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:
- tumor phylogeny inference,
- cancer immunotherapy,
- driver mutation identification,
- 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
- Class participation: 20%
- Asking critical questions
- Peer review
- Paper presentation: 30%
- Project: 50%
- Proposal
- Report/paper
- Presentation
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.
- TBD: Pick paper to present
- TBD: Project proposal
- TBD: Proposal peer reviews
- TBD: Initial project report submission
- TBD: Initial project report peer reviews
- TBD: Final project report submission
Further instructions are on piazza.
Papers
See schedule.
Project
Example projects:
- Analyze cancer progression using SEER data
- Non-uniqueness and consensus tree clustering of 1-Dollo phylogenies
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 Center | 217-333-3704 | 610 East John Street Champaign, IL 61820 |
McKinley Health Center | 217-333-2700 | 1109 South Lincoln Avenue, Urbana, Illinois 61801 |