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Lecture Notes

CB = Professor Chris Burge
AK = Professor Amy Keating
MY = Professor Michael Yaffe

1 Introduction/Sequence Comparison and Dynamic Programming (PDF - 2.6 MB) MY
2 Multiple Sequence Alignments I (PDF) MY
3 Multiple Sequence Alignments II (PDF) MY
4 Phylogenetic Analysis (PDF) MY
5 Literature Discussion (PDF) MY
6 Genome Sequencing and DNA Sequence Analysis (PDF) CB
7 DNA Sequence Comparison and Alignment (PDF) CB
8 DNA Motif Modeling and Discovery (PDF) CB
9 Markov and Hidden Markov Models for DNA Sequences (PDF) CB
10 DNA Sequence Evolution (PDF) CB
11 RNA Secondary Structure Prediction (PDF) CB
12 Literature Discussion on Predicting the Functions of DNA/RNA Sequences CB
13 Midterm Exam – in class – Protein and DNA Sequence Analysis
14 Protein Secondary Structure Prediction (PDF) MY
15 Introduction to Protein Structure and Classification (PDF - 1.8 MB) AK
16 Comparing Protein Structures

Molecular Modeling: Methods and Applications (PDF)
17 Using Computational Methods to Analyze, Predict, and Design Protein Sequences and Structures

Solving Structures using X-ray Crystallographpy and NMR (PDF)
18 Solving Structures using X-ray Crystallographpy and NMR (cont.)

Homology Modeling (PDF)
19 Methods for Protein Structure Prediction: Homology Modeling and Fold Recognition (PDF) AK
20 Threading and ab initio Structure Prediction

Computational Protein Design (PDF)
21 Introduction to Systems Biology MY
22 Feedback Systems and Coupled Differential Equations MY
23 DNA Microarrays and Clustering (PDF - 1.8 MB) CB
24 Literature Discussion on DNA Microarrays and Clustering CB
25 Computational Annotation of the Proteome (PDF) AK
26 Literature Discussion on Computational Annotation of the Proteome AK