CSE / BMMB 566, Spring 2016, Algorithms and Data Structures in Bioinformatics
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TopicAnnouncements / HandoutsReferences
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CSE / BMMB 566, Spring 2016, Algorithms and Data Structures in Bioinformatics
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Instructor: Paul Medvedev (pzm11)
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Link to Syllabus
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Link to Piazza page
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Scheduled Lectures
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1/11/2016Bio review & Next Generation Sequencing & Genome Assembly
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1/13/2016Exact string matching -- Z-algorithm, Boyer MooreFirst batch of programming due, Jan 18th, 11pm
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1/29/2016Boyer Moore / Suffix Trees Gusfield book, Chapter 1
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2/8/2016Suffix Trees/ArraysGusfield Ch 2.2, Haubold and Wiehe, Chapter 3
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2/10/2016Burrows-Wheeler Transformhttp://schatzlab.cshl.edu/teaching/2012/BWT.pdf
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2/12/2016BWT, FM-Index
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2/15/2016Needleman-Wunsch / Smith WatermanHaubold and Wiehe, subset of Chapter 2.
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http://en.wikipedia.org/wiki/Needleman%E2%80%93Wunsch_algorithm
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2/17/2016Modeling gap costs, Hirschberg's AlgorithmProblems 13, 14, and 15 of programming due, 11pmHirschberg's original paper
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http://en.wikipedia.org/wiki/Hirschberg%27s_algorithm
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2/19/2016Four Russians Speed-up, Heuristic Pairwise alignmentGusfield, Ch 12.7
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Haubold and Wiehe, Chapter 4
http://mummer.sourceforge.net/MUMmer.pdf
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2/22/2016Mutliple Sequence Alignment
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2/24/2016Genome assembly
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2/26/2016no classProblems 16,17, and 18 of programming due, 11pm
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2/29/2016Genome assembly
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3/2/2016Genome assemblyRanked list of papers due (will be postponed, stay tuned)
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3/4/2016Genome assembly11pm deadline for Assignment 1/2/3 regrades
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3/14/2016Structural Variation Detectionhttp://dx.doi.org/10.1038/nmeth.1374
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3/16/2016Hidden Markov ModelsRanked list of papers due 11amChapter 3 of Durbin et al. book
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3/18/2016Hidden Markov ModelsProblems 8-12 of programming due, 11pm
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3/21/2016Hidden Markov Models
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3/23/2016Profile HMMsChapter 7 of Durbin et al. book
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3/24/2016no class (not a class time)Prior meetings for paper presentations
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3/25/2016Mayank, Iyswarya, Tao-yang, Prasanna
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3/28/2016Wentao, Weining, Quoc, Athar
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3/30/2016Jiaqi, Tianqi, Valleri, Frank
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4/1/2016Kaiyu (kfw), Hui-ju, Dafang, Xiao
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4/4/2016Khushboo, Chun-Yang, Kaiyu (kuw), RoksanaWritten report due, if you did not do the presentation (4 pages)
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4/6/2016Phylogeny introduction, UPGMAProject Plan Due (11pm)Chapter 7 of Durbin et al. book
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4/8/2016Phylogeny (neighbor joining, Fitch's algorithm, Sankoff's)
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4/25 - 4/29(tent) no lectures
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4/29/2016no lecture, but Optional Preliminary Report due at 10am Optional Preliminary Report due 10am
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5/4/2016Project Report Due at 10am, no classProject Report Due
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Future topics (tentative)
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Groups
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athar21
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frank khushboo15
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Quoc Valleri
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Tianqi
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kuw Jiaqi
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kfw Xiao
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Roksana
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Chun-Yang
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Iyswarya
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Prasanna
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Wentao
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Hui-ju Tao-Yang
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Dafang Weining
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Mayank
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