Introduction to Computational Molecular Biology: Molecular Evolution

GENOME 541
Department of Genome Sciences
University of Washington
Spring Quarter, 2009


Course description:

Instructional staff

Meeting times and locations

Prerequisites

Course materials

Course requirements

Examinations

Course grade

Home page

Class schedule

Date            Instructor Topic Reading Homework
Tue Mar 31 Felsenstein Trees, parsimony, compatibility Ewens 497-499, 511-512, 517-521; Durbin 160-163, 173-176, 188-189  
Thu Apr 2 Felsenstein Counting trees, searching tree space Ewens 511-512; Durbin 163-165, 176-179 HW1 (tree)
Tue Apr 7 Felsenstein Distances and distance matrix methods Ewens 499-511; Durbin 165-173, 189-191  
Thu Apr 9
Class cancelled due to illness
Tue Apr 14 Felsenstein Models of DNA and protein change Ewens 475-496; Durbin 193-197 HW2 (primates.dna)
Thu Apr 16 Felsenstein Likelihood and Bayesian methods Ewens 512-516, 409-416; Durbin. 197-210, 215-217 HW3
Tue Apr 21 Felsenstein Testing and bootstraps Ewens 295-300, 308-309, 313-318, 522-535; Durbin 179-180, 212-215  
Tue Apr 23 Felsenstein Coalescents Durbin 211-212 HW4
Tue Apr 28 Felsenstein Inference with coalescents Ewens 392-398; Durbin 206-207, 211-212  
Thu Apr 30
Class re-scheduled due to Genome Sciences Symposium
Fri May 1 Noble Microarray analysis (Pavlidis 2003)
(Storey and Tibshirani 2003)
(Brown et al. 2000)
(Ramaswamy et al. 2001)
 
Tue May 5 Noble Predicting protein function from heterogeneous data (Lee et al. 2004)
(Troyanskaya et al. 2003)
(Lanckriet et al. 2004)
(Noble 2006 or long version)
HW5
Thu May 7 Noble Protein identification from tandem mass spectra (Sadygov et al. 2004)  
Fri May 8 Noble Motif discovery   HW6
Tue May 12 Ruzzo Modeling and searching for non-coding RNA Durbin, ch. 10  
Thu May 14 Ruzzo Modeling and searching for non-coding RNA   HW7
Tue May 19 Tompa Comparative sequence analysis and phylogenetic footprinting (Xie et al.)
(Bejerano et al.)
(Siepel et al.)
(Blanchette and Tompa)
(Neph and Tompa)
(Prakash and Tompa)
 
Thu May 21 Tompa Comparative sequence analysis and phylogenetic footprinting   HW8
Tue May 26 Bradley Computational structural biology    
Thu May 28 Bradley Computational structural biology   HW9
Tue Jun 2 Bradley Computational structural biology    
Thu Jun 4 Bradley Computational structural biology   HW10