Simon Fraser University
Engaging the World

Course Outlines

Fall 2025 - CMPT 711 G100

Bioinformatics Algorithms (3)

Class Number: 5541

Delivery Method: In Person

Overview

  • Course Times + Location:

    Sep 3 – Dec 2, 2025: Mon, 4:30–5:20 p.m.
    Burnaby

    Sep 3 – Dec 2, 2025: Wed, 4:30–6:20 p.m.
    Burnaby

  • Exam Times + Location:

    Dec 6, 2025
    Sat, 8:30–11:30 a.m.
    Burnaby

Description

CALENDAR DESCRIPTION:

Fundamental algorithmic techniques used to solve computational problems encountered in molecular biology. This area is usually referred to as Bioinformatics or Computational Biology. Students who have taken CMPT 881 (Bioinformatics) in 2007 or earlier may not take CMPT 711 for further credit.

COURSE DETAILS:

This is an upper division/graduate course on fundamental algorithmic techniques used to solve computational problems encountered in molecular biology. The course will investigate both traditional deterministic algorithms such as dynamic programming as well as machine learning and AI methods in Computational Biology. We will focus on practical algorithmic solutions as well as theoretical challenges. We will discuss several standard application areas and also discuss some of my current research and novel approaches.

This is a computational science course that will help students develop their problem solving skills and help them make practical decisions when it comes to algorithm design in the context of a variety of problems in molecular biology and genomics. Bioinformatics is a huge industry and current hot research area. Bioinformaticians and Comutational Biologists work in a variety of settings including Cancer Agencies, Therapeutics, Pharmacology, Research Labs, Genomics Companies, and the Pharmaceutical Industry. 

COURSE-LEVEL EDUCATIONAL GOALS:

Topics

  • Molecular biology basics
  • Public Databases and Tools
  • Sequence Analysis (local and global alignments)
  • Multiple Sequence Alignments
  • Dynamic Programming
  • Markov Chains and Hidden Markov Models (HMMs)
  • Sequence Similarity Search
  • RNA secondary Structure Prediction
  • Thermodynamic Models
  • Machine Learning: Evolutionary Computation, Neural Networks

Grading

NOTES:

There will be assignments, a midterm, and a final exam. Details will be discussed in class in the first week of classes.

Students must attain an overall passing grade on the final exam in order to pass the course.

Materials

REQUIRED READING:

  • An Introduction to Bioinformatics Algorithms, Neil Jones and Pavel Pevzner, MIT Press, 2004

ISBN: ISBN: 9780262101066

RECOMMENDED READING:

  • Biological Sequence Analysis: Probabilistic Models of Proteins & Nucleic acids, R. Durbin, S. Eddy, A. Krogh, G. Mitchison, Cambridge University Press, 1998

ISBN: ISBN: 9780521629713

  • Bioinformatics: The Machine Learning Approach, Pierre Baldi, Sren Brunak, MIT Press, 2001

ISBN: ISBN: 9780262025065

REQUIRED READING NOTES:

Your personalized Course Material list, including digital and physical textbooks, are available through the SFU Bookstore website by simply entering your Computing ID at: shop.sfu.ca/course-materials/my-personalized-course-materials.

Department Graduate Notes:

The following are default policies in the School of Computing Science. Please check your course syllabus whether the instructor has chosen a different policy for your class, otherwise the following policies apply.
 
  • Students must attain an overall passing grade on the weighted average of exams in the course in order to get a C- or higher.
  • All student requests for accommodations for their religious practices must be made in writing by the end of the first week of classes, or no later than one week after a student adds a course. After considering a request, an instructor may provide a concession or may decline to do so. Students requiring accommodations as a result of a disability can contact the Centre for Accessible Learning (caladmin@sfu.ca).

Graduate Studies Notes:

Important dates and deadlines for graduate students are found here: http://www.sfu.ca/dean-gradstudies/current/important_dates/guidelines.html. The deadline to drop a course with a 100% refund is the end of week 2. The deadline to drop with no notation on your transcript is the end of week 3.

Registrar Notes:

ACADEMIC INTEGRITY: YOUR WORK, YOUR SUCCESS

At SFU, you are expected to act honestly and responsibly in all your academic work. Cheating, plagiarism, or any other form of academic dishonesty harms your own learning, undermines the efforts of your classmates who pursue their studies honestly, and goes against the core values of the university.

To learn more about the academic disciplinary process and relevant academic supports, visit: 


RELIGIOUS ACCOMMODATION

Students with a faith background who may need accommodations during the term are encouraged to assess their needs as soon as possible and review the Multifaith religious accommodations website. The page outlines ways they begin working toward an accommodation and ensure solutions can be reached in a timely fashion.