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 SIGACT International Conference on Computational Molecular Biology (RECOMB). Topic areas include original research (both theoretical and experimental) in genomics, molecular sequence analysis, recognition of genes and regulatory elements, molecular evolution, protein structure, and combinatorial libraries and 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 Mondays will be guest lecturers who will present various research topics. Abstracts will be sent by email prior to each talk.

The class meeting on Wednesdays 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:

Monday, Feb 20; the week of Mar 27; and Apr 17.

Prerequisites: 18.417 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: in The Theory of Computation Lab Room Building 32, Room G575 on Mondays & in room 2-105 on Wednesdays

Office Hours for Professor Berger: 1-2pm, Wednesdays (room TBA) or by appointment.

General Directions to MIT:
Direction to Building 32:

Direction to Building 2:


Date Lecture
Feb 8 Bonnie Berger Lecture: Introduction to the Course
Feb 13 Guest Lecturer Joachim Theilhaber, Aventis
Feb 15 Class Discussion Student Presentations: Nathan Palmer & Rohit Singh
Feb 20 Holiday (President's Day)
No Meeting
Feb 22 Class Discussion Student Presentations: Oaz Nir & Patrick Schmid
Feb 27 Guest Lecturer
Paul de Bakker, MGH-Molecular Biology
Mar 1 Class Discussion Student Presentations: Manuel Rivas
Mar 6 Guest Lecturer: William M. Gelbart, Harvard
Mar 8 Class Discussion Student Presentations: Philip Cassel, Manuel Rivas & Yahli Becker
Mar 13 Guest Lecturer: Jacques Cohen, Brandeis
Mar 15 Class Discussion Student Presentations: Sophie Rapoport & Lele Yin
Mar 20 Guest Lecturer: Karen Sachs, MIT
Mar 22 No Class Student Presentations: NO CLASS
Mar 27 Spring Break No Meeting
Mar 29 Spring Break No Meeting
Apr 3 Guest Lecturer: Michael Zuker, RPI
Apr 5 Class Discussion Student Presentations: Frances Ragoz, Sarah Lee & Caroline Jordan
Apr 10 Guest Lecturer:  Amy Keating, MIT
Apr 12 Class Discussion Student Presentations:Luke Hutchison
Apr 17 Holiday (Patriot's Day) No Meeting
Apr 19 Class Discussion Student Presentations: Allen Bryan
Apr 24 Guest Lecturer: Manolis Kellis, MIT
Apr 26 Class Discussion Student Presentations: Helen Belogolova, Alexander Chernyakov & Michael Beregovsky
May 1 Guest Lecturer: Serafim Batzoglou, Stanford
May 3 Class Discussion Student Presentations: Amjad Afanah & Abdul Tarbzouni
May 8 Guest Lecturer: Mona Singh, Princeton
May 11 Class Discussion Student Presentations: Phil Murray & Danny Kanamori
May 15 Guest Lecturer: Jinbo Xu , TTI
May 17 Class Discussion Informal Discussions : Meet in 32-G574 if you want to touch base with Professor Berger, class not mandatory
May 22 Finals Week No Meeting
May 24 Finals Week No Meeting

Instructor: Bonnie Berger
Contact Information:, x3-1827, 2-373.
Course Support: Kathleen Dickey
Contact, x3-3037, 32-G591a.

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

To join the class email list, please email


Site last updated 16 May, 2006 23:12

Massachusetts Institute
of Technology
77 Massachusetts Avenue
Cambridge, MA 02139