Lectures

You can download the lectures here (in PDF format). I will try to upload lectures prior to their corresponding classes.

• 

  Introduction
  tl;dr: Introduction to the class and some basic bio.
  

  [slides]
• 

  Computer Science for Biology
  tl;dr: Quiz 0 recap; posing biological questions computationally
  

  [slides]
• 

  Exact pattern matching
  tl;dr: The Z algorithm and KMP
  

  [slides]
• 

  Suffix tries and trees
  tl;dr: Matching the forest through the tries
  

  [slides]
• 

  Suffix Arrays
  tl;dr: Trees -> Arrays
  

  [slides]
• 

  BWT and FM-index
  tl;dr: It's crazy that this works
  

  [slides]
• 

  Global alignment and dynamic programming
  tl;dr: Not just exact matches any more.
  

  [slides]
• 

  Local alignment and affine gap penalties
  tl;dr: Playing at the boundaries.
  

  [slides]
• 

  Linear space alignment
  tl;dr: About as good as we can do!
  

  [slides]
• 

  RNA-seq and gene expression inference
  tl;dr: Estimating gene and transcript abundance from RNA-seq
  

  [slides]
• 

  The small and large phylogeny problems
  tl;dr: Tracing evolution via sequence similarity.
  

  [slides]
• 

  The de Bruijn graph and genome assembly
  tl;dr: Finally, some graphs.
  

  [slides]
• 

  Efficient representation of the dBG
  tl;dr: Bloom filters, basically.
  

  [slides]