CS 598MEB: Computational Cancer Genomics

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Semester Spring 2021
Instructor Prof. Mohammed El-Kebir
Time TR 2:00-3:15 PM
Location Zoom: [link] (requires Illinois Zoom account)
Office hours Tuesdays 3:15-4:15 PM in 3216 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.

Prerequisites

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

Grading

Course schedule

Date Presenter Slides Reading
01/26/2021 Mohammed El-Kebir Introduction [slides] [recording]
  • Biology for Computer Scientists -- Lawrence Hunter [link]
01/28/2021 Mohammed El-Kebir Cancer Phylogenetics I [slides] [recording]
02/02/2021 Mohammed El-Kebir Cancer Phylogenetics II [slides] [recording]
02/04/2021 Mohammed El-Kebir Cancer Phylogenetics III [slides] [recording]
02/09/2021 Mohammed El-Kebir Consensus Trees [slides] [recording]
02/11/2021 Mohammed El-Kebir Single-cell Phylogenetics [slides] [recording]
02/16/2021 Mohammed El-Kebir Mutation Clusters I [slides] [recording]
  • G. Satas, S. Zaccaria, M. El-Kebir and B.J. Raphael. DeCiFering the Elusive Cancer Cell Fraction in Tumor Heterogeneity and Evolution. [see piazza]
02/18/2021 Mohammed El-Kebir Mutation Clusters II [slides] [notes] [recording]
  • G. Satas, S. Zaccaria, M. El-Kebir and B.J. Raphael. DeCiFering the Elusive Cancer Cell Fraction in Tumor Heterogeneity and Evolution. [see piazza]
02/23/2021 Mohammed El-Kebir Signatures [slides] [recording]
02/25/2021 Mohammed El-Kebir RECAP [slides] [recording]
03/02/2021 Simone Zaccaria CNA Calling I [recording]
  • S. Zaccaria S and B.J. Raphael. Accurate quantification of copy-number aberrations and whole-genome duplications in multi-sample tumor sequencing data. Nat Commun. 2020;11(1):4301
03/04/2021 Simone Zaccaria CNA Calling II
03/09/2021 Mohammed El-Kebir Metastasis I [slides]
03/11/2021 Mohammed El-Kebir Metastasis II [slides]

Deadlines

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

Papers

See schedule.

Project

Example projects:

Statement on Mental Health

Diminished mental health, including significant stress, mood changes, excessive worry, substance/alcohol abuse, or problems with eating and/or sleeping can interfere with optimal academic performance, social development, and emotional wellbeing. The University of Illinois offers a variety of confidential services including individual and group counseling, crisis intervention, psychiatric services, and specialized screenings at no additional cost. If you or someone you know experiences any of the above mental health concerns, it is strongly encouraged to contact or visit any of the University’s resources provided below. Getting help is a smart and courageous thing to do -- for yourself and for those who care about you.

Counseling Center217-333-3704610 East John Street Champaign, IL 61820
McKinley Health Center217-333-27001109 South Lincoln Avenue, Urbana, Illinois 61801