October 30
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?
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 15
Human genome project and GenBank
BLAST
gapped BLAST
November 20
Multiple sequence alignment and phylogeny
MSA Notes
Phylogeny Notes
Daily Dozen
Making trees
Relating multiple sequences
Frightening flaw in the algorithm
November 27
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
November 29
Homework 1 due

Hidden Markov Models
Going forward, going backward
December 4
HMMs, continued
Notes
Daily Dozen
Baum-Welch
Applications
December 6
High throughput sequencing: Experimental applications and associated analysis methodology
ChIP notes
Variant calling notes
Daily Dozen
ChIPseq
variant calling
December 11
Gene expression: approaches and statistics
RNAseq notes
Alignment-free sequence comparison
Notes for alignment-free comparison
Spliced alignment
Gene expression measurements
Spatial comparisons
Alignment-free sequence comparison methods
December 13
Alignment
Assigning OTUs
Counting and comparing
December 18
Guest lecture: Elana Fertig, PhD
Data display
Notes
Visualizing big data
Circos
Hive plots