Special Topics: Bioinformatics Computing

COSC 494/594 - Spring 2018

Instructor

Scott Emrich
Office: 608 Min Kao
Phone: (865) 974-3891; E-mail: semrich at utk.edu
Office hours: Tues 3:30-4:30pm; and by appointment

Overview

Broad overview of bioinformatics with a substantial problem-solving component. Topics include: generative models for sequences, pairwise sequence alignment, basic methods in molecular phylogeny and evolution, ab initio gene prediction, whole genome comparisons, genome assembly and analysis.

Text and syllabus

Introduction to Computational Genomics by Cristianini and Hahn.

The syllabus can be found here

Draft schedule

Date Topic Homework Notes
1/11/2018 DNA, genes and the genome Hw #1 out, due 1/23 see Piazza
1/16/2018 Sequence statistics   [PDF]
1/18/2018 Finalize stats; Intro to sequence alignment   [PDF]
1/23/2018 Sequence alignment Hw #2 out, due 2/6 [PDF]
1/25/2018 Sequence alignment heuristics   [PDF]
1/30/2018 Variation and natural selection   [PDF]
2/01/2018 Affine gap penalties; Intro to Markov Models   [PDF]
2/06/2018 Hidden Markov Models (Forward algorithm) Hw #3 out, due 2/20
File 1   File 2
[PDF]
2/08/2018 Hidden Markov Models (Viterbi)   [PDF]
2/13/2018 Gene finding using IMMs and HMMs   [PDF]
2/15/2018 Intro to whole genome alignment   [PDF]
2/20/2018 Midterm review, suffix trees and suffix arrays   [PDF]
2/22/2018 In-class midterm    
2/27/2018 Suffix arrays (cont.) Hw #4 out, due 3/27 See Piazza
3/01/2018 Genome assembly   [PDF]
3/06/2018 Genome assembly: hands on   [PDF]
3/08/2018 Asm validation (finish); Phylogenetics   [PDF]
Spring Break!
3/20/2018 Phylogenetic analysis (cont)   [PDF]
3/22/2018 Phylogenetic trees: distance   [PDF]
3/27/2018 Other approaches for determining trees, intro to metagenomics Hw #5 out, due 4/10 [PDF]
3/29/2018 Galaxy and outsourcing analysis   [PDF]
4/03/2018 Multiple sequence alignent   [PDF]
4/05/2018 Personalized medicine and human demographics Group update #1 due  
4/10/2018 Project-linked #1: cloud and HPC for sequencing    
4/12/2018 Project-linked #2: randomized algs (LSH, minhash)    
4/17/2018 Special topic: k-mer driven analysis    
4/19/2018 Special topic: Genomics in the news Group update #2 due  
4/24/2018 TBD    
4/26/2018 Project presentations    

Academic dishonesty

All are required to abide by the University honor code. Discussions are encouraged, but all answers/programs must be written/developed individually.

Final projects will be performed as a group with peer assessments.