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 |
| 8/23/2018 | DNA, genes and the genome | Hw #1 out, due 9/3 | see Piazza |
| 8/28/2018 | Sequence statistics | ||
| 8/30/2018 | Finalize stats; Intro to sequence alignment | ||
| 9/04/2018 | Sequence alignment | Hw #2 out, due 9/18 | |
| 9/06/2018 | Sequence alignment heuristics | ||
| 9/11/2018 | Variation and natural selection | ||
| 9/13/2018 | Affine gap penalties; Intro to Markov Models | ||
| 9/18/2018 | Hidden Markov Models (Forward algorithm) | Hw #3 out, due 10/2 | |
| 9/20/2018 | Hidden Markov Models (Viterbi) | ||
| 9/25/2018 | Gene finding using IMMs and HMMs | 9/27/2018 | Special topic: Bioinformatics and Plant tech (at Calhoun's) |
| 10/02/2018 | Midterm review, suffix trees and suffix arrays | Fall break! | |
| 10/9/2018 | In-class midterm | ||
| 10/11/2018 | Suffix arrays | Hw #4 out, due 10/30 [AFG for asm][reference] |
See Piazza |
| 10/16/2018 | Finish genome alignment | ||
| 10/18/2018 | Genome assembly | 10/23/2018 | Genome assembly: hands on |
| 10/25/2018 | Engineering day | ||
| 10/30/2018 | Phylogenetic analysis | ||
| 11/01/2018 | Phylogenetic trees: distance | Hw #5 out, due 11/15 [small FASTA] [Large Phylip file] |
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| 11/06/2018 | Other approaches for determining trees, intro to metagenomics | ||
| 11/08/2018 | Multiple sequence alignent | Group update #1 due | |
| 11/13/2018 | Sequencing, Galaxy and outsourcing analysis | ||
| 11/15/2018 | Personalized medicine and human demographics | ||
| 11/20/2018 | Project-linked #1: cloud and HPC for sequencing | Thanksgiving! | |
| 11/27/2018 | Project-linked #2: randomized algs (LSH, minhash) | Group update #2 due | |
| 11/29/2018 | Special topic: Genomics in the news | ||
| 12/04/2018 | 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.