Peter Clote

Publication Activity (10 Years)

Years Active: 1983-2019
Publications (10 Years): 6

Top Topics

Fast Fourier Transform

Diversity Measures

Top Venues

J. Comput. Biol.

Nucleic Acids Res.

Publications

Defne Surujon, Yann Ponty, Peter Clote
Small-World Networks and RNA Secondary Structures. J. Comput. Biol. 26 (1) (2019)
Amir H. Bayegan, Peter Clote
Minimum length RNA folding trajectories. CoRR (2018)
Amir H. Bayegan, Peter Clote
An IP Algorithm for RNA Folding Trajectories. WABI (2017)
Amir H. Bayegan, Juan Antonio García-Martín, Peter Clote
New tools to analyze overlapping coding regions. BMC Bioinform. 17 (2016)
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) (2016)
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 (2016)
Amir H. Bayegan, Peter Clote
Structural diversity measures for RNA. BCB (2015)
Juan Antonio García-Martín, Peter Clote
Poster abstract: RNA thermodynamic conformational entropy. BCB (2015)
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) (2015)
Evan Senter, Peter Clote
Fast, Approximate Kinetics of RNA Folding. J. Comput. Biol. 22 (2) (2015)
Peter Clote
Expected degree for RNA secondary structure networks. J. Comput. Chem. 36 (2) (2015)
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) (2014)
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)
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)
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) (2013)
Peter Clote, Evangelos Kranakis, Danny Krizanc
Asymptotic structural properties of quasi-random saturated structures of RNA. Algorithms Mol. Biol. 8 (2013)
Peter Clote, Feng Lou, William Andrew Lorenz
Maximum expected accuracy structural neighbors of an RNA secondary structure. BMC Bioinform. 13 (S-5) (2012)
Iván Dotú, Manuel Cebrián, Pascal Van Hentenryck, Peter Clote
On Lattice Protein Structure Prediction Revisited. IEEE ACM Trans. Comput. Biol. Bioinform. 8 (6) (2011)
Feng Lou, Peter Clote
Maximum expected accurate structural neighbors of an RNA secondary structure. ICCABS (2011)
Iván Dotú, W. A. Lorenz, Pascal Van Hentenryck, Peter Clote
RNA Structural Segmentation. Pacific Symposium on Biocomputing (2010)
Feng Lou, Peter Clote
Thermodynamics of RNA structures by Wang-Landau sampling. Bioinform. 26 (12) (2010)
Peter Clote, Evangelos Kranakis, Danny Krizanc
Asymptotics of Canonical RNA Secondary Structures. BIBE (2009)
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) (2009)
Peter Clote, Evangelos Kranakis, Danny Krizanc, Bruno Salvy
Asymptotics of Canonical and Saturated RNA Secondary Structures. J. Bioinform. Comput. Biol. 7 (5) (2009)
Yann Ponty, R. Istrate, E. Porcelli, Peter Clote
LocalMove: computing on-lattice fits for biopolymers. Nucleic Acids Res. 36 (Web-Server-Issue) (2008)
W. A. Lorenz, Yann Ponty, Peter Clote
Asymptotics of RNA Shapes. J. Comput. Biol. 15 (1) (2008)
Iván Dotú, Manuel Cebrián, Pascal Van Hentenryck, Peter Clote
Protein Structure Prediction with Large Neighborhood Constraint Programming Search. CP (2008)
Jérôme Waldispühl, Srinivas Devadas, Bonnie Berger, Peter Clote
Efficient Algorithms for Probing the RNA Mutation Landscape. PLoS Comput. Biol. 4 (8) (2008)
Manuel Cebrián, Iván Dotú, Pascal Van Hentenryck, Peter Clote
Protein Structure Prediction on the Face Centered Cubic Lattice by Local Search. AAAI (2008)
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) (2007)
Eva Freyhult, Vincent Moulton, Peter Clote
RNAbor: a web server for RNA structural neighbors. Nucleic Acids Res. 35 (Web-Server-Issue) (2007)
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) (2007)
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) (2007)
Eva Freyhult, Vincent Moulton, Peter Clote
Boltzmann probability of RNA structural neighbors and riboswitch detection. Bioinform. 23 (16) (2007)
Peter Clote
Combinatorics of Saturated Secondary Structures of RNA. J. Comput. Biol. 13 (9) (2006)
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) (2006)
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) (2006)
Fabrizio Ferrè, Peter Clote
BTW: a web server for Boltzmann time warping of gene expression time series. Nucleic Acids Res. 34 (Web-Server-Issue) (2006)
