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2010 – 2019
- 2019
[j51]Defne Surujon
, Yann Ponty, Peter Clote:
Small-World Networks and RNA Secondary Structures. J. Comput. Biol. 26(1): 16-26 (2019)- 2018
- [i1]Amir H. Bayegan, Peter Clote:
Minimum length RNA folding trajectories. CoRR abs/1802.06328 (2018) - 2017
- [c25]Amir H. Bayegan, Peter Clote:
An IP Algorithm for RNA Folding Trajectories. WABI 2017: 6:1-6:16 - 2016
- [j50]Juan Antonio García-Martín, Iván Dotú, Javier Fernandez-Chamorro, Gloria Lozano, Jorge Ramajo, Encarnacion Martinez-Salas, Peter Clote:
RNAiFold2T: Constraint Programming design of thermo-IRES switches. Bioinform. 32(12): 360-368 (2016) - [j49]Juan Antonio García-Martín, Amir H. Bayegan, Iván Dotú, Peter Clote:
RNAdualPF: software to compute the dual partition function with sample applications in molecular evolution theory. BMC Bioinform. 17: 424 (2016) - [j48]Amir H. Bayegan, Juan Antonio García-Martín, Peter Clote:
New tools to analyze overlapping coding regions. BMC Bioinform. 17: 530:1-530:15 (2016) - 2015
- [j47]Evan Senter, Peter Clote:
Fast, Approximate Kinetics of RNA Folding. J. Comput. Biol. 22(2): 124-144 (2015) - [j46]Peter Clote:
Expected degree for RNA secondary structure networks. J. Comput. Chem. 36(2): 103-117 (2015) - [j45]Juan Antonio García-Martín, Iván Dotú, Peter Clote:
RNAiFold 2.0: a web server and software to design custom and Rfam-based RNA molecules. Nucleic Acids Res. 43(Webserver-Issue): W513-W521 (2015) - [c24]Juan Antonio García-Martín, Peter Clote:
Poster abstract: RNA thermodynamic conformational entropy. BCB 2015: 482-483 - [c23]Amir H. Bayegan, Peter Clote:
Structural diversity measures for RNA. BCB 2015: 501-502 - 2014
- [j44]Yang Ding, William Andrew Lorenz, Iván Dotú, Evan Senter, Peter Clote:
Computing the Probability of RNA Hairpin and Multiloop Formation. J. Comput. Biol. 21(3): 201-218 (2014) - 2013
- [j43]Peter Clote, Evangelos Kranakis, Danny Krizanc:
Asymptotic structural properties of quasi-random saturated structures of RNA. Algorithms Mol. Biol. 8: 24 (2013) - [j42]Juan Antonio García-Martín, Peter Clote, Iván Dotú:
Rnaifold: a Constraint Programming Algorithm for RNA inverse Folding and molecular Design. J. Bioinform. Comput. Biol. 11(2) (2013) - [j41]Juan Antonio García-Martín, Peter Clote, Iván Dotú:
RNAiFold: a web server for RNA inverse folding and molecular design. Nucleic Acids Res. 41(Webserver-Issue): 465-470 (2013) - [c22]Evan Senter, Saad Sheikh, Iván Dotú, Yann Ponty, Peter Clote:
Abstract: Using the Fast Fourier Transform to Accelerate the Computational Search for RNA Conformational Switches. RECOMB 2013: 264-265 - 2012
- [j40]Peter Clote, Feng Lou, William Andrew Lorenz:
Maximum expected accuracy structural neighbors of an RNA secondary structure. BMC Bioinform. 13(S-5): S6 (2012) - 2011
- [j39]Iván Dotú, Manuel Cebrián, Pascal Van Hentenryck, Peter Clote:
On Lattice Protein Structure Prediction Revisited. IEEE ACM Trans. Comput. Biol. Bioinform. 8(6): 1620-1632 (2011) - [c21]Feng Lou, Peter Clote:
