CS 598MEB: Computational Cancer Genomics

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Semester	Spring 2022
Instructor	Prof. Mohammed El-Kebir
Time	TR 3:30-4:45 PM
Location	1302 in Siebel Center and Zoom: [link] (requires Illinois Zoom account)
Office hours	Tuesdays 2:15-3:15 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

• Class participation: 20%
• Asking critical questions
• Peer review
• Paper presentation: 30%
• Project: 50%
• Proposal
• Report/paper
• Presentation

Course schedule

Date	Presenter	Slides	Reading
01/18/2022	Mohammed El-Kebir	Introduction [slides] [recording]	Biology for Computer Scientists -- Lawrence Hunter [link]
01/20/2022	Mohammed El-Kebir	Cancer Phylogenetics I [slides] [recording]	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
01/25/2022	Mohammed El-Kebir	Cancer Phylogenetics II [slides] [recording]	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
01/27/2022	Mohammed El-Kebir	Cancer Phylogenetics III [slides I] [slides II] [recording]	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 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
02/01/2022	Mohammed El-Kebir	Cancer Phylogenetics IV [slides I] [slides II] [recording]	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 M. El-Kebir. SPhyR: Tumor Phylogeny Estimation from Single-Cell Sequencing Data under Loss and Error. Bioinformatics (ECCB 2018), 34(17):i671-679, 2018
02/03/2022	Mohammed El-Kebir	Single-cell Phylogenetics [slides] [recording]	M. El-Kebir. SPhyR: Tumor Phylogeny Estimation from Single-Cell Sequencing Data under Loss and Error. Bioinformatics (ECCB 2018), 34(17):i671-679, 2018
02/08/2022	Mohammed El-Kebir	SCS Design [slides] [recording]	L. Weber, N. Aguse, N. Chia and M. El-Kebir. PhyDOSE: Design of Follow-up Single-cell Sequencing Experiments of Tumors. PLoS Computational Biology, 16(10):e1008240, 2020.
02/10/2022	Mohammed El-Kebir	Signatures [slides] [recording]	S. Christensen, M.D.M. Leiserson, M. El-Kebir. PhySigs: Phylogenetic Inference of Mutational Signature Dynamics. Pacific Symposium on Biocomputing, 25:226-237, 2021
02/15/2022	Mohammed El-Kebir	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
02/17/2022	Mohammed El-Kebir	CNA Calling I [recording] [recording II]	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 Z. Lalani*, G. Chu*, S. Hsu, S. Zaccaria† and M. El-Kebir†. User-guided local and global copy-number segmentation for tumor sequencing data
02/22/2022	Mohammed El-Kebir	Metastasis I [slides] [recording]	M. El-Kebir, G. Satas and B.J. Raphael. Inferring parsimonious migration histories for metastatic cancers. Nature Genetics, 50:718-726, 2018 M. El-Kebir. Parsimonious Migration History Problem: Complexity and Algorithms. WABI 2018.
03/01/2022	Mohammed El-Kebir	Metastasis II + Evolutionary Trajectories [slides I] [slides II] [recording]	M. El-Kebir, G. Satas and B.J. Raphael. Inferring parsimonious migration histories for metastatic cancers. Nature Genetics, 50:718-726, 2018 M. El-Kebir. Parsimonious Migration History Problem: Complexity and Algorithms. WABI 2018. S. Christensen, J. Kim, N. Chia, O. Koyejo and M. El-Kebir†. Detecting Evolutionary Patterns of Cancers using Consensus Trees. Bioinformatics (ECCB 2020), 36:i362–i370, 2020.
03/08/2022	Mohammed El-Kebir	Clone Tree Integration [recording]	P. Sashittal, S. Zaccaria and M. El-Kebir†. Parsimonious Clone Tree Reconciliation in Cancer. WABI 2021, Workshop on Algorithms in Bioinformatics, Chicago, IL (virtual), August 2-4, 2021.
03/10/2022	Mohammed El-Kebir	Phyolin + DoubletD [recording]	L.L. Weber and M. El-Kebir†. Distinguishing linear and branched evolution given single-cell DNA sequencing data of tumors. Algorithms for Molecular Biology, 16(1):14, 2021. L.L. Weber*, P. Sashittal* and M. El-Kebir†. doubletD: detecting doublets in single-cell DNA sequencing data. Bioinformatics (ISMB/ECCB 2021), 37:i214-i221, 2021
03/22/2022	Leah Weber	Cancer Immunology [slides] [recording]
03/24/2022	Mohammed El-Kebir	Mutation Clustering [slides] [recording]	G. Satas*, S. Zaccaria*, M. El-Kebir*†, B.J. Raphael†. DeCiFering the elusive cancer cell fraction in tumor heterogeneity and evolution. Cell Systems.
03/29/2022	Students	Papers 1-2 [recording]	TBD TBD
03/31/2022	Students	Papers 3-4 [recording]	TBD TBD
04/05/2022	Students	Papers 5-6 [recording]	TBD TBD
04/07/2022	Students	Papers 7-8 [recording]	TBD TBD
04/12/2022	Students	Papers 9-10 [recording]	TBD TBD
04/14/2022	Students	Paper 11 [recording]	TBD TBD
04/26/2022	Students	Projects [recording]	TBD TBD
04/28/2022	Students	Projects [recording]	TBD TBD
05/03/2022	Students	Projects [recording]	TBD TBD
05/05/2022	Students	Projects [recording]	TBD TBD

Deadlines

All deadlines are 11:59pm CST.

• 03/11/2022: Pick paper to present
• 04/01/2022: Project proposal
• 04/08/2022: Proposal peer reviews
• 05/01/2022: Initial project report submission
• 05/08/2022: Initial project report peer reviews
• 05/15/2022: Final project report submission

Further instructions are on piazza.

Statement on Anti-racism and Inclusivity

The Grainger College of Engineering is committed to the creation of an anti-racist, inclusive community that welcomes diversity along a number of dimensions, including, but not limited to, race, ethnicity and national origins, gender and gender identity, sexuality, disability status, class, age, or religious beliefs. The College recognizes that we are learning together in the midst of the Black Lives Matter movement, that Black, Hispanic, and Indigenous voices and contributions have largely either been excluded from, or not recognized in, science and engineering, and that both overt racism and micro-aggressions threaten the well-being of our students and our university community.

The effectiveness of this course is dependent upon each of us to create a safe and encouraging learning environment that allows for the open exchange of ideas while also ensuring equitable opportunities and respect for all of us. Everyone is expected to help establish and maintain an environment where students, staff, and faculty can contribute without fear of personal ridicule, or intolerant or offensive language. If you witness or experience racism, discrimination, micro-aggressions, or other offensive behavior, you are encouraged to bring this to the attention of the course director if you feel comfortable. You can also report these behaviors to the Bias Assessment and Response Team (BART) (https://bart.illinois.edu/). Based on your report, BART members will follow up and reach out to students to make sure they have the support they need to be healthy and safe. If the reported behavior also violates university policy, staff in the Office for Student Conflict Resolution may respond as well and will take appropriate action.

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Statement on Mental Health

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Counseling Center	217-333-3704	610 East John Street Champaign, IL 61820
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