Peter Clote - RankMe

81 papers A* 5A 1B 4C 3Misc 3Journal 52Unranked 10

Year	Rank	Type	Title / Venue / Authors
2019	J	`jnl`	Small-World Networks and RNA Secondary Structures. J. Comput. Biol. Defne Surujon, Yann Ponty, Peter Clote
2018	J	`jnl`	Minimum length RNA folding trajectories. CoRR Amir H. Bayegan, Peter Clote
2017	C	`conf`	An IP Algorithm for RNA Folding Trajectories. WABI Amir H. Bayegan, Peter Clote
2016	J	`jnl`	New tools to analyze overlapping coding regions. BMC Bioinform. Amir H. Bayegan, Juan Antonio García-Martín, Peter Clote
2016	J	`jnl`	RNAdualPF: software to compute the dual partition function with sample applications in molecular evolution theory. BMC Bioinform. Juan Antonio García-Martín, Amir H. Bayegan, Iván Dotú, Peter Clote
2016	J	`jnl`	RNAiFold2T: Constraint Programming design of thermo-IRES switches. Bioinform. Juan Antonio García-Martín, Iván Dotú, Javier Fernandez-Chamorro, Gloria Lozano, Jorge Ramajo, Encarnacion Martinez-Salas, Peter Clote
2015	J	`jnl`	Expected degree for RNA secondary structure networks. J. Comput. Chem. Peter Clote
2015	J	`jnl`	Fast, Approximate Kinetics of RNA Folding. J. Comput. Biol. Evan Senter, Peter Clote
2015	—	`conf`	Poster abstract: RNA thermodynamic conformational entropy. BCB Juan Antonio García-Martín, Peter Clote
2015	J	`jnl`	RNAiFold 2.0: a web server and software to design custom and Rfam-based RNA molecules. Nucleic Acids Res. Juan Antonio García-Martín, Iván Dotú, Peter Clote
2015	—	`conf`	Structural diversity measures for RNA. BCB Amir H. Bayegan, Peter Clote
2014	J	`jnl`	Computing the Probability of RNA Hairpin and Multiloop Formation. J. Comput. Biol. Yang Ding, William Andrew Lorenz, Iván Dotú, Evan Senter, Peter Clote
2013	B	`conf`	Abstract: Using the Fast Fourier Transform to Accelerate the Computational Search for RNA Conformational Switches. RECOMB Evan Senter, Saad Sheikh, Iván Dotú, Yann Ponty, Peter Clote
2013	J	`jnl`	Asymptotic structural properties of quasi-random saturated structures of RNA. Algorithms Mol. Biol. Peter Clote, Evangelos Kranakis, Danny Krizanc
2013	J	`jnl`	RNAiFold: a web server for RNA inverse folding and molecular design. Nucleic Acids Res. Juan Antonio García-Martín, Peter Clote, Iván Dotú
2013	J	`jnl`	Rnaifold: a Constraint Programming Algorithm for RNA inverse Folding and molecular Design. J. Bioinform. Comput. Biol. Juan Antonio García-Martín, Peter Clote, Iván Dotú
2012	J	`jnl`	Maximum expected accuracy structural neighbors of an RNA secondary structure. BMC Bioinform. Peter Clote, Feng Lou, William Andrew Lorenz
2011	—	`conf`	Maximum expected accurate structural neighbors of an RNA secondary structure. ICCABS Feng Lou, Peter Clote
2011	J	`jnl`	On Lattice Protein Structure Prediction Revisited. IEEE ACM Trans. Comput. Biol. Bioinform. Iván Dotú, Manuel Cebrián, Pascal Van Hentenryck, Peter Clote
2010	Misc	`conf`	RNA Structural Segmentation. Pacific Symposium on Biocomputing Iván Dotú, W. A. Lorenz, Pascal Van Hentenryck, Peter Clote
2010	J	`jnl`	Thermodynamics of RNA structures by Wang-Landau sampling. Bioinform. Feng Lou, Peter Clote
2009	C	`conf`	Asymptotics of Canonical RNA Secondary Structures. BIBE Peter Clote, Evangelos Kranakis, Danny Krizanc
2009	J	`jnl`	Asymptotics of Canonical and Saturated RNA Secondary Structures. J. Bioinform. Comput. Biol. Peter Clote, Evangelos Kranakis, Danny Krizanc, Bruno Salvy
