Introduction to Computational Molecular Biology

Department of Genome Sciences
University of Washington
Spring Quarter

Course description:

Instructional staff

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Meeting times and locations


Course materials

Course requirements


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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
(peptide_database.txt, peptide_msms.txt)
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 Transcription factor binding motifs    
Thu May 10 Supervised learning for transcription factor binding
Keras from here.
  Homework #7
Thu May 17 Semi-automated genome annotation and epigenomic imputation    
Fri May 18 Chromatin 3D architecture
This class will start at 1pm in Foege S040.
  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