CS 466: Introduction to Bioinformatics

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Semester Fall 2019
Instructor Prof. Mohammed El-Kebir
TA Ashwin Ramesh (aramesh7)
Time WF 2:00-3:15 PM
Location 0216 Siebel Center
Office hours Wednesdays 3:15-4:15 PM in 3216 Siebel Center
TA office hours Fridays 11-11:59 AM in 3405 Siebel Center

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.


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.


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

3-credit students: 4-credit students:

Course schedule

Date Presenter Slides Reading
08/28/2019 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]
08/30/2019 Mohammed El-Kebir Sequence alignment I [slides]
  • Jones and Pevzner: Chapters 2.7-2.9 and 6.1-6.4
  • Lecture notes on Big Oh [link]
09/04/2019 Mohammed El-Kebir Sequence alignment II [slides]
  • Jones and Pevzner: Chapters 6.6, 6.8 and 6.9.
  • Lecture notes [link]
09/06/2019 Mohammed El-Kebir Sequence alignment III [slides]
  • Jones and Pevzner: Chapters 6.7-6.9
  • Affine gap penalties example [link]
  • Lecture notes [link]
09/11/2019 Mohammed El-Kebir Sequence alignment IV [slides]
  • Jones and Pevzner: Chapters 7.1-7.4
  • Lecture notes [link]
09/13/2019 Mohammed El-Kebir Multiple Sequence Alignment I [slides]
  • Jones and Pevzner: Chapter 6.10
09/18/2019 Mohammed El-Kebir Multiple Sequence Alignment II [slides]
09/20/2019 Mohammed El-Kebir Multiple Sequence Alignment III [slides]
09/25/2019 Mohammed El-Kebir Multiple Sequence Alignment IV [slides]
9/27/2019 Mohammed El-Kebir Midterm review
10/02/2019 Ashwin Ramesh Midterm review
10/04/2019 Midterm
10/09/2019 Mohammed El-Kebir RNA Secondary Structure Prediction [slides]
10/11/2019 Mohammed El-Kebir Protein Structure Alignment [slides]
10/16/2019 Mohammed El-Kebir Phylogeny I [slides]
  • Jones and Pevzner: Chapter 10.2, 10.5-10.8
10/18/2019 Mohammed El-Kebir Phylogeny II [slides]
  • Jones and Pevzner: Chapter 10.2, 10.5-10.9
10/23/2019 Mohammed El-Kebir Phylogeny III [slides]
10/25/2019 Mohammed El-Kebir Phylogeny IV [slides]
10/30/2019 Mohammed El-Kebir Cancer Phylogenetics I [slides] & [slides]
11/01/2019 Mohammed El-Kebir Cancer Phylogenetics II [slides] [slides]
11/06/2019 Mohammed El-Kebir HMM I [slides]
  • Jones and Pevzner: Chapter 11.1-11.3
  • Lecture notes [link]
11/08/2019 Mohammed El-Kebir HMM II
  • Jones and Pevzner: Chapter 11.1-11.3
  • Lecture notes [link]
11/13/2019 Mohammed El-Kebir HMM III
  • Jones and Pevzner: Chapter 11.1-11.3
  • Lecture notes [link]
11/15/2019 Canceled Canceled
11/20/2019 Mohammed El-Kebir Genome Assembly I [slides1] [slides2]
  • Jones and Pevzner: Chapter 8.1-8.4
  • Handout [link]
11/22/2019 Mohammed El-Kebir Genome Assembly II [slides1] [slides2]
  • Jones and Pevzner: Chapter 8.1-8.4
12/04/2019 Students Project presentations
12/06/2019 Students Project presentations
12/11/2019 TBD Final review


  1. Homework 1 will be released on 9/11/2019 and will be due on 9/18/2019.
  2. Homework 2 will be released on 9/25/2019 and will be due on 10/2/2019.
  3. Homework 3 will be released on 10/25/2019 and will be due on 11/2/2019.
  4. Homework 4 will be released on 11/15/2019 and will be due on 11/22/2019.
  5. Homework 5 will be released on 12/2/2019 and will be due on 12/9/2019.
Late policy:


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.
Some implementation-based project ideas: Deadlines: