Special Topics: Bioinformatics Computing

COSC 494/594 - Fall 2019

Instructor

Scott Emrich
Office: 608 Min Kao
Phone: (865) 974-3891; E-mail: semrich at utk.edu
Office hours: Mondays, 4-5pm 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
8/22/2019 DNA, genes and the genome Hw #1, due 9/3 see Piazza
8/27/2019 Sequence statistics   PDF
8/29/2019 Finalize stats; Intro to sequence alignment   PDF
9/03/2019 Sequence alignment Hw #2, due 9/17 PDF
9/05/2019 Sequence alignment heuristics   PDF
9/10/2019 Variation and natural selection   PDF
9/12/2019 Affine gap penalties; Intro to Markov Models   PDF
9/17/2019 Hidden Markov Models (Forward algorithm) Hw #3 out, due 10/3 PDF
9/19/2019 Hidden Markov Models (Viterbi)    
9/24/2019 Gene finding using IMMs and HMMs    
9/26/2019 Midterm review, suffix trees and suffix arrays    
10/01/2019 Suffix arrays    
10/03/2019 Genome alignment Hw #4 out, due 10/29
 
10/08/2019 In-class midterm    
10/10/2019 Genome assembly    
10/15/2019 Genome assembly: hands on    
Fall break!
10/22/2019 TBD    
10/24/2019 Engineering day (no class)    
10/29/2019 Phylogenetic analysis    
10/31/2019 Phylogenetic trees: distance Hw #5 out, due 11/14
 
11/05/2019 Other approaches for determining trees, intro to metagenomics    
11/07/2019 Multiple sequence alignent Group update #1 due  
11/12/2019 Sequencing, Galaxy and outsourcing analysis    
11/14/2019 Personalized medicine and human demographics    
11/19/2019 Project-linked #1: cloud and HPC for sequencing    
11/21/2019 Project-linked #2: randomized algs (LSH, minhash) Group update #2 due  
11/26/2019 Special topic: Genomics in the news    
Thanksgiving!
12/03/2019 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.