October 24
Welcome!
Notes
Daily Dozen
Overview of the a day in the life of a cell
Finding signals in DNA—the cell does it, can we?
October 26
First generation sequencing
Notes
Daily Dozen
First generation sequencing technology
Base calling
Pairwise sequence alignment
Dot plots
Needleman-Wunsch and Smith-Waterman
October 31
Human genome project and GenBank
BLAST
gapped BLAST
November 2
Relating multiple sequences
Frightening flaw in the algorithm
November 7
Phylogeny
Notes
Daily Dozen
November 9
Next (and nextnext) generation sequencing
Notes
Daily Dozen
Second generation sequencing technology
Third generation sequencing technology
New algorithmic challenges
Short read alignment
Not-so-short read alignment
Hidden Markov Models
Going forward, going backward
November 16
HMMs, continued
Notes
Daily Dozen
Baum-Welch
Applications
November 21
High throughput sequencing: Experimental applications and associated analysis methodology
Notes
Daily Dozen
ChIPseq
November 28
High throughput sequencing: Experimental applications, continued
Notes
Daily Dozen
variant calling
November 30
Homework 2 due today
High throughput genomics: Experimental applications, continued
Variant calling, continued
December 5
Gene expression: approaches and statistics
Notes
Spliced alignment
Gene expression measurements
December 7
Functional analysis in genome space
Alignment-free sequence comparison
Notes
Spatial comparisons
Alignment-free sequence comparison methods
December 12
Metagenomics
Notes
Alignment
Assigning OTUs
Counting and comparing
December 14
Visualizing big data
December 19
Homework 3 and final project due today
Markov Chain Monte Carlo (Alexander Favorov)
Notes