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Peter Clote

professor of biology

Peter Clote

Ph.D., Duke University
D.Sc., University of Paris VII

Phone: 617-552-1332

Dr. Clote's website

Dr. Clote's Lab website

Fields of Interest

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).

Academic Profile

It has emerged that RNA plays a wide range of previously unsuspected roles in many biological processes, including retranslation of the genetic code (selenocysteine insertion, ribosomal frameshift transcriptional and translational gene regulation, temperature sensitive conformational switches, chemical modification of specific nucleotides in the ribosome, regulation of alternative splicing, etc.

It is now understood that RNA is pervasively expressed in the human genome, many of the transcripts of no known function, while mRNA, tRNA, rRNA and small RNAs (microRNA, piRNA, etc.) account only for a fraction of the total human transcriptome. What is the function of this RNA? What new regulatory roles are played by RNA? What is the fingerprint of small RNAs of healthy versus tumorous cells?

Our lab is interested in such questions, especially in the development of new thermodynamics-based algorithms to better understand such RNA. Such ab initio free energy based modeling is the only possible method for the study of orphan RNAs and especially in the design of novel RNA molecules in synthetic biology.

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RNA1 diagram RNA2 diagram



Representative Publications

More publications can be viewed on Dr. Clote's Website

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.

Waldispühl, J., Berger, B., Clote, P., and Steyaert, J.-M. 2006. Predicting transmembrane beta-barrels and interstrand residue interactions from sequence. Proteins 65(1): 61–74.

Ferre, F., Clote, P. 2006. BTW: A web server for Boltzmann time warping of gene expression time series. Nucleic Acids Research (Web Server issue) 34: W482–5.

Ferre, F., Clote, P. 2006. DiANNA 1.1: An extension of the DiANNA web server for ternary cysteine classification. Nucleic Acids Research (Web Server issue) 34: W182–5.

Clote, P., Waldispühl, J., Behzadi, B., and Steyaert, J.-M. 2005. Energy landscape of k-point mutants of an RNA molecule. Bioinformatics 21: 4140–4147.

Clote, P. 2005. 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 12(1): 83–101.

Clote, P., Ferre, F., Kranakis, E., Krizanc, D. 2005. Structural RNA has lower folding energy than random RNA of the same dinucleotide frequency. RNA 11(5): 578–591.

Clote, P., Ferre, F. 2005. Disulfide connectivity prediction using secondary structure information and diresidue frequencies. Bioinformatics 21(10): 2336–2346.

Clote, P., and Kranakis, E. 2002. Boolean Functions and Computation Models. Springer-Verlag, 601 pages.

Clote, P., and Backofen, R. 2000. Computational Molecular Biology: An Introduction. Wiley & Sons, 286 pages, Japanese translation (2005).

** The conference proceedings publications are peer-reviewed and very competitive, with an acceptance rate of about 20%.