Department of Mathematics

18.418: Topics in Computational Molecular Biology

Covers current research topics in computational molecular biology. Recent research papers presented from leading conferences such as the International Conference on Computational Molecular Biology (RECOMB), the Pacific Symposium on Biocomputing (PSB), and the Intelligent Systems for Molecular Biology (ISMB). Topic areas include original research (both theoretical and experimental) in genomics, molecular sequence analysis, recognition of genes and regulatory elements, molecular evolution, protein, and RNA structure, and combinatorial libraries for drug design. Recent research by course participants also covered.


Attendance is mandatory and it will be taken at each meeting and count toward your overall grade. Participation will also factor into your grade.

The class meeting on Wednesdays will be guest lecturers who will present various research topics. Information concerning the series can be found at the seminar's web page:

The class meeting on Mondays will be either group or individual (depending upon enrollment) projects by student seminar members. A copy of the powerpoint presentation or your notes (typed preferred) with bibliography will be due the day of your talk.

There is not a final for this class.

The class will not meet the following days: Feb 16, Mar 23, Mar 25, and May 20.

Prerequisites: 18.417, 6.085, 6.8745 or permission of instructor.

Please note that only graduate students may repeat the class for credit; undergrads (Juniors and Seniors) are welcomed to take the class once for credit & encouraged to sit in as listeners if they wish to repeat the class. Freshmen and Sophmores are welcome as listeners only & only with permission of the instructor.

Please note that this page and the information on it are subject to change.

Time & Location

Class Meeting Time: 11:30 - 1:00 in The Theory of Computation Lab Room Building 32, Room G575

Office Hours for Professor Berger: 10:30-11:30am, Wednesdays (CSAIL office, 32G-574) or by appointment.


Date Lecture
Feb 4 Bonnie Berger Lecture: Introduction to the Course
Feb 9 Guest Lecturer Michael Baym
Feb 11 Guest Lecturer Lenore Cowan, Tufts
Feb 16 Holiday (President's Day) No Meeting
Feb 17 Class Discussion Student Presentations
Feb 18 Guest Lecturer Shuba Gopal, formerly Rochester Institute of Technology
Feb 23 Class Discussion Student Presentations: Po-Ru Loh
Feb 25 Guest Lecturer Francois-Major, University of Montreal
Mar 2 Special Guest Lecturer POSTPONED Amy Keating, MIT
Mar 4 Guest Lecturer Amy Keating, MIT
Mar 9 Class Discussion Student Presentations: Michael Yu
Mar 11 Guest Lecturer Rolf Backofen, Universitat Freiburg
Mar 16 Guest Lecturer Peter Clote, BC
Mar 18 Guest Lecturer Tobias Bollenbach, Harvard
Mar 23 Spring Break No Meeting
Mar 25 Spring Break No Meeting
Mar 30 Guest Lecturer Jinbo Xu, Toyota Technological Institute of Chicago
Apr 1 Guest Lecturer David Reich, Harvard School of Public Health
Apr 6 Class Discussion Student Presentations: Ardavan F. Oskooi
Apr 8 Guest Lecturer Samuel Kou, Harvard
Apr 13 Class Discussion Student Presentations: Arjun Manrai
Apr 15 Guest Lecturer Austin Che
Apr 20 Holiday (Patriots Day) No Meeting
Apr 22 Guest Lecturer Charles W. O'Donnell
Apr 27 Class Discussion Student Presentations: Jiawei Chiu
Apr 29 Guest Lecturer Ivan Dotu, Brown
May 4 Class Discussion Student Presentations: Irene Kaplow
May 6 Guest Lecturer Jim Collins, BU
May 11 Class Discussion Student Presentations: Alex Levin/Leonid Chindelevitch
May 13 Guest Lecturer Jin Liu, Harvard
May 18 Final Exams No Meeting

Instructor: Bonnie Berger, Assistant: Patrice Macaluso
Contact Information: bab at mit dot edu, x3-1827, 32-G574, 2-373.
Contact Information: macaluso at mit dot edu, x3-3037, 32-G568.

Please contact Professor Berger via email directly for further information concerning this class.

Site last updated 2 February, 2009 16:48

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