P. Clote

发表

Performance comparison of generalized PSSM in in signal peptide cleavage site and disulfide bond recognition

P. Clote, P. Clote, 2003, Third IEEE Symposium on Bioinformatics and Bioengineering, 2003. Proceedings..

Efficient Algorithms for Probing the RNA Mutation Landscape

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

Computing folding pathways between RNA secondary structures

P. Clote, Iván Dotú, W. Lorenz, 2009, Nucleic acids research.

Energy landscape of k-point mutants of an RNA molecule

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

Structural RNA has lower folding energy than random RNA of the same dinucleotide frequency.

P. Clote, E. Kranakis, D. Krizanc, 2005, RNA.

On realizing shapes in the theory of RNA neutral networks.

P. Clote, E. Kranakis, D. Krizanc, 2005, Journal of theoretical biology.

First Order Bounded Arithmetic and Small Boolean Circuit Complexity Classes

P. Clote, G. Takeuti, 1995 .

Arithmetic, proof theory, and computational complexity

P. Clote, J. Krajícek, 1993 .

Sequential, machine-independent characterizations of the parallel complexity classes AlogTIME, AC k , NC k and NC

P. Clote, 1990 .

Cutting planes, connectivity, and threshold logic

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

Asymptotics of Canonical RNA Secondary Structures

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

RNA folding pathways and kinetics using 2D energy landscapes

P. Clote, Iván Dotú, Evan Senter, 2015, Journal of mathematical biology.

RNA Thermodynamic Structural Entropy

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

Asymptotic connectivity for the network of RNA secondary structures

P. Clote, 2015, 1508.03815.

Combinatorics of locally optimal RNA secondary structures

P. Clote, Éric Fusy, 2011, Journal of Mathematical Biology.

On the page number of RNA secondary structures with pseudoknots

P. Clote, J. Urrutia, E. Kranakis, 2012, Journal of mathematical biology.

On the Page Number of Secondary Structures with Pseudoknots

P. Clote, J. Urrutia, E. Kranakis, 2011 .

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.

Computing the Partition Function for Kinetically Trapped RNA Secondary Structures

P. Clote, W. Lorenz, 2011, PloS one.

OPTIMAL BOUNDS FOR O RDINAL C OMPARISON MAPS*' 1,2

P. Clote, 1985 .

Designing synthetic RNAs to determine the relevance of structural motifs in picornavirus IRES elements

P. Clote, Iván Dotú, J. A. García-Martín, 2016, Scientific Reports.

BOOLEAN FUNCTIONS, INVARIANCE GROUPS AND PARALLEL COMPLEXITY (Extended Abstract)

P. Clote, E. Kranakis, 1989 .

Modeling ensembles of transmembrane beta-barrel proteins.

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

Modeling ensembles of transmembrane β‐barrel proteins

Srinivas Devadas, Peter Clote, Bonnie Berger, 2008 .

RNA folding kinetics using Monte Carlo and Gillespie algorithms

Amir H. Bayegan, P. Clote, 2017, Journal of Mathematical Biology.

On the scale-free nature of RNA secondary structure networks

P. Clote, 2018, 1807.00215.

Asymptotic Number of Hairpins of Saturated RNA Secondary Structures

P. Clote, E. Kranakis, D. Krizanc, 2013, Bulletin of mathematical biology.

Fragmentation‐free LC‐MS can identify hundreds of proteins

P. Clote, B. Schwikowski, D. Goodlett, 2011, Proteomics.

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

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

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..

Applications of RNA minimum free energy computations

P. Clote, 2005 .

RNA SECONDARY STRUCTURE PREDICTION USING APPLICATIONS OF THE PARTITION FUNCTION by Timothy Wake Boston College 2003

P. Clote, T. Wake, Timothy Wake Advisor, 2022 .

Biologically significant sequence alignments using Boltzmann probabilities

P. Clote, 2022 .

Computational prediction of riboswitches.

P. Clote, 2015, Methods in enzymology.

Review: Jan Krajicek, Bounded Arithmetic, Propositional Logic, and Complexity Theory

P. Clote, 1999, Journal of Symbolic Logic.

Signal peptide cleavage site prediction using variants of PSSM

P. Clote, 2022 .

Combinatorics of Saturated Secondary Structures of Rna Au1 Au2

P. Clote, 2022 .

Introduction to special issue on RNA

P. Clote, 2007, Journal of mathematical biology.

Combinatorics of locally optimal RNA secondary structures

P. Clote, Éric Fusy, 2012, Journal of Mathematical Biology.

RNA folding kinetics using Monte Carlo and Gillespie algorithms

Amir H. Bayegan, P. Clote, 2017, Journal of Mathematical Biology.

RNA folding pathways and kinetics using 2D energy landscapes

P. Clote, Iván Dotú, Evan Senter, 2014, Journal of Mathematical Biology.

Expected distance between terminal nucleotides of RNA secondary structures

P. Clote, J. Steyaert, Yann Ponty, 2011, Journal of Mathematical Biology.

DiANNA: a web server for disulfide connectivity prediction

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

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

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

Are RNA networks scale-free?

