Peter Clote

According to our database, Peter Clote authored at least 80 papers between 1983 and 2019.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2019

Small-World Networks and RNA Secondary Structures.

Defne Surujon, Yann Ponty, Peter Clote

J. Comput. Biol., 2019

2018

Minimum length RNA folding trajectories.

Amir H. Bayegan, Peter Clote

CoRR, 2018

2017

An IP Algorithm for RNA Folding Trajectories.

Amir H. Bayegan, Peter Clote

Proceedings of the 17th International Workshop on Algorithms in Bioinformatics, 2017

2016

RNAdualPF: software to compute the dual partition function with sample applications in molecular evolution theory.

Juan Antonio García-Martín, Amir H. Bayegan, Iván Dotú, Peter Clote

BMC Bioinform., 2016

New tools to analyze overlapping coding regions.

Amir H. Bayegan, Juan Antonio García-Martín, Peter Clote

BMC Bioinform., 2016

RNAiFold2T: Constraint Programming design of thermo-IRES switches.

Juan Antonio García-Martín, Iván Dotú, Javier Fernandez-Chamorro, Gloria Lozano, Jorge Ramajo, Encarnacion Martinez-Salas, Peter Clote

Bioinform., 2016

2015

RNAiFold 2.0: a web server and software to design custom and Rfam-based RNA molecules.

Juan Antonio García-Martín, Iván Dotú, Peter Clote

Nucleic Acids Res., 2015

Expected degree for RNA secondary structure networks.

Peter Clote

J. Comput. Chem., 2015

Fast, Approximate Kinetics of RNA Folding.

Evan Senter, Peter Clote

J. Comput. Biol., 2015

Poster abstract: RNA thermodynamic conformational entropy.

Juan Antonio García-Martín, Peter Clote

Proceedings of the 6th ACM Conference on Bioinformatics, 2015

Structural diversity measures for RNA.

Amir H. Bayegan, Peter Clote

Proceedings of the 6th ACM Conference on Bioinformatics, 2015

2014

Computing the Probability of RNA Hairpin and Multiloop Formation.

Yang Ding, William Andrew Lorenz, Iván Dotú, Evan Senter, Peter Clote

J. Comput. Biol., 2014

2013

RNAiFold: a web server for RNA inverse folding and molecular design.

Juan Antonio García-Martín, Peter Clote, Iván Dotú

Nucleic Acids Res., 2013

Rnaifold: a Constraint Programming Algorithm for RNA inverse Folding and molecular Design.

Juan Antonio García-Martín, Peter Clote, Iván Dotú

J. Bioinform. Comput. Biol., 2013

Asymptotic structural properties of quasi-random saturated structures of RNA.

Peter Clote, Evangelos Kranakis, Danny Krizanc

Algorithms Mol. Biol., 2013

Abstract: Using the Fast Fourier Transform to Accelerate the Computational Search for RNA Conformational Switches.

Evan Senter, Saad Sheikh, Iván Dotú, Yann Ponty, Peter Clote

Proceedings of the Research in Computational Molecular Biology, 2013

2012

Maximum expected accuracy structural neighbors of an RNA secondary structure.

Peter Clote, Feng Lou, William Andrew Lorenz

BMC Bioinform., 2012

2011

On Lattice Protein Structure Prediction Revisited.

Iván Dotú, Manuel Cebrián, Pascal Van Hentenryck, Peter Clote

IEEE ACM Trans. Comput. Biol. Bioinform., 2011

Maximum expected accurate structural neighbors of an RNA secondary structure.

Feng Lou, Peter Clote

Proceedings of the IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences, 2011

2010

Thermodynamics of RNA structures by Wang-Landau sampling.

Feng Lou, Peter Clote

Bioinform., 2010

RNA Structural Segmentation.

Iván Dotú, W. A. Lorenz, Pascal Van Hentenryck, Peter Clote

Proceedings of the Biocomputing 2010: Proceedings of the Pacific Symposium, 2010

2009

RNAmutants: a web server to explore the mutational landscape of RNA secondary structures.

Jérôme Waldispühl, Srinivas Devadas, Bonnie Berger, Peter Clote

Nucleic Acids Res., 2009

Asymptotics of Canonical and Saturated RNA Secondary Structures.

Peter Clote, Evangelos Kranakis, Danny Krizanc, Bruno Salvy

J. Bioinform. Comput. Biol., 2009

Asymptotics of Canonical RNA Secondary Structures.

Peter Clote, Evangelos Kranakis, Danny Krizanc

Proceedings of the Ninth IEEE International Conference on Bioinformatics and Bioengineering, 2009

2008

Efficient Algorithms for Probing the RNA Mutation Landscape.

