18.417 | Fall 2004 | Graduate

Introduction to Computational Molecular Biology

Calendar

LEC # TOPICS KEY Dates
Introduction to Biology
1 The Central Dogma: Some Algorithms Introduction

Enumerative Solutions: Partial Digest Problem and Median Strings
2 Partial Digest Problem Problem set 1 out
3 Motifs and Median Strings

Dynamic Programming: Sequence Alignments
4 Global Alignment Problem set 2 out
5 Local Alignment

6 Spliced Alignment

7 More Efficient Alignment

Graph Theory: Sequencing Genes and Proteins
8 Genomics and SBH Graphs Problem set 3 out
9 Peptide Graphs

Pattern Matching: Exact Matches, Gapless Alignments, and BLAST
10 Exact Pattern Matching Problem set 4 out
11 Suffix Trees

12 Suffix Arrays and BWTs

13 BLAST

Clustering: Microarrays and Phylogeny
14 Clustering (Guest Lecturer) Problem set 5 out
15 Trees

Neighbor Joining
16 Review of Phylogenetic Analysis

Coalescent Theory in Biology

17 Application: Microarrays (Guest Lecturer)

Probabilistic Models and Machine Learning: Gene Annotation and Evolution
18 Hidden Markov Models I Problem set 6 out
19 Hidden Markov Models II

20 Gibbs Sampling

21 Random Projections

22 MCMC and Bayesian Networks

Horizons
23 The Future: Protein Structure (Guest Lecturer)

24 The Future: Haplotype Mapping (Guest Lecturer)

25 Presentations of Final Projects

26 Presentations of Final Projects (cont.)

Course Info

Instructor
Departments
As Taught In
Fall 2004
Level
Learning Resource Types
Lecture Notes
Projects with Examples
Problem Sets