Introduction to Computational Molecular Biology

GENOME 541
Department of Genome Sciences
University of Washington
Spring Quarter


Course description:

Instructional staff

Please click on the links above for email addresses and office locations.

Meeting times and locations

Prerequisites

Course materials

Course requirements

Examinations

Course grade

Home page

Class schedule

Date            Topic References Homework
Assigned
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
(
scores.txt)
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