CSE / BMMB 566, Spring 2018, 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
 
 
ABCDEFGHIJKLMNOPQRST
1
TopicAnnouncements / HandoutsReferences
2
CSE / BMMB 566, Spring 2018, Algorithms and Data Structures in Bioinformatics
3
Instructor: Paul Medvedev (pzm11)
4
Link to Syllabus
5
Link to Canvas page
6
7
Completed Lectures
8
1/8/2018Class Into and Bio Review
9
1/10/2018Knuth-Morris-Pratt algorithmhttp://jakeboxer.com/blog/2009/12/13/the-knuth-morris-pratt-algorithm-in-my-own-words/
10
1/15/2018MLK day -- Holiday
11
1/17/2018Suffix TreesProgramming Assignment 1 dueGusfield Ch 2.2, Haubold and Wiehe, Chapter 3
12
1/19/2018Suffix tree applications / Suffix array
13
1/22/2018Suffix array construction
14
1/24/2018Burrows-Wheeler Transformhttps://www.youtube.com/watch?v=4n7NPk5lwbI
15
1/26/2018FM-index and Sequence AlignmentHaubold and Wiehe, subset of Chapter 2.
16
http://en.wikipedia.org/wiki/Needleman%E2%80%93Wunsch_algorithm
17
1/31/2018Needleman-Wunsch, Smith WatermanHomework Assignment 2 due
18
2/2/2018Gotoh's algorithm and Linear-space alignmentHirschberg's original paper (see canvas)
19
http://en.wikipedia.org/wiki/Hirschberg%27s_algorithm
20
2/5/2018Four Russians Speed-up / Heuristic Pairwise alinmentGusfield, Ch 12.7 (see canvas)
21
2/7/2018University cancels classes
22
2/12/2018Mutliple Sequence AlignmentHaubold and Wiehe, Chapter 4, http://mummer.sourceforge.net/MUMmer.pdf
23
2/14/2018Structural Variation DetectionHomework Assignment 3 due
24
2/19/2018Structural Variation Detection / Modeling Biological Problems
25
2/21/2018Modeling Biological Problems
26
2/23/2018Modeling Biological Problems / Genome Assemblyhttps://arxiv.org/pdf/1706.05429
27
2/26/2018Genome assembly
28
2/28/2018Hidden Markov Models
29
3/2/2018Hidden Markov Models
30
3/5-3/9spring break
31
3/12/2018Hidden Markov Models
32
3/16/2018Profile HMMsPaper choices due
33
3/23/2018Prior Meetings on paper presentations
34
3/26/2018Paper Presentations: Kushal, Anish, Natasha
35
3/28/2018Paper Presentations: Mihir, Mahdi, Tsung-Yu
36
3/30/2018Paper Presentations: Nathan, Debolina, Jordan
37
38
Scheduled Lectures
39
4/9/2018Phylogeny introduction, UPGMAChapter 7 of Durbin et al. book
40
4/11/2018Phylogeny (neighbor joining)
41
4/13/2018Phylogeny (Fitch's algorithm, Sankoff's)
42
4/25/2018Final Project presentation: Jordan/Debolina/Nathan/Tsung-Yu
43
4/27/2018Final Project presentation: Mahdi / Mihir+Kushal / Natasha / Anish
44
5/2/2018report due
45
4 on 3/16
46
47
48
49
50
Papers:Kushal, Compacting de Bruijn graphs from sequencing data quickly and in low memory
51
Anish, Succinct Colored de Bruijn Graphs
52
Natasha, AllSome Sequence Bloom Trees
53
54
Mihir, Bloom Filter Trie: an alignment-free and reference-free data structure for pan-genome storage
55
Mahdi, TBD
56
Tsung Yu, Epileptic seizure detection based on EEG signal analysis using hierarchy based Hidden Markov Model
57
58
Nathan, Joint sparse canonical correlation analysis for detecting differential imaging genetics modules
59
Debolina, Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data
60
Jordan, Inferring hidden causal relations between pathway members using reduced Google matrix of directed biological networks.
61
62
Loading...
Main menu