CS 598MEB: Computational Cancer Genomics

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Semester Spring 2020
Instructor Prof. Mohammed El-Kebir
TA Sarah Christensen (sac2)
Time TR 2:00-3:15 PM
Location 1214 Siebel Center
Office hours Tuesdays 3:15-4:15 PM in 3216 Siebel Center
TA office hours Wednesdays 11-11:59 AM in Siebel Center

Course description

This course introduces fundamental problems and algorithmic approaches in cancer genomics. Covered topics include:

  1. tumor phylogeny inference,
  2. cancer immunotherapy,
  3. driver mutation identification,
  4. somatic variant calling.
This course will not teach you how to run popular bioinformatics tools. Rather, we will focus on the underlying algorithmic ideas and the issues that arise when translating a biological problem into a computational problem and ultimately an accurate tool for biologists to use. In addition, this course will teach you how to read scientific papers and how to propose and conduct independent research.


This course is appropriate for graduate students in computer science, bioengineering, mathematics and statistics. Familiarity with basic statistics, probability and algorithms is expected.


Course schedule

Date Presenter Slides Reading
01/21/2020 Mohammed El-Kebir Introduction [slides]
  • Biology for Computer Scientists -- Lawrence Hunter [link]
01/23/2020 Mohammed El-Kebir Cancer Phylogenetics I [slides]
01/28/2020 Mohammed El-Kebir Cancer Phylogenetics II [slides]
01/30/2020 Mohammed El-Kebir Cancer Phylogenetics III [slides]
02/04/2020 Mohammed El-Kebir Consensus Trees [slides]
02/06/2020 Mohammed El-Kebir Single-cell Phylogenetics [slides]
02/11/2020 Mohammed El-Kebir CNA/SNV Interplay [slides]
  • M. El-Kebir, G. Satas , L. Oesper and B.J. Raphael. Inferring the Mutational History of a Tumor using Multi-State Perfect Phylogeny Mixtures. Cell Systems, 3(1):43-53, 2016
02/13/2020 Mohammed El-Kebir Mutation Clusters I [slides on Piazza]
02/18/2020 Mohammed El-Kebir Mutation Clusters II [notes]
02/20/2020 Sarah Christensen Signatures [slides]
02/25/2020 Mohammed El-Kebir Metastasis I [slides]
02/27/2020 Mohammed El-Kebir Metastasis II [slides]
03/03/2020 Mohammed El-Kebir CNA Phylogeny [slides]
03/05/2020 Mohammed El-Kebir ILP [slides] [notebook] [clique]
  • Tyler Camp
  • Mohammed El-Kebir
Paper presentations [slides I] [slides II]
03/12/2020 TBD Paper presentations [slides I] [slides II]
03/24/2020 TBD Paper presentations [slides I] [slides II]
03/26/2020 TBD Paper presentations [slides I] [slides II]
03/31/2020 TBD Paper presentations [slides I] [slides II]
04/02/2020 TBD Paper presentations [slides I] [slides II]
04/07/2020 TBD Paper presentations [slides I] [slides II]
04/09/2020 TBD Paper presentations [slides I] [slides II]
04/14/2020 TBD Paper presentations [slides I] [slides II]
04/16/2020 TBD Paper presentations [slides I] [slides II]
04/21/2020 TBD Paper presentations [slides I] [slides II]
04/23/2020 TBD Projects I [slides I] [slides II]
04/28/2020 TBD Projects II [slides I] [slides II]
04/30/2020 TBD Projects III [slides I] [slides II]
05/05/2020 TBD Projects IV [slides I] [slides II]


All deadlines are 11:59pm CST. Further instructions are on piazza.


See schedule.


Example projects: