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. Abstracts will be sent by email prior to each talk.

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:

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 7 Bonnie Berger Lecture: Introduction to the Course
Feb 12 Class Discussion Student Presentations: Mitchell Guttman and Leonid Chindelevitch
Feb 14 Guest Lecturer Jadwiga Bienkowska, biogen/BU
Feb 19 Holiday (President's Day)
No Meeting
Feb 21 Guest Lecturer Vladimer Kuznetsov, Genome Institute of Singapore
Feb 26 Class Discussion
Student Presentations: Michael Schnall-Levin and Xia Hua
Feb 28 Guest Lecturer Vincent Danos, CNRS, University of Paris Diderot-Paris 7
Mar 5 Class Discussion
Student Presentations:
Mar 7 Guest Lecturer Aedin Culhane, Harvard School of Public Health
Mar 12 Class Discussion
Student Presentations:
Mar 14 Guest Lecturer Chris Bakal, Harvard Medical
Mar 19 Class Discussion
Student Presentations: Xia Carol Hua
Mar 21 Guest Lecturer Alexander Stark, Broad Institute
Mar 26 Spring Break
No Meeting
Mar 28 Spring Break
No Meeting
Apr 2 Guest Lecturer Nancy Amato, Texas A&M
Apr 4 Guest Lecturer Marco Ramoni, HMS/HST
Apr 9 Class Discussion
Student Presentations:
Apr 11 Guest Lecturer Borya Shakhnovich, Broad Institute
Apr 16 Holiday (Patriot's Day) No Meeting
Apr 18 Guest Lecturer Dana Peer, Columbia
Apr 23 Class Discussion
Student Presentations: Daniel Schultz, Michal Wexler
Apr 25 Guest Lecturer Eytan Domany, Weizmann Institute for Science
Apr 30 Class Discussion
Student Presentations:David Dryjanksi, Charles O'Donnell
May 2 Guest Lecturer Yann Ponty, BC
May 7 Class Discussion
Student Presentations:
May 9 Guest Lecturer Yi-Kuo Yu, NIH
May 14 Class Discussion
Student Presentations:
May 16 Class Discussion
Informal Discussions: Meet in 32-575 if you want to touch base with Prof. Berger. Class not mandatory.
May 21 Finals Week No Meeting
May 23 Finals Week No Meeting

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

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

Site last updated 07 February 2007

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