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Peter Clote

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TOP 3
Juan Antonio Garcia-Martin; Peter Clote; Ivan Dotu
RNAiFOLD: A CONSTRAINT PROGRAMMING ALGORITHM FOR RNA INVERSE FOLDING AND MOLECULAR DESIGN.
Peter Clote; Stefan Dobrev; Ivan Dotu; Evangelos Kranakis; Danny Krizanc; Jorge Urrutia
On the page number of RNA secondary structures with pseudoknots.
Peter Clote; Yann Ponty; Jean-Marc Steyaert
Expected distance between terminal nucleotides of RNA secondary structures.

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All Publications

2013: Juan Antonio Garcia-Martin; Peter Clote; Ivan Dotu
RNAiFOLD: A CONSTRAINT PROGRAMMING ALGORITHM FOR RNA INVERSE FOLDING AND MOLECULAR DESIGN.
Journal of bioinformatics and computational biology 2013;11(2):1350001.
2012: Peter Clote; Stefan Dobrev; Ivan Dotu; Evangelos Kranakis; Danny Krizanc; Jorge Urrutia
On the page number of RNA secondary structures with pseudoknots.
Journal of mathematical biology 2012;65(6-7):1337-57.
2012: Peter Clote; Yann Ponty; Jean-Marc Steyaert
Expected distance between terminal nucleotides of RNA secondary structures.
Journal of mathematical biology 2012;65(3):581-99.
2012: Evan Senter; Saad Sheikh; Ivan Dotu; Yann Ponty; Peter Clote
Using the fast fourier transform to accelerate the computational search for RNA conformational switches.
PloS one 2012;7(12):e50506.
2012: Kourosh Zarringhalam; Jeffrey H Chuang; Ivan Dotu; Michelle M Meyer; Peter Clote
Integrating chemical footprinting data into RNA secondary structure prediction.
PloS one 2012;7(10):e45160.
2012: Peter Clote; Feng Lou; William A Lorenz
Maximum expected accuracy structural neighbors of an RNA secondary structure.
BMC bioinformatics 2012;13 Suppl 5():S6.
2011: Ivan Dotu; Pascal Van Hentenryck; Manuel Cebrián; Peter Clote
On lattice protein structure prediction revisited.
IEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM 2011;8(6):1620-32.
2011: William A Lorenz; Peter Clote
Computing the partition function for kinetically trapped RNA secondary structures.
PloS one 2011;6(1):e16178.
2011: Pascal Bochet; Frank Rügheimer; Tina Guina; Peter Brooks; David R Goodlett; Peter Clote; Benno Schwikowski
Fragmentation-free LC-MS can identify hundreds of proteins.
Proteomics 2011;11(1):22-32.
2010: Feng Lou; Peter Clote
Thermodynamics of RNA structures by Wang-Landau sampling.
Bioinformatics (Oxford, England) 2010;26(12):i278-86.
2010: Ivan Dotu; William A Lorenz; Pascal Van Hentenryck; Peter Clote
Computing folding pathways between RNA secondary structures.
Nucleic acids research 2010;38(5):1711-22.
2010: Ivan Dotú; William A Lorenz; Pascal VAN Hentenryck; Peter Clote
RNA structural segmentation.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2010;():57-68.
2009: Peter Clote; Evangelos Kranakis; Danny Krizanc; Bruno Salvy
Asymptotics of canonical and saturated RNA secondary structures.
Journal of bioinformatics and computational biology 2009;7(5):869-93.
2009: Jerome Waldispühl; Srinivas Devadas; Bonnie Berger; Peter Clote
RNAmutants: a web server to explore the mutational landscape of RNA secondary structures.
Nucleic acids research 2009;37(Web Server issue):W281-6.
2008: Y Ponty; R Istrate; E Porcelli; Peter Clote
LocalMove: computing on-lattice fits for biopolymers.
Nucleic acids research 2008;36(Web Server issue):W216-22.
2008: Jérôme Waldispühl; Charles W O'Donnell; Srinivas Devadas; Peter Clote; Bonnie Berger
Modeling ensembles of transmembrane beta-barrel proteins.
Proteins 2008;71(3):1097-112.
2008: Jérôme Waldispühl; Srinivas Devadas; Bonnie Berger; Peter Clote
