Lectures

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

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

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  Shortest Common Superstring & LW Statistics
  tl;dr: Thinking computationally about sequencing and assembly
  

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  Exact pattern matching & Z-algorithm
  tl;dr: A first surprising result
  

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  Exact pattern matching (Rabin-Karp)
  tl;dr: A different approach to speeding up exact matching
  

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  String indexing (suffix trie / tree)
  tl;dr: Fun with suffixes, part 1
  

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  String indexing (suffix arrays)
  tl;dr: Fun with suffixes, part 2
  

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  BWT & FM-index
  tl;dr: Fun with suffixes, part 3
  

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  Sequence similarity & alignment
  tl;dr: Global sequence alignment
  

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  Local alignment & gap penalties
  tl;dr: more alignment
  

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  Linear space alignment
  tl;dr: aligning in linear space
  

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  Phylogenomics
  tl;dr: Building the tree of life
  

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  gene & transcript expression estimation
  tl;dr: how to count
  

  [slides] [notes]
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  Assembling transcripts from RNA-seq data
  tl;dr: finding the path and walking the path
  

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  Assembly with the de Bruijn Graph
  tl;dr: Back to genome assembly
  

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