Biology Department Faculty
Peter Clote
Professor
Peter Clote
Ph.D.
Contact
Higgins Hall 577
Telephone: 617-552-1332
Email: peter.clote@bc.edu
ORCID 0000-0003-3628-2874
Education
- Sc.B., Massachusetts Institute of Technology
- Ph.D., Duke University
- Doctorat d'Etat, University of Paris VII
Research Interests
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).
Department
Research
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.).
Our lab is interested in such questions, especially in the development of new thermodynamics-based algorithms to better understand the folding and folding kinetics of such RNA. We are interested in the computational design of synthetic ribozymes (ribonucleic acid enzymes), synthetic riboswitches (RNAs that regulate genes by allostery), synthetic thermozymes (regulatory RNAs that are triggered by temperature change) and other RNA classes -- work that contributes to synthetic biology, the "wet" analogue of nanotechnology, a field that could be dominant in the 21st century.
Selected Publications
More publications can be viewed on Dr. Clote's Website
- P. Clote, A. Bayegan. RNA folding kinetics using Monte Carlo and Gillespie algorithms. J Math Biol, in press (2017), arXiv article ID 1707.03922.
- Bayegan AH and Clote P. "An IP algorithm for RNA folding trajectories", Workshop on Algorithms in Bioinformatics (WABI 2017), August 21-23, 2017, Boston, MA. WABI2017 is part of the eighth ACM-BCB 2017 (ACM Conference on Bioinformatics, Computational Biology and Health Informatics).
- Bayegan AH, Garcia-Martin JA, and Clote P. New tools to analyze overlapping coding regions. BMC Bioinformatics. 2016 Dec 13;17(1):530.
- Garcia-Martin JA, Dotu I, Fernandez-Chamorro J, Lozano G, Ramajo J, Martinez-Salas E, Clote P. RNAiFold2T: Constraint Programming design of thermo-IRES switches. Bioinformatics. 2016 Jun 15;32(12):i360-i368. doi: 10.1093/bioinformatics/btw265.
- Clote P, Bayegan A. Network Properties of the Ensemble of RNA Structures. PLoS One. 2015 Oct 21;10(10):e0139476. doi: 10.1371/journal.pone.0139476.
- Garcia-Martin JA, Dotu I, Clote P. 1. RNAiFold 2.0 A web server and software to design custom and Rfam-based RNA molecules. Nucleic Acids Research Web Server issue, 2015, doi: 10.1093/nar/gkv460
- Senter E, Clote P. Fast, approximate kinetics of RNA folding. J Comp Biol, Vol. 22, No. 2, February 2015: 124-144.
- Dotu I, Garcia-Martin JA, Slinger BL, Mechery V, Meyer MM, Clote P. Complete RNA inverse folding: computational design of functional hammerhead ribozymes. Nucleic Acids Res. 2015 Feb 1;42(18):11752-62. doi: 10.1093/nar/gku740.
- Clote P. Expected degree of RNA secondary structure networks. J Comput Chem. 2015 Jan 15;36(2):103-17. doi: 10.1002/jcc.23776.
- Dotu I, Lozano G, Clote P, Martinez-Salas E. Using RNA inverse folding to identify IRES-like structural subdomains. RNA Biol. 2013 Dec 1;10(12):1842-52. doi: 10.4161/rna.26994.
- Senter E, Sheikh S, Dotu I, Ponty Y, Clote P. Using the Fast Fourier Transform to accelerate the computational search for RNA conformational switches. PLoS One. 2012;7(12):e50506. doi: 10.1371/journal.pone.0050506.
- 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. doi: 10.1371/journal.pone.0045160.
- 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.
- 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.
- Feng Lou, Peter Clote. Thermodynamics of RNA structures by Wang-Landau sampling. ISMB2010, Bioinformatics 2010 Jun 15;26(12):i278-86.
- 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.
- Eva Freyhult; Vincent Moulton; Peter Clote. Boltzmann probability of RNA structural neighbors and riboswitch detection. Bioinformatics. 2007 Aug 15;23(16):2054-62.
- F. Ferre, P. Clote. DiANNA 1.1: An extension of the DiANNA web server for ternary cysteine classification, Nucleic Acids Res. 34(Web Server issue):W182-5 (2006).
- P. Clote, F. Ferre, E. Kranakis, D. Krizanc. Structural RNA has lower folding energy than random RNA of the same dinucleotide frequency. RNA, 11(5):578-591 (2005).
- F. Ferre and P. Clote. Disulfide connectivity prediction using secondary structure information and diresidue frequencies, Bioinformatics 21(10):2336-2346 (2005). BibTeX entry
- P. Clote and R. Backofen. Computational Biology: an Introduction. John Wiley & Sons, Ltd., 286 pages (2000), ISBN 0-471-87251-2. Japanese translation (2005). ISBN 4-320-05615-9.
- P. Clote and E. Kranakis. Boolean Functions and Computation Models. Springer-Verlag, 601 pages (2002), ISBN 3-540-59436-1.
- S.R. Buss and P. Clote. Solving the Fisher-Wright and coalescence problems with a discrete Markov chain analysis. Advances in Applied Probability, 36(3), 1175-1197 (2004).