P Clote, P. Clote, 2020, Journal of Mathematical Biology.

Using RNA inverse folding to identify IRES-like structural subdomains

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

Boltzmann probability of RNA structural neighbors and riboswitch detection

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

Fast, Approximate Kinetics of RNA Folding

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

Expected degree for RNA secondary structure networks

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

Complete RNA inverse folding: computational design of functional hammerhead ribozymes

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

Computing the Probability of RNA Hairpin and Multiloop Formation

YANG DING, WILLIAM A. LORENZ, IVAN DOTU, 2014, J. Comput. Biol..

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

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

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

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

Maximum expected accuracy structural neighbors of an RNA secondary structure

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

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).

Network Properties of the Ensemble of RNA Structures

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

Integrating Chemical Footprinting Data into RNA Secondary Structure Prediction

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

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..

RNAiFold2T: Constraint Programming design of thermo-IRES switches

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

How optimal is the genetic code?

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

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..

Bounded arithmetic and computational complexity

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

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..

Evolution as a Computational Engine

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

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..

On the page number of RNA secondary structures with pseudoknots

P. Clote, J. Urrutia, E. Kranakis, 2011, Journal of Mathematical Biology.

Asymptotics of Canonical and Saturated RNA Secondary Structures

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

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..

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

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

RNAbor: a web server for RNA structural neighbors

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

Computation Models and Function Algebras

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

Computational Models and Function Algebras

Peter Clote, P. Clote, 1994, LCC.

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 for NC, ALogTIME, L and NL

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

Predicting transmembrane β‐barrels and interstrand residue interactions from sequence

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

Applications of the low-basis theorem in arithmetic

Peter Clote, P. Clote, 1985 .

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

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

Minimum length RNA folding trajectories pdf

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

RNALOSS: a web server for RNA locally optimal secondary structures

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

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..

Expected Distance between Terminal Nucleotides of Rna Secondary Structures

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

Disulfide connectivity prediction using secondary structure information and diresidue frequencies

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

RNA Structural Segmentation

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

On the Finite Containment Problem for Petri Nets

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

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

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

A new approach to suboptimal pairwise sequence alignment

Peter Clote, Alain Denise, Lou Feng, 2011 .

Asymptotics of RNA Shapes

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

Nondeterministic Stack Register Machines

Peter Clote, P. Clote, 1997, Theor. Comput. Sci..

On Lattice Protein Structure Prediction Revisited

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

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

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

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.

Small-World Networks and RNA Secondary Structures

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

New tools to analyze overlapping coding regions

Amir H. Bayegan, P. Clote, J. A. García-Martín, 2016, BMC Bioinformatics.

Boolean Functions and Computation Models

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

Thermodynamics of RNA structures by Wang–Landau sampling

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

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

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

Cutting plane and Frege proofs

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

The metamathematics of Fraïssé's order type conjecture

Peter Clote, P. Clote, 1990 .

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

Peter Clote, P. Clote, 1981 .

A generalization of the limit lemma and clopen games

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

Optimal bounds for ordinal comparison maps

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

A recursion theoretic analysis of the clopen Ramsey theorem

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

Partition relations in arithmetic

Peter Clote, P. Clote, 1985 .

Weak partition relations, finite games, and independence results in Peano arithmetic

P. Clote, 1980 .

Asymptotic Number of Hairpins of Saturated RNA Secondary Structures

P. Clote, E. Kranakis, D. Krizanc, 2013, Bulletin of Mathematical Biology.

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

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

On some formalized conservation results in arithmetic

Petr Hájek, Jeff B. Paris, Peter Clote, 1990, Arch. Math. Log..

Ultrafilters on Definable Sets in Arithmetic

Peter Clote, P. Clote, 1986 .

Protein Structure Prediction with Large Neighborhood Constraint Programming Search

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

Expected distance between terminal nucleotides of RNA secondary structures

P. Clote, Y. Ponty, J. Steyaert, 2011, Journal of Mathematical Biology.

COMPUTATIONAL MOLECULAR BIOLOGY: AN INTRODUCTION

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

Members of countable π10 classes

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

Exponential Time and Bounded Arithmetic

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

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.

RNA folding pathways and kinetics using 2D energy landscapes

P. Clote, Iván Dotú, Evan Senter, 2014, Journal of Mathematical Biology.

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

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

Fragmentation‐free LC‐MS can identify hundreds of proteins

P. Clote, B. Schwikowski, D. Goodlett, 2011, Proteomics.

New tools to analyze overlapping coding regions

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

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

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

Combinatorics of Saturated Secondary Structures of RNA

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

LocalMove: computing on-lattice fits for biopolymers

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

Deep sea microbes and DNA cloning.

P. Clote, V. Moulton, E. Freyhult, 1996, Nucleic Acids Res..

SUPPLEMENTARY INFORMATION FOR “NEW TOOLS TO ANALYZE OVERLAPPING CODING REGIONS”

P. Clote, J. A. García-Martín, 2016 .