Bioinformatics Computing

CSE 40532/60532 - Fall 2012

Instructor

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

Schedule

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Date Topic Homework Notes
08/21/2012 DNA, genes and the genome   Syllabus video
Intro lecture
[PDF]
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  

Academic dishonesty

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.