Peter Clote, Ph.D., Doctorat d'Etat

Professor, Dept of Biology
Dept of Computer Science (courtesy appointment)

Biology Department, Higgins Hall 577, Boston College
140 Commonwealth Avenue
Chestnut Hill, MA 02467
Email: clote@bc.edu
Tel: (617) 552-1332, Fax: (617) 552-2011
Map to Boston College: approach maps, enlarged campus map

See CLOTE Computational Biology LAB for lab members, publications, web servers, etc.


Research Interests

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 kinetics?


Recent Grants

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).


Brief Bio

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, etc.

Full publication list is HERE. For PDF files of articles since around 2000, go here.

Current Courses

Jazz

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.

jazz group


Graduate training in bioinformatics at BC | MIT Bioinformatics Seminar | Research Interests | Current Courses | Publications in Computational Biology | Publications | Boolean Functions and Computation Models | Computational Molecular Biology: An Introduction | Recent Papers | Jazz trio Sharp Eleventh


Last update: Mon Mar 2 16:20:44 EST 2015

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Peter Clote, clote@bc.edu