Spring 2015
(For Fall 2010 offering, which was focused mostly on population genetics, click here.)

[Staff] [Information] [Materials]


. Name Email address Office hours
Instructor Luay K. Nakhleh by appointment, DH 3119
Teaching Assistant Dingqiao Wen by appointment, DH 3117

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Course Information

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Course Material

Course material (homework assignments, schedule of topics, slides, etc.) will be posted in this section.

Slides Set # Topic Slides Homework assignments
1 Administrivia and background material PDF
2 Sequence alignment: General overview PDF
3 Sequence alignment: Scoring schemes PDF
4 Sequence alignment: Dynamic programming algorithms for pairwise alignment PDF
5 Significance of estimated sequence alignments PDF
6 Markov chains and hidden Markov models PDF
7 Pairwise HMMs and sequence alignment PDF
8 Profiles and multiple sequence alignments PDF homework 1
9 Phylogenetics: Recovering Evolutionary History PDF
10 Phylogenetics: Building Phylogenetic Trees PDF
11 Phylogenetics: Distance-based Methods PDF homework 2
12 Phylogenetics: Parsimony and Likelihood PDF homework 3
13 Phylogenetics: Bayesian Analysis PDF
14 Phylogenomics PDF
15 Genome characteristics and annotation PDF homework 4
16 Networks in biology PDF
17 Graph-theoretic properties of networks PDF
18 Network motifs PDF
19 Boolean network modeling of regulatory networks PDF
20 Probabilistic modeling: Bayesian networks PDF

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