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The reading assignments for the course are provided below. The abbreviations in the table refer to chapters and sections in the following textbooks:
D = Durbin, Richard, Sean R. Eddy, Anders Krogh, and Graeme Mitchison. Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids. Reprint ed. Cambridge, UK: Cambridge University Press, 1999. ISBN: 0521629713.
J = Jones, Neil, and Pavel Pevzner. An Introduction to Bioinformatics Algorithms. Cambridge, MA: MIT Press, 2004. ISBN: 0262101068.
Course readings.
| SES # |
TOPICS |
READINGS |
| L1 |
Algorithms; Machine Learning; Biology |
J: 3.1-3.7, 2.8-2.10
D: 11 |
| R1 |
Running Times, Molecular Biology and Probability |
|
| L2 |
Evolutionary Models; Seq Alignment; Dynamic Programming |
D: 2.1-2.3
J: 6.4-6.9 |
| L3 |
Local/Global Alignments; Variations on Dynamic Programming |
D: 2.1-2.3
J: 6.4-6.9 |
| R2 |
Python and Dynamic Programming and Alignments |
|
| L4 |
Linear Time String Searching; Suffix Trees; String Preprocessing |
J: 9.1-9.8 |
| L5 |
Database Search; Hashing; Random Projections |
J: 9.1-9.8 |
| R3 |
Randomization, Modulus, Hashing, Random Projections, BLAST, Suffix Trees |
|
| L6 |
Biological Signals; HMMs |
D: 3.1-3.2 |
| L7 |
CpG Islands/Simple ORFs; Learning with HMMs |
D: 3.3 |
| R4 |
Hidden Markov Models |
|
| L8 |
Expression Analysis; Clustering |
J: 10.1-10.3 |
| L9 |
Multi-dimensional Clustering; Feature Selection |
J: 10.1-10.3 |
| L10 |
Regulatory Motifs; Gibbs Sampling; Expectation Maximization |
J: 4.4-4.9, 5.5, and 12.2 |
| R5 |
Motif Finding Using EM and Gibbs Sampling |
|
| L11 |
Biological Networks; Graph Algorithms |
J: 8.1-8.2 |
| L12 |
Phylogenetic Trees; Greedy Algorithms; Parsimony; EM |
D: 7.1-7.5 |
| R6 |
UPGMA, Neighbor Joining, Parsimony |
|
| L13 |
Multiple Alignment; Profile Alignment; Iterative Alignment |
J: 6.10 |
| L14 |
Midterm |
|
| L15 |
RNA Folding; Context-free Grammars; Phylo-CFGs |
D: 9 |
| L16 |
Combine Alignment and Feature Finding; Pair HMM |
D: 4 |
| R7 |
RNA Folding, Context Free Grammars and Related Algorithms |
|
| L17 |
Gene Finding; Generalized HMMs |
|
| L18 |
Comparative Gene Finding; Phylogenetic HMMs |
|
| L19 |
microRNA Regulation; Target Prediction |
|
| L20 |
Regulatory Relationships; Bayesian Networks |
|
| R8 |
Sequencing by Hybridization |
|
| L21 |
Generative Models of Regulation; Bayesian Graphs |
|
| L22 |
Genome Assembly; Euler Graphs |
J: 8.4 |
| L23 |
Genome Duplication; Genome Rearrangements |
J: 5.1-5.4 |
| L24 |
Whole-genome Comparative Genomics |
|
| L25-L26 |
Final Presentations |
|