CS 466: Introduction to Bioinformatics

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Semester	Fall 2020
Instructor	Prof. Mohammed El-Kebir
TA	Sarah Christensen (sac2), Wesley Wei Qian (weiqian3)
Time	WF 2:00-3:15 PM
Location	Zoom: [link] (PW on piazza, starting week 2)
Office hours	Wednesdays 3:15-4:15 PM in 3216 Siebel Center
TA office hours	Mondays, 3-4 PM; Fridays 9-10 AM on Zoom [link]
Piazza	[link]

Course description

This course introduces fundamental problems and algorithmic approaches in computational biology. Covered topics include:

1. sequence alignment,
2. genome assembly,
3. phylogenetics,
4. pattern matching,
5. cancer genomics.

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.
Book: Jones and Pevzner, An Introduction to Bioinformatics Algorihms.

Prerequisites

Programming skills (equivalent to CS 225) for doing the mini-project. No background in biology is required. If you did not take CS 225 and its prerequisites at UIUC, you will need to get permission from me to stay in the course.

Grading

Undergraduates will receive 3 undergraduate credits; graduate students can enroll for 3 or 4 graduate credits.

3-credit students:

• Five problem sets (30%)
• Midterm (25%)
• Final (25%)
• Team-based (3-4 people) mini-project and report (20%)

4-credit students:

• Five problem sets (20%)
• Midterm (25%)
• Final (25%)
• Small team-based (1-2 people) mini-project and report (30%)

Course schedule

This is a tentative schedule and subject to change.

Date	Presenter	Slides	Reading
08/26/2020	Mohammed El-Kebir	Introduction [slides] [recording] [jupyter]	Jones and Pevzner: Chapters 2.1, 2.3, 2.4 and 6.2 Biology for Computer Scientists -- Lawrence Hunter [link]
08/28/2020	Mohammed El-Kebir	Sequence alignment I [slides] [recording]	Jones and Pevzner: Chapters 2.7-2.9 and 6.1-6.4 Lecture notes on Big Oh [link]
09/02/2020	Mohammed El-Kebir	Sequence alignment II [slides] [recording]	Jones and Pevzner: Chapters 6.6, 6.8 and 6.9. Lecture notes [link]
09/04/2020	Mohammed El-Kebir	Sequence alignment III [slides] [recording]	Jones and Pevzner: Chapters 6.7-6.9 Affine gap penalties example [link] Lecture notes [link]
09/09/2020	Mohammed El-Kebir	Sequence alignment IV [slides] [annotated slides] [recording]	Jones and Pevzner: Chapters 7.1-7.4 Lecture notes [link]
09/11/2020	Mohammed El-Kebir	Multiple Sequence Alignment I [slides] [recording]	Jones and Pevzner: Chapter 6.10
09/16/2020	Mohammed El-Kebir	Multiple Sequence Alignment II [slides] [annotated slides] [recording]	Lecture notes [link]
09/18/2020	Mohammed El-Kebir	Multiple Sequence Alignment III [slides] [annotated slides] [recording]	Lecture notes [link]
09/23/2020	Mohammed El-Kebir	Multiple Sequence Alignment IV [slides] [annotated slides] [recording]	Lecture notes [link]
09/25/2020	Mohammed El-Kebir	HW1 discussion
09/30/2020	Chuanyi Zhang, Palash Sashittal	Research talk [recording]
10/02/2020	Wesley Wei Qian	Midterm review [slides] [recording]
10/07/2020		Midterm (7-10pm CT)
10/09/2020	Mohammed El-Kebir	RNA Secondary Structure Prediction [slides] [annotated slides] [recording]	Lecture notes [link] Nussinov example [link]
10/14/2020	Mohammed El-Kebir	Phylogeny I [slides] [annotated slides] [recording]	Jones and Pevzner: Chapter 10.2, 10.5-10.8
10/16/2020	Mohammed El-Kebir	Phylogeny II [slides] [annotated slides] [recording]	Jones and Pevzner: Chapter 10.2, 10.5-10.8
10/21/2020	Mohammed El-Kebir	Phylogeny III [slides I] [annotated slides I] [slides II] [annotated slides II] [recording]	Jones and Pevzner: Chapter 10.2, 10.5-10.8
10/23/2020	Mohammed El-Kebir	Phylogeny IV [slides] [annotated slides] [recording]	Lecture notes [link]
10/28/2020	Mohammed El-Kebir	Phylogeny V [slides] [annotated slides] [recording]
10/30/2020	Mohammed El-Kebir	Cancer Phylogenetics I [slides] [recording]
11/04/2020	Sarah Christensen	Cancer Phylogenetics II [slides] [recording]
11/06/2020	Mohammed El-Kebir	HMM I [slides] [annotated slides] [recording]	Jones and Pevzner: Chapter 11.1-11.3 Lecture notes [link]
11/11/2020	Mohammed El-Kebir	HMM II [slides] [annotated slides] [recording]	Jones and Pevzner: Chapter 11.1-11.3 Lecture notes [link]
11/13/2020	Mohammed El-Kebir	HMM III [slides] [annotated slides] [recording]	Jones and Pevzner: Chapter 11.1-11.3 Lecture notes [link]
11/18/2020	Mohammed El-Kebir	Genome Assembly I [slides1] [slides2] [recording]	Jones and Pevzner: Chapter 8.1-8.4 Handout [link]
11/20/2020	Mohammed El-Kebir	Genome Assembly II [slides1] [slides2] [recording]	Jones and Pevzner: Chapter 8.1-8.4
12/02/2020	Students	Project presentations [recording]
12/04/2020	Students	Project presentations [recording]
12/09/2020	Sarah Christensen	Final review [slides] [recording]

Homework

1. Homework 1 will be released on 09/09/2020 and will be due on 09/17/2020.
2. Homework 2 will be released on 09/23/2020 and will be due on 10/01/2020.
3. Homework 3 will be released on 10/28/2020 and will be due on 11/05/2020.
4. Homework 4 will be released on 11/13/2020 and will be due on 11/21/2020.
5. Homework 5 will be released on 11/29/2020 and will be due on 12/07/2020.

Late policy:

• Students may request one 3-day extension in the semester for full credit.
• Otherwise, late submission within 3 days results in at most 80% of credits. Submission later than 3 days results in 0% of credits.

Project

There are three kinds of projects.

1. Implement an algorithm discussed in class, and make it available on Github.
2. Benchmark algorithms discussed in class that solve the same problem on simulated or real data. Write a report about your findings.
3. Write a small survey paper, summarizing state-of-the-art algorithms for a specific computational biology problem.

Deadlines:

• Project proposal: 11/05/2020
• Project report: 12/20/2020

Some implementation-based project ideas:

• Extend Needleman-Wunsch aligner to support fitting alignments and local alignments. [link] [Github]
• Extend Needleman-Wunsch aligner to support affine gap penalties. [link] [Github]
• Implement linear space global alignment algorithm.
• Implement Nussinov algorithm.
• Benchmark current multiple sequence alignment algorithms.
• Study, implement and extend HMM described in Shihab, H. A., Gough, J., Cooper, D. N., Day, I. N. M. & Gaunt, T. R. Predicting the functional consequences of cancer-associated amino acid substitutions. Bioinformatics 29, 1504–1510 (2013).

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