BCB410/CSC 2417 -- Syllabus

Algorithms for Genome Analysis
Syllabus & Reading

This is a more of a "What's Happened" than a "What's Coming Up" syllabus. Lectures are subject to adjustment depending on the pace of the class. Readings for future weeks are "approximations"; required reading will be posted by Wednesday before the class.

There will not be a required book for this class, most topics will be covered by research papers. This is mainly due to the fact that the field changes rapidly and many books are dated by the time they hit the shelves.

Having said that, for a lot of the topics in this class a copy of Durbin, Eddy, Krogh & Mitchison's book Biological Sequence Analysis is good reading. It is especially good at covering HMM's and other probabilistic approaches. It is "suggested" but not "required".

Two optional "reference" books are Waterman's Introduction to Computational Biology and Gusfield's Algorithms on Strings Trees and Sequences.

Lec #	Topic	Date	Reading	Handouts & Slides
	Genomes, Assembly & Evolution
1.	Overview: what is the genome, and where does it come from?	Sept 13	EBI's Intro to Biology: Sections 1-3 JGI's Intro to Genomics Weber & Myers: Human Whole-Genome Shotgun Sequencing Green: Against a Whole-Genome Shotgun	Lecture slides
2.	Genome assembly & String Graphs	Sept 20	Medvedev et al: Models for Genome Assembly Batzoglou, et al: Arachne Butler, et al: AllPaths
3.	Basic Evolution & Variation Detection	Sept 27	Section 1 of Speed's notes on Evolution and Phylogeny Chapter 9 of the Haubold book (only available from on-campus).
	Alignment & Phylogeny
4.	Pairwise Alignment: Longest common subsequence, Substitution matrices, Global v Local	Oct 4	Speed: Lecture Notes on Sequence Alignment Myers & Miller: Alignments in Linear Space More Lecture Notes on Alignment	HW1 out Project Description
5.	Modern Alignment programs: Gap penalties, Anchored Alignment	Oct 18	Reduction from LIS to LCS (Gusfield 12.4-12.5) Brudno & Dubchak: Comparisons of Long Genomic Sequences (Chapter 14 from Aluru's Handbook)	HW1 due on Thurs Oct 21 @10am
6.	Multiple Alignment & Phylogenetic Tree Reconstruction	Oct 25	Thompson et al: CLUSTALW Loytinoja & Golding: Progressive Alignment Lecture notes on phylogenetic trees
7.	Rearrangements & Hannenhali-Pevzner Theory	Nov 1	Bergeron's presentation of Hannenhali-Pevzner	Project proposal due! HW2 out
	Genes & Regulation
8.	Biology of genes & Motifs; Microarrays	Nov 15	Microarray Overview Eisen et al: Microarray Clustering	Lecture slides
9.	Hidden Markov Models & Comparative Genomics	Nov 22	Rabiner's tutorial on HMMs Huson's notes on HMMs & CpGs	HW2 Due!
10.	Gene finding	Nov 29	Zhang's Review of Gene-Finding Brent & Guigo's Review of Comparative Gene-Finding	HW3 out; due Dec 9 Genome for HW3
11.	Motif finding	Dec 6	Blanchette et al.: Footprinter Lawrence et al.: Gibbs Sampling Bailey et al.: EM for Motif Finding (MEME)

Algorithms for Genome Analysis Syllabus & Reading

Algorithms for Genome Analysis
Syllabus & Reading