Peter Clote

发表

Algorithmic approach to quantifying the hydrophobic force contribution in protein folding

Rolf Backofen, Sebastian Will, Peter Clote, 1999, German Conference on Bioinformatics.

Asymptotics of Canonical RNA Secondary Structures

Peter Clote, Evangelos Kranakis, Danny Krizanc, 2009, 2009 Ninth IEEE International Conference on Bioinformatics and BioEngineering.

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

Peter Clote, Fabrizio Ferrè, P. Clote, 2006, Nucleic Acids Res..

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

Peter Clote, Juan Antonio García-Martín, Iván Dotú, 2013, Nucleic Acids Res..

Editor's Introduction

Peter Clote, 1995, Notre Dame J. Formal Log..

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

Peter Clote, Jérôme Waldispühl, P. Clote, 2007, J. Comput. Biol..

DiANNA: a web server for disulfide connectivity prediction

Peter Clote, Fabrizio Ferrè, P. Clote, 2005, Nucleic Acids Res..

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

Peter Clote, Juan Antonio García-Martín, Iván Dotú, 2013, J. Bioinform. Comput. Biol..

RNAmountAlign: Efficient software for local, global, semiglobal pairwise and multiple RNA sequence/structure alignment

Peter Clote, Amir H Bayegan, 2020, PloS one.

How optimal is the genetic code?

Peter Clote, Stefan Schönauer, P. Clote, 1997, German Conference on Bioinformatics.

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

Peter Clote, P. Clote, 2005, J. Comput. Biol..

Combinatorics of Saturated Secondary Structures of RNA

Peter Clote, P. Clote, 2006, J. Comput. Biol..

Two further combinatorial theorems equivalent to the 1-consistency of peano arithmetic

Peter Clote, Kenneth McAloon, P. Clote, 1983, Journal of Symbolic Logic.

Protein Folding, the Levinthal Paradox and Rapidly Mixing Markov Chains

Peter Clote, 1999, ICALP.

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

Peter Clote, Evan Senter, Saad Sheikh, 2012, PloS one.

COMPUTATIONAL MOLECULAR BIOLOGY: AN INTRODUCTION

Rolf Backofen, Peter Clote, P. Clote, 2000 .

Complete RNA inverse folding: computational design of functional hammerhead ribozymes

Peter Clote, Ivan Dotu, Juan Antonio Garcia-Martin, 2014, Nucleic acids research.

Symmetric time warping, Boltzmann pair probabilities and functional genomics

Peter Clote, Jürg Straubhaar, 2006, Journal of mathematical biology.

Small-World Networks and RNA Secondary Structures

Peter Clote, Yann Ponty, Defne Surujon, 2018, J. Comput. Biol..

A Note on the Monotone Complexity of 2-REF

Peter Clote, 1996, Inf. Process. Lett..

Expected degree for RNA secondary structure networks

Peter Clote, P. Clote, 2014, J. Comput. Chem..

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

Peter Clote, Fabrizio Ferrè, P. Clote, 2006, Nucleic Acids Res..

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

Peter Clote, Juan Antonio García-Martín, Iván Dotú, 2016, BMC Bioinformatics.

A time-space hierarchy between polynomial time and polynomial space

Peter Clote, 2008, Mathematical systems theory.

Proteins: Structure, Function and Evolution - Session Introduction

Peter Clote, Ziheng Yang, Gavin J. P. Naylor, 2002, Pacific Symposium on Biocomputing.

Computational Models and Function Algebras

Peter Clote, P. Clote, 1994, LCC.

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

Peter Clote, F. Ferrè, Y. Ponty, 2007, Nucleic Acids Res..

Disulfide connectivity prediction using secondary structure information and diresidue frequencies

Peter Clote, Fabrizio Ferrè, P. Clote, 2005, Bioinform..

A new approach to suboptimal pairwise sequence alignment

Peter Clote, Alain Denise, Lou Feng, 2011 .

New tools to analyze overlapping coding regions

Peter Clote, Juan Antonio García-Martín, Amir H. Bayegan, 2016, BMC Bioinformatics.

The metamathematics of scattered linear orderings

Peter Clote, 1989, Arch. Math. Log..

Asymptotic structural properties of quasi-random saturated structures of RNA

Peter Clote, Evangelos Kranakis, Danny Krizanc, 2011, Algorithms for Molecular Biology.

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

Peter Clote, 1995, CSL.

Efficient Algorithms for Probing the RNA Mutation Landscape

Srinivas Devadas, Peter Clote, Bonnie Berger, 2008, PLoS Comput. Biol..

An IP Algorithm for RNA Folding Trajectories

Peter Clote, Amir H. Bayegan, 2017, WABI.

A generalization of the limit lemma and clopen games

Peter Clote, P. Clote, 1986, Journal of Symbolic Logic.