Maximum expected accurate structural neighbors of an RNA secondary structure. ICCABS 2011: 123-128 - 2010
- [j38]Feng Lou, Peter Clote:
Thermodynamics of RNA structures by Wang-Landau sampling. Bioinform. 26(12): 278-286 (2010) - [c20]Iván Dotú, W. A. Lorenz, Pascal Van Hentenryck, Peter Clote:
RNA Structural Segmentation. Pacific Symposium on Biocomputing 2010: 57-68
2000 – 2009
- 2009
- [j37]Peter Clote, Evangelos Kranakis, Danny Krizanc, Bruno Salvy:
Asymptotics of Canonical and Saturated RNA Secondary Structures. J. Bioinform. Comput. Biol. 7(5): 869-893 (2009) - [j36]Jérôme Waldispühl, Srinivas Devadas, Bonnie Berger, Peter Clote:
RNAmutants: a web server to explore the mutational landscape of RNA secondary structures. Nucleic Acids Res. 37(Web-Server-Issue): 281-286 (2009) - [c19]Peter Clote, Evangelos Kranakis, Danny Krizanc:
Asymptotics of Canonical RNA Secondary Structures. BIBE 2009: 184-191 - 2008
- [j35]W. A. Lorenz, Yann Ponty, Peter Clote:
Asymptotics of RNA Shapes. J. Comput. Biol. 15(1): 31-63 (2008) - [j34]Yann Ponty, R. Istrate, E. Porcelli, Peter Clote:
LocalMove: computing on-lattice fits for biopolymers. Nucleic Acids Res. 36(Web-Server-Issue): 216-222 (2008) - [j33]Jérôme Waldispühl, Srinivas Devadas, Bonnie Berger, Peter Clote:
Efficient Algorithms for Probing the RNA Mutation Landscape. PLoS Comput. Biol. 4(8) (2008) - [c18]Manuel Cebrián, Iván Dotú, Pascal Van Hentenryck, Peter Clote:
Protein Structure Prediction on the Face Centered Cubic Lattice by Local Search. AAAI 2008: 241-246 - [c17]Iván Dotú, Manuel Cebrián, Pascal Van Hentenryck, Peter Clote:
Protein Structure Prediction with Large Neighborhood Constraint Programming Search. CP 2008: 82-96 - 2007
- [j32]Eva Freyhult, Vincent Moulton, Peter Clote:
Boltzmann probability of RNA structural neighbors and riboswitch detection. Bioinform. 23(16): 2054-2062 (2007) - [j31]Peter Clote, Evangelos Kranakis, Danny Krizanc, Ladislav Stacho:
Asymptotic expected number of base pairs in optimal secondary structure for random RNA using the Nussinov-Jacobson energy model. Discret. Appl. Math. 155(6-7): 759-787 (2007) - [j30]Jérôme Waldispühl, Peter Clote:
Computing the Partition Function and Sampling for Saturated Secondary Structures of RNA, with Respect to the Turner Energy Model. J. Comput. Biol. 14(2): 190-215 (2007) - [j29]Eva Freyhult, Vincent Moulton, Peter Clote:
RNAbor: a web server for RNA structural neighbors. Nucleic Acids Res. 35(Web-Server-Issue): 305-309 (2007) - [j28]Fabrizio Ferrè, Yann Ponty, W. A. Lorenz, Peter Clote:
DIAL: a web server for the pairwise alignment of two RNA three-dimensional structures using nucleotide, dihedral angle and base-pairing similarities. Nucleic Acids Res. 35(Web-Server-Issue): 659-668 (2007) - 2006
- [j27]Peter Clote:
Combinatorics of Saturated Secondary Structures of RNA. J. Comput. Biol. 13(9): 1640-1657 (2006) - [j26]Fabrizio Ferrè, Peter Clote:
DiANNA 1.1: an extension of the DiANNA web server for ternary cysteine classification. Nucleic Acids Res. 34(Web-Server-Issue): 182-185 (2006) - [j25]Jérôme Waldispühl, Bonnie Berger, Peter Clote, Jean-Marc Steyaert:
