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 Mar 27 Protein structure    
Thu Mar 29 Molecular modeling—Macromolecular forcefields   Homework #1
Tue Apr 3 Molecular modeling—optimization methods    
Thu Apr 5 Nucleic acid structure   Homework #2
Proteomics—Brian Searle
Tue Apr 10 Mass spectrometry and de novo sequencing    
Thu Apr 12 Database searching and E-value estimation   Homework #3
Tue Apr 17 Mixture model analysis and target/decoy evaluation    
Thu Apr 19 Searching for post-translational modifications   Homework #4
RNA-seq analysis—Sreeram Kannan
Tue Apr 24 Transcriptome quantification and differential expression    
Thu Apr 26 Transcriptome assembly   Homework #5
Tue May 1 Single-cell RNA-seq analytics: dimensionality reduction, clustering    
Thu May 3 scRNA-Seq: Lineage estimation, regulatory network inference   Homework #6
Epigenomics—Bill Noble
Tue May 8 Supervised learning from epigenomic data    
Thu May 10 Semi-automated genome annotation   Homework #7
Tue May 15 Analysis of Hi-C data    
Thu May 17 3D modeling of DNA in the nucleus   Homework #8
Phylogenetics—Erick Matsen
Tue May 22 Phylogenetics motivation and intro    
Thu May 24 Phylogenetics methods   Homework #9
Tue May 29 Theory and codon models    
Thu May 31 Further topics   Homework #10