Introduction to Computational Molecular Biology

Department of Genome Sciences
University of Washington
Spring Quarter

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Class schedule

Date            Topic References Homework
Proteins and proteomics—Bill Noble
Tue Mar 31 Protein remote homology detection HHPred, SVM primer, Fisher SVM, RankProp, Protembed  
Thu Apr 2 Predicting protein function from heterogeneous data Bayesian networks, multiple kernel SVMs, GeneMania Homework #1
Tue Apr 7 Analysis of tandem mass spectra - I Review, SEQUEST, X!Tandem, Target-decoy search, MS-GF+  
Thu Apr 9 Analysis of tandem mass spectra - II Percolator, IDPicker, EVD, Barista Homework #2
Protein structure—Frank DiMaio
Tue Apr 14 Protein structure    
Thu Apr 16 Molecular modeling—Macromolecular forcefields   Homework #3
Tue Apr 21 Molecular modeling—optimization methods    
Thu Apr 23 Nucleic acid structure   Homework #4
Metagenomics—Ohad Manor
Tue Apr 28 Metagenomics    
Thu Apr 30 Deconvolution and linear regression   Homework #5
Tue May 5 Pathway analysis in metagenomics    
Thu May 7 Predicting disease state with k-nearest-neighbour and random forest   Homework #6
Gene regulation and epigenomics—Max Libbrecht
Tue May 12 Transcription factor binding    
Thu May 14 Transcription factor binding   Homework #7
Tue May 19 Functional element discovery    
Thu May 21 Chromatin 3D modeling   Homework #8
Phylogenetics—Jesse Bloom
Tue May 26 Molecular evolution (Zuckerkand and Pauling)  
Thu May 28 Molecular evolution   Homework #9
Tue Jun 2 Phylogenetic inference   Homework #10
Thu Jun 4 Phylogenetic inference    

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