Special Topics: Bioinformatics Computing

COSC 494/594 - Spring 2022


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


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
8/24/2023 DNA, genes and the genome Hw #1, due 9/4 see Piazza
8/29/2023 Sequence statistics   PDF
8/31/2023 Finalize stats; Intro to sequence alignment   PDF
9/05/2023 Sequence alignment Hw #2, due 9/18 PDF
9/07/2023 Sequence alignment heuristics   PDF
9/12/2023 Variation and natural selection   PDF
9/14/2023 Affine gap penalties; Intro to Markov Models   PDF
9/19/2023 Hidden Markov Models (Forward algorithm) Hw #3, due 10/2 PDF
9/21/2023 Hidden Markov Models (Viterbi)   PDF
9/26/2023 Gene finding using HMMs   PDF
9/28/2023 IMMs, midterm review (syncronous)   PDF
10/03/2023 Genome alignments Hw #4, due 10/16
[AFG] [Reference]
10/05/2023 Midterm    
Fall Break!
10/12/2023 suffix arrays, intro to genome assembly   PDF
10/17/2023 Genome assembly: hands on   PDF
10/19/2023 Multiple sequence alignment   PDF
10/24/2023 Phylogenetic analysis   PDF
10/26/2023 Phylogenetic trees: distance   PDF
10/31/2023 Other approaches for determining trees Hw #5, due 11/09
[small file] [Large file]
11/02/2023 Personalized medicine and human demographics   PDF
11/07/2023 Sequencing, Galaxy and outsourcing analysis    
11/09/2023 Project #1: a comparison of dimensionality reduction/deep learning for classification    
11/14/2023 Project-linked #2: TBD Group update #1 due  
11/16/2023 Guest lecture: NLP/deep learning and bioinformatics
(student choice)
11/21/2023 TBD    
11/28/2023 Project-linked #3: TBD Group update #2 due  
11/30/2023 Special topic: Genomics in the news    
12/05/2023 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.