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.

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
01/21/2020	Mohammed El-Kebir	Introduction [slides]	Biology for Computer Scientists -- Lawrence Hunter [link]
01/23/2020	Mohammed El-Kebir	Cancer Phylogenetics I [slides]	Lecture notes [link] M. El-Kebir, L. Oesper, H. Acheson-Field and B. J. Raphael. Reconstruction of clonal trees and tumor composition from multi-sample sequencing data. Bioinformatics (Special Issue: Proceedings of ISMB), 31(12):i62-i70, 2015
01/28/2020	Mohammed El-Kebir	Cancer Phylogenetics II [slides]	M. El-Kebir, L. Oesper, H. Acheson-Field and B. J. Raphael. Reconstruction of clonal trees and tumor composition from multi-sample sequencing data. Bioinformatics (Special Issue: Proceedings of ISMB), 31(12):i62-i70, 2015 Y. Qi, D. Pradhan and M. El-Kebir. Implications of non-uniqueness in phylogenetic deconvolution of bulk DNA samples of tumors. Algorithms for Molecular Biology, 14:19, 2019
01/30/2020	Mohammed El-Kebir	Cancer Phylogenetics III [slides]	Y. Qi, D. Pradhan and M. El-Kebir. Implications of non-uniqueness in phylogenetic deconvolution of bulk DNA samples of tumors. Algorithms for Molecular Biology, 14:19, 2019
02/04/2020	Mohammed El-Kebir	Consensus Trees [slides]	N. Aguse, Y. Qi and M. El-Kebir. Summarizing the Solution Space in Tumor Phylogeny Inference using Multiple Consensus Trees. Bioinformatics (ISMB/ECCB 2019), 35:i408-i146, 2019
02/06/2020	Mohammed El-Kebir	Single-cell Phylogenetics [slides]	M. El-Kebir. SPhyR: Tumor Phylogeny Estimation from Single-Cell Sequencing Data under Loss and Error. Bioinformatics (ECCB 2018), 34(17):i671-679, 2018
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]	S. Christensen, M.D.M. Leiserson, M. El-Kebir. PhySigs: Phylogenetic Inference of Mutational Signature Dynamics. Pacific Symposium on Biocomputing, 25:226-237, 2020
02/25/2020	Mohammed El-Kebir	Metastasis I [slides]	M. El-Kebir, G. Satas and B.J. Raphael. Inferring parsimonious migration histories for metastatic cancers. Nature Genetics, 50:718-726, 2018
02/27/2020	Mohammed El-Kebir	Metastasis II [slides]	M. El-Kebir, G. Satas and B.J. Raphael. Inferring parsimonious migration histories for metastatic cancers. Nature Genetics, 50:718-726, 2018
03/03/2020	Mohammed El-Kebir	CNA Phylogeny [slides]	M. El-Kebir, B.J. Raphael, R. Shamir, R. Sharan, S. Zaccaria, M. Zehavi and R. Zeira. Complexity and algorithms for copy-number evolution problems. Algorithms for Molecular Biology, 12(1), 2017.
03/05/2020	Mohammed El-Kebir	ILP [slides] [notebook] [clique]
03/10/2020	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]

Deadlines

All deadlines are 11:59pm CST.

• 3/4: Pick paper to present
• 3/22: Project proposal
• 3/27: Proposal peer reviews
• 5/1: Initial project report submission
• 5/8: Initial project report peer reviews
• 5/15: 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