October 27
Welcome!
Notes
Overview of the a day in the life of a cell
Finding signals in DNA—the cell does it, can we?
November 1
First generation sequencing
Notes
Daily Dozen
First generation sequencing technology
Base calling
Pairwise sequence alignment
Dot plots
Needleman-Wunsch and Smith-Waterman
November 3
Human genome project and GenBank
BLAST
gapped BLAST
November 8
Multiple sequence alignment
Notes
Daily Dozen
Extra topics
Relating multiple sequences
Frightening flaw in the algorithm
November 10
Next (and nextnext) generation sequencing
Notes
extra notes
Second generation sequencing technology
Third generation sequencing technology
New algorithmic challenges
Short read alignment
Not-so-short read alignment
November 15 Homework #1 due today
Hidden Markov Models
Going forward, going backward
November 17
HMMs, continued
Notes
Daily Dozen
Baum-Welch
Applications
November 22
Interpreting HTS results
Notes
Daily Dozen
Phylogeny, PCA
November 29
High throughput sequencing: Experimental applications and associated analysis methodology
Notes
ChIPseq
December 1
no class
December 6
Homework #2 due today
High throughput sequencing: Experimental applications, continued
Notes
variant calling
December 8
High throughput genomics: Experimental applications, continued
Notes
Measuring gene expression I: alignment
December 13
Gene expression: approaches and statistics
Notes
Gene expression measurements
Statistics
December 15
Functional analysis in genome space
Alignment-free sequence comparison
Alignment-free notes
Spatial comparisons
Alignment-free sequence comparison methods
December 20
Guest speaker: Jonathan Pevsner
Notes
December 22
Homework #3 and final project due today
Data display
Notes
Big data
Visualization