You can download the lectures here. We will try to upload lectures prior to their corresponding classes.

  • Introduction
    tl;dr: Introduction to the class and some basic bio.
    [slides]
  • Computational framing of Biological Problems
    tl;dr: Lander Waterman & SCS as examples.
    [slides]
  • Exact string matching using the Z-algorithm
    tl;dr: Z-boxes everywhere!
    [slides]
  • Exact string matching using hashing
    tl;dr: All I need is your fingerprint
    [slides]
  • Suffix Tries and Suffix Trees
    tl;dr: Organizing strings by their suffixes
    [slides]
  • Suffix Arrays
    tl;dr: Just keep a sorted list!
    [slides]
  • BWT and FM-index
    tl;dr: This feels like magic
    [slides]
  • Global Alignment and Dynamic Programming
    tl;dr: How similar are these strings?
    [slides]
  • Semi-global and local alignment
    tl;dr: Finding similar parts?
    [slides]
  • Linear-space string alignment
    tl;dr: Combining DP & divide-and-conquer for better bounds
    [slides]
  • Phylogenomics
    tl;dr: How are these organisms related?
    [slides]
  • The de Bruijn Graph and Assembly
    tl;dr: Assembling from k-mers
    [slides]
  • Efficient, approximate representations of (multi-)sets
    tl;dr: K-mer counting and efficient dBG representation
    [slides]
  • RNA-seq and transcript expression estimation
    tl;dr: Counting under uncertainty
    [slides] [supplement_slides]
  • Course wrapup
    tl;dr: That's all folks
    [slides]