Clote, Peter - Boston College - Department of Biology

研究领域

Computational biology/bioinformatics, synthetic biology,structural and systems biology, RNA molecular design, kinetics, RNA tertiary structure motifs, macromolecular structure, molecular evolution, machine learning in bioinformatics (neural nets, support vector machines).

近期论文

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Juan Antonio Garcia-Martin, Peter Clote, Ivan Dotu. RNAiFold: A constraint programming algorithm for RNA inverse folding and molecular design. J Bioinform Comput Biol. 11(2): 1350001, 2013. E. Senter, S. Sheik, I. Dotu, Y. Ponty, P. Clote. Using the Fast Fourier Transform to accelerate the computational search for RNA conformational switches. PLoS One. 2012;7(12):e50506. K. Zarringhalam, M.M. Meyer, I. Dotu, J.H. Chuang, P.Clote. Integrating chemical footprinting data into RNA secondary structure prediction. PLoS One. 2012;7(10):e45160. Clote P, Lou F, Lorenz WA. Maximum expected accuracy structural neighbors of an RNA secondary structure. BMC Bioinformatics. 2012 Apr 12;13 Suppl 5:S6. doi: 10.1186/1471-2105-13-S5-S6. Clote P, Dobrev S, Dotu I, Kranakis E, Krizanc D, Urrutia J. On the page number of RNA secondary structures with pseudoknots. J Math Biol. 2012 Dec;65(6-7):1337-57. P. Clote, Y. Ponty, J.-M. Steyaert. Expected distance between terminal nucleotides of RNA secondary structures. J Math Biol. 2012 Sep;65(3):581-99. Epub 2011 Oct 9. Feng Lou, Alain Denise and Peter Clote. A new approach to suboptimal pairwise sequence alignment. IASTED conference CompBio. 2011, July 11-13, 2011, Cambridge, UK. P. Bochet, F. Rüheimer, T. Guina, P. Brooks, D. Goodlett, P. Clote, B. Schwikowski. Fragmentation-free LC-MS can identify hundreds of proteins. Proteomics, 2011 Jan;11(1):22-32. W.A. Lorenz, P. Clote. Computing the partition function for kinetically trapped RNA secondary structures. Public Library of Science One (PLoS ONE), (2011) PLoS ONE 6(1): e16178. doi:10.1371/journal.pone.0016178. I. Dotú, W.A. Lorenz, P. Van Hentenryck, P. Clote. Computing folding pathways between RNA secondary structures. Nucleic Acids Res. 2010 Mar 1;38(5):1711-22. Feng Lou, Peter Clote. Thermodynamics of RNA structures by Wang-Landau sampling. ISMB 2010, Bioinformatics 2010 Jun 15;26(12):i278-86. Dotú, I., Lorenz, W.A., Van Hentenryck, P., Clote, P. 2010. RNA Structural Segmentation. Proceedings of the Pacific Symposium, Biocomputing 2010: 57–68. Clote, P., Kranakis, E., Krizanc, D., Salvy, B. 2009. Asymptotics of canonical and saturated RNA secondary structures. Journal of Bioinformatics and Computational Biology 7(5): 869–93. Waldispühl, J., Devadas, S., Berger, B., Clote, P. 2009. RNAmutants: A web server to explore the mutational landscape of RNA secondary structures. Nucleic Acids Research (Web Server issue) 37: W281–6. Clote, P., Kranakis, E., Krizanc, D. 2009. Asymptotics of canonical RNA secondary structures. 9th IEEE Conference on Bioinformatics and Bioengineering (BIBE 2009) Proceedings**. June 22-24, 2009, Taichung, Taiwan. Waldispühl, J., Devadas, S., Berger, B., Clote, P. 2008. Efficient algorithms for probing the RNA mutation landscape. PLoS Computational Biology 4(8): e1000124. Dotú, I., Cebrián, M., Van Hentenryck, P., Clote, P. 2008. Protein structure prediction with large neighborhood constraint programming search. Principles and Practice of Constraint Programming **(pp. 82-96), 14th International Conference, CP 2008, Sydney, Australia, September 14-18, 2008, Proceedings Series: Lecture Notes in Computer Science Subseries: Programming and Software Engineering , Vol. 5202 Stuckey, Peter J. (Ed.) 2008, XVII, 648 p., Softcover ISBN: 978-3-540-85957-4. Ponty, Y., Istrate, R., Porcelli, E., Clote, P. 2008. LocalMove: Computing on-lattice fits for biopolymers. Nucleic Acids Research (Web Server issue) 36: W216–W222. Dotú, I., Cebrián, M., Van Hentenryck, P., Clote, P. 2008. A local search approach to protein structure prediciton on the face centered cubic lattice. Twenty-Third Association for the Advancement of Artificial Intelligence Conference on Artificial Intelligence (AAAI-08)**, July 13-17, 2008. Lorenz, W.A., Ponty, Y., and Clote, P. 2008. Asymptotics of RNA shapes. Journal of Computational Biology 15(1): 31–63. Clote, P. 2008. Introduction to special issue on RNA. Journal of Mathematical Biology 56 (1–2): 3–13. Freyhult, E., Moulton, V., Clote, P. 2007. Boltzmann probability of RNA structural neighbors and riboswitch detection. Bioinformatics 23(16): 2054–62. Ferre, F., Ponty, Y., Lorenz, W. A., Clote, P. 2007. 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 (Web Server issue) 35: W659–W668. Waldispühl, J., Clote, P. 2007. Computing the partition function and sampling for saturated secondary structures of RNA, with respect to the Turner energy model. Journal of Computational Biology 14(2): 190–215. Clote, P. 2006. Combinatorics of saturated secondary structures of RNA. Journal of Computational Biology 13(9): 1640–1657.