CSE / BMMB 566, Spring 2017, Algorithms and Data Structures in Bioinformatics

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2	CSE / BMMB 566, Spring 2017, Algorithms and Data Structures in Bioinformatics
3	Instructor: Paul Medvedev (pzm11)
4	Link to Syllabus
5	Link to Piazza page
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7	Completed Lectures
8	1/9/2017	Class Into and Bio Review
9	1/11/2017	Bio Review & Knuth-Morris-Pratt		http://jakeboxer.com/blog/2009/12/13/the-knuth-morris-pratt-algorithm-in-my-own-words/
10	1/13/2017	KMP & Suffix trees
11	1/18/2017	Suffix Trees	Second Homwork posted, First batch of programming due, Jan 18th, 11pm	Gusfield Ch 2.2, Haubold and Wiehe, Chapter 3
12	1/20/2017	Suffix tree applications / Suffix array		Gusfield Ch 2.2, Haubold and Wiehe, Chapter 3
13	1/23/2017	Suffix array construction
14	1/25/2017	Burrows-Wheeler Transform		http://schatzlab.cshl.edu/teaching/2012/BWT.pdf
15	1/30/2017	BWT
16	2/6/2017	FM-index and Needleman-Wunsch		Haubold and Wiehe, subset of Chapter 2.
17				http://en.wikipedia.org/wiki/Needleman%E2%80%93Wunsch_algorithm
18	2/8/2017	Smith Waterman, Modeling gap costs		Hirschberg's original paper
19				http://en.wikipedia.org/wiki/Hirschberg%27s_algorithm
20	2/10/2017	Four Russians Speed-up, Linear-space alignment		Gusfield, Ch 12.7
21	2/13/2017	Heuristic Pairwise alignment, Mutliple Sequence Alignment		Haubold and Wiehe, Chapter 4 http://mummer.sourceforge.net/MUMmer.pdf
22	2/15/2017	Mutliple Sequence Alignment and SV detection
23	2/17/2017	Structural Variation Detection	Homework 3 due	http://dx.doi.org/10.1038/nmeth.1374
24	2/24/2017	Genome assembly
25	2/27/2017	Genome assembly		Modeling Biological Problems in Computer Science (see dropbox)
26	3/1/2017	Genome assembly
27	3/3/2017	Genome assembly
28	3/13/2017	Hidden Markov Models	Paper choices due	Chapter 3 of Durbin et al. book
29	3/17/2017	Hidden Markov Models	Homework 4 due
30	3/20/2017	Hidden Markov Models
31	3/22/2017	Profile HMMs
32	3/29/2017	Saurabh Kaul, chikhi informed
33	3/29/2017	Lidong Luo, zhang, these are
34	3/29/2017	Hongyuan Zhan, Melsted
35	3/29/2017	john hutton, Salmela
36	3/31/2017	Asha Veerabhadraiah, Muggli
37	3/31/2017	Chun-Yi Liu, Minkin
38	3/31/2017	Sravya Adavi, Simpson
39	3/31/2017	Priyasha Pratik, Langmead ultrafast
40	4/3/2017	Hanling Zhang, Liu
41	4/3/2017	Ayaan Hossain, Sun varmatch
42	4/3/2017	Huaipan Jiang, Sun allsome
43	4/5/2017	Adam Mohammed, kingsford
44	4/5/2017	Yunqi Zhang, Tomescu
45	4/5/2017	Yiwei Sun, epitopes
46	4/24/2017	Adam Mohammed, Yunqi Zhang, Yiwei Sun, Qichen Yan, Jing Zhao
47	4/26/2017	Chun-Yi Liu, Sravya Adavi, Priyasha Pratik / Ayaan Hossain, Hanling Zhang, Huaipan Jiang
48	4/28/2017	Saurabh Kaul, Lidong Luo, Hongyuan Zhan, John Hutton, Asha Veerabhadraiah
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50	Scheduled Lectures
51	5/1/2017	no class	Project report due
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66	Future topics (tentative and will change)
67				Chapter 7 of Durbin et al. book
68	4/6/2016	Phylogeny introduction, UPGMA		Chapter 7 of Durbin et al. book
69	4/8/2016	Phylogeny (neighbor joining, Fitch's algorithm, Sankoff's)
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