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Computational Biology: Genomes, Networks, Evolution >> Content Detail



Calendar / Schedule



Calendar

The calendar below provides information on the course's lecture (L) and recitation (R) sessions.


SES #tOPICSKEY DATES
L1Algorithms; Machine Learning; Biology
R1Running Times, Molecular Biology and Probability
L2Evolutionary Models; Sequence Alignment; Dynamic ProgrammingProblem set 1 out
L3Local/Global Alignments; Variations on Dynamic Programming
R2Python and Dynamic Programming and Alignments
L4Linear Time String Searching; Suffix Trees; String Preprocessing
L5Database Search; Hashing; Random Projections
R3Randomization, Modulus, Hashing, Random Projections, BLAST, Suffix Trees
L6Biological Signals; HMMsProblem set 1 due one day before Lec #6

Problem set 2 out
L7CpG Islands/Simple ORFs; Learning with HMMs
R4Hidden Markov Models
L8Expression Analysis; Clustering
L9Multi-dimensional Clustering; Feature Selection
L10Regulatory Motifs; Gibbs Sampling; Expectation MaximizationProblem set 2 due three days before Lec #10

Problem set 3 out
R5Motif Finding Using EM and Gibbs Sampling
L11Biological Networks; Graph Algorithms
L12Phylogenetic Trees; Greedy Algorithms; Parsimony; EM
R6UPGMA, Neighbor Joining, Parsimony
L13Multiple Alignment; Profile Alignment; Iterative AlignmentProblem set 3 due one day before Lec #13

Practice midterm out
L14Midterm
L15RNA Folding; Context-free Grammars; Phylo-CFGsProblem set 4 out
L16Combine Alignment and Feature Finding; Pair HMM
R7RNA Folding, Context Free Grammars and Related Algorithms
L17Gene Finding; Generalized HMMs
L18Comparative Gene Finding; Phylogenetic HMMs
L19microRNA Regulation; Target PredictionProblem set 4 due one day before Lec #19

Project proposals due one day before Lec #19

Problem set 5 out
L20Regulatory Relationships; Bayesian Networks
R8Sequencing by Hybridization
L21Generative Models of Regulation; Bayesian GraphsProblem set 5 due one day after Lec #21

Revised project proposals due one day after Lec #21
L22Genome Assembly; Euler Graphs
L23Genome Duplication; Genome Rearrangements
L24Whole-genome Comparative Genomics
L25-L26Final PresentationsFinal projects due one day after Lec #26

 








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