Bioinformatik - Aktuelles Schlagwort

Hans-Peter Kriegel, Rolf Backofen, Peter Clote, 1999, Inform. Spektrum.

Parallel computable higher type functionals

Bruce M. Kapron, Peter Clote, Aleksandar Ignjatovic, 1993, Proceedings of 1993 IEEE 34th Annual Foundations of Computer Science.

Bounded arithmetic and computational complexity

Peter Clote, P. Clote, 1990, Proceedings Fifth Annual Structure in Complexity Theory Conference.

Proceedings of the 14th Annual Conference of the EACSL on Computer Science Logic

Peter Clote, Helmut Schwichtenberg, P. Clote, 2000 .

RNALOSS: a web server for RNA locally optimal secondary structures

Peter Clote, P. Clote, 2005, Nucleic Acids Res..

Exponential Time and Bounded Arithmetic

Peter Clote, Gaisi Takeuti, P. Clote, 1986, SCT.

On Lattice Protein Structure Prediction Revisited

Pascal Van Hentenryck, Peter Clote, Manuel Cebrián, 2011, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

RNAiFold2T: Constraint Programming design of thermo-IRES switches

Peter Clote, Juan Antonio García-Martín, Iván Dotú, 2016, Bioinform..

Evolution as a Computational Engine

Rolf Backofen, Peter Clote, P. Clote, 1997, CSL.

On the Finite Containment Problem for Petri Nets

Peter Clote, P. Clote, 1986, Theor. Comput. Sci..

A Safe Recursion Scheme for Exponential Time

Peter Clote, 1997, LFCS.

Maximum expected accuracy structural neighbors of an RNA secondary structure

Peter Clote, William Andrew Lorenz, Feng Lou, 2012, BMC Bioinformatics.

Bounded Arithmetic for NC, ALogTIME, L and NL

Peter Clote, Gaisi Takeuti, P. Clote, 1992, Ann. Pure Appl. Log..

Performance Comparison of Generalized PSSM in Signal Peptide Cleavage Site

Peter Clote, 2003, BIBE.

Minimum length RNA folding trajectories pdf

Peter Clote, Amir H. Bayegan, P. Clote, 2018, ArXiv.

Asymptotics of Canonical and Saturated RNA Secondary Structures

Peter Clote, Evangelos Kranakis, Danny Krizanc, 2009, J. Bioinform. Comput. Biol..

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

Peter Clote, Bonnie Berger, Jean-Marc Steyaert, 2006, Nucleic Acids Res..

RNAbor: a web server for RNA structural neighbors

Peter Clote, Vincent Moulton, Eva Freyhult, 2007, Nucleic Acids Res..

Boolean functions, invariance groups and parallel complexity

Peter Clote, 1989, [1989] Proceedings. Structure in Complexity Theory Fourth Annual Conference.

Thermodynamics of RNA structures by Wang–Landau sampling

Peter Clote, Feng Lou, P. Clote, 2010, Bioinform..

Maximum expected accurate structural neighbors of an RNA secondary structure

Peter Clote, Feng Lou, P. Clote, 2011, 2011 IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences (ICCABS).

RNAmountAlign: Efficient software for local, global, semiglobal pairwise and multiple RNA sequence/structure alignment

Peter Clote, Amir H. Bayegan, P. Clote, 2018, bioRxiv.

Members of countable π10 classes

Peter Clote, Douglas A. Cenzer, Robert I. Soare, 1986, Ann. Pure Appl. Log..

A recursion theoretic analysis of the clopen Ramsey theorem

Peter Clote, P. Clote, 1984, Journal of Symbolic Logic.

Cutting planes and constant depth Frege proofs

Peter Clote, P. Clote, 1992, [1992] Proceedings of the Seventh Annual IEEE Symposium on Logic in Computer Science.

Computation Models and Function Algebras

Peter Clote, P. Clote, 1999, Handbook of Computability Theory.

Cutting planes, connectivity, and threshold logic

Peter Clote, Samuel R. Buss, P. Clote, 1996, Arch. Math. Log..

Boltzmann probability of RNA structural neighbors and riboswitch detection

Peter Clote, Vincent Moulton, Eva Freyhult, 2007, Bioinform..

Asymptotics of RNA Shapes

Peter Clote, Yann Ponty, William Andrew Lorenz, 2008, J. Comput. Biol..

Boolean Functions and Computation Models

Peter Clote, Evangelos Kranakis, P. Clote, 2002, Texts in Theoretical Computer Science. An EATCS Series.

Fast, Approximate Kinetics of RNA Folding

Peter Clote, Evan Senter, P. Clote, 2015, J. Comput. Biol..

Computer Science Logic: 14th International Workshop, CSL 2000 Annual Conference of the EACSL Fischbachau, Germany, August 21-26, 2000 Proceedings

Peter Clote, Helmut Schwichtenberg, 2000 .

