You can download the lectures here. We will try to upload lectures prior to their corresponding classes. Majority of slides used in this class were originally created by Prof. Robert Beiko and modified (to greater and lesser degrees) by myself.

  • 01 Course Overview & Life at Resolution
    tl;dr: Overview of the course, motivational plagues, and biology background from DNA to Ecosystems
    [slides] [recording]
  • 02 Central Dogma & Pathways
    tl;dr: Foundational material on biochemical pathways and how central dogma determines how biological data is copied and interpreted by cells
    [slides] [recording]
  • 03 Molecular Evolution
    tl;dr: Foundational material on molecular evolution
    [slides] [recording]
  • 04 Sequence Representations
    tl;dr: Strings and structures for encoding biological sequence data for computation
    [slides] [recording]
  • 05 Sequence Alignment - Definitions and Scoring
    tl;dr: How we define and score sequence alignments
    [slides] [recording]
  • 06 Optimal Alignment - Dynamic Programming
    tl;dr: How dynamic programming approaches can be used to generate optimal alignments
    [slides] [recording]
  • 07 Fast Sequence Searches: BLAST and friends
    tl;dr: Overview of the BLAST algorithm and related approaches
    [slides] [recording]
  • 08 Algorithms and Data Structures for Read Mapping
    tl;dr: An overview of algorithms for mapping reads to a genome (suffix trees, suffix arrays, and burrows-wheeler transform
    [slides] [recording]
  • 09 Efficient MSA and HMMs
    tl;dr: An overview of algorithms for efficient multiple sequence alignment and introduction to Hidden Markov Models
    [slides] [recording]
  • 10 Genomic Assembly - Overlap Layout Consensus
    tl;dr: OLC algorithm for recovering genomes from sequencing data
    [slides]