Efficient algorithms for probing the RNA mutation landscape.
PLoS computational biology 2008;4(8):e1000124.
2008: W A Lorenz; Y Ponty; Peter Clote
Asymptotics of RNA shapes.
Journal of computational biology : a journal of computational molecular cell biology 2008;15(1):31-63.
2008: Peter Clote
Introduction to special issue on RNA.
Journal of mathematical biology 2008;56(1-2):3-13.
2007: Eva Freyhult; Vincent Moulton; Peter Clote
Boltzmann probability of RNA structural neighbors and riboswitch detection.
Bioinformatics (Oxford, England) 2007;23(16):2054-62.
2007: Fabrizio Ferrè; Y Ponty; W A Lorenz; Peter Clote
DIAL: a web server for the pairwise alignment of two RNA three-dimensional structures using nucleotide, dihedral angle and base-pairing similarities.
Nucleic acids research 2007;35(Web Server issue):W659-68.
2007: Eva Freyhult; Vincent Moulton; Peter Clote
RNAbor: a web server for RNA structural neighbors.
Nucleic acids research 2007;35(Web Server issue):W305-9.
2007: J Waldispühl; Peter Clote
Computing the partition function and sampling for saturated secondary structures of RNA, with respect to the Turner energy model.
Journal of computational biology : a journal of computational molecular cell biology 2007;14(2):190-215.
2006: Peter Clote
Combinatorics of saturated secondary structures of RNA.
Journal of computational biology : a journal of computational molecular cell biology 2006;13(9):1640-57.
2006: J Waldispühl; Bonnie Berger; Peter Clote; Jean-Marc Steyaert
Predicting transmembrane beta-barrels and interstrand residue interactions from sequence.
Proteins 2006;65(1):61-74.
2006: Fabrizio Ferrè; Peter Clote
BTW: a web server for Boltzmann time warping of gene expression time series.
Nucleic acids research 2006;34(Web Server issue):W482-5.
2006: J Waldispühl; Bonnie Berger; Peter Clote; Jean-Marc Steyaert
transFold: a web server for predicting the structure and residue contacts of transmembrane beta-barrels.
Nucleic acids research 2006;34(Web Server issue):W189-93.
2006: Fabrizio Ferrè; Peter Clote
DiANNA 1.1: an extension of the DiANNA web server for ternary cysteine classification.
Nucleic acids research 2006;34(Web Server issue):W182-5.
2006: Peter Clote; Jürg Straubhaar
Symmetric time warping, Boltzmann pair probabilities and functional genomics.
Journal of mathematical biology 2006;53(1):135-61.
2005: Peter Clote; J Waldispühl; B Behzadi; Jean-Marc Steyaert
Energy landscape of k-point mutants of an RNA molecule.
Bioinformatics (Oxford, England) 2005;21(22):4140-7.
2005: Peter Clote; Leszek Gasieniec; Roman Kolpakov; Evangelos Kranakis; Danny Krizanc
On realizing shapes in the theory of RNA neutral networks.
Journal of theoretical biology 2005;236(2):216-27.
2005: Peter Clote
RNALOSS: a web server for RNA locally optimal secondary structures.
Nucleic acids research 2005;33(Web Server issue):W600-4.
2005: Fabrizio Ferrè; Peter Clote
DiANNA: a web server for disulfide connectivity prediction.
Nucleic acids research 2005;33(Web Server issue):W230-2.
2005: Fabrizio Ferrè; Peter Clote
Disulfide connectivity prediction using secondary structure information and diresidue frequencies.
Bioinformatics (Oxford, England) 2005;21(10):2336-46.
2005: Peter Clote; Fabrizio Ferré; Evangelos Kranakis; Danny Krizanc
Structural RNA has lower folding energy than random RNA of the same dinucleotide frequency.
RNA (New York, N.Y.) 2005;11(5):578-91.
2005: Peter Clote
An efficient algorithm to compute the landscape of locally optimal RNA secondary structures with respect to the Nussinov-Jacobson energy model.
Journal of computational biology : a journal of computational molecular cell biology 2005;12(1):83-101.