Special Topics: Bioinformatics Computing

COSC 494/594 - Spring 2022

Instructor

Scott Emrich
Office: 608 Min Kao
Phone: (865) 974-3891; E-mail: semrich at utk.edu
Office hours: Tuesdays, 3-4pm 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
1/25/2022 DNA, genes and the genome Hw #1, due 2/2 see Piazza
1/27/2022 Sequence statistics   PDF
2/01/2022 Finalize stats; Intro to sequence alignment   PDF
2/03/2022 Sequence alignment Hw #2, due 2/16 PDF
2/08/2022 Sequence alignment heuristics   PDF
2/10/2022 Variation and natural selection   PDF
2/15/2022 Affine gap penalties; Intro to Markov Models   PDF
2/17/2022 Hidden Markov Models (Forward algorithm) Hw #3, due 3/7 PDF
2/22/2022 Hidden Markov Models (Viterbi)   PDF
2/24/2022 Gene finding using HMMs   PDF
3/01/2022 IMMs, midterm review (syncronous)   PDF
3/03/2022 Genome alignments   PDF
3/08/2022 suffix arrays, intro to genome assembly Hw #4, due 4/4
[AFG] [Reference]
PDF
3/10/2022 Midterm    
Spring Break!
3/22/2022 Multiple sequence alignment   PDF
3/24/2022 Genome assembly: hands on   PDF
3/29/2022 Phylogenetic analysis   PDF
3/31/2022 Phylogenetic trees: distance   PDF
4/05/2022 Other approaches for determining trees Hw #5, due 4/21
[small file] [Large file]
PDF
4/07/2022 Sequencing, Galaxy and outsourcing analysis   PDF
4/12/2022 Student choice: feature selection for bacteria genomics    
4/19/2022 Personalized medicine and human demographics    
4/21/2022 Project-linked #1: deep learning for -omics/bioinformatics Group update #1 due  
4/26/2022 Project-linked #2: TBD    
4/28/2022 study hall / open for projects    
5/03/2022 Project-linked #3: NGS tools / analysis Group update #2 due  
5/05/2022 Special topic: Genomics in the news    
5/10/2022 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.