October 27
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 29
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 5
Measuring distances
Making trees
November 10
Multiple sequence alignment
Notes
Daily Dozen
Relating multiple sequences
Frightening flaw in the algorithm
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 17
Hidden Markov Models
Going forward, going backward
November 19
HMMs, continued
Notes
Daily Dozen
Baum-Welch
Applications
November 24
High throughput sequencing: Experimental applications and associated analysis methodology
Notes
Daily Dozen
ChIPseq
December 1
High throughput sequencing: Experimental applications and associated analysis methodology, continued
Notes
Daily Dozen
Variant calling
Gene expression: approaches and statistics
Daily Dozen
Spliced alignment
Gene expression measurements
December 8
Alignment-free sequence comparison
Spatial comparisons
Alignment-free sequence comparison methods
December 10
Metagenomics
Alignment
Assigning OTUs
Counting and comparing
December 15
Data display
Visualizing big data
Circos
Hive plots
Guest lecture: Alexander Favorov
MCMC