Computational Biology: an Introduction , P. Clote and R. Backofen, John Wiley & Sons, Ltd., 286 pages (2000), ISBN 0-471-87251-2 (hardback) and ISBN 0-471-87251-0 (paperback). BibTeX entry


  5. 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.

  6. Feasible Mathematics II, Birkhäuser Inc., eds. P. Clote and J. Remmel, in series Progress in Computer Science and Applied Logic, Volume 13, (1995) 447 pages.


  7. Arithmetic, Proof Theory and Computational Complexity , Oxford University Press, eds. P. Clote and J. Krajicek, in series Oxford Logic Guides, volume 23, (1993) 428 pages.

Selected articles prior to 2005

  1. 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). BibTeX entry
  2. "Performance comparison of generalized PSSM in signal peptide cleavage site and disulfide bond recognition", P. Clote, Third IEEE Symposium on BioInformatics and BioEngineering (BIBE'03), Ed. N. Bourbakis, pp 37-44 (2003)
  3. "Proteins: Structure, Function and Evolution", Peter Clote, Gavin J.P. Naylor, Ziheng Yang, Pacific Symposium on Biocomputing, 7:548-551 (2002).
  4. "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.
  5. "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.
  6. "Protein folding, the Levinthal paradox and rapidly mixing Markov chains", ICALP 99, Springer Lecture Notes in Computer Science (August 1999).
  7. "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.
  8. "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).

Journal articles in pure mathematics or theoretical computer science

  1. "Reverse mathematics of some topics from algorithmic graph theory" , P. Clote, J. Hirst, Fundamenta Mathematica 157(1), 1-13 (1998).
  2. "Nondeterministic stack register machines", P. Clote, Theoretical Computer Science 178 (June 1997) 37-76.
  3. "Note on monotonic complexity of 2-REF" , P. Clote, Information Processing Letters 57, 117-123 (1996).
  4. "Cutting planes, connectivity and threshold logic", S.R. Buss, P. Clote, Archive for Mathematical Logic 35, 33-62 (1995). See additional supplement.
  5. "Cutting plane and Frege proofs", P. Clote, Information and Computation, 121(1) 103-122 (1995).
  6. ALOGTIME and a conjecture of S.A. Cook", P. Clote, 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.
  7. "Bounded arithmetic for NC, ALOGTIME, L and NL", P. Clote, G. Takeuti, Annals of Pure and Applied Logic 56 73-117 (1992).
  8. "A time-space hierarchy between P and NP", P. Clote, Mathematical Systems Theory 25 77-92 (1992).
  9. "On some formalized consistency statements in arithmetic", P. Clote, P. Hájek, J.B. Paris, Archive for Mathematical Logic 30(4) 201-221 (1991).
  10. "Boolean functions, invariance groups, and parallel complexity", P. Clote, 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.
  11. "The metamathematics of scattered linear orderings", P. Clote, Archive for Mathematical Logic 29 9-20 (1989).
  12. "A note on the MacDowell-Specker Theorem", P. Clote, Fundamenta Mathematicae 127 (1986), 163-170.
  13. "Members of PI1 classes", P. Clote, D. Cenzer, R. Smith, R. Soare, S. Wainer, Annals of Pure and Applied Logic 31 (1986), 145-161.
  14. "On the finite containment problem for Petri nets", P. Clote, Theoretical Computer Science 43 (1986), 99-105.
  15. "A generalization of the limit lemma and clopen games", P. Clote, Journal of Symbolic Logic 51 (1986), 273-291.
  16. "Sharp bounds on ordinal comparison maps", P. Clote, Archiv für Mathematische Logik und Grundlagenforschung 25 (1985), 99-107.
  17. "On recursive trees with a unique infinite branch", P. Clote, Proceedings of the American Mathematical Society 93 (1985), 335-342.
  18. "A recursion theoretic analysis of the clopen Ramsey theorem", P. Clote, Journal of Symbolic Logic 49 (1984), 376-400.
  19. "Two further combinatorial theorems equivalent to the 1-consistency of Peano arithmetic", P. Clote, K. McAloon, Journal of Symbolic Logic 48 (1983), 1090-1104.

