Two Further Combinatorial Theorems Equivalent to the 1-Consistency of Peano Arithmetic. - Peter Clote; Kenneth McAloon (J. Symb. Log., 1983)

A Recursion Theoretic Analysis of the Clopen Ramsey Theorem. - Peter Clote (J. Symb. Log., 1984)

Optimal bounds for ordinal comparison maps. - Peter Clote (Arch. Math. Log., 1985)

Exponential Time and Bounded Arithmetic. - Peter Clote; Gaisi Takeuti (SCT, 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)

A Generalization of the Limit Lemma and Clopen Games. - Peter Clote (J. Symb. Log., 1986)

On the Finite Containment Problem for Petri Nets. - Peter Clote (Theor. Comput. Sci., 1986)

Boolean Functions, Invariance Groups and Parallel Complexity. - Peter Clote (SCT, 1989)

The metamathematics of scattered linear orderings. - Peter Clote (Arch. Math. Log., 1989)

Bounded Arithmetic and Computational Complexity. - Peter Clote (SCT, 1990)

ALOGTIME and a Conjecture of S. A. Cook (Extended Abstract) - Peter Clote (LICS, 1990)

On some formalized conservation results in arithmetic. - Peter Clote; Petr Hájek 001; Jeff B. Paris (Arch. Math. Log., 1990)

Boolean Functions, Invariance Groups, and Parallel Complexity. - Peter Clote; Evangelos Kranakis (SIAM J. Comput., 1991)

Cutting Planes and constant depth Frege proofs - Peter Clote (LICS, 1992)

ALOGTIME and a Conjecture of S. A. Cook. - Peter Clote (Ann. Math. Artif. Intell., 1992)

Bounded Arithmetic for NC, ALogTIME, L and NL. - Peter Clote; Gaisi Takeuti (Ann. Pure Appl. Log., 1992)

A Time-Space Hierarchy Between Polynomial Time and Polynomial Space. - Peter Clote (Math. Syst. Theory, 1992)

Parallel computable higher type functionals (Extended Abstract) - Peter Clote; Aleksandar Ignjatovic; Bruce M. Kapron (FOCS, 1993)

Computational Models and Function Algebras. - Peter Clote (LCC, 1994)

A Note on the Relation Between Polynomial Time Functionals and Constable's Class K. - Peter Clote (CSL, 1995)

Editor's Introduction. - Peter Clote (Notre Dame J. Formal Log., 1995)

Cutting plane and Frege proofs - Peter Clote (Inf. Comput., 1995)

On PHP st-connectivity, and odd charged graphs. - Peter Clote; Anton Setzer (Proof Complexity and Feasible Arithmetics, 1996)

Cutting planes, connectivity, and threshold logic. - Samuel R. Buss; Peter Clote (Arch. Math. Log., 1996)

A Note on the Monotone Complexity of 2-REF. - Peter Clote (Inf. Process. Lett., 1996)

Evolution as a Computational Engine. - Rolf Backofen; Peter Clote (CSL, 1997)

How optimal is the genetic code? - Stefan Schönauer; Peter Clote (German Conference on Bioinformatics, 1997)

A Safe Recursion Scheme for Exponential Time. - Peter Clote (LFCS, 1997)

Nondeterministic Stack Register Machines. - Peter Clote (Theor. Comput. Sci., 1997)

Computation Models and Function Algebras. - Peter Clote (Handbook of Computability Theory, 1999)

Algorithmic approach to quantifying the hydrophobic force contribution in protein folding. - Rolf Backofen; Sebastian Will; Peter Clote (German Conference on Bioinformatics, 1999)

Protein Folding, the Levinthal Paradox and Rapidly Mixing Markov Chains. - Peter Clote (ICALP, 1999)

Bioinformatik - Aktuelles Schlagwort. - Rolf Backofen; François Bry; Peter Clote; Hans-Peter Kriegel; Thomas Seidl 001; Klaus U. Schulz (Inform. Spektrum, 1999)

Proteins: Structure, Function and Evolution - Session Introduction. - Peter Clote; Gavin J. P. Naylor; Ziheng Yang (Pacific Symposium on Biocomputing, 2002)

Boolean Functions and Computation Models - Peter Clote; Evangelos Kranakis (Springer, 2002)

Performance Comparison of Generalized PSSM in Signal Peptide Cleavage Site. - Peter Clote (BIBE, 2003)

Computational molecular biology - an introduction. - Peter Clote; Rolf Backofen (Wiley-VCH, 2005)

