CSE / BMMB 566, Spring 2017, Algorithms and Data Structures in Bioinformatics
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TopicAnnouncements / HandoutsReferences
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CSE / BMMB 566, Spring 2017, 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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Completed Lectures
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1/9/2017Class Into and Bio Review
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1/11/2017Bio Review & Knuth-Morris-Pratthttp://jakeboxer.com/blog/2009/12/13/the-knuth-morris-pratt-algorithm-in-my-own-words/
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1/13/2017KMP & Suffix trees
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1/18/2017Suffix TreesSecond Homwork posted,
First batch of programming due, Jan 18th, 11pm
Gusfield Ch 2.2, Haubold and Wiehe, Chapter 3
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1/20/2017Suffix tree applications / Suffix arrayGusfield Ch 2.2, Haubold and Wiehe, Chapter 3
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1/23/2017Suffix array construction
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1/25/2017Burrows-Wheeler Transformhttp://schatzlab.cshl.edu/teaching/2012/BWT.pdf
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1/30/2017BWT
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2/6/2017FM-index and Needleman-WunschHaubold and Wiehe, subset of Chapter 2.
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http://en.wikipedia.org/wiki/Needleman%E2%80%93Wunsch_algorithm
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2/8/2017Smith Waterman, Modeling gap costsHirschberg's original paper
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http://en.wikipedia.org/wiki/Hirschberg%27s_algorithm
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2/10/2017Four Russians Speed-up, Linear-space alignmentGusfield, Ch 12.7
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2/13/2017Heuristic Pairwise alignment, Mutliple Sequence AlignmentHaubold and Wiehe, Chapter 4
http://mummer.sourceforge.net/MUMmer.pdf
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2/15/2017Mutliple Sequence Alignment and SV detection
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2/17/2017Structural Variation DetectionHomework 3 duehttp://dx.doi.org/10.1038/nmeth.1374
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2/24/2017Genome assembly
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2/27/2017Genome assemblyModeling Biological Problems in Computer Science (see dropbox)
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3/1/2017Genome assembly
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3/3/2017Genome assembly
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3/13/2017Hidden Markov ModelsPaper choices dueChapter 3 of Durbin et al. book
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3/17/2017Hidden Markov ModelsHomework 4 due
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3/20/2017Hidden Markov Models
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3/22/2017Profile HMMs
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3/29/2017Saurabh Kaul, chikhi informed
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3/29/2017Lidong Luo, zhang, these are
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3/29/2017Hongyuan Zhan, Melsted
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3/29/2017john hutton, Salmela
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3/31/2017Asha Veerabhadraiah, Muggli
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3/31/2017Chun-Yi Liu, Minkin
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3/31/2017Sravya Adavi, Simpson
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3/31/2017Priyasha Pratik, Langmead ultrafast
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4/3/2017Hanling Zhang, Liu
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4/3/2017Ayaan Hossain, Sun varmatch
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4/3/2017Huaipan Jiang, Sun allsome
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4/5/2017Adam Mohammed, kingsford
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4/5/2017Yunqi Zhang, Tomescu
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4/5/2017Yiwei Sun, epitopes
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4/24/2017Adam Mohammed, Yunqi Zhang, Yiwei Sun, Qichen Yan, Jing Zhao
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4/26/2017
Chun-Yi Liu, Sravya Adavi, Priyasha Pratik / Ayaan Hossain, Hanling Zhang, Huaipan Jiang
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4/28/2017Saurabh Kaul, Lidong Luo, Hongyuan Zhan, John Hutton, Asha Veerabhadraiah
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Scheduled Lectures
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5/1/2017no classProject report due
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Future topics (tentative and will change)
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Chapter 7 of Durbin et al. book
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4/6/2016Phylogeny introduction, UPGMAChapter 7 of Durbin et al. book
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4/8/2016Phylogeny (neighbor joining, Fitch's algorithm, Sankoff's)
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