Introduction to Computational Molecular Biology

Department of Genome Sciences
University of Washington
Spring Quarter

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Class schedule

Date            Topic References Homework
Protein structure—Frank DiMaio
Tue Apr 2 Protein structure    
Thu Apr 4 Molecular modeling—Macromolecular forcefields   Homework #1
Tue Apr 9 Molecular modeling—optimization methods    
Thu Apr 11 Nucleic acid structure   Homework #2
Epigenomics—Bill Noble
Tue Apr 16 Transcription factor binding motifs    
Thu Apr 18 Supervised learning for transcription factor binding   Homework #5
Thu Apr 23 Semi-automated genome annotation and epigenomic imputation    
Fri Apr 25 Chromatin 3D architecture   Homework #6
RNA-seq analysis—Sreeram Kannan
Tue Apr 30 Transcriptome quantification and differential expression    
Thu May 2 Transcriptome assembly   Homework #5
Tue May 7 Single-cell RNA-seq analytics: dimensionality reduction, clustering    
Thu May 9 scRNA-Seq: Lineage estimation, regulatory network inference   Homework #6
Phylogenetics—Erick Matsen
Tue May 14 Phylogenetics motivation and intro    
Thu May 16 Phylogenetics methods   Homework #7
Tue May 21 MCMC: general case and theory    
Thu May 23 Phylogenetic MCMC   Homework #8
Phylogenetics—Jesse Bloom
Tue May 28 Protein evolution    
Thu May 30 Substitution models   Homework #9
Tue June 4 Codon models    
Thu June 6 More phylogenetics   Homework #10