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.


Time & Location

Class Meeting Time: Mondays & Wednesdays, 11:30 am to 1 pm in The Applied Mathematics Conference Room Building 2, Room 338

Office Hours for Professor Berger: Wednesdays, 1 to 2pm in 2-373.

General Directions to MIT:
Location of Building 2:


Date Lecture
Feb 4 Bonnie Berger Lecture: Introduction to the Course
Feb 9 Guest Lecturer:John Aach, Harvard Multicellular genetic network modeling: directions and issues
Feb 11 Class Discussion  
Feb 16 Holiday (President's Day) No Lecture
Feb 18 Class Discussion  
Feb 23 Guest Lecturer: Phil Bradley, University of Washington
Howard Hughes Medical Institute
Folding Algorithms for Protein Structure Prediction
*Note Special Time of 4.15 in room 2-105-- please refer to email abstract for details
Feb 25 Class Discussion  
Mar 1 Guest Lecturer: Peter Clote, Boston College Efficiently computing the landscape of
locally optimal RNA secondary structures
Mar 3 Class Discussion  
Mar 8 Class Discussion  
Mar 10 Guest Lecturer: Matt Menke, Berger Lab Memeber Wrap-and-Pack: A New Paradigm for Beta Structural Motif Recognition with Application to Recognizing Beta Trefoils
Mar 15 TBA TBA
Mar 17 Guest Lecturer: Alex Coventry, MIT- Berger Lab Post-Doc Further recent work on MSARi, a program for detection of conserved RNA secondary structure in large multiple sequence alignments of orthologs.
Mar 22 Spring Vacation No Lecture
Mar 25 Spring Vacation No Lecture
Mar 29 Tandy Warnow, Department of Computer Sciences
University of Texas at Austin
The CIPRES Project: Inferring the Tree of Life
Apr 1 RECOMB 2004  No Lecture
Apr 5 Guest Lecturer: Shamil Sunyaev, Harvard Medical School and Brigham and Women's Hospital TBA
Apr 7 Class Discussion  
Apr 12 Guest Lecturer: Temple Smith, Boston University  The tale of two protein domain problems ...
Apr 15 Class Discussion  
Apr 19 Holiday (Patriot's Day) No Lecture
Apr 21 Class Discussion  
Apr 26 Bonnie Berger Mathematical Challenges in Molecular Biology
Apr 28 Class Discussion  
May 3 Guest Lecturer: Gary Benson Searching for Inverted Repeats in Genomic Sequences
May 5 Guest Lecturer: Sorin Istrail  
May10 Qicheng Ma, Novartis Clustering protein sequences with a novel metric transformed from seq uence similarity scores and sequence alignments with neural networks
May12 Class Discussion & Guest Lecturer Final Lecture, presentation by J Goler
 A printable version of the schedule is available here in PDF format.

Instructor: Bonnie Berger
Contact Information: bab at mit dot edu, x3-1827, 2-373.
Course Support: Kathleen Dickey
Contact, x3-3037, NE43-330.

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

To join the class email list, please email


Site last updated 8 December, 2006 15:50

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