Introduction to Computational Molecular Biology

GENOME 541
Department of Genome Sciences
University of Washington
Spring Quarter


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Class schedule

All lectures will be delivered via Zoom, accessible via the Canvas page above. Lectures will be recorded and made available via Canvas.

Date            Topic References Homework
Assigned
Protein structure—Frank DiMaio
Tue Mar 31 Protein structure    
Thu Apr 1 Molecular modeling—Macromolecular forcefields   Homework #1
Tue Apr 7 Molecular modeling—optimization methods    
Thu Apr 9 Nucleic acid structure   Homework #2
Epigenomics—Bill Noble
Tue Apr 14 Transcription factor binding motifs compute-motif-pvalue.py small.txt (Noble 2009)  
Thu Apr 16 Supervised learning for transcription factor binding (Agius 2012) (Noble 2006) (Zhou 2015) Homework #3
Thu Apr 21 Semi-automated genome annotation and epigenomic imputation    
Fri Apr 23 Chromatin 3D architecture   Homework #4
Cancer genomics—Gavin Ha
Tue Apr 28 Introduction to cancer genome analysis    
Thu Apr 30 Probabilistic methods for mutation detection   Homework #5
Tue May 5 Probabilistic methods for copy number alteration detection    
Thu May 7 Additional topics: structural variation, signature analysis   Homework #6
Phylogenetics—Erick Matsen
Tue May 12 Phylogenetics motivation and intro    
Thu May 14 Phylogenetics methods   Homework #7
Tue May 19 Recombination and trees as data structures    
Thu May 21 Further topics   Homework #8
Phylogenetics—Trevor Bedford
Tue May 26      
Thu May 28     Homework #9
Population genetics—Will DeWitt
Tue June 2 Population genetics    
Thu June 4 Population genetics   Homework #10