Simon Fraser University
Engaging the World

Course Outlines

Spring 2018 - CMPT 829 G100

Special Topics in Bioinformatics (3)

Bioinformatics

Class Number: 10848

Delivery Method: In Person

Overview

  • Course Times + Location:

    Jan 3 – Apr 10, 2018: Tue, 2:30–3:50 p.m.
    Burnaby

    Jan 3 – Apr 10, 2018: Thu, 2:30–3:50 p.m.
    Burnaby

  • Prerequisites:

    Permission of the instructor.

Description

CALENDAR DESCRIPTION:

Examination of recent literature and problems in bioinformatics. Within the CIHR graduate bioinformatics training program, this course will be offered alternatively as the problem-based learning course and the advanced graduate seminar in bioinformatics (both concurrent with MBB 829).

COURSE DETAILS:

This course is open to interested graduate students from Computing Science, Math, Engineering, Biology, and MBB. It is also open to interested senior undergraduate students. The first part of the course will review some of the basic and more advanced topics in bioinformatics.This will include select chapters from several reference text books, but also selected papers from the literature. The course will be offered in a mixed lecture style/seminar style format. Lectures are given by the instructor or a guest lecturer. The seminar part of the course will include student presentations on selected topics/papers/chapters.

Topics

  • - Exhaustive Search: Restriction Mapping, Profiles, Motif Finding, Search Trees
  • - Greedy Algorithms: Genome Re-arrangements, Reversal Sorting, Motif Finding
  • - Dynamic Programming: Edit Distance and Alignments, LCS, Local Alignment, Gap Penalties, Gene Predi
  • - Divide and Conquer Algorithms: Space efficient Sequence Alignment, Block Alignment and Four Russia
  • - Graph Algorithms: DNA Sequencing, Shortest Superstring Problem, DNA Arrays, Fragment Assembly in D
  • - Combinatorial Pattern Matching: Repeat Finding, Exact Pattern Matching, Suffix Trees, Heuristic Si
  • - Clustering and Trees: Gene Expression Analysis, Evolutionary Trees, Parsimony Problem
  • - Hidden Markov Models: HMM Parameter Estimation, Profile HMM Alginment
  • - RNA secondary structure prediction, RNA Gene Finding, RNA Design
  • - RNA and Protein Visualization

Grading

NOTES:

There will be assignments, student presentations, a project and an exam. Students will also be graded based on participation. Details of grading will be discussed in the first week of classes.

Students must attain an overall passing grade on the weighted average of exams in the course in order to obtain a clear pass (C- or better).

Materials

MATERIALS + SUPPLIES:

Reference Books

  • Biological Sequence Analysis, Durbin, Eddy, Krogh, and Mitchison, Cambridge, 1998, 9780521629713
  • Computational Intelligence in Bioinformatics, Gary B. Fogel, David W. Corne, Yi Pan, IEEE Press/Wiley Interscience , 2008, 9780470105269
  • Evolutionary Computation in Bioinformatics, Gary B. Fogel and David W. Corne, Morgan Kaufmann, 2003, 9781558607972

REQUIRED READING:

An Introduction to Bioinformatics Algorithms,
Neil C. Jones and Pavel A. Pevzner,
The MIT Press, 2004
ISBN: 9780262101066

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:

SFU’s Academic Integrity web site http://students.sfu.ca/academicintegrity.html is filled with information on what is meant by academic dishonesty, where you can find resources to help with your studies and the consequences of cheating.  Check out the site for more information and videos that help explain the issues in plain English.

Each student is responsible for his or her conduct as it affects the University community.  Academic dishonesty, in whatever form, is ultimately destructive of the values of the University. Furthermore, it is unfair and discouraging to the majority of students who pursue their studies honestly. Scholarly integrity is required of all members of the University. http://www.sfu.ca/policies/gazette/student/s10-01.html

ACADEMIC INTEGRITY: YOUR WORK, YOUR SUCCESS