Scott Emrich
Office: 211B Cushing Hall
Phone: (574) 631-0353; E-mail: semrich at nd.edu
Office hours: Mon 4:30-5:30pm, Tues 3:30-4:30 pm; 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
Announcements
| Date | Topic | Homework | Notes | |
| 08/21/2012 | DNA, genes and the genome | Syllabus video Intro lecture [PDF] |
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| 08/23/2012 | Sequence statistics | Hw #1 | [PDF] | |
| 08/28/2012 | Stats; Intro to Sequence alignment | [Notes] | ||
| 08/30/2012 | Sequence alignment | [PDF] | ||
| 09/04/2012 | Sequence alignment | Hw #2 out | [PDF] | |
| 09/06/2012 | Sequence alignment | [PDF] | ||
| 09/11/2010 | Intro to Hidden Markov Models | [PDF] | ||
| 09/13/2012 | Forward and Viterbi algorithms | [PDF] | ||
| 09/18/2012 | Hidden Markov Models | Hw #3 out | [PDF] | |
| 09/20/2012 | Ab initio gene finding | [PDF] | ||
| 9/25/2012 | Variation | [PDF] | ||
| 09/27/2012 | Variation and natural selection | [PDF] | ||
| 10/02/2012 | midterm review, intro to whole genome alignment | Hw #4 out | [PDF] | |
| 10/04/2012 | In-class midterm | |||
| 10/09/2012 | Whole genome comparisons | [PDF] | ||
| 10/11/2012 | Whole genome comparisons | [PDF] | ||
| Midterm Break! | ||||
| 10/23/2012 | Intro to genome sequencing and assembly | [PDF] | ||
| 10/25/2012 | Genome sequencing and assembly | Hw #5 out | [PDF] | |
| 10/30/2012 | Genome sequencing and assembly | [PDF]< | ||
| 11/01/2012 | Assembly validation | [PDF] | ||
| 11/06/2012 | Intro to phylogentic analysis | [PDF] | ||
| 11/08/2012 | Phylogenetic analysis: distance | [PDF] | ||
| 11/13/2012 | Phylogenetic analysis: parsimony | Hw #6 out | [PDF] | |
| 11/15/2012 | Multiple sequence alignment | [PDFs] | ||
| 11/20/2012 | Metagenomics | |||
| Happy Thanksgiving! | ||||
| 11/27/2012 | Genomics in the news | |||
| 11/29/2012 | Special topics | |||
| 12/04/2012 | Special topics | |||
| 12/06/2012 | Project presentations | Project due | ||
All are required to abide by the CSE and University honor code. Discussions are encouraged, but all answers/programs must be written/developed individually. Final projects will be performed as a group.