CSE / BMMB 566, Spring 2017, Algorithms and Data Structures in Bioinformatics
 Share
The version of the browser you are using is no longer supported. Please upgrade to a supported browser.Dismiss

 
View only
 
 
Still loading...
ABCDEFGHIJKLMNOPQRST
1
TopicAnnouncements / HandoutsReferences
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
6
7
Completed Lectures
8
1/9/2017Class Into and Bio Review
9
1/11/2017Bio Review & Knuth-Morris-Pratthttp://jakeboxer.com/blog/2009/12/13/the-knuth-morris-pratt-algorithm-in-my-own-words/
10
1/13/2017KMP & Suffix trees
11
1/18/2017Suffix TreesSecond Homwork posted,
First batch of programming due, Jan 18th, 11pm
Gusfield Ch 2.2, Haubold and Wiehe, Chapter 3
12
1/20/2017Suffix tree applications / Suffix arrayGusfield Ch 2.2, Haubold and Wiehe, Chapter 3
13
1/23/2017Suffix array construction
14
1/25/2017Burrows-Wheeler Transformhttp://schatzlab.cshl.edu/teaching/2012/BWT.pdf
15
1/30/2017BWT
16
2/6/2017FM-index and Needleman-WunschHaubold and Wiehe, subset of Chapter 2.
17
http://en.wikipedia.org/wiki/Needleman%E2%80%93Wunsch_algorithm
18
2/8/2017Smith Waterman, Modeling gap costsHirschberg's original paper
19
http://en.wikipedia.org/wiki/Hirschberg%27s_algorithm
20
2/10/2017Four Russians Speed-up, Linear-space alignmentGusfield, Ch 12.7
21
2/13/2017Heuristic Pairwise alignment, Mutliple Sequence AlignmentHaubold and Wiehe, Chapter 4
http://mummer.sourceforge.net/MUMmer.pdf
22
2/15/2017Mutliple Sequence Alignment and SV detection
23
2/17/2017Structural Variation DetectionHomework 3 duehttp://dx.doi.org/10.1038/nmeth.1374
24
2/24/2017Genome assembly
25
2/27/2017Genome assemblyModeling Biological Problems in Computer Science (see dropbox)
26
3/1/2017Genome assembly
27
3/3/2017Genome assembly
28
3/13/2017Hidden Markov ModelsPaper choices dueChapter 3 of Durbin et al. book
29
3/17/2017Hidden Markov ModelsHomework 4 due
30
3/20/2017Hidden Markov Models
31
3/22/2017Profile HMMs
32
3/29/2017Saurabh Kaul, chikhi informed
33
3/29/2017Lidong Luo, zhang, these are
34
3/29/2017Hongyuan Zhan, Melsted
35
3/29/2017john hutton, Salmela
36
3/31/2017Asha Veerabhadraiah, Muggli
37
3/31/2017Chun-Yi Liu, Minkin
38
3/31/2017Sravya Adavi, Simpson
39
3/31/2017Priyasha Pratik, Langmead ultrafast
40
4/3/2017Hanling Zhang, Liu
41
4/3/2017Ayaan Hossain, Sun varmatch
42
4/3/2017Huaipan Jiang, Sun allsome
43
4/5/2017Adam Mohammed, kingsford
44
4/5/2017Yunqi Zhang, Tomescu
45
4/5/2017Yiwei Sun, epitopes
46
47
Scheduled Lectures
48
4/24/2017Adam Mohammed, Yunqi Zhang, Yiwei Sun, Qichen Yan, Jing Zhao
49
4/26/2017
Chun-Yi Liu, Sravya Adavi, Priyasha Pratik / Ayaan Hossain, Hanling Zhang, Huaipan Jiang
50
4/28/2017Saurabh Kaul, Lidong Luo, Hongyuan Zhan, John Hutton, Asha Veerabhadraiah
51
5/1/2017no classProject report due
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
Future topics (tentative and will change)
67
Chapter 7 of Durbin et al. book
68
4/6/2016Phylogeny introduction, UPGMAChapter 7 of Durbin et al. book
69
4/8/2016Phylogeny (neighbor joining, Fitch's algorithm, Sankoff's)
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
Loading...
 
 
 
Sheet1