Lecture 1 - Course overview
Lecture 2 - Molecular biology and high-throughput sequencing
Lecture 3 - Data structures/Algorithms Warmup
Lecture 4 - Bitvector rank operations
Lecture 5 - Demo for constructing rank data structure
Lecture 6 - Z-algorithm
Lecture 7 - Suffix Arrays
Lecture 8 - Suffix array construction using prefix doubling
Lecture 9 - Demo for constructing suffix array
Lecture 10 - Suffix Tree
Lecture 11 - Building Suffix Trees
Lecture 12 - Building Suffix Trees (Continued...)
Lecture 13 - Applications of suffix trees
Lecture 14 - Burrows Wheeler Indexes
Lecture 15 - Burrows Wheeler Indexes (Continued...)
Lecture 16 - How is BWT useful for indexing genomes ?
Lecture 17 - Sequence Alignment and Edit Distance
Lecture 18 - Global and semi-global alignment
Lecture 19 - Local alignment
Lecture 20 - Scoring gaps in alignments
Lecture 21 - Alignment significance statitstics
Lecture 22 - Alignment demonstration
Lecture 23 - Heuristics for genome-scale alignment
Lecture 24 - Maximal unique matches
Lecture 25 - Co-linear chaining
Lecture 26 - Incorporating gaps into the chaining algorithm
Lecture 27 - IGV Demonstration
Lecture 28 - Genome assembly
Lecture 29 - Shortest common superstring
Lecture 30 - Greedy algorithm for genome assembly
Lecture 31 - Genome assembly using de Bruijn graphs
Lecture 32 - Multiplex de Bruijn graphs and Overlap graphs
Lecture 33 - Assembly Demonstration
Lecture 34 - Introduction to phylogeny trees
Lecture 35 - Distance based tree reconstruction
Lecture 36 - Character based tree reconstruction
Lecture 37 - Phylogenetic trees Demo
Lecture 38 - Hidden Markov Models
Lecture 39 - Hidden Markov Models (Continued...)
Lecture 40 - ProtGPT2 Demo
Lecture 41 - Pangenome Graphs
Lecture 42 - Pangenome Demo
Lecture 43 - Multiple Sequence Alignment
Lecture 44 - Multiple Sequence Alignment Demo
Lecture 45 - Sequence alignment to pangenome graphs
Lecture 46 - Genomic Large Language Models
Lecture 47 - Course Summary
