Fields of Interest

Computational biology/bioinformatics, structural and systems biology, RNA folding landscape, RNA tertiary motifs, RNA kinetics, protein 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.

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Representative Publications

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

Dotú, I., Lorenz, W.A., Van Hentenryck, P., Clote, P. 2010. RNA Structural Segmentation. Proceedings of the Pacific Symposium, Biocomputing 2010: 57–68.

Dotú, I., Lorenz, W.A., Van Hentenryck, P., Clote, P. 2010. Computing folding pathways between RNA secondary structures. Nucleic Acids Research 38(5): 1711–1722.

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%.