Introduction to Computational Molecular Biology

GENOME 541
Department of Genome Sciences
University of Washington
Spring Quarter, 2011


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Class schedule

Date            Instructor Topic Reading Homework
Tue Mar 29 Ruzzo Modeling and searching for non-coding RNA    
Thu Mar 31 Ruzzo Modeling and searching for non-coding RNA   Homework #1
Tue Apr 5 Noble Gene expression analysis (Pavlidis 2003) (Storey and Tibshirani 2003) (Noble 2009) (D'haeseleer 2005) (Brown et al. 2000) (Ramaswamy et al. 2001)  
Thu Apr 7 Noble Predicting protein function from heterogeneous data (Lee et al. 2004) (Troyanskaya et al. 2003) (Lanckriet et al. 2004) (Noble 2006 or long version) Homework #2
Tue Apr 12 Noble Protein identification from tandem mass spectra (Sadygov et al. 2004) (Marcotte 2007)  
Thu Apr 14 Noble Motif discovery   Homework #3
Tue Apr 19 Minin Introduction to phylogenetics    
Thu Apr 21 Minin Introduction to phylogenetics   Homework #4
Tue Apr 26 Lee Haplotype reconstruction    
Thu Apr 28 Lee Analysis of genome-wide association study data   Homework #5
Tue May 3 Borenstein Complex biological networks    
Thu May 5 Borenstein Complex biological networks   Homework #6
Tue May 10 Tompa Comparative sequence analysis and phylogenetic footprinting    
Thu May 12 Tompa Comparative sequence analysis and phylogenetic footprinting   Homework #7
Tue May 17 Qian Computational cell biology: thermodynamics and kinetics Readings  
Thu May 19 Qian Computational cell biology: thermodynamics and kinetics   Homework #8
Tue May 24 Bradley Computational structural biology    
Thu May 26 Bradley Computational structural biology   Homework #9
Tue May 31 Bradley Computational structural biology    
Thu Jun 2 Bradley Computational structural biology   Homework #10