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) (2005)
Peter Clote
RNALOSS: a web server for RNA locally optimal secondary structures. Nucleic Acids Res. 33 (Web-Server-Issue) (2005)
Fabrizio Ferrè, Peter Clote
DiANNA: a web server for disulfide connectivity prediction. Nucleic Acids Res. 33 (Web-Server-Issue) (2005)
Fabrizio Ferrè, Peter Clote
Disulfide connectivity prediction using secondary structure information and diresidue frequencies. Bioinform. 21 (10) (2005)
Peter Clote, Jérôme Waldispühl, Behshad Behzadi, Jean-Marc Steyaert
-point mutants of an RNA molecule. Bioinform. 21 (22) (2005)
Peter Clote
Performance Comparison of Generalized PSSM in Signal Peptide Cleavage Site. BIBE (2003)
Peter Clote, Gavin J. P. Naylor, Ziheng Yang
Proteins: Structure, Function and Evolution - Session Introduction. Pacific Symposium on Biocomputing (2002)
Rolf Backofen, Sebastian Will, Peter Clote
Algorithmic approach to quantifying the hydrophobic force contribution in protein folding. German Conference on Bioinformatics (1999)
Rolf Backofen, François Bry, Peter Clote, Hans-Peter Kriegel, Thomas Seidl, Klaus U. Schulz
Bioinformatik - Aktuelles Schlagwort. Inform. Spektrum 22 (5) (1999)
Peter Clote
Protein Folding, the Levinthal Paradox and Rapidly Mixing Markov Chains. ICALP (1999)
Stefan Schönauer, Peter Clote
How optimal is the genetic code? German Conference on Bioinformatics (1997)
Peter Clote
Nondeterministic Stack Register Machines. Theor. Comput. Sci. 178 (1-2) (1997)
Peter Clote
A Safe Recursion Scheme for Exponential Time. LFCS (1997)
Rolf Backofen, Peter Clote
Evolution as a Computational Engine. CSL (1997)
Peter Clote
A Note on the Monotone Complexity of 2-REF. Inf. Process. Lett. 57 (3) (1996)
Samuel R. Buss, Peter Clote
Cutting planes, connectivity, and threshold logic. Arch. Math. Log. 35 (1) (1996)
Peter Clote, Anton Setzer
-connectivity, and odd charged graphs. Proof Complexity and Feasible Arithmetics (1996)
Peter Clote
A Note on the Relation Between Polynomial Time Functionals and Constable's Class K. CSL (1995)
Peter Clote
Cutting plane and Frege proofs Inf. Comput. 121 (1) (1995)
Peter Clote
Editor's Introduction. Notre Dame J. Formal Log. 36 (4) (1995)
Peter Clote
Computational Models and Function Algebras. LCC (1994)
Peter Clote, Aleksandar Ignjatovic, Bruce M. Kapron
Parallel computable higher type functionals (Extended Abstract) FOCS (1993)
Peter Clote
A Time-Space Hierarchy Between Polynomial Time and Polynomial Space. Math. Syst. Theory 25 (2) (1992)
Peter Clote, Gaisi Takeuti
Bounded Arithmetic for NC, ALogTIME, L and NL. Ann. Pure Appl. Log. 56 (1-3) (1992)
Peter Clote
Cutting Planes and constant depth Frege proofs LICS (1992)
Peter Clote
ALOGTIME and a Conjecture of S. A. Cook. Ann. Math. Artif. Intell. 6 (1-3) (1992)
Peter Clote, Evangelos Kranakis
Boolean Functions, Invariance Groups, and Parallel Complexity. SIAM J. Comput. 20 (3) (1991)
Peter Clote, Petr Hájek, Jeff B. Paris
On some formalized conservation results in arithmetic. Arch. Math. Log. 30 (4) (1990)
Peter Clote
Bounded Arithmetic and Computational Complexity. Computational Complexity Conference (1990)
Peter Clote
ALOGTIME and a Conjecture of S. A. Cook (Extended Abstract) LICS (1990)
Peter Clote
The metamathematics of scattered linear orderings. Arch. Math. Log. 29 (1) (1989)
Peter Clote
Boolean Functions, Invariance Groups and Parallel Complexity. Computational Complexity Conference (1989)
Peter Clote, Gaisi Takeuti
Exponential Time and Bounded Arithmetic. Computational Complexity Conference (1986)
Douglas A. Cenzer, Peter Clote, Rick L. Smith, Robert I. Soare, Stanley S. Wainer
classes. Ann. Pure Appl. Log. 31 (1986)
Peter Clote
On the Finite Containment Problem for Petri Nets. Theor. Comput. Sci. 43 (1986)
Peter Clote
A Generalization of the Limit Lemma and Clopen Games. J. Symb. Log. 51 (2) (1986)
Peter Clote
Optimal bounds for ordinal comparison maps. Arch. Math. Log. 25 (1) (1985)
Peter Clote
A Recursion Theoretic Analysis of the Clopen Ramsey Theorem. J. Symb. Log. 49 (2) (1984)
Peter Clote, Kenneth McAloon
Two Further Combinatorial Theorems Equivalent to the 1-Consistency of Peano Arithmetic. J. Symb. Log. 48 (4) (1983)