CSE597C / BMMB598F, Spring 2014, Algorithms and Data Structures in Bioinformatics
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TopicAnnouncements / HandoutsReferences
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CSE597C / BMMB598F, Spring 2014, 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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For up to date Instructor's office hours and location, see http://www.cse.psu.edu/~pashadag/medvedev.html
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For access to references, refer to Lessons tab in Angel
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1/14/2014Introduction to course & Genome Assemblylec1.pdf
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1/16/2014Genome Assembly
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1/21/2014Genome AssemblyHW1 is out, due Jan 30th 9am (postponed till 2/6 at 9am)
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hw1.pdf
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1/23/2014Bidirected Graphs, Z-Algorithm for exact string matchinglec2.pdfGusfield book, Chapter 1 (see angel)
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1/28/2014Boyer Moore, Suffix Treeslec3.pdfGusfield Ch 2.2 (see angel), Haubold and Wiehe, Chapter 3
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PaperPresentation.pdf
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CourseProject.pdf
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1/30/2014Suffix Trees / Suffix Arrays
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2/4/2014Burrows-Wheeler TransformlecBWT.pdfhttp://schatzlab.cshl.edu/teaching/2012/BWT.pdf
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2/6/2014Burrows-Wheeler Transform / FM-indexHW1 due 9am
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hw2.pdf
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2/11/2014no class
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2/13/2014no class
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2/18/2014Needleman-Wunsch & Smith-WatermanlecSeqAl.pdfHaubold and Wiehe, subset of Chapter 2.
Alternatively, you can look at: http://en.wikipedia.org/wiki/Needleman%E2%80%93Wunsch_algorithm
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2/20/2014Modeling gap costsHW2 due at 9amHaubold and Wiehe, parts of Chapter 2.
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2/25/2014Hirschberg's Algorithm & Four Russians Speed-up (not finished)FourRussiansSlidesByChristianPedersen.pdfGusfield, Ch 12.7
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lecHirschberg.pdfHirschberg's original paper
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hw3.pdfhttp://en.wikipedia.org/wiki/Hirschberg%27s_algorithm
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2/27/2014paper presentationsYao, Manjari/Abhishek
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3/4/2014paper presentationsColleen/Chen, Kai/Gang
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3/6/2014paper presentationsGeorge
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3/11/2014Spring Break
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3/13/2014Spring Break
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3/18/2014paper presentationsMeiram
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3/20/2014Four Russians, Anchor Based AlignmentHW3 dueHaubold and Wiehe, Chapter 4
http://mummer.sourceforge.net/MUMmer.pdf
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3/25/2014no class, no office hoursProject Plan Due
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3/27/2014Mutliple Sequence AlignmentlecMultAl.pdf
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4/1/2014Hidden Markov ModelsChapter 3 of Durbin et al. book
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4/3/2014no class
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4/8/2014Hidden Markov Models
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4/10/2014Hidden Markov Models
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4/15/2014Profile HMMs and Phylogeny Introduction
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4/17/2014Phylogeny (UPGMA)Chapter 7 of Durbin et al. book
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4/22/2014Neighbor Joining and Fitch's algorithm
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4/24/2014Structural Variation DetectionSVtutorial.pdfhttp://dx.doi.org/10.1038/nmeth.1374
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4/29/2014project presentations (15mins each)Chen, Meiram, George
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5/1/2014project presentationsAbhishek/Colleen, Manjari, Kai/Gang, Yao
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5/3/2014Project Report Due
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