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: 4-credit students:

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]
09/18/2020 Mohammed El-Kebir Multiple Sequence Alignment III [slides] [annotated slides] [recording]
09/23/2020 Mohammed El-Kebir Multiple Sequence Alignment IV [slides] [annotated slides] [recording]
09/25/2020 Mohammed El-Kebir Midterm review
09/30/2020 TBD Midterm review
10/07/2020 Midterm (7-10pm CT)
10/07/2020 Mohammed El-Kebir RNA Secondary Structure Prediction [slides]
10/09/2020 Mohammed El-Kebir Protein Structure Alignment [slides]
10/14/2020 Mohammed El-Kebir Phylogeny I [slides]
  • Jones and Pevzner: Chapter 10.2, 10.5-10.8
10/16/2020 Mohammed El-Kebir Phylogeny II [slides]
  • Jones and Pevzner: Chapter 10.2, 10.5-10.9
10/21/2020 Mohammed El-Kebir Phylogeny III [slides]
10/23/2020 Mohammed El-Kebir Phylogeny IV [slides]
10/28/2020 Mohammed El-Kebir Cancer Phylogenetics I [slides] & [slides]
10/30/2020 Mohammed El-Kebir Cancer Phylogenetics II [slides] [slides]
11/04/2020 Mohammed El-Kebir HMM I [slides]
  • Jones and Pevzner: Chapter 11.1-11.3
  • Lecture notes [link]
11/06/2020 Mohammed El-Kebir HMM II
  • Jones and Pevzner: Chapter 11.1-11.3
  • Lecture notes [link]
11/11/2020 Mohammed El-Kebir HMM III
  • Jones and Pevzner: Chapter 11.1-11.3
  • Lecture notes [link]
11/13/2020 Mohammed El-Kebir TBD
11/18/2020 Mohammed El-Kebir Genome Assembly I [slides1] [slides2]
  • Jones and Pevzner: Chapter 8.1-8.4
  • Handout [link]
11/20/2020 Mohammed El-Kebir Genome Assembly II [slides1] [slides2]
  • Jones and Pevzner: Chapter 8.1-8.4
12/02/2020 Students Project presentations
12/04/2020 Students Project presentations
12/09/2020 Students Project presentations
12/11/2020 TBD Final review

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 10/23/2020 and will be due on 10/31/2020.
  4. Homework 4 will be released on 11/11/2020 and will be due on 11/19/2020.
  5. Homework 5 will be released on 11/20/2020 and will be due on 12/01/2019.
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.
Some implementation-based project ideas: Deadlines:

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