Bioinformatics Algorithms (Part 2)

University of California, San Diego

This is the second course in a two-part series on bioinformatics algorithms, covering the following topics: evolutionary tree reconstruction, applications of combinatorial pattern matching for read mapping, gene regulatory analysis, protein classification, computational proteomics, and computational aspects of human genetics.

This course is the second in a two-part series that begins with Bioinformatics Algorithms (Part 1).  It will build upon the biological and computational material covered in the first course to cover additional topics in modern computational biology.

The format for this course will be the same as that of Part 1. Each chapter of course material will cover a single biological question and slowly build the algorithmic knowledge required to address this challenge.  Along the way, coding challenges and exercises (many of which ask you to apply your skills to real genetic data) will be directly integrated into the text at the exact moment they are needed.


The course will be based on six "chapters" covering the following central questions, with the algorithmic ideas that we will use to solve them in parentheses:
  • How Do We Locate Disease-Causing Mutations? (Combinatorial Pattern Matching)
  • Which Animal Gave Us SARS? (Evolutionary Trees)
  • How Did Yeast Become Such a Good Wine Brewer? (Clustering Algorithms)
  • Why Do We Still Not Have an HIV Vaccine? (Hldden Markov Models)
  • Was T. rex Just a Big Chicken? (Computational Proteomics)
The grading for the course will be based on several weekly programming challenges, as well as a comprehension quiz at the end of each chapter.

Recommended Background

Bioinformatics Algorithms (Part 1) is a suggested prerequisite for this course, but it is not required for experienced programmers.  The material in Part 1 is covered by the first six chapters of Bioinformatics Algorithms: An Active Learning Approach.

Course Format

The class will offer two ways of learning the material.  In addition to a collection of lecture videos, we are currently developing additional textbook chapters for this class that will supplement the existing material in Bioinformatics Algorithms: An Active Learning Approach, by Compeau & Pevzner.


  • Can I get a Statement of Accomplishment after completing this class?

Yes. Students who successfully complete the class will receive a Statement of Accomplishment signed by the instructor.

  • Can I receive a Verified Certificate for this course?

Yes. Students who would like a Verified Certificate can sign up for the course's Signature Track option.

  • 16 March 2015, 10 weeks
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  • Language: English Gb


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