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, and Mar 25.

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: Monday & Wednesday 11:30 - 1:00. We meet in two different classrooms. On Mondays, the class is in 56-180, and on Wednesdays, it is in 32-G575 (Gates Tower of the Stata Center)

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 Class Discussion Student Presentations
Feb 11 Guest Lecturer Noam Kaplan, UMass Medical
Feb 16 President's Day No Meeting
Feb 18 Guest Lecturer Po-Ru Loh, Harvard Medical
Feb 23 Class Discussion Student Presentations
Feb 25 Guest Lecturer Uri Alon, Weizmann Institute of Science
Mar  2 Class Discussion Student Presentations
Mar  4 Guest Lecturer Jerome Waldispuhl, McGill
Mar  9 Class Discussion Student Presentations
Mar 11 Guest Lecturer David Reich, Harvard Medical
Mar 16 Class Discussion Student Presentations
Mar 18 Guest Lecturer TBA
Mar 23  Spring Break No Meeting
Mar 30 Class Discussion Student Presentations
Apr   1 Guest Lecturer Michael Baym
Apr   6 Class Discussion Student Presentations
Apr   8 Guest Lecturer Ben Raphael, Brown
Apr 13 Class Discussion Student Presentations
Apr 15 Guest Lecturer Jadwiga Bienkowski
Apr 20 Class Discussion Student Presentations
Apr 22 Bonnie Berger Computational biology in the 21st century: Algorithms that scale
Apr 27 Class Discussion Student Presentations
Apr 29 Guest Lecturer Eric Kelsic, Wyss Institute at Harvard
May  4 Class Discussion Student Presentations
May  6 Guest Lecturer Konstantin Zeldovich, UMass Medical School
May 11 Class Discussion Student Presentations
May 13 Guest Lecturer Jennifer Listgarten

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, 2013 16:48

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