CSE597A / BMMB598F, Spring 2015, Algorithms and Data Structures in Bioinformatics

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1		Topic	Announcements / Handouts	References

2	CSE597A / BMMB598F, Spring 2015, Algorithms and Data Structures in Bioinformatics
3	Instructor: Paul Medvedev (pzm11)
4	Link to Syllabus
5	Office hours are by appointment after class
6	For access to references without links, refer to Lessons tab in Angel
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8	Past Lectures
9	1/13/2015	Bio review & Next Generation Sequencing & Genome Assembly	http://www.cse.psu.edu/~pashadag/teaching/597s15/slides1.pdf
10	1/15/2015	Genome Assembly	Programming Assignment
11	1/20/2015	Genome Assembly
12	1/22/2015	Bidirected Graphs, Z-Algorithm for exact string matching	slides2.pdf	Gusfield book, Chapter 1
13	1/27/2015	Z-algorithm proof, Boyer Moore	First batch of programming assignment due	Gusfield Ch 2.2, Haubold and Wiehe, Chapter 3
14			slides3.pdf
15	1/29/2015	Boyer Moore / Suffix Trees
16	2/3/2015	Suffix Trees/Arrays	slides4.pdf
17	2/5/2015	Burrows-Wheeler Transform / FM-index	blackboard	http://schatzlab.cshl.edu/teaching/2012/BWT.pdf
18	2/10/2015		Second batch of programming assignment due
19	2/12/2015	Burrows-Wheeler Transform / FM-index	PaperPresentations.pdf
20			CourseProject.pdf
21	2/17/2015	FM-index wrap-up, Needleman-Wunsch	slides5.pdf	Haubold and Wiehe, subset of Chapter 2.
22				http://en.wikipedia.org/wiki/Needleman%E2%80%93Wunsch_algorithm
23	2/19/2015	Smith-Waterman, Modeling gap costs, Hirschberg's Algorithm	slides6.pdf	Haubold and Wiehe, parts of Chapter 2.
24			slides7.pdf	Hirschberg's original paper
25				http://en.wikipedia.org/wiki/Hirschberg%27s_algorithm
26	2/24/2015	Hirschberg's Algorithm & Four Russians Speed-up	Assignment due date extended to 2/25, 11pm	Gusfield, Ch 12.7
27	2/26/2015	Whole-genome alignment	Paper preferences due	Haubold and Wiehe, Chapter 4 http://mummer.sourceforge.net/MUMmer.pdf
28	3/3/2015	Mutliple Sequence Alignment
29	3/5/2015	Structural Variation Detection	Fourth batch of programming assignment due	http://dx.doi.org/10.1038/nmeth.1374
30			SVtutorial.pdf
31	3/10/2015	Spring Break
32	3/12/2015	Spring Break
33	3/17/2015	Hidden Markov Models		Chapter 3 of Durbin et al. book
34	3/19/2015	Hidden Markov Models	Prior meetings for paper presentations
35	3/24/2015	HMMs / paper presentations
36	3/26/2015	paper presentations
37	3/31/2015	paper presentations	Project Plan Due
38	4/2/2015	paper presentations
39	4/7/2015	Profile HMMs and Phylogeny Introduction		Chapter 7 of Durbin et al. book
40	4/9/2015
41	4/14/2015		Paper Report Due (for those who did not do the presentation)
42	4/16/2015	UPGMA and Neighbor joining algorithms
43	4/21/2015	Fitch's algorithm
44	4/23/2015	Sankoff's Algorithm / project presentations
45	4/28/2015	project presentations
46	4/30/2015	project presentations
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48	Upcoming Lectures (subject to most likely change)
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