Introduction to Computational Molecular Biology

GENOME 541
Department of Genome Sciences
University of Washington
Spring Quarter, 2013


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Class schedule

Date            Instructor Topic References Homework
Assigned
Tue Apr 2 Noble Predicting protein function from heterogeneous data (Part 1) (Noble 2006)  
Thu Apr 4 Noble Predicting protein function from heterogeneous data (Part 2) (Brown et al. 2000) (Ramaswamy et al. 2001) (Lanckriet et al. 2004) Homework #1
Tue Apr 9 Noble Motif discovery (D'Haeseleer 2006) (Noble 2009)  
Thu Apr 11 Noble Protein identification from tandem mass spectra (Sadygov et al. 2004) (Marcotte 2007) Homework #2
Tue Apr 16 Borenstein Complex biological networks    
Thu Apr 18 Borenstein Complex biological networks   Homework #3
Tue Apr 23 Tompa Comparative sequence analysis and phylogenetic footprinting    
Thu Apr 25 Tompa Comparative sequence analysis and phylogenetic footprinting   Homework #4
Tue Apr 30 Bloom Phylogenetic inference: what can it tell us about the origins of new influenza strains such as H7N9?   Homework #5 is described.
Thu May 2 Bloom What type of evolutionary process is being assumed in phylogenetic inference? The concept of evolutionary distance and the molecular clock.    
Tue May 7 Bloom Likelihood calculations on a tree. Bayesian phylogenetics.   Homework 5 is due before class, and is briefly discussed. Homework 6 is described.
Thu May 9 Bloom Bayesian phylogenetics continued. Introduction to BEAST. Inference of ancestral states (if time is available).    
Tue May 14 Lee Reconstructing the transcriptional regulatory network I    
Thu May 16 Lee Reconstructing the transcriptional regulatory network II   Homework #7
Tue May 21 Lee Statistical genetics I (Genome-wide association studies)    
Thu May 23 Lee Statistical genetics II (Haplotype reconstruction)   Homework #8
Tue May 28 Bradley Protein structure    
Thu May 30 Bradley Protein sequence analysis   Homework #9
Tue Jun 3 Bradley Molecular modeling    
Thu Jun 5 Bradley Nucleic acid structure   Homework #10