Lecture topics are organized by course unit. Materials will be added as we cover them. In general, you can expect the slides for a lecture to go up the day of that lecture before class. The unit structure below is broad and we will generally follow it; some specific lectures may be added, removed, or rearranged based on the speed at which we cover topics.

Unit 01

Foundations

  1. Introduction

    Introduction to the class and some basic bio.

    slides

  2. Computational framing of Biological Problems

    Lander Waterman & SCS as examples.

    slides
Unit 02

Exact string matching

  1. Exact matching and the Z-box algorithm

    Linear time exact matching

    slides

  2. Semi-numerical string matching (Rabin-Karp)

    Treating strings as numbers & hashing

    slides
Unit 03

Indexing

  1. Suffix Tries and Suffix Trees

    The power of indexing

    slides

  2. Suffix Arrays

    binary search FTW

    slides

  3. BWT & FM-index

    Optimal search in small space

    slides
Unit 04

Sequence alignment

  1. Edit distance and global alignment

    How to compare strings

    slides

  2. Semi-global alignment and gap penalties

    More dynamic programming

    slides

  3. Linear Space Alignment

    Don't keep the whole matrix

    slides
Unit 05

Phylogenomics

  1. Phylogenomics

    Dynamic programming on trees

    slides
Unit 06

Gene expression

  1. Gene expression estimation from RNA-seq

    How to count

    Materials coming soon
Unit 07

Genome assembly

  1. The de Bruijn Graph

    Thinking about k-mers

    Materials coming soon

  2. Efficient representation of the de Bruijn graph

    small space dBG

    Materials coming soon