CSE597A / BMMB598F, Spring 2015, Algorithms and Data Structures in Bioinformatics
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TopicAnnouncements / HandoutsReferences
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CSE597A / BMMB598F, Spring 2015, 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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Office hours are by appointment after class
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For access to references without links, refer to Lessons tab in Angel
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Past Lectures
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1/13/2015Bio review & Next Generation Sequencing & Genome Assemblyhttp://www.cse.psu.edu/~pashadag/teaching/597s15/slides1.pdf
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1/15/2015Genome AssemblyProgramming Assignment
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1/20/2015Genome Assembly
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1/22/2015Bidirected Graphs, Z-Algorithm for exact string matchingslides2.pdfGusfield book, Chapter 1
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1/27/2015Z-algorithm proof, Boyer MooreFirst batch of programming assignment dueGusfield Ch 2.2, Haubold and Wiehe, Chapter 3
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slides3.pdf
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1/29/2015Boyer Moore / Suffix Trees
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2/3/2015Suffix Trees/Arraysslides4.pdf
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2/5/2015Burrows-Wheeler Transform / FM-indexblackboardhttp://schatzlab.cshl.edu/teaching/2012/BWT.pdf
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2/10/2015Second batch of programming assignment due
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2/12/2015Burrows-Wheeler Transform / FM-indexPaperPresentations.pdf
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CourseProject.pdf
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2/17/2015FM-index wrap-up, Needleman-Wunsch slides5.pdfHaubold and Wiehe, subset of Chapter 2.
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http://en.wikipedia.org/wiki/Needleman%E2%80%93Wunsch_algorithm
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2/19/2015Smith-Waterman, Modeling gap costs, Hirschberg's Algorithmslides6.pdfHaubold and Wiehe, parts of Chapter 2.
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slides7.pdfHirschberg's original paper
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http://en.wikipedia.org/wiki/Hirschberg%27s_algorithm
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2/24/2015Hirschberg's Algorithm & Four Russians Speed-upAssignment due date extended to 2/25, 11pmGusfield, Ch 12.7
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2/26/2015Whole-genome alignmentPaper preferences dueHaubold and Wiehe, Chapter 4
http://mummer.sourceforge.net/MUMmer.pdf
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3/3/2015Mutliple Sequence Alignment
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3/5/2015Structural Variation DetectionFourth batch of programming assignment duehttp://dx.doi.org/10.1038/nmeth.1374
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SVtutorial.pdf
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3/10/2015Spring Break
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3/12/2015Spring Break
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3/17/2015Hidden Markov ModelsChapter 3 of Durbin et al. book
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3/19/2015Hidden Markov ModelsPrior meetings for paper presentations
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3/24/2015HMMs / paper presentations
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3/26/2015paper presentations
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3/31/2015paper presentationsProject Plan Due
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4/2/2015paper presentations
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4/7/2015Profile HMMs and Phylogeny IntroductionChapter 7 of Durbin et al. book
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4/9/2015
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4/14/2015Paper Report Due (for those who did not do the presentation)
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4/16/2015UPGMA and Neighbor joining algorithms
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4/21/2015Fitch's algorithm
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4/23/2015Sankoff's Algorithm / project presentations
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4/28/2015project presentations
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4/30/2015project presentations
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Upcoming Lectures (subject to most likely change)
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