The calendar below provides information on the course's lecture (L) and recitation (R) sessions.
Course schedule.
| SES # |
tOPICS |
KEY DATES |
| L1 |
Algorithms; Machine Learning; Biology |
|
| R1 |
Running Times, Molecular Biology and Probability |
|
| L2 |
Evolutionary Models; Sequence Alignment; Dynamic Programming |
Problem set 1 out |
| L3 |
Local/Global Alignments; Variations on Dynamic Programming |
|
| R2 |
Python and Dynamic Programming and Alignments |
|
| L4 |
Linear Time String Searching; Suffix Trees; String Preprocessing |
|
| L5 |
Database Search; Hashing; Random Projections |
|
| R3 |
Randomization, Modulus, Hashing, Random Projections, BLAST, Suffix Trees |
|
| L6 |
Biological Signals; HMMs |
Problem set 1 due one day before Lec #6
Problem set 2 out |
| L7 |
CpG Islands/Simple ORFs; Learning with HMMs |
|
| R4 |
Hidden Markov Models |
|
| L8 |
Expression Analysis; Clustering |
|
| L9 |
Multi-dimensional Clustering; Feature Selection |
|
| L10 |
Regulatory Motifs; Gibbs Sampling; Expectation Maximization |
Problem set 2 due three days before Lec #10
Problem set 3 out |
| R5 |
Motif Finding Using EM and Gibbs Sampling |
|
| L11 |
Biological Networks; Graph Algorithms |
|
| L12 |
Phylogenetic Trees; Greedy Algorithms; Parsimony; EM |
|
| R6 |
UPGMA, Neighbor Joining, Parsimony |
|
| L13 |
Multiple Alignment; Profile Alignment; Iterative Alignment |
Problem set 3 due one day before Lec #13
Practice midterm out |
| L14 |
Midterm |
|
| L15 |
RNA Folding; Context-free Grammars; Phylo-CFGs |
Problem set 4 out |
| L16 |
Combine Alignment and Feature Finding; Pair HMM |
|
| 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 |
Problem set 4 due one day before Lec #19
Project proposals due one day before Lec #19
Problem set 5 out |
| L20 |
Regulatory Relationships; Bayesian Networks |
|
| R8 |
Sequencing by Hybridization |
|
| L21 |
Generative Models of Regulation; Bayesian Graphs |
Problem set 5 due one day after Lec #21
Revised project proposals due one day after Lec #21 |
| L22 |
Genome Assembly; Euler Graphs |
|
| L23 |
Genome Duplication; Genome Rearrangements |
|
| L24 |
Whole-genome Comparative Genomics |
|
| L25-L26 |
Final Presentations |
Final projects due one day after Lec #26 |