CSE / BMMB 566, Spring 2019 Algorithms and Data Structures in Bioinformatics

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2	CSE / BMMB 566, Spring 2019, Algorithms and Data Structures in Bioinformatics
3	Instructor: Paul Medvedev (pzm11)
4	Link to Syllabus		0
5	Link to Canvas page
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7	Completed Lectures
8	1/7/19	Class intro and bio background
9	1/11/19	Knuth-Morris-Pratt algorithm		http://jakeboxer.com/blog/2009/12/13/the-knuth-morris-pratt-algorithm-in-my-own-words/
10	1/14/19	KMP continued, Suffix tries	Programming Assignment 1 due	Gusfield Ch 2.2, Haubold and Wiehe, Chapter 3
11	1/16/19	Suffix trees
12	1/21/19	MLK day, no classes
13	1/23/19	suffix trees, suffix arrays
14	1/25/19	suffix array construction
15	1/28/19	Suffix array construction and BWT		https://www.youtube.com/watch?v=4n7NPk5lwbI
16	1/30/19	BWT	Homework 2 is due
17	2/1/19	BWT & Needleman-Wunsch		Haubold and Wiehe, subset of Chapter 2.
18				http://en.wikipedia.org/wiki/Needleman%E2%80%93Wunsch_algorithm
19	2/8/19	Smith Waterman, Gotoh's algorithm
20	2/11/19	Linear-space alignment		Hirschberg's original paper (see canvas)
21	2/13/19	Four Russians Speed-up		Gusfield, Ch 12.7 (see canvas)
22	2/15/19	Heuristic Pairwise alinment / Mutliple Sequence Alignment		Haubold and Wiehe, Chapter 4, http://mummer.sourceforge.net/MUMmer.pdf
23	2/18/19	Modeling Biological Problems		https://arxiv.org/pdf/1706.05429
24	2/20/19	PSU Classes cancelled
25	2/22/19	Modeling Biological Problems	Homework 3 due
26	2/25/19	Genome assembly
27	2/27/19	Genome assembly
28	3/11/19	Hidden Markov Models	Homework 4 due	Chapter 3 in Durbin et al
29	3/13/19	Hidden Markov Models
30	3/15/19	Hidden Markov Models	Paper choices due
31	3/18/19	(tent) Profile HMMs		Chapter 7 in Durbin et al
32	3/25/19	paper prior meetings
33	3/29/19	Paper presentations	Michael, Praneet, Soodabeh, Mengran, Mahdi
34	4/1/19	Paper presentations	Amatur, Geesun, Sen, Yuchen, Yunju
35	4/3/19	Paper presentations	Qi, Alejandro, Qian, Ashirbad
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38	Scheduled Lectures
39	4/8/19	no class but project plan due	project plan due
40	4/24/19	(tent) final project presentations	Geesun, Sen, Qi/Yuchen, Ashirbad, Qian, Alejandro
41	4/26/19	(tent) final project presentations	Yunju, Amatur, Michael, Praneet, Soodabeh, Mengran, Mahdi
42	5/1/19	no class	project report due
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45	Remaining topics (tenative)
46		Structural Variation Detection
47		Structural Variation Detection
48		Phylogeny introduction, UPGMA	Chapter 7 of Durbin et al. book
49		Phylogeny (neighbor joining)
50		Phylogeny (Fitch's algorithm, Sankoff's)
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54	Paper Presentation assignments (http://www.citeulike.org/user/pashadag/tag/cse566)
55	Yunju Lee	A space and time-efficient index for the compacted colored de Bruijn graph
56	Mengran Fan	Rapid Flexible Docking Using a Stochastic Rotamer Library of Ligands
57	Geesun Jang	Compacting de Bruijn graphs from sequencing data quickly and in low memory
58	Amatur Rahman	Fast and Scalable Minimal Perfect Hashing for Massive Key Sets
59	Sen Lu	Minimap2: pairwise alignment for nucleotide sequences
60	Soodabeh	Automatic Prediction of Protein 3D Structures by Probabilistic Multi-template Homology Modeling.
61	Yuchen Sun	LoRDEC: accurate and efficient long read error correction
62	Michael Meehan	A General-Purpose Counting Filter: Making Every Bit Count
63	Qi Chang	U-Net: Convolutional Network for Biomedical Image Segmentation.
64	Alejandro	Informed and automated k-mer size selection for genome assembly
65	Qian Shi	OLego: fast and sensitive mapping of spliced mRNA-Seq reads using small seeds.
66	Praneet	SeqOthello: querying RNA-seq experiments at scale
67	Ashirbad	Parallel de Bruijn graph construction and traversal for de novo genome assembly
68	Mahdi	Rapid construction of metabolic models for a family of Cyanobacteria using a multiple source annotation workflow
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