Energy landscape of k-point mutants of an RNA molecule

Peter Clote, Jean-Marc Steyaert, Jérôme Waldispühl, 2005, Bioinform..

On PHP st-connectivity, and odd charged graphs

Peter Clote, Anton Setzer, 1996, Proof Complexity and Feasible Arithmetics.

LocalMove: computing on-lattice fits for biopolymers

Peter Clote, Yann Ponty, R. Istrate, 2008, Nucleic Acids Res..

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, 2007, Discret. Appl. Math..

Poster abstract: RNA thermodynamic conformational entropy

Peter Clote, Juan Antonio García-Martín, 2015, BCB.

Optimal bounds for ordinal comparison maps

Peter Clote, P. Clote, 1985, Arch. Math. Log..

An Application of Time Warping to Functional Genomics

Peter Clote, Joseph D. Straubhaar, V. Ewell, 2003 .

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

Pascal Van Hentenryck, Peter Clote, Manuel Cebrián, 2008, AAAI.

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

Peter Clote, Yann Ponty, Iván Dotú, 2013, RECOMB.

Protein Structure Prediction with Large Neighborhood Constraint Programming Search

Pascal Van Hentenryck, Peter Clote, Manuel Cebrián, 2008, CP.

Cutting plane and Frege proofs

Peter Clote, P. Clote, 1995, Inf. Comput..

Computer Science Logic

Peter Clote, Helmut Schwichtenberg, 2001, Lecture Notes in Computer Science.

ALOGTIME and a conjecture of S.A. Cook

Peter Clote, 1990, [1990] Proceedings. Fifth Annual IEEE Symposium on Logic in Computer Science.

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

Srinivas Devadas, Peter Clote, Bonnie Berger, 2009, Nucleic Acids Res..

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

Peter Clote, Juan Antonio García-Martín, Iván Dotú, 2015, Nucleic Acids Res..

ALOGTIME and a conjecture of S.A. Cook

Peter Clote, 2005, Annals of Mathematics and Artificial Intelligence.

RNA Structural Segmentation

Pascal Van Hentenryck, Peter Clote, Iván Dotú, 2010, Pacific Symposium on Biocomputing.

Structural diversity measures for RNA

Peter Clote, Amir H. Bayegan, 2015, BCB.

Feasible Mathematics II

Peter Clote, Jeffrey B. Remmel, 2011 .

Anti-Basis theorems and their relation to independence results in Peano arithmetic

Peter Clote, P. Clote, 1981 .

On recursive trees with a unique infinite branch

Peter Clote, 1985 .

Predicting transmembrane β‐barrels and interstrand residue interactions from sequence

Peter Clote, Bonnie Berger, B. Berger, 2006, Proteins.

Solving the Fisher-Wright and coalescence problems with a discrete Markov chain analysis

Peter Clote, Samuel R. Buss, P. Clote, 2004, Advances in Applied Probability.

Energy Parameters and Novel Algorithms for an Extended Nearest Neighbor Energy Model of RNA

Peter Clote, Ivan Dotu, Vinodh Mechery, 2014, PloS one.

Integrating Chemical Footprinting Data into RNA Secondary Structure Prediction

Peter Clote, Kourosh Zarringhalam, Jeffrey H. Chuang, 2012, PloS one.

Using RNA inverse folding to identify IRES-like structural subdomains

Peter Clote, Ivan Dotu, P. Clote, 2013, RNA biology.

Expected Distance between Terminal Nucleotides of Rna Secondary Structures

Peter Clote, Jean-Marc Steyaert, Yann Ponty, 2011 .

Modeling ensembles of transmembrane beta-barrel proteins.

Srinivas Devadas, Peter Clote, Bonnie Berger, 2008, Proteins.

RNA Thermodynamic Structural Entropy

Peter Clote, Juan Antonio Garcia-Martin, P. Clote, 2015, PloS one.

The metamathematics of Fraïssé's order type conjecture

Peter Clote, P. Clote, 1990 .

Ultrafilters on Definable Sets in Arithmetic

Peter Clote, P. Clote, 1986 .

Finite Notations for Innnite Terms

Peter Clote, Helmut Schwichtenberg, Wilfried Buchholz, 1998 .

Modeling ensembles of transmembrane β‐barrel proteins

Srinivas Devadas, Peter Clote, Bonnie Berger, 2008 .

Partition relations in arithmetic

Peter Clote, P. Clote, 1985 .

A Note on Degen's Generalization of the Pigeonhole Principle, St-connectivity, and Odd Charged Graphs

Peter Clote, Anton Setzer, P. Clote, 1996 .

Applications of the low-basis theorem in arithmetic

Peter Clote, P. Clote, 1985 .

Network Properties of the Ensemble of RNA Structures

Peter Clote, Amir H. Bayegan, P. Clote, 2015, PloS one.