Peer-refereed math/cs articles appearing in books

  1. "Computation models and function algebras" , P. Clote, Handbook of Computability Theory, ed. E.R. Griffor, Elsevier Science B.V. (1999). pp. 589-681.
  2. "On PHP, st-connectivity and odd charged graphs", P. Clote, 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.
  3. "First order bounded arithmetic and small boolean circuit complexity classes", P. Clote, G. Takeuti, in Feasible Mathematics II, eds. P. Clote and J. Remmel, Birkhäuser Inc. (1995).
  4. "Polynomial size Frege proofs of certain combinatorial principles", P. Clote, Arithmetic, Proof Theory and Computational Complexity, Oxford University Press, eds. P. Clote and J. Krajicek (1993).
  5. "Sequential, machine independent characterizations of the parallel complexity classes ACk, NCk and NC" P. Clote, Feasible Mathematics, eds. S. Buss and P. Scott, Birkhäuser, 49-70 (1990).
  6. "Théorème de Cantor-Bendixson", P. Clote, Séminaire Général de Logique, Publications Mathématiques de l'Université Paris VII 27 (1983-84), 73-88, ISSN 0073-8301 (in French).

Peer-refereed math/cs proceedings articles

  1. "A safe recursion scheme for exponential time", P. Clote, 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).
  2. "A note on the relation between polynomial time functionals and Constable's class K", P. Clote, Computer Science Logic, Springer Lecture Notes in Computer Science 1092, ed. Hans Kleine-Büning, 145-160 (1996).
  3. "Computation models and function algebras (extended abstract}", P. Clote, Logic and Computational Complexity, Springer Lecture Notes in Computer Science 960, ed. D. Leivant, 98--130 (1995).
  4. "Parallel computable higher type functionals", P. Clote, B. Kapron, A. Ignjatovic, Thirty-Fourth IEEE Symposium on Foundations of Computer Science, Nov 3-5, 1993.
  5. "The metamathematics of Fraissé's order type conjecture", P. Clote, 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).
  6. "A smash-based hierarchy between P and PSPACE", P. Clote, Logic and Computation, Contemporary Mathematics 106, ed. W. Sieg, American Mathematical Society, 85-100 (1990).
  7. "Exponential time and bounded arithmetic", P. Clote and G. Takeuti, Springer Lecture Notes in Computer Science 223, Structure in Complexity Theory, (1986), 125-143.
  8. "Ultrafilters on definable sets in arithmetic", P. Clote, Logic Colloquium '84, eds. J.B. Paris, A.J. Wilkie, and G.M.Wilmers, 37-58, North Holland Elsevier Science (1986).
  9. "Partition relations in arithmetic", P. Clote, Springer Lecture Notes in Mathematics 1130, Methods in Mathematical Logic, (1985), ed. C. A. DiPrisco, 32-68.
  10. "Applications of the low basis theorem in arithmetic", P. Clote, Springer Lecture Notes in Mathematics 1141, Recursion Theory Week, Proceedings Oberwolfach 1984, eds. H.D. Ebbinghaus, G.H. Müller, G. E. Sacks (1985), 65-88.
  11. "A note on the leftmost infinite branch of a recursive tree", P. Clote, Open Days in Model Theory and Set Theory, eds. W. Guzicki, Z. Marek, A. Pelc, C. Rauszer, (1984), 93-102, published by University of Leeds (England).
  12. "A note on decidable model theory", P. Clote, Model Theory and Arithmetic, Springer Lecture Notes in Mathematics 890 (1981), 134-142.
  13. "Anti-basis theorems and their relation to independence results in Peano arithmetic", P. Clote, Model Theory and Arithmetic, Springer Lecture Notes in Mathematics 890 (1981), 115-133.
  14. "Weak partition relations, finite games and independence results in Peano arithmetic", P. Clote, Model Theory of Algebra and Arithmetic, Springer Lecture Notes in Mathematics 834, (1980), 92-107.

Computer Science Professional Publications

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