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Week Date Topic Slides / notes Reading Assignment
1 8/27 Introduction Slides
 What is Bioinfo, Jones&Pevzner Chap3, MBWB Chap1.A, Chap3.A, 3.B, 3.E  
2 9/1 No class (labor day)  
9/3 Introduction to molecular biology  
3 9/8 Global sequence alignment Slides

What is Dynamic Programming, J&P Ch 6.1-6.6, 7.2, Durbin Ch 2 linear-space alg review,

 
9/10 Local alignment, linear-space alignment, bounded alignment Slides HW 1 | Solution
4 9/15 Affine gap alignment, Alignment statistics Slides J&P Ch 6.7-6.9, Durbin 2.3 BLOSUM62 Substitution Matrix  
9/17 Alignment Statistics Slides

J&P 6.6-6.8, Durbin 2.5-2.6,

  
5 9/22 BLAST Slides BLAST J&P 9.8  
9/24 Multiple sequence alignment Slides

J&P 6.10, Durbin 6.1-6.4
MSA review 1 MSA review 2

 
6 9/29 String matching algorithms Slides

Pattern Matching in Strings
J&P Ch 9.3-9.5

 
10/1  
7 10/6 HW2 | seq files
10/8 Combinatorial motif finding Slides What are DNA motifs?
Weeder
MultiProfiler		  
8 10/13  
10/15 Intro to Prob and HMM Slides

Intro to Prob and Stat
Durbin Ch 3-5, J&P 6.11-6.14; J&P 11
What is a HMM?
What is Expectation Maximization?
 GeneScan
Hmm in speech recognition

 
9 10/20  
10/22  
10 10/27 HW3 | seq files | Example | Viterbi Training
10/29 Probabilistic motif finding Slides How to find motifs?
Gibbs Sampling
Practical strategies		  
11 11/3

IDEAL Survey
ENCODE (Guest lecturer: Dr. Livi)

 Slides    
11/5 Phylogeny (Guest lecturer: Dr. Livi) Slides    
12 11/10 RNA secondary structure prediction Slides How do RNA folding algorithms work?  
11/12    
13 11/17 Microarray data analysis Slides

Review on normalization 1, 2

Review on analysis 1, 2

 
11/19  
14 11/24 Microarray data analysis    
11/26    
15 12/1 Biological networks Slides    
12/3      
16 12/8        
12/10 Final presentation