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