CS 466: Introduction to Bioinformatics

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Semester	Fall 2024
Instructor	Prof. Mohammed El-Kebir
TAs	Claire Chou (czchou2), Nicole Dong (nsdong2), Mrinmoy Roddur (mroddur2)
Time	WF 2:00-3:15 PM
Location	151 Loomis Laboratory
Instructor office hours	Wednesdays 3:30-4:30 PM in 3216 Siebel Center
TA office hours	Nicole (nsdong2): Mondays 4-5pm in CS Tutoring Center (Siebel basement) Claire (czchou2): Tuesdays 2-3pm in CS Tutoring Center (Siebel basement) Mrinmoy (mroddur2): Thursdays 2-3pm in CS Tutoring Center (Siebel basement)
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 (25%)
• Midterm (25%)
• Final (25%)
• Team-based (3-4 people) mini-project and report (25%)

4-credit students:

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

Course schedule

This is a tentative schedule and subject to change. Recordings are available on mediaspace. To access slides and other materials, log in to Google drive using your Illinois email address; *not* your personal gmail. If your Google account has not been activated yet, please follow the instructions here.

Date	Presenter	Slides	Reading
08/28/2024	Mohammed El-Kebir	Introduction [slides] [jupyter]	Jones and Pevzner: Chapters 2.1, 2.3, 2.4 and 6.2 Biology for Computer Scientists -- Lawrence Hunter [link]
08/30/2024	Mohammed El-Kebir	Sequence alignment I [slides]	Jones and Pevzner: Chapters 2.7-2.9 and 6.1-6.4 Lecture notes [link]
09/04/2024	Mohammed El-Kebir	No class
09/06/2024	Mohammed El-Kebir	Sequence alignment II [slides]	Jones and Pevzner: Chapters 6.6, 6.8 and 6.9. Lecture notes [link]
09/11/2024	Mohammed El-Kebir	Sequence alignment III [slides]	Jones and Pevzner: Chapters 6.7-6.9 Affine gap penalties example [link] [recording] Lecture notes [link]
09/13/2024	Mohammed El-Kebir	Sequence alignment IV [slides] [annotated slides]	Jones and Pevzner: Chapters 7.1-7.4 Lecture notes [link]
09/18/2024	Mohammed El-Kebir	Multiple Sequence Alignment I [slides]	Jones and Pevzner: Chapter 6.10
09/20/2024	Mohammed El-Kebir	Multiple Sequence Alignment II [slides]	Lecture notes [link]
09/25/2024	Mohammed El-Kebir	Multiple Sequence Alignment III [slides] [annotated slides]	Lecture notes [link]
09/27/2024	Mohammed El-Kebir	Multiple Sequence Alignment IV [slides] [annotated slides]	Lecture notes [link]
10/02/2024	Mohammed El-Kebir	RNA Secondary Structure Prediction [slides]	Lecture notes [link] Nussinov example [link]
10/04/2024	Canceled	Canceled
10/09/2024	Mohammed El-Kebir	Midterm Review
10/11/2024	Mohammed El-Kebir	Research Presentation [paper] [slides]
10/16/2024	Mohammed El-Kebir	Phylogeny I [slides]	Jones and Pevzner: Chapter 10.2, 10.5-10.8 Derivation for n=3 sequences [link]
10/18/2024	Mohammed El-Kebir	Phylogeny II [slides]	Jones and Pevzner: Chapter 10.2, 10.5-10.8 Derivation for n=3 sequences [link]
10/23/2024	Mohammed El-Kebir	Phylogeny III [slides]	Jones and Pevzner: Chapter 10.2, 10.5-10.8
10/25/2024	Mohammed El-Kebir	Phylogeny IV [slides]	Lecture notes [link]
10/30/2024	Mohammed El-Kebir	Phylogeny V [slides]	Lecture notes [link]
11/01/2024	Mohammed El-Kebir	Phylogeny VI [slides]	Lecture notes [link]
11/06/2024	Mohammed El-Kebir	HMM I [slides] [annotated slides]	Jones and Pevzner: Chapter 11.1-11.3 Lecture notes [link]
11/08/2024	Mohammed El-Kebir	HMM II [slides] [annotated slides]	Jones and Pevzner: Chapter 11.1-11.3 Lecture notes [link]
11/13/2024	Mohammed El-Kebir	HMM III [slides I] [slides II] [annotated slides]	Jones and Pevzner: Chapter 11.1-11.3 Lecture notes [link]
11/15/2024	Mohammed El-Kebir	Genome Assembly I [slides 0] [slides I] [slides II] [slides III]	Jones and Pevzner: Chapter 8.1-8.4 Handout [link]
11/20/2024	Mohammed El-Kebir	Genome Assembly II [slides I] [slides II] [slides III]	Jones and Pevzner: Chapter 8.1-8.4 T2T [1] Transcript assembly: [1], [2], [3] Ribo-seq: [1]
11/22/2024	Mohammed El-Kebir	Project Presentations I
12/04/2024	Mohammed El-Kebir	Project Presentations II
12/06/2024	Mohammed El-Kebir	Project Presentations III
12/11/2024	Mohammed El-Kebir	Final Review

Homework

1. Homework 1 will be released on 09/13/2024 and will be due on 09/21/2024.
2. Homework 2 will be released on 09/27/2024 and will be due on 10/05/2024.
3. Homework 3 will be released on 11/01/2024 and will be due on 11/09/2024.
4. Homework 4 will be released on 11/13/2024 and will be due on 11/23/2024.
5. Homework 5 will be released on 11/20/2024 and will be due on 12/04/2024.

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:

• Midterm exam: Oct. 9, 7-9:45 PM in CIF 3039
• Project proposal: Nov. 17
• Final exam: Dec. 17, 1:30-4:30 PM in 1024 Chemistry Annex
• Project report: Dec. 20

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 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.

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

Statement on CS CARES and CS Values and Code of Conduct

All members of the Illinois Computer Science department - faculty, staff, and students - are expected to adhere to the CS Values and Code of Conduct. The CS CARES Committee is available to serve as a resource to help people who are concerned about or experience a potential violation of the Code. If you experience such issues, please contact the CS CARES Committee. The instructors of this course are also available for issues related to this class.