Jérôme Waldispühl, Srinivas Devadas, Bonnie Berger, Peter Clote

PLoS Comput. Biol., 2008

LocalMove: computing on-lattice fits for biopolymers.

Yann Ponty, R. Istrate, E. Porcelli, Peter Clote

Nucleic Acids Res., 2008

Asymptotics of RNA Shapes.

W. A. Lorenz, Yann Ponty, Peter Clote

J. Comput. Biol., 2008

Protein Structure Prediction with Large Neighborhood Constraint Programming Search.

Iván Dotú, Manuel Cebrián, Pascal Van Hentenryck, Peter Clote

Proceedings of the Principles and Practice of Constraint Programming, 2008

Protein Structure Prediction on the Face Centered Cubic Lattice by Local Search.

Manuel Cebrián, Iván Dotú, Pascal Van Hentenryck, Peter Clote

Proceedings of the Twenty-Third AAAI Conference on Artificial Intelligence, 2008

2007

RNAbor: a web server for RNA structural neighbors.

Eva Freyhult, Vincent Moulton, Peter Clote

Nucleic Acids Res., 2007

DIAL: a web server for the pairwise alignment of two RNA three-dimensional structures using nucleotide, dihedral angle and base-pairing similarities.

Fabrizio Ferrè, Yann Ponty, W. A. Lorenz, Peter Clote

Nucleic Acids Res., 2007

Computing the Partition Function and Sampling for Saturated Secondary Structures of RNA, with Respect to the Turner Energy Model.

Jérôme Waldispühl, Peter Clote

J. Comput. Biol., 2007

Asymptotic expected number of base pairs in optimal secondary structure for random RNA using the Nussinov-Jacobson energy model.

Peter Clote, Evangelos Kranakis, Danny Krizanc, Ladislav Stacho

Discret. Appl. Math., 2007

Boltzmann probability of RNA structural neighbors and riboswitch detection.

Eva Freyhult, Vincent Moulton, Peter Clote

Bioinform., 2007

2006

transFold: a web server for predicting the structure and residue contacts of transmembrane beta-barrels.

Jérôme Waldispühl, Bonnie Berger, Peter Clote, Jean-Marc Steyaert

Nucleic Acids Res., 2006

BTW: a web server for Boltzmann time warping of gene expression time series.

Fabrizio Ferrè, Peter Clote

Nucleic Acids Res., 2006

DiANNA 1.1: an extension of the DiANNA web server for ternary cysteine classification.

Fabrizio Ferrè, Peter Clote

Nucleic Acids Res., 2006

Combinatorics of Saturated Secondary Structures of RNA.

Peter Clote

J. Comput. Biol., 2006

2005

DiANNA: a web server for disulfide connectivity prediction.

Fabrizio Ferrè, Peter Clote

Nucleic Acids Res., 2005

RNALOSS: a web server for RNA locally optimal secondary structures.

Peter Clote

Nucleic Acids Res., 2005

An Efficient Algorithm to Compute the Landscape of Locally Optimal RNA Secondary Structures with Respect to the NussinovJacobson Energy Model.

Peter Clote

J. Comput. Biol., 2005

Disulfide connectivity prediction using secondary structure information and diresidue frequencies.

Fabrizio Ferrè, Peter Clote

Bioinform., 2005

Energy landscape of <i>k</i>-point mutants of an RNA molecule.

Peter Clote, Jérôme Waldispühl, Behshad Behzadi, Jean-Marc Steyaert

Bioinform., 2005

Computational molecular biology - an introduction.

Peter Clote, Rolf Backofen

Wiley series in mathematical and computational biology, Wiley-VCH, ISBN: 978-0-471-87252-8, 2005

2003

Performance Comparison of Generalized PSSM in Signal Peptide Cleavage Site.

Peter Clote

Proceedings of the 3rd IEEE International Symposium on BioInformatics and BioEngineering (BIBE 2003), 2003

2002

Boolean Functions and Computation Models

Peter Clote, Evangelos Kranakis

Texts in Theoretical Computer Science. An EATCS Series, Springer, ISBN: 3540594361, 2002

Proteins: Structure, Function and Evolution - Session Introduction.

Peter Clote, Gavin J. P. Naylor, Ziheng Yang

Proceedings of the 7th Pacific Symposium on Biocomputing, 2002

1999

Bioinformatik - Aktuelles Schlagwort.

Rolf Backofen, François Bry, Peter Clote, Hans-Peter Kriegel, Thomas Seidl, Klaus U. Schulz

Inform. Spektrum, 1999

Protein Folding, the Levinthal Paradox and Rapidly Mixing Markov Chains.

