18.417: Introduction to Computational Molecular Biology

With the availability of genomic, expression, and structural data, math and computer science have changed the face of modern biology. This course introduces the basic computational methods used to understand the cell on a molecular level. We first focus on sequence alignment algorithms: dynamic programming, hashing, suffix trees, Gibbs sampling. We then cover computational approaches to: genetic and physical mapping, DNA sequencing, genome assembly and gene annotation; RNA expression and secondary structure; protein structure and folding; and molecular interactions and dynamics.

InstructorBonnie Berger
Time and PlaceTuesdays and Thursdays, 1-2:30pm, 2-139 (Map1, Map2, floorplan).
Prerequisites6.001 or 18.410J/6.046J or permission of instructor. No biology background is assumed.
LecturersBonnie Berger and Manolis Kamvysselis
TAsManolis Kamvysselis and Alex Coventry
Contact Information Email Office Office Hours Phone
Bonnie Berger bab@mit.edu 2-373 TBA 617-253-1827
Manolis Kamvysselis manoli@mit.edu NE43-336 TBA 617-452-2274
Alex Coventry alex_c@mit.edu 2-229 Wed 2-3, Fri 1-2, Student Center Coffee House 617-253-7788
Course Support Jessica Baum jbaum@theory.lcs.mit.edu NE43-330 Thu-Fri 617-253-3037

This page will contain lectures and handouts from Fall 2001. Lecture notes from previous offerings can be found online for the Fall of 1999 and the Spring of 1998. Because the content of this class will differ markedly from the last time it was offered, the new lecture notes this year will appear some time after the material has been covered. Even the lecture notes on similar material are being updated. However, some of you may want to be able to look at the lecture notes from the last time the course was offered - this may be a valuable addition to your own notes for the purposes of doing the homework.


Schedule

(class days in red, holidays in blue, reg/add/drop dates in green)
      September                 October               November               December       
Su Mo Tu We Th Fr Sa     Su Mo Tu We Th Fr Sa  Su Mo Tu We Th Fr Sa   Su Mo Tu We Th Fr Sa 
                   1         1  2  3  4  5  6               1  2  3                      1
 2  3  4  5  6  7  8      7  8  9 10 11 12 13   4  5  6  7  8  9 10    2  3  4  5  6  7  8
 9 10 11 12 13 14 15     14 15 16 17 18 19 20  11 12 13 14 15 16 17    9 10 11 12 13 14 15
16 17 18 19 20 21 22     21 22 23 24 25 26 27  18 19 20 21 22 23 24   16 17 18 19 20 21 22
23 24 25 26 27 28 29     28 29 30 31           25 26 27 28 29 30      23 24 25 26 27 28 29
30                                                                    30 31

Lectures


Introduction
Sequence Alignments
Genome
Transcriptome and Evolution
Protein Structure
Protein Dynamics

Handouts


Homework and Grading

Problem Sets: Final Project: Groups: Scribes and Editors:

Further Reading: Reference Books

No book is mandatory for the class, and no book will treat all the topics we cover. Since people ask us for book advice though, here's a list of books you can consult for your personnal interest, and for further information on individual topics.


Bonnie Berger (bab@mit.edu) and Manolis Kamvysselis (manoli@mit.edu)