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TopicAnnouncements / HandoutsReferences
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CSE / BMMB 566, Spring 2018, 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 Canvas page
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Completed Lectures
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1/8/2018Class Into and Bio Review
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1/10/2018Knuth-Morris-Pratt algorithmhttp://jakeboxer.com/blog/2009/12/13/the-knuth-morris-pratt-algorithm-in-my-own-words/
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1/15/2018MLK day -- Holiday
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1/17/2018Suffix TreesProgramming Assignment 1 dueGusfield Ch 2.2, Haubold and Wiehe, Chapter 3
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1/19/2018Suffix tree applications / Suffix array
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1/22/2018Suffix array construction
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1/24/2018Burrows-Wheeler Transformhttps://www.youtube.com/watch?v=4n7NPk5lwbI
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1/26/2018FM-index and Sequence AlignmentHaubold and Wiehe, subset of Chapter 2.
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http://en.wikipedia.org/wiki/Needleman%E2%80%93Wunsch_algorithm
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1/31/2018Needleman-Wunsch, Smith WatermanHomework Assignment 2 due
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2/2/2018Gotoh's algorithm and Linear-space alignmentHirschberg's original paper (see canvas)
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http://en.wikipedia.org/wiki/Hirschberg%27s_algorithm
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2/5/2018Four Russians Speed-up / Heuristic Pairwise alinmentGusfield, Ch 12.7 (see canvas)
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2/7/2018University cancels classes
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2/12/2018Mutliple Sequence AlignmentHaubold and Wiehe, Chapter 4, http://mummer.sourceforge.net/MUMmer.pdf
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2/14/2018Structural Variation DetectionHomework Assignment 3 due
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2/19/2018Structural Variation Detection / Modeling Biological Problems
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2/21/2018Modeling Biological Problems
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2/23/2018Modeling Biological Problems / Genome Assemblyhttps://arxiv.org/pdf/1706.05429
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2/26/2018Genome assembly
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2/28/2018Hidden Markov Models
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3/2/2018Hidden Markov Models
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3/5-3/9spring break
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3/12/2018Hidden Markov Models
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3/16/2018Profile HMMsPaper choices due
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3/23/2018Prior Meetings on paper presentations
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3/26/2018Paper Presentations: Kushal, Anish, Natasha
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3/28/2018Paper Presentations: Mihir, Mahdi, Tsung-Yu
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3/30/2018Paper Presentations: Nathan, Debolina, Jordan
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Scheduled Lectures
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4/9/2018Phylogeny introduction, UPGMAChapter 7 of Durbin et al. book
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4/11/2018Phylogeny (neighbor joining)
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4/13/2018Phylogeny (Fitch's algorithm, Sankoff's)
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4/25/2018Final Project presentation: Jordan/Debolina/Nathan/Tsung-Yu
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4/27/2018Final Project presentation: Mahdi / Mihir+Kushal / Natasha / Anish
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5/2/2018report due
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Papers:Kushal, Compacting de Bruijn graphs from sequencing data quickly and in low memory
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Anish, Succinct Colored de Bruijn Graphs
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Natasha, AllSome Sequence Bloom Trees
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Mihir, Bloom Filter Trie: an alignment-free and reference-free data structure for pan-genome storage
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Mahdi, TBD
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Tsung Yu, Epileptic seizure detection based on EEG signal analysis using hierarchy based Hidden Markov Model
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Nathan, Joint sparse canonical correlation analysis for detecting differential imaging genetics modules
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Debolina, Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data
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Jordan, Inferring hidden causal relations between pathway members using reduced Google matrix of directed biological networks.
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