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 6
BLAST
Human genome project and GenBank
BLAST
gapped BLAST
November 8
Multiple sequence alignment
Relating multiple sequences
Frightening flaw in the algorithm
November 13
Phylogeny
November 15
Homework 1 due today
Next (and nextnext) generation sequencing
Second generation sequencing technology
Third generation sequencing technology
New algorithmic challenges
Short read alignment
Not-so-short read alignment
November 20
HMMs
Hidden Markov Models
Going forward, going backward
November 27
HMMs, continued
Baum-Welch
Applications
November 29
High throughput sequencing: Experimental applications and associated analysis methodology
ChIPseq
December 4
High throughput sequencing: Experimental applications, continued
variant calling
December 6
Gene expression: approaches and statistics
Spliced alignment
Gene expression measurements
December 11
Functional analysis in genome space
Alignment-free sequence comparison
Spatial comparisons
Alignment-free sequence comparison methods
December 13
Metagenomics
Alignment
Assigning OTUs
Counting and comparing
December 18
Guest lecture
December 20
Data display
Visualizing big data
Circos
Hive plots