Introduction to Computational Molecular Biology

GENOME 541
Department of Genome Sciences
University of Washington
Spring Quarter


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Class schedule

Date            Topic References Homework
Assigned
Proteins and proteomics—Bill Noble
Tue Mar 29 Protein remote homology detection HHPred, SVM primer, Fisher SVM, RankProp, Protembed  
Thu Mar 31 Predicting protein function from heterogeneous data Bayesian networks, multiple kernel SVMs, Critical assessment Homework #1
Tue Apr 5 Analysis of tandem mass spectra - I Review, SEQUEST, X!Tandem, Target-decoy search, MS-GF+  
Thu Apr 7 Analysis of tandem mass spectra - II Percolator, IDPicker, EVD, Barista Homework #2
Metagenomics—Ohad Manor
Tue Apr 12 Metagenomics    
Thu Apr 14 Deconvolution and linear regression   Homework #3
Tue Apr 19 Pathway analysis in metagenomics    
Thu Apr 21 Predicting disease state with k-nearest-neighbour and random forest   Homework #4
Gene regulation and epigenomics—Max Libbrecht
Tue Apr 26 Transcription factor binding    
Thu Apr 28 Transcription factor binding   Homework #5
Tue May 3 Functional element discovery    
Thu May 5 Chromatin 3D modeling   Homework #6
Phylogenetics—Jesse Bloom
Tue May 10 Molecular evolution (Zuckerkand and Pauling)  
Thu May 12 Molecular evolution   Homework #7
Tue May 17 Phylogenetic inference   Homework #8
Thu May 19 Phylogenetic inference    
Protein structure—Frank DiMaio
Tue May 24 Protein structure    
Thu May 26 Molecular modeling—Macromolecular forcefields   Homework #9
Tue May 31 Molecular modeling—optimization methods    
Thu Jun 2 Nucleic acid structure   Homework #10

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