transFold: a web server for predicting the structure and residue contacts of transmembrane beta-barrels. Nucleic Acids Res. 34(Web-Server-Issue): 189-193 (2006) - [j24]Fabrizio Ferrè, Peter Clote:
BTW: a web server for Boltzmann time warping of gene expression time series. Nucleic Acids Res. 34(Web-Server-Issue): 482-485 (2006) - 2005
- [b2]Peter Clote, Rolf Backofen:
Computational molecular biology - an introduction. Wiley series in mathematical and computational biology, Wiley-VCH 2005, ISBN 978-0-471-87252-8, pp. I-IX, 1-286 - [j23]Fabrizio Ferrè, Peter Clote:
Disulfide connectivity prediction using secondary structure information and diresidue frequencies. Bioinform. 21(10): 2336-2346 (2005) - [j22]Peter Clote, Jérôme Waldispühl, Behshad Behzadi, Jean-Marc Steyaert:
Energy landscape of k-point mutants of an RNA molecule. Bioinform. 21(22): 4140-4147 (2005) - [j21]Peter Clote:
An Efficient Algorithm to Compute the Landscape of Locally Optimal RNA Secondary Structures with Respect to the NussinovJacobson Energy Model. J. Comput. Biol. 12(1): 83-101 (2005) - [j20]Fabrizio Ferrè, Peter Clote:
DiANNA: a web server for disulfide connectivity prediction. Nucleic Acids Res. 33(Web-Server-Issue): 230-232 (2005) - [j19]Peter Clote:
RNALOSS: a web server for RNA locally optimal secondary structures. Nucleic Acids Res. 33(Web-Server-Issue): 600-604 (2005) - 2003
- [c16]Peter Clote:
Performance Comparison of Generalized PSSM in Signal Peptide Cleavage Site. BIBE 2003: 37-44 - 2002
- [b1]Peter Clote, Evangelos Kranakis:
Boolean Functions and Computation Models. Texts in Theoretical Computer Science. An EATCS Series, Springer 2002, ISBN 978-3-642-08217-7, pp. 1-602 - [c15]Peter Clote, Gavin J. P. Naylor, Ziheng Yang:
Proteins: Structure, Function and Evolution - Session Introduction. Pacific Symposium on Biocomputing 2002: 548-551 - 2000
- [e1]Peter Clote, Helmut Schwichtenberg:
Computer Science Logic, 14th Annual Conference of the EACSL, Fischbachau, Germany, August 21-26, 2000, Proceedings. Lecture Notes in Computer Science 1862, Springer 2000, ISBN 3-540-67895-6 [contents]
1990 – 1999
- 1999
- [j18]Rolf Backofen, François Bry, Peter Clote, Hans-Peter Kriegel, Thomas Seidl, Klaus U. Schulz:
Bioinformatik - Aktuelles Schlagwort. Inform. Spektrum 22(5): 376-378 (1999) - [c14]Rolf Backofen, Sebastian Will, Peter Clote:
Algorithmic approach to quantifying the hydrophobic force contribution in protein folding. German Conference on Bioinformatics 1999: 93-106 - [c13]Peter Clote:
Protein Folding, the Levinthal Paradox and Rapidly Mixing Markov Chains. ICALP 1999: 240-249 - [p1]Peter Clote:
Computation Models and Function Algebras. Handbook of Computability Theory 1999: 589-681 - 1997
- [j17]Peter Clote:
Nondeterministic Stack Register Machines. Theor. Comput. Sci. 178(1-2): 37-76 (1997) - [c12]Rolf Backofen, Peter Clote:
Evolution as a Computational Engine. CSL 1997: 35-55 - [c11]Stefan Schönauer, Peter Clote:
How optimal is the genetic code? German Conference on Bioinformatics 1997: 65-67 - [c10]Peter Clote:
