CS 466: Introduction to Bioinformatics

Jump to: description | schedule | homework | project | mental health statement

Semester Fall 2021
Instructor Prof. Mohammed El-Kebir
TA Yuanyuan Qi (yq7), Leah Weber (leahlw2)
Time WF 2:00-3:15 PM
Location 1302 Everitt Lab, or Zoom: [link] (only accessible with Illinois Zoom account)
Instructor office hours Wednesdays 3:30-4:30 PM in 3216 Siebel Center, or Zoom: [link] (only accessible with Illinois Zoom account)
TA office hours Mondays, 4-5 PM (Leah); Fridays 9-10 AM (Yuanyuan) 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: 4-credit students:

Course schedule

This is a tentative schedule and subject to change.

Date Presenter Slides Reading
08/25/2021 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]
08/27/2021 Mohammed El-Kebir Sequence alignment I [slides] [recording]
  • Jones and Pevzner: Chapters 2.7-2.9 and 6.1-6.4
  • Lecture notes [link]
09/01/2021 Mohammed El-Kebir Sequence alignment II [slides] [recording]
  • Jones and Pevzner: Chapters 6.6, 6.8 and 6.9.
  • Lecture notes [link]
09/03/2021 Mohammed El-Kebir Sequence alignment III [slides] [recording]
09/08/2021 Mohammed El-Kebir Sequence alignment IV [slides] [recording]
  • Jones and Pevzner: Chapters 7.1-7.4
  • Lecture notes [link]
09/10/2021 Mohammed El-Kebir Multiple Sequence Alignment I [slides] [recording]
  • Jones and Pevzner: Chapter 6.10
09/15/2021 Mohammed El-Kebir Multiple Sequence Alignment II [slides] [recording I] [recording II]
09/17/2020 Mohammed El-Kebir Multiple Sequence Alignment III [slides] [recording]
09/22/2021 Mohammed El-Kebir Multiple Sequence Alignment IV [slides] [recording]
09/24/2021 Mohammed El-Kebir Multiple Sequence Alignment V [recording]
09/29/2021 Mohammed El-Kebir Research talk [recording]
10/01/2021 TBD Research talk + Midterm review [slides] [recording]
10/06/2021 Midterm (7-10pm CT)
10/08/2021 No class
10/13/2021 Mohammed El-Kebir Phylogeny I [slides] [recording]
  • Jones and Pevzner: Chapter 10.2, 10.5-10.8
10/15/2021 Mohammed El-Kebir Phylogeny II [slides] [recording]
  • Jones and Pevzner: Chapter 10.2, 10.5-10.8
10/20/2021 Mohammed El-Kebir Phylogeny III [slides I] [slides II] [recording]
  • Jones and Pevzner: Chapter 10.2, 10.5-10.8
10/22/2021 Mohammed El-Kebir Phylogeny IV [slides] [recording]
10/27/2021 Mohammed El-Kebir Phylogeny V [slides] [recording]
11/03/2021 Mohammed El-Kebir RNA Secondary Structure Prediction [slides] [recording]
11/05/2021 Mohammed El-Kebir Genome Sequencing [slides] [recording]
11/10/2021 Mohammed El-Kebir Genome Assembly [slides I] [slides II] [slides III] [recording]
  • Jones and Pevzner: Chapter 8.1-8.4
  • Handout [link]
11/12/2021 Mohammed El-Kebir HMM I [slides] [recording]
  • Jones and Pevzner: Chapter 11.1-11.3
  • Lecture notes [link]
11/17/2021 Mohammed El-Kebir HMM II [slides] [recording]
  • Jones and Pevzner: Chapter 11.1-11.3
  • Lecture notes [link]
11/19/2021 Mohammed El-Kebir HMM III [slides] [recording]
  • Jones and Pevzner: Chapter 11.1-11.3
  • Lecture notes [link]
12/01/2020 Students Project presentations [recording]
12/03/2020 Students Project presentations [recording]
12/08/2021 TBD Final review [slides] [recording]
12/10/2021 Final (7-10pm CT)

Homework

  1. Homework 1 will be released on 09/08/2021 and will be due on 09/16/2021.
  2. Homework 2 will be released on 09/22/2021 and will be due on 09/30/2021.
  3. Homework 3 will be released on 10/29/2021 and will be due on 11/06/2021.
  4. Homework 4 will be released on 11/10/2021 and will be due on 11/17/2021.
  5. Homework 5 will be released on 11/19/2021 and will be due on 12/04/2021.
Late policy:

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: Some implementation-based project ideas:

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 Center217-333-3704610 East John Street Champaign, IL 61820
McKinley Health Center217-333-27001109 South Lincoln Avenue, Urbana, Illinois 61801