Computing Science Course Outlines

Course Outline - CMPT 711 - Bioinformatics Algorithms

Information

Subject

Catalog Number

Section

Semester

Title

Instructor(s)

Campus

CMPT

711

G100

2015 Fall (1157)

Bioinformatics Algorithms

Leonid Chindelevitch   

Burnaby Mountain Campus

Calendar Objective/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.

Instructor's Objectives

The goal of this course is to provide a solid foundation in the algorithmic techniques, such as dynamic programming, graph theory and probabilistic modelling, that computational biologists use on a daily basis, as well as present a sampling of applications to the analysis of metabolites, proteins, genes, and their interactions. The course targets both graduate and advanced undergraduate students in computing science, molecular biology, biochemistry, biophysics, mathematics and biostatistics with minimal or no background in computational biology.

Prerequisites

None

Topics

  • Sequence alignment, global and local
  • Phylogenetics - inferring evolutionary trees
  • RNA secondary structure prediction
  • Biological networks analysis

Grading

Option 1: 10% participation, 30% assignments (best 3 out of 4), 20% midterm, 40% final exam Option 2: 100% final exam While I highly recommend option 1, you will automatically get the higher of the two grades.

Recommended Books

  • An Introduction to Bioinformatics Algorithms, Neil Jones, Pavel Pevzner, MIT Press, 2004, 9780262101066
  • Biological Sequence Analysis, Richard Durbin, Sean Eddy, Anders Krogh, Graeme Mitchison, Cambridge University Press, 1998, 9780521629713

Academic Honesty Statement

Academic honesty plays a key role in our efforts to maintain a high standard of academic excellence and integrity. Students are advised that ALL acts of intellectual dishonesty will be handled in accordance with the SFU Academic Honesty and Student Conduct Policies ( http://www.sfu.ca/policies/gazette/student.html ).

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