Energy landscape of k-point mutants of an RNA molecule. - Peter Clote; Jérôme Waldispühl; Behshad Behzadi; Jean-Marc Steyaert (Bioinform., 2005)

Disulfide connectivity prediction using secondary structure information and diresidue frequencies. - Fabrizio Ferrè; Peter Clote (Bioinform., 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)

RNALOSS: a web server for RNA locally optimal secondary structures. - Peter Clote (Nucleic Acids Res., 2005)

DiANNA: a web server for disulfide connectivity prediction. - Fabrizio Ferrè; Peter Clote (Nucleic Acids Res., 2005)

Combinatorics of Saturated Secondary Structures of RNA. - Peter Clote (J. Comput. Biol., 2006)

DiANNA 1.1: an extension of the DiANNA web server for ternary cysteine classification. - Fabrizio Ferrè; Peter Clote (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)

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)

Boltzmann probability of RNA structural neighbors and riboswitch detection. - Eva Freyhult; Vincent Moulton; Peter Clote (Bioinform., 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)

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)

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)

RNAbor: a web server for RNA structural neighbors. - Eva Freyhult; Vincent Moulton; Peter Clote (Nucleic Acids Res., 2007)

Protein Structure Prediction on the Face Centered Cubic Lattice by Local Search. - Manuel Cebrián; Iván Dotú; Pascal Van Hentenryck; Peter Clote (AAAI, 2008)

Protein Structure Prediction with Large Neighborhood Constraint Programming Search. - Iván Dotú; Manuel Cebrián; Pascal Van Hentenryck; Peter Clote (CP, 2008)

Asymptotics of RNA Shapes. - W. A. Lorenz; Yann Ponty; Peter Clote (J. Comput. Biol., 2008)

LocalMove: computing on-lattice fits for biopolymers. - Yann Ponty; R. Istrate; E. Porcelli; Peter Clote (Nucleic Acids Res., 2008)

Efficient Algorithms for Probing the RNA Mutation Landscape. - Jérôme Waldispühl; Srinivas Devadas; Bonnie Berger; Peter Clote (PLoS Comput. Biol., 2008)

Asymptotics of Canonical RNA Secondary Structures. - Peter Clote; Evangelos Kranakis; Danny Krizanc (BIBE, 2009)

Asymptotics of Canonical and Saturated RNA Secondary Structures. - Peter Clote; Evangelos Kranakis; Danny Krizanc; Bruno Salvy (J. Bioinform. Comput. Biol., 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)

RNA Structural Segmentation. - Iván Dotú; W. A. Lorenz; Pascal Van Hentenryck; Peter Clote (Pacific Symposium on Biocomputing, 2010)

Thermodynamics of RNA structures by Wang-Landau sampling. - Feng Lou; Peter Clote (Bioinform., 2010)

Maximum expected accurate structural neighbors of an RNA secondary structure. - Feng Lou; Peter Clote (ICCABS, 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 accuracy structural neighbors of an RNA secondary structure. - Peter Clote; Feng Lou; William Andrew Lorenz (BMC Bioinform., 2012)

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 (RECOMB, 2013)

Asymptotic structural properties of quasi-random saturated structures of RNA. - Peter Clote; Evangelos Kranakis; Danny Krizanc (Algorithms Mol. Biol., 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)

RNAiFold: a web server for RNA inverse folding and molecular design. - Juan Antonio García-Martín; Peter Clote; Iván Dotú (Nucleic Acids Res., 2013)

Computing the Probability of RNA Hairpin and Multiloop Formation. - Yang Ding; William Andrew Lorenz; Iván Dotú; Evan Senter; Peter Clote (J. Comput. Biol., 2014)

Structural diversity measures for RNA. - Amir H. Bayegan; Peter Clote (BCB, 2015)

Poster abstract: RNA thermodynamic conformational entropy. - Juan Antonio García-Martín; Peter Clote (BCB, 2015)

Fast, Approximate Kinetics of RNA Folding. - Evan Senter; Peter Clote (J. Comput. Biol., 2015)

Expected degree for RNA secondary structure networks. - Peter Clote (J. Comput. Chem., 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)

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)

New tools to analyze overlapping coding regions. - Amir H. Bayegan; Juan Antonio García-Martín; Peter Clote (BMC Bioinform., 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)

An IP Algorithm for RNA Folding Trajectories. - Amir H. Bayegan; Peter Clote (WABI, 2017)

Minimum length RNA folding trajectories. - Amir H. Bayegan; Peter Clote (CoRR, 2018)

Small-World Networks and RNA Secondary Structures. - Defne Surujon; Yann Ponty; Peter Clote (J. Comput. Biol., 2019)