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TopicAnnouncements / HandoutsReferences
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CSE / BMMB 566, Spring 2019, Algorithms and Data Structures in Bioinformatics
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Instructor: Paul Medvedev (pzm11)
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Link to Syllabus0
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Link to Canvas page
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Completed Lectures
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1/7/19Class intro and bio background
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1/11/19Knuth-Morris-Pratt algorithmhttp://jakeboxer.com/blog/2009/12/13/the-knuth-morris-pratt-algorithm-in-my-own-words/
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1/14/19KMP continued, Suffix triesProgramming Assignment 1 dueGusfield Ch 2.2, Haubold and Wiehe, Chapter 3
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1/16/19Suffix trees
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1/21/19MLK day, no classes
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1/23/19suffix trees, suffix arrays
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1/25/19suffix array construction
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1/28/19Suffix array construction and BWThttps://www.youtube.com/watch?v=4n7NPk5lwbI
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1/30/19BWTHomework 2 is due
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2/1/19BWT & 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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2/8/19Smith Waterman, Gotoh's algorithm
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2/11/19Linear-space alignmentHirschberg's original paper (see canvas)
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2/13/19Four Russians Speed-up Gusfield, Ch 12.7 (see canvas)
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2/15/19Heuristic Pairwise alinment / Mutliple Sequence AlignmentHaubold and Wiehe, Chapter 4, http://mummer.sourceforge.net/MUMmer.pdf
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2/18/19Modeling Biological Problemshttps://arxiv.org/pdf/1706.05429
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2/20/19PSU Classes cancelled
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2/22/19Modeling Biological Problems Homework 3 due
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2/25/19Genome assembly
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2/27/19Genome assembly
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3/11/19Hidden Markov ModelsHomework 4 dueChapter 3 in Durbin et al
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3/13/19Hidden Markov Models
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3/15/19Hidden Markov ModelsPaper choices due
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3/18/19(tent) Profile HMMsChapter 7 in Durbin et al
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3/25/19paper prior meetings
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3/29/19Paper presentationsMichael, Praneet, Soodabeh, Mengran, Mahdi
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4/1/19Paper presentationsAmatur, Geesun, Sen, Yuchen, Yunju
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4/3/19Paper presentationsQi, Alejandro, Qian, Ashirbad
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Scheduled Lectures
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4/8/19no class but project plan dueproject plan due
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4/24/19(tent) final project presentationsGeesun, Sen, Qi/Yuchen, Ashirbad, Qian, Alejandro
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4/26/19(tent) final project presentationsYunju, Amatur, Michael, Praneet, Soodabeh, Mengran, Mahdi
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5/1/19no classproject report due
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Remaining topics (tenative)
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Structural Variation Detection
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Structural Variation Detection
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Phylogeny introduction, UPGMAChapter 7 of Durbin et al. book
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Phylogeny (neighbor joining)
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Phylogeny (Fitch's algorithm, Sankoff's)
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Paper Presentation assignments (http://www.citeulike.org/user/pashadag/tag/cse566)
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Yunju LeeA space and time-efficient index for the compacted colored de Bruijn graph
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Mengran FanRapid Flexible Docking Using a Stochastic Rotamer Library of Ligands
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Geesun JangCompacting de Bruijn graphs from sequencing data quickly and in low memory
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Amatur RahmanFast and Scalable Minimal Perfect Hashing for Massive Key Sets
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Sen LuMinimap2: pairwise alignment for nucleotide sequences
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SoodabehAutomatic Prediction of Protein 3D Structures by Probabilistic Multi-template Homology Modeling.
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Yuchen SunLoRDEC: accurate and efficient long read error correction
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Michael MeehanA General-Purpose Counting Filter: Making Every Bit Count
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Qi ChangU-Net: Convolutional Network for Biomedical Image Segmentation.
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AlejandroInformed and automated k-mer size selection for genome assembly
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Qian ShiOLego: fast and sensitive mapping of spliced mRNA-Seq reads using small seeds.
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PraneetSeqOthello: querying RNA-seq experiments at scale
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AshirbadParallel de Bruijn graph construction and traversal for de novo genome assembly
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MahdiRapid construction of metabolic models for a family of Cyanobacteria using a multiple source annotation workflow
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