Bioinformatics Computing

CSE 40532/60532 - Fall 2008

Instructor

Scott Emrich
Office: 351 Fitzpatrick Hall
Phone: (574)631-0353; E-mail: semrich at nd.edu
Office hours: Mon 11am-noon and 4:30-6:00 PM; Wed 4:30-6:00 PM; and by appointment

Teaching Assistant

Santanu Chatterjee
Office: 325 Cushing Hall
Phone: (574)631-3906; E-mail: schatter at nd.edu
Office hours: Tues 3:30-5:30 pm

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

Course material wiki

Schedule

Date Topic Homework Notes
08/26/2008 DNA, genes and the genome   PDF
08/28/2008 Sequence statistics HW #1 out PDF
09/02/2008 Sequence alignment   PDF
09/04/2008 Sequence alignment   PDF
09/09/2008 Sequence alignment HW #1 answers
HW #2 out
PDF
09/11/2008 Sequence alignment   PDF
09/16/2008 Hidden Markov Models   PDF
09/18/2008 Hidden Markov Models   PDF
09/23/2008 Hidden Markov Models HW #2 answers
HW #3 out
PDF
09/25/2008 Ab initio gene finding   PDF
09/30/2008 Variation   PDF
10/02/2008 Variation and natural selection   PDF
10/07/2008 In-class midterm HW #3 due
10/09/2008 Whole genome comparisons   PDF
Add info
10/14/2008 Whole genome comparisons   PDF
10/16/2008 Whole genome comparisons   PDF
Add info
Midterm Break!
10/28/2008 Genome sequencing and assembly HW #4 out Video 1
Video 2
10/30/2008 Genome sequencing and assembly   PDF
11/04/2008 Assembly validation HW #4 due PDF
11/06/2008 Intro to phylogentic analysis HW #5 out PDF
11/11/2008 Phylogenetic analysis   >PDF
11/13/2008 Phylogenetic analysis HW #5 due
HW #6 out
PDF
11/18/2008 Genome annotation   PDF
11/20/2008 Next-gen sequencing   PDF
11/25/2008 Motifs HW #6 due
HW #7 out
PDF
Happy Thanksgiving!
12/02/2008 Genomics in the news  
12/04/2008 Special topics HW #7 due
12/09/2008 Special topics  
12/11/2008 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.