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



Study Materials



Readings

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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.


SES #TOPICSREADINGS
L1Algorithms; Machine Learning; BiologyJ: 3.1-3.7, 2.8-2.10

D: 11
R1Running Times, Molecular Biology and Probability
L2Evolutionary Models; Seq Alignment; Dynamic ProgrammingD: 2.1-2.3

J: 6.4-6.9
L3Local/Global Alignments; Variations on Dynamic ProgrammingD: 2.1-2.3

J: 6.4-6.9
R2Python and Dynamic Programming and Alignments
L4Linear Time String Searching; Suffix Trees; String PreprocessingJ: 9.1-9.8
L5Database Search; Hashing; Random ProjectionsJ: 9.1-9.8
R3Randomization, Modulus, Hashing, Random Projections, BLAST, Suffix Trees
L6Biological Signals; HMMsD: 3.1-3.2
L7CpG Islands/Simple ORFs; Learning with HMMsD: 3.3
R4Hidden Markov Models
L8Expression Analysis; ClusteringJ: 10.1-10.3
L9Multi-dimensional Clustering; Feature SelectionJ: 10.1-10.3
L10Regulatory Motifs; Gibbs Sampling; Expectation MaximizationJ: 4.4-4.9, 5.5, and 12.2
R5Motif Finding Using EM and Gibbs Sampling
L11Biological Networks; Graph AlgorithmsJ: 8.1-8.2
L12Phylogenetic Trees; Greedy Algorithms; Parsimony; EMD: 7.1-7.5
R6UPGMA, Neighbor Joining, Parsimony
L13Multiple Alignment; Profile Alignment; Iterative AlignmentJ: 6.10
L14Midterm
L15RNA Folding; Context-free Grammars; Phylo-CFGsD: 9
L16Combine Alignment and Feature Finding; Pair HMMD: 4
R7RNA Folding, Context Free Grammars and Related Algorithms
L17Gene Finding; Generalized HMMs
L18Comparative Gene Finding; Phylogenetic HMMs
L19microRNA Regulation; Target Prediction
L20Regulatory Relationships; Bayesian Networks
R8Sequencing by Hybridization
L21Generative Models of Regulation; Bayesian Graphs
L22Genome Assembly; Euler GraphsJ: 8.4
L23Genome Duplication; Genome RearrangementsJ: 5.1-5.4
L24Whole-genome Comparative Genomics
L25-L26Final Presentations

 








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