Peter Clote, Ph.D., Doctorat d'Etat
Professor, Dept of Biology
Dept of Computer Science (courtesy appointment)
Biology Department, Higgins Hall 577,
140 Commonwealth Avenue
Chestnut Hill, MA 02467
Tel: (617) 552-1332, Fax: (617) 552-2011
Map to Boston College:
enlarged campus map
CLOTE Computational Biology LAB
for lab members,
web servers, etc.
Our lab is driven by an interest to develop novel algorithmic approaches
to fundamental problems of molecular biology, with a focus on aspects of
RNA structure. Since RNA can fulfill both an information
coding as well as a catalytic role, it is a promising
molecule of choice for synthetic design and application. Indeed,
it is now commonly believed that prior to the
emergence of DNA and protein, there was a primeval "RNA world" (W. Gilbert's
RNA world hypothesis). Moreover, RNA secondary structure enjoys a
coarse-grained, yet reasonably accurate physics-based model, which allows
the development of algorithms to predict how RNA folds, to determine those
RNA sequences that fold into a target structure, to solve coarse-grained
folding kinetics using rate matrices, etc. Take a look at out
publications to see our work on the following questions:
How can one design synthetic RNAs that are likely to perform the same
function as that of a particular Rfam family of RNAs?
How can one compute fast, approximate folding kinetics, given the fact that
there are exponentially many structures and the Gillespie algorithm is slow
and must be iterated an enormous number of times for reasonably accurate
NSF project in synthetic biology DBI-1262439 (current),
Guggenheim Fellowship in Applied Mathematics (8/2013-7/2014),
Deutscher Akademischer Austauschdienst 2014,
NSF DMS-1016618 (9/2010-8/2013),
NSF DMS-0817971 (9/2008-8/2011),
Digiteo Foundation Chair of Excellence (Ecole
Polytechnique and l'Université Paris-Sud 7/2008-8/2012).
Deutscher Akademischer Austauschdienst (7/2008 and 8/2009),
NSF DBI-0543506 (4/2006-3/2011).
Dr. Clote has an unusual background, having held faculty positions in
Mathematics, Computer Science and Biology in France, Germany and the
United States, including the tenured Gentzen Computer Science Chair in
Munich, and a visiting Digiteo Chair of Excellence at Ecole Polytechnique.
This unique experience, including biochemistry lab work as an
undergraduate, provides for an interest and familiarity with the
mathematical, algorithmic and physical chemical issues that concern the
research in computational biology – especially RNA and protein structural
bioinformatics. Some recent computational research of Dr. Clote and co-workers:
Dr. Clote has co-written 2 books, co-edited 3 books, and published over
100 peer-reviewed journal articles and book chapters, in subjects ranging
from synthetic biology, riboswitch prediction using thermodynamic methods,
disulfide bond topology prediction using novel neural net architecture and
support vector machines, design of programming languages that capture
fast parallel complexity classes, boolean circuit complexity upper bounds using
classification of finite simple groups, ultraproducts, fast-growing
combinatorial functions, combinatorial independence results in Peano arithmetic,
Algorithm using the fast Fourier transform to compute 1D and 2D
projections of RNA energy landscapes with applications to conformational
switch detection and RNA kinetics.
Algorithm to predict
RNA secondary structure prediction that incorporates in-line probing and
SHAPE (selective 2’hydroxyl acylation analyzed by primer extension) data.
Algorithm for RNA inverse folding and molecular design (work of Ivan Dotu
and Juan-Antonio Garcia-Martin).
Design of synthetic hammerhead ribozymes, experimentally confirmed to be
Various additional algorithms including thermodynamic structural entropy,
expected degree of the network of RNA secondary structures, etc.
Full publication list is
PDF files of articles since around 2000, go
an Introduction to Bioinformatics.
Semi-professional jazz musician
(sax, flute). I compose for our trio
Sharp Eleventh. We perform
especially for conference banquets and
international meetings. For full-length sample recordings, go to
Sharp Eleventh Web Site.
Graduate training in bioinformatics at BC
MIT Bioinformatics Seminar
Publications in Computational Biology
Boolean Functions and Computation Models
Computational Molecular Biology: An Introduction
Jazz trio Sharp Eleventh
Last update: Mon Mar 2 16:20:44 EST 2015
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Peter Clote, email@example.com