Links to lecture notes and lab handouts will be made active each week

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	Date	Subject (click for lecture notes)	Instructor	HW Due	Lab Material	Readings
1	Wed 9/8	Introduction to the course: administrivia and example problem	Ungar			Sequence & Genome Analysis. Chapter 1 & 2: skim for background only
2	Mon 9/13	Dynamic programming	Hannenhalli			Sequence & Genome Analysis. Chapter 3: p. 65-74, 79-112
3	Wed 9/15	Sequence alignment	Hannenhalli	HW1 Due 09/22/04 solutions	Lab 1	same as above
4	Mon 9/20	BLAST & its variants	Hannenhalli			Sequence & Genome Analysis. Chapter 6: p. 227-258, 269-270
5	Wed 9/22	Statistics in BLAST I (hardcopy handout)	Ewens	HW2 Due 09/29/04 solutions	Lab 2	Sequence & Genome Analysis. Chapter 4: mostly unnecessary; read p. 126, p. 140, p. 147-148
6	Mon 9/27	Statistics in BLAST II (hardcopy handout)	Ewens			same as above
7	Wed 9/29	Motif finding I	Hannenhalli	No homework this week	Lab 3	Sequence & Genome Analysis. Chapter 5: p. 192-193, skim p. 194-204 (read the supplementary handout), p. 210-215; Chapter 9: p. 385-396
8	Mon 10/4	Motif finding II Supplementary handout on motif finding	Hannenhalli			same as above
9	Wed 10/6	Promoter Prediction	Hannenhalli	HW3 Due 10/13/04 HW3 clarification solutions	Lab 4	same as above
10	Mon 10/11	Comparative genomics & rVista	Hannenhalli			Sequence & Genome Analysis. Chapter 11: gives an overview, but nothing specific about what we covered
11	Wed 10/13	Gene finding Pt I Summary so far	Ungar			Sequence & Genome Analysis. Chapter 11: p. 366-375, skim p. 375-383 for the biology
12	Mon 10/18	Genefinding Pt 2 regression and neural nets	Ungar			Sequence & Genome Analysis. Chapter 11: p. 372-385
13	Wed 10/20	Gene finding III [pdf]	Ungar			same as above
	Fri 10/22	MIDTERM I (Towne 321 at 2 pm) Review questions and study guide Midterm I solutions
	Mon 10/25	No class (Fall break)
14	Wed 10/27	Gene finding IV (HMMs)	Ungar		Lab 5	same as above & supplementary web resource
15	Mon 11/1	Gene Expression I	Cheung	HW4 Due 11/10/04 UPDATED to fix typo data files for regression problem solutions		Sequence & Genome Analysis. Chapter 13 p. 616-621 & supplementary web resources
16	Wed 11/3	Gene Expression II [B/W pdf] [color pdf]	Tobias		Lab 6	Sequence & Genome Analysis. Chapter 13
17	Mon 11/8	Gene Expression III [B/W pdf] [color pdf]	Tobias			Sequence & Genome Analysis. Chapter 13
18	Wed 11/10	Gene Expression IV	Ungar		Lab 7	Sequence & Genome Analysis. Chapter 13
19	Mon 11/15	Gene Expression V	Tobias	HW5 Due 11/22/04 Q4 data file (Updated) solutions		Sequence & Genome Analysis. Chapter 13
20	Wed 11/17	Gene Regulatory Networks	Ungar			Sequence & Genome Analysis. Chapter 13
21	Mon 11/22	Proteomics I [pdf]	Hippler			A review for reading before class Supplementary proteomics paper Supplementary MS paper
	Wed 11/24	No class (Thanksgiving)
22	Mon 11/29	Proteomics II	Hippler	HW6 part I Due 12/6/04 solutions HW6 part II Due 12/8/04 (UPDATED) Part II solutions
23	Wed 12/1	Proteomics III (same handout as above)	Hippler		Lab 8
24	Mon 12/6	Proteomics IV	Hippler
25	Wed 12/8	Midterm review questions and study guide Summary by Dr. Ungar	TAs
26	Fri 12/10	MIDTERM II: Towne 303, 2-3pm Midterm II solutions