A Safe Recursion Scheme for Exponential Time. LFCS 1997: 44-52 - 1996
- [j16]Samuel R. Buss, Peter Clote:
Cutting planes, connectivity, and threshold logic. Arch. Math. Log. 35(1): 33-62 (1996) - [j15]Peter Clote:
A Note on the Monotone Complexity of 2-REF. Inf. Process. Lett. 57(3): 117-123 (1996) - [c9]Peter Clote, Anton Setzer:
On PHP st-connectivity, and odd charged graphs. Proof Complexity and Feasible Arithmetics 1996: 93-117 - 1995
- [j14]Peter Clote:
Cutting plane and Frege proofs. Inf. Comput. 121(1): 103-122 (1995) - [j13]Peter Clote:
Editor's Introduction. Notre Dame J. Formal Log. 36(4): 499-501 (1995) - [c8]Peter Clote:
A Note on the Relation Between Polynomial Time Functionals and Constable's Class K. CSL 1995: 145-160 - 1994
- [c7]Peter Clote:
Computational Models and Function Algebras. LCC 1994: 98-130 - 1993
- [c6]Peter Clote, Aleksandar Ignjatovic, Bruce M. Kapron:
Parallel computable higher type functionals (Extended Abstract). FOCS 1993: 72-81 - 1992
- [j12]Peter Clote:
ALOGTIME and a Conjecture of S. A. Cook. Ann. Math. Artif. Intell. 6(1-3): 57-106 (1992) - [j11]Peter Clote, Gaisi Takeuti:
Bounded Arithmetic for NC, ALogTIME, L and NL. Ann. Pure Appl. Log. 56(1-3): 73-117 (1992) - [j10]Peter Clote:
A Time-Space Hierarchy Between Polynomial Time and Polynomial Space. Math. Syst. Theory 25(2): 77-92 (1992) - [c5]Peter Clote:
Cutting Planes and constant depth Frege proofs. LICS 1992: 296-307 - 1991
- [j9]Peter Clote, Evangelos Kranakis:
Boolean Functions, Invariance Groups, and Parallel Complexity. SIAM J. Comput. 20(3): 553-590 (1991) - 1990
- [j8]Peter Clote, Petr Hájek, Jeff B. Paris:
On some formalized conservation results in arithmetic. Arch. Math. Log. 30(4): 201-218 (1990) - [c4]Peter Clote:
Bounded Arithmetic and Computational Complexity. SCT 1990: 186-199 - [c3]Peter Clote:
ALOGTIME and a Conjecture of S. A. Cook (Extended Abstract). LICS 1990: 181-189
1980 – 1989
- 1989
- [j7]Peter Clote:
The metamathematics of scattered linear orderings. Arch. Math. Log. 29(1): 9-20 (1989) - [c2]Peter Clote:
Boolean Functions, Invariance Groups and Parallel Complexity. SCT 1989: 55-66 - 1986
- [j6]Douglas A. Cenzer, Peter Clote, Rick L. Smith, Robert I. Soare, Stanley S. Wainer:
Members of countable π10 classes. Ann. Pure Appl. Log. 31: 145-163 (1986) - [j5]Peter Clote:
A Generalization of the Limit Lemma and Clopen Games. J. Symb. Log. 51(2): 273-291 (1986) - [j4]Peter Clote:
On the Finite Containment Problem for Petri Nets. Theor. Comput. Sci. 43: 99-105 (1986) - [c1]Peter Clote, Gaisi Takeuti:
Exponential Time and Bounded Arithmetic. SCT 1986: 125-143 - 1985
- [j3]Peter Clote:
Optimal bounds for ordinal comparison maps. Arch. Math. Log. 25(1): 99-107 (1985) - 1984
- [j2]Peter Clote:
A Recursion Theoretic Analysis of the Clopen Ramsey Theorem. J. Symb. Log. 49(2): 376-400 (1984) - 1983
- [j1]Peter Clote, Kenneth McAloon:
Two Further Combinatorial Theorems Equivalent to the 1-Consistency of Peano Arithmetic. J. Symb. Log. 48(4): 1090-1104 (1983)
Coauthor Index
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