2009	J	`jnl`	RNAmutants: a web server to explore the mutational landscape of RNA secondary structures. Nucleic Acids Res. Jérôme Waldispühl, Srinivas Devadas, Bonnie Berger, Peter Clote
2008	J	`jnl`	Asymptotics of RNA Shapes. J. Comput. Biol. W. A. Lorenz, Yann Ponty, Peter Clote
2008	J	`jnl`	Efficient Algorithms for Probing the RNA Mutation Landscape. PLoS Comput. Biol. Jérôme Waldispühl, Srinivas Devadas, Bonnie Berger, Peter Clote
2008	J	`jnl`	LocalMove: computing on-lattice fits for biopolymers. Nucleic Acids Res. Yann Ponty, R. Istrate, E. Porcelli, Peter Clote
2008	A*	`conf`	Protein Structure Prediction on the Face Centered Cubic Lattice by Local Search. AAAI Manuel Cebrián, Iván Dotú, Pascal Van Hentenryck, Peter Clote
2008	A	`conf`	Protein Structure Prediction with Large Neighborhood Constraint Programming Search. CP Iván Dotú, Manuel Cebrián, Pascal Van Hentenryck, Peter Clote
2007	J	`jnl`	Asymptotic expected number of base pairs in optimal secondary structure for random RNA using the Nussinov-Jacobson energy model. Discret. Appl. Math. Peter Clote, Evangelos Kranakis, Danny Krizanc, Ladislav Stacho
2007	J	`jnl`	Boltzmann probability of RNA structural neighbors and riboswitch detection. Bioinform. Eva Freyhult, Vincent Moulton, Peter Clote
2007	J	`jnl`	Computing the Partition Function and Sampling for Saturated Secondary Structures of RNA, with Respect to the Turner Energy Model. J. Comput. Biol. Jérôme Waldispühl, Peter Clote
2007	J	`jnl`	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. Fabrizio Ferrè, Yann Ponty, W. A. Lorenz, Peter Clote
2007	J	`jnl`	RNAbor: a web server for RNA structural neighbors. Nucleic Acids Res. Eva Freyhult, Vincent Moulton, Peter Clote
2006	J	`jnl`	BTW: a web server for Boltzmann time warping of gene expression time series. Nucleic Acids Res. Fabrizio Ferrè, Peter Clote
2006	J	`jnl`	Combinatorics of Saturated Secondary Structures of RNA. J. Comput. Biol. Peter Clote
2006	J	`jnl`	DiANNA 1.1: an extension of the DiANNA web server for ternary cysteine classification. Nucleic Acids Res. Fabrizio Ferrè, Peter Clote
2006	J	`jnl`	transFold: a web server for predicting the structure and residue contacts of transmembrane beta-barrels. Nucleic Acids Res. Jérôme Waldispühl, Bonnie Berger, Peter Clote, Jean-Marc Steyaert
2005	J	`jnl`	An Efficient Algorithm to Compute the Landscape of Locally Optimal RNA Secondary Structures with Respect to the NussinovJacobson Energy Model. J. Comput. Biol. Peter Clote
2005	—	`book`	Computational molecular biology - an introduction. Peter Clote, Rolf Backofen
2005	J	`jnl`	DiANNA: a web server for disulfide connectivity prediction. Nucleic Acids Res. Fabrizio Ferrè, Peter Clote
2005	J	`jnl`	Disulfide connectivity prediction using secondary structure information and diresidue frequencies. Bioinform. Fabrizio Ferrè, Peter Clote
2005	J	`jnl`	Energy landscape of Bioinform. Peter Clote, Jérôme Waldispühl, Behshad Behzadi, Jean-Marc Steyaert
2005	J	`jnl`	RNALOSS: a web server for RNA locally optimal secondary structures. Nucleic Acids Res. Peter Clote
2003	C	`conf`	Performance Comparison of Generalized PSSM in Signal Peptide Cleavage Site. BIBE Peter Clote
2002	—	`book`	Boolean Functions and Computation Models Peter Clote, Evangelos Kranakis
2002	Misc	`conf`	Proteins: Structure, Function and Evolution - Session Introduction. Pacific Symposium on Biocomputing Peter Clote, Gavin J. P. Naylor, Ziheng Yang
2000	B	`ed.`	Computer Science Logic, 14th Annual Conference of the EACSL, Fischbachau, Germany, August 21-26, 2000, Proceedings CSL Peter Clote, Helmut Schwichtenberg
