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.

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 & encouraged to sit in as listeners if they wish to repeat the class. Freshmen and Sophmores are welcome as listeners only.

Abstracts will be sent by email prior to each talk.

Time & Location

Class Meeting Time: Mondays & Wednesdays, 11:30 am to 1 pm in The Theory of Computation Lab Room Building 32, Room G575

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

General Directions to MIT:
Direction to Building 32:


Date Lecture
Feb 2 Bonnie Berger Lecture: Introduction to the Course
Feb 7 Lecturer: Jinbo Xu Two recent results presented
Feb 9 Class Discussion  
Feb 14 Guest Lecturer: Michael Jordan Bayesian Bioinformatics
Feb 16 Class Discussion  
Feb 21 Holiday (President's Day)
No Lecture
Feb 23 Class Discussion  
Feb 28 Guest Lecturer: Peter Clote Structural RNA, folding energy and asymptotic Z-scores
Mar 2 Class Discussion  
Mar 7 Guest Lecturer: Jerome Waldispuhl Modeling and predicting the structure of
transmembrane proteins
Mar 9 Class Discussion  
Mar 14 Guest Lecturer: Elizabeth Thomas Doublets: a new player in genome evolution
Mar 16 Class Discussion  
Mar 21 Spring Vacation No Lecture
Mar 23 Spring Vacation No Lecture
Mar 28 Guest Lecturer: Norbert Perrimon Functional genomic and network analysis in Drosophila
Mar 30 Class Discussion  
Apr 4 Guest Lecturer: Rohit Singh TBA
Apr 6 Class Discussion  
Apr 11 Guest Lecturer: Huajan Wang SED, a Normalization Free Method for DNA Microarray Data Analysis
Apr 13 Class Discussion  
Apr 18 Holiday (Patriot's Day) No Lecture
Apr 20 Class Discussion  
Apr 25 Guest Lecturer: Garbor Marth TBA
Apr 27 Class Discussion  
May 2 Guest Lecturer: David Mathews Tentative topic RNA
May 4 Class Discussion  
May 9 Guest Lecturer: Jim Collins TBA
May 11 Class Discussion Last Class, Summation of Class

Instructor: Bonnie Berger
Contact Information:, x3-1827, 2-373.
Course Support: Kathleen Dickey
Contact, x3-3037, 32-G568.

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

To join the class email list, please email


Site last updated 29 December, 2005 23:31

Massachusetts Institute
of Technology
77 Massachusetts Avenue
Cambridge, MA 02139