CSCI1950-Z: Computational Methods in Biology Schedule

Date

Subject and Slides

Reading

1/21 W

Intro: Trees & Graphs
Phylogeny

Graph primer: J&P 237-60
Molecular Biology primer: J&P 57-78
Shamir notes

1/26 M

Parsimony:
Sankoff and Fitch

Shamir (8.2.2-8.2.7)

1/28 W

Parsimony 2:
Perfect Phylogeny & Compatibility

Fel Ch.8
Shamir notes: 8.2.9

2/2 M

Distances: Additive & Quartets, UPGMA & Ultrametric

P&J 358-367
Fel: Ch11(pp. 161-166)
Ch12 (pp. 176-178)
Neighbor Joining Revealed

2/4 W

Distances: Neighbor joining

Fel: Ch11 (pp. 166-170)

2/9 M

Markov chains, Jukes-Cantor, Likelihood

Fel: Ch11 (p. 155-159)

2/11 W

Likelihood

Fel: Ch16 (pp. 248-260)

2/16 M

HOLIDAY

Godel, Escher, Bach
Just kidding!

2/18 W

Tree space and Searching:
EM for branch lengths
Splits-metric vs. branch-swapping

Fel: Ch4-5, Ch30 (pp. 528-534)
Branch Length EM (works!)

2/23 M

Branch swapping, Bayesian & MCMC, Consensus trees

Fel Ch30 (pp. 521-524), Ch18 (pp. 288-296)

2/25 W

Bootstrapping trees,
supertrees, Aho's algorithm

Ch12 (pp. 189-191)
Fel: Ch20 (pp. 335-342)
P&J 125-138
Shamir

3/2 M

Gene Trees vs. Species Trees
Reconciliation
Orthologs vs. Paralogs

Fel: Ch29 (pp. 509-519)

3/4 W

Distances between trees, Consensus/super-trees

Fel Ch. 30

3/9 M

Clustering 1: Hierarchical, cliques, biclustering <soon>

J&P 339-354
Shamir Lec.3
Shamir Lec.4
Shamir Lec.5

3/11 W

Clustering 2: PCA, SVD, Linear algebra

3/16 M

HMMs & EM

P&J 387-402

3/18 W

Functional enrichment (distributions and correlation)

Parida p.198-200

3/21-3/29

SPRING BREAK

3/30 M

Binary classification & Support vector machines (SVM)

Shamir Lec.6
Shamir Lec.7
Kernel methods p.71-92

4/1 W
April Fools!

Bayesian networks

Shamir Lec.10

4/6 M

TBA

4/8 W

Intro: Networks in Biology

Shamir Lec.9

4/13 M

Network motifs

Parida Ch.12

4/15 W

Random network models

4/20 M

Network alignment

Shamir Lec.10 (05)

4/22 W

Network integration

Shamir Lec.11

4/27 M

Network integration

4/29 W

TBA