Peter Clote

Proceedings of the Automata, 1999

Algorithmic approach to quantifying the hydrophobic force contribution in protein folding.

Rolf Backofen, Sebastian Will, Peter Clote

Proceedings of the German Conference on Bioinformatics, 1999

Computation Models and Function Algebras.

Peter Clote

Proceedings of the Handbook of Computability Theory, 1999

1997

Nondeterministic Stack Register Machines.

Peter Clote

Theor. Comput. Sci., 1997

A Safe Recursion Scheme for Exponential Time.

Peter Clote

Proceedings of the Logical Foundations of Computer Science, 4th International Symposium, 1997

How optimal is the genetic code?

Stefan Schönauer, Peter Clote

Proceedings of the German Conference on Bioinformatics, 1997

Evolution as a Computational Engine.

Rolf Backofen, Peter Clote

Proceedings of the Computer Science Logic, 11th International Workshop, 1997

1996

A Note on the Monotone Complexity of 2-REF.

Peter Clote

Inf. Process. Lett., 1996

Cutting planes, connectivity, and threshold logic.

Samuel R. Buss, Peter Clote

Arch. Math. Log., 1996

On <i>PHP st</i>-connectivity, and odd charged graphs.

Peter Clote, Anton Setzer

Proceedings of the Proof Complexity and Feasible Arithmetics, 1996

1995

Cutting plane and Frege proofs

Peter Clote

Inf. Comput., August, 1995

Editor's Introduction.

Peter Clote

Notre Dame J. Formal Log., 1995

A Note on the Relation Between Polynomial Time Functionals and Constable's Class K.

Peter Clote

Proceedings of the Computer Science Logic, 9th International Workshop, 1995

1994

Computational Models and Function Algebras.

Peter Clote

Proceedings of the Logical and Computational Complexity. Selected Papers. Logic and Computational Complexity, 1994

1993

Parallel computable higher type functionals (Extended Abstract)

Peter Clote, Aleksandar Ignjatovic, Bruce M. Kapron

Proceedings of the 34th Annual Symposium on Foundations of Computer Science, 1993

1992

A Time-Space Hierarchy Between Polynomial Time and Polynomial Space.

Peter Clote

Math. Syst. Theory, 1992

Bounded Arithmetic for NC, ALogTIME, L and NL.

Peter Clote, Gaisi Takeuti

Ann. Pure Appl. Log., 1992

ALOGTIME and a Conjecture of S. A. Cook.

Peter Clote

Ann. Math. Artif. Intell., 1992

Cutting Planes and constant depth Frege proofs

Peter Clote

Proceedings of the Seventh Annual Symposium on Logic in Computer Science (LICS '92), 1992

1991

Boolean Functions, Invariance Groups, and Parallel Complexity.

Peter Clote, Evangelos Kranakis

SIAM J. Comput., 1991

1990

On some formalized conservation results in arithmetic.

Peter Clote, Petr Hájek, Jeff B. Paris

Arch. Math. Log., 1990

ALOGTIME and a Conjecture of S. A. Cook (Extended Abstract)

Peter Clote

Proceedings of the Fifth Annual Symposium on Logic in Computer Science (LICS '90), 1990

Bounded Arithmetic and Computational Complexity.

Peter Clote

Proceedings of the Proceedings: Fifth Annual Structure in Complexity Theory Conference, 1990

1989

The metamathematics of scattered linear orderings.

Peter Clote

Arch. Math. Log., 1989

Boolean Functions, Invariance Groups and Parallel Complexity.

Peter Clote

Proceedings of the Proceedings: Fourth Annual Structure in Complexity Theory Conference, 1989

1986

On the Finite Containment Problem for Petri Nets.

Peter Clote

Theor. Comput. Sci., 1986

A Generalization of the Limit Lemma and Clopen Games.

Peter Clote

J. Symb. Log., 1986

Members of countable π₁⁰ classes.

Douglas A. Cenzer, Peter Clote, Rick L. Smith, Robert I. Soare, Stanley S. Wainer

Ann. Pure Appl. Log., 1986

Exponential Time and Bounded Arithmetic.

Peter Clote, Gaisi Takeuti

Proceedings of the Structure in Complexity Theory, 1986

1985

Optimal bounds for ordinal comparison maps.

Peter Clote

Arch. Math. Log., 1985

1984

A Recursion Theoretic Analysis of the Clopen Ramsey Theorem.

Peter Clote

J. Symb. Log., 1984

1983

Two Further Combinatorial Theorems Equivalent to the 1-Consistency of Peano Arithmetic.

Peter Clote, Kenneth McAloon

J. Symb. Log., 1983