Biography

Since September 1st 2009, I am assistant professor in the School of Computer Science at McGill University. My area of research is computation structural biology. I am a member of the McGill Centre for Bioinformatics.

I did my PHD in the computer science laboratory (LIX) of Ecole Polytechnique, where I worked on transmembrane protein structure prediction algorithms under the mentorship of Jean-Marc Steyaert.

In January 2005, I moved to Boston to work with Peter Clote on RNA secondary structure prediction algorithms. I resumed a work started during my PhD on the development of algorithms for exploring the RNA mutation landscape. This project has been subsequently funded by the NSF.

Six month later, I joined silmutaneously the Bonnie Berger and Srinivas Devadas groups to extend my work on protein structure prediction.

In July 2006, I joined the Applied Mathematics Department at MIT as an Instructor.

From July 1st 2006 to June 30-th 2009, I have been an Instructor in Applied Mathematics in the Department of Mathematics of the Massachusetts Institute of Technology. I was a member of both Bonnie Berger and Srinivas Devadas groups. I remain affiliated to the MIT Computer Science and Artificial Intelligence Laboratory (CSAIL) as a research affiliate.

Curriculum Vitæ [Link to PDF]

Research Interests

Protein and RNA folding, formal language theory, statistical mechanics, evolution.

Current position

Sep. 2009	Assistant Professor of Computer Science, McGill University.
	Member of the McGill Centre for Bioinformatics.
	Research affiliate at the MIT Computer Science and AI Laboratory.

Education

Nov. 2004	PhD in Computer Science with honors.
	École Polytechnique (France)
	Title: “Modeling and Predicting the Structure of Transmembrane Proteins”
	Supervisor: Jean-Marc Steyaert.
	Referees: Peter Clote, Marie-France Sagot.
	Committee: Christian Choffrut (Chair), Alessandra Carbone, Philippe Dessen, Thomas Simonson.
Jul. 2000	M.S. in Computer Science with honors.
	University of Paris VII Denis Diderot (France)
	Majors: computer algebra, algorithm analysis, combinatorics.
	M.S. thesis: “Analysis of Combinatorial Properties of Protein Folding”.
	Supervisor: Jean-Marc Steyaert.
Jun. 1999	B.S. in Mathematics with honors.
	University of Nice and Sophia-Antipolis (France)
	Algebra, complex analysis, differential calculus, geometry, numerical analysis, probability, statistics, topology.
	B.S. thesis: “Ehrhart Polynomial, Cooccurence Matrices and Applications to Medical Imaging”.
	Supervisor: Loic Pottier.

Past Experience

2006-2009	Instructor, Applied Mathematics, M.I.T., USA.
2005-2009	Postdoctoral Associate, Computer Science and AI Laboratory, M.I.T., USA.
2005-2006	Postdoctoral Associate, Department of Biology, Boston College, USA.
2003-2004	Instructor in Computer Science, University of Paris VII, France.
2000-2003	Teaching assistant in Computer Science, École Polytechnique, France.

Awards and Honors

2000-2003	PhD Fellowship from the French Ministry for Research.
2000-2003	Teaching Fellowship (monitorat) from the Academy of Versailles (France).
1999-2000	Master Fellowship from the University of Paris VII (France).

Contributions to the Community

Selected invited talks (Conferences, Symposiums, Workshops):

MonBUG symposium, Montreal, Canada, September 2009.
Symposium of the Cluster of Excellence "Multimodal Computing and Interaction", Saarland University, Saarbrucken, Germany, March 2009.
Thirteenth Annual Meeting of the RNA society, Berlin, Germany, July 2008
IMA Workshop on Protein Folding, Minneapolis, USA, January 2008.

Program Committees:

Program Committee Member of the Fourteenth Annual International Conference on Research in Computational Molecular Biology (RECOMB 2010), Lisbon, April 2010.
Program Committee Member of the Eightteenth Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2010), Cambridge, July 2010.

Organizing Committees:

Organizing commitee of the McGill System Biology training program open house, Montreal, February 4th, 2010.
Organizing commitee of the LIX symposium: “Bioinformatics: algorithms, structures and statistics”, Palaiseau, December 2005.
Chief of the technical staff of the South West European Regional programming Contest of ACM, École Polytechnique, Palaiseau, France, November 2004.
Member of the technical staff of the South West European Regional programming Contest of ACM, École Polytechnique, Palaiseau, France, November 2003.

Administrative duties:

SOCS PhD committee, School of Computer Science (SOCS), McGill, Since 2009.
PhD student representative (elected) at the computer science department council, École Polytechnique, Palaiseau, France, 2003-2005.
PhD student representative (elected) at the Academy of Versailles council, France, 2001-2002.

Teachings:

McGill (Since 2010): 1 Undergraduate Class (Lecturer).
MIT (2006-2009): 3 Graduate Classes (Lecturer), 3 Undergraduate Classes (TA).
University Paris VII (2002-2004): 2 Graduate Classes (Lecturer), 4 Undergraduate Classes (1 as Lecturer & 3 as TA).
École Polytechnique (2000-2004): 9 Undergraduate Classes (TA).

Training of Highly Qualified Personnel

Masters

Philippe Antoine, “Using NMR data for Transmembrane β-barrel structure prediction”, M.S.École Polytechnique, France, 2007.

Undergraduates

Solomon Shenker, “Ensemble Modeling of β-structures”, McGill, 2010.
Kelley Bailey, “Analysis of Protein Loop Flexibility”, MIT, 2008.
Natasha Plotkins, “Reconstruction of Transmembrane β-barrel from contacts”, MIT, 2008.

This document was translated from L^AT_EX by H^EV^EA.