1999	—	`conf`	Algorithmic approach to quantifying the hydrophobic force contribution in protein folding. German Conference on Bioinformatics Rolf Backofen, Sebastian Will, Peter Clote
1999	J	`jnl`	Bioinformatik - Aktuelles Schlagwort. Inform. Spektrum Rolf Backofen, François Bry, Peter Clote, Hans-Peter Kriegel, Thomas Seidl, Klaus U. Schulz
1999	—	`ch.`	Computation Models and Function Algebras. Handbook of Computability Theory Peter Clote
1999	A*	`conf`	Protein Folding, the Levinthal Paradox and Rapidly Mixing Markov Chains. ICALP Peter Clote
1997	Misc	`conf`	A Safe Recursion Scheme for Exponential Time. LFCS Peter Clote
1997	B	`conf`	Evolution as a Computational Engine. CSL Rolf Backofen, Peter Clote
1997	—	`conf`	How optimal is the genetic code? German Conference on Bioinformatics Stefan Schönauer, Peter Clote
1997	J	`jnl`	Nondeterministic Stack Register Machines. Theor. Comput. Sci. Peter Clote
1996	J	`jnl`	A Note on the Monotone Complexity of 2-REF. Inf. Process. Lett. Peter Clote
1996	J	`jnl`	Cutting planes, connectivity, and threshold logic. Arch. Math. Log. Samuel R. Buss, Peter Clote
1996	—	`conf`	On Proof Complexity and Feasible Arithmetics Peter Clote, Anton Setzer
1995	B	`conf`	A Note on the Relation Between Polynomial Time Functionals and Constable's Class K. CSL Peter Clote
1995	J	`jnl`	Cutting plane and Frege proofs Inf. Comput. Peter Clote
1995	J	`jnl`	Editor's Introduction. Notre Dame J. Formal Log. Peter Clote
1994	—	`conf`	Computational Models and Function Algebras. LCC Peter Clote
1993	A*	`conf`	Parallel computable higher type functionals (Extended Abstract) FOCS Peter Clote, Aleksandar Ignjatovic, Bruce M. Kapron
1992	J	`jnl`	A Time-Space Hierarchy Between Polynomial Time and Polynomial Space. Math. Syst. Theory Peter Clote
1992	J	`jnl`	ALOGTIME and a Conjecture of S. A. Cook. Ann. Math. Artif. Intell. Peter Clote
1992	J	`jnl`	Bounded Arithmetic for NC, ALogTIME, L and NL. Ann. Pure Appl. Log. Peter Clote, Gaisi Takeuti
1992	A*	`conf`	Cutting Planes and constant depth Frege proofs LICS Peter Clote
1991	J	`jnl`	Boolean Functions, Invariance Groups, and Parallel Complexity. SIAM J. Comput. Peter Clote, Evangelos Kranakis
1990	A*	`conf`	ALOGTIME and a Conjecture of S. A. Cook (Extended Abstract) LICS Peter Clote
1990	—	`conf`	Bounded Arithmetic and Computational Complexity. SCT Peter Clote
1990	J	`jnl`	On some formalized conservation results in arithmetic. Arch. Math. Log. Peter Clote, Petr Hájek, Jeff B. Paris
1989	—	`conf`	Boolean Functions, Invariance Groups and Parallel Complexity. SCT Peter Clote
1989	J	`jnl`	The metamathematics of scattered linear orderings. Arch. Math. Log. Peter Clote
1986	J	`jnl`	A Generalization of the Limit Lemma and Clopen Games. J. Symb. Log. Peter Clote
1986	—	`conf`	Exponential Time and Bounded Arithmetic. SCT Peter Clote, Gaisi Takeuti
1986	J	`jnl`	Members of countable π Ann. Pure Appl. Log. Douglas A. Cenzer, Peter Clote, Rick L. Smith, Robert I. Soare, Stanley S. Wainer
1986	J	`jnl`	On the Finite Containment Problem for Petri Nets. Theor. Comput. Sci. Peter Clote
1985	J	`jnl`	Optimal bounds for ordinal comparison maps. Arch. Math. Log. Peter Clote
1984	J	`jnl`	A Recursion Theoretic Analysis of the Clopen Ramsey Theorem. J. Symb. Log. Peter Clote
1983	J	`jnl`	Two Further Combinatorial Theorems Equivalent to the 1-Consistency of Peano Arithmetic. J. Symb. Log. Peter Clote, Kenneth McAloon