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 | |
| 8/19/2025 | DNA, genes and the genome | Hw #1, due 8/28 | see Piazza | |
| 8/21/2025 | Sequence statistics | |||
| 8/26/2025 | Finalize stats; Intro to sequence alignment | |||
| 8/28/2025 | Sequence alignment | Hw #2, due 9/11 | ||
| 9/02/2025 | Sequence alignment heuristics | |||
| 9/04/2025 | Variation and natural selection | |||
| 9/09/2025 | Affine gap penalties; Intro to Markov Models | |||
| 9/11/2025 | Hidden Markov Models (Forward algorithm) | Hw #3, due 9/25 | ||
| 9/16/2025 | Hidden Markov Models (Viterbi) | |||
| 9/18/2025 | Gene finding using HMMs | 9/23/2025 | Scalable genome alignment: Classical to modern | |
| 9/25/2025 | Intro to genome assembly | Hw #4, due 10/14 [Draft] [Reference] |
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| 9/30/2025 | Midterm | |||
| 10/02/2025 | Genome assembly (hands on) | |||
| Fall Break! | ||||
| 10/09/2025 | Multiple sequence alignment | |||
| 10/14/2025 | Class choice: study hall to start projects | 10/16/2025 | Phylogenetic analysis | |
| 10/21/2025 | Phylogenetic trees: distance | |||
| 10/23/2025 | Other approaches for determining trees | Hw #5, due 11/09 [small file] [Large file] |
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| 10/28/2025 | Personalized medicine and human demographics | |||
| 10/30/2025 | From sequencing to workflows: Using Galaxy and external tools | |||
| 11/04/2025 | No class Election day | |||
| 11/06/2025 | Modern genomics search (sketching, compressed data structures, GPT) | Group update #1 due | ||
| 11/11/2025 | Project-linked lecture: large language models for sequences | |||
| 11/13/2025 | Reproducibility and open science | |||
| 11/18/2025 | Special topic: Genomics in the news | Group update #2 due | ||
| 11/20/2025 | Team Science and technical collaboration: Lessons learned | |||
| 11/25/2025 | Study hall / project time | |||
| 12/02/2025 | Project presentations | |||
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.