Bioinformatics Computing

CSE 40532/60532 - Fall 2017

Instructor

Scott Emrich
Office: 211B Cushing Hall
Phone: (574) 631-0353; E-mail: semrich at nd.edu
Tentative office hours: TBD; 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
08/22/2017 DNA, genes and the genome Hw #1 out, due 8/31 [PDF] see Piazza
08/24/2017 Sequence statistics   [PDF]
08/29/2017 Finalize stats; Intro to Sequence alignment   [PDF]
08/31/2017 Sequence alignment Hw #2 out, due 9/14 [PDF] [PDF]
09/05/2017 Sequence alignment heuristics   [PDF]
09/07/2017 Variation and natural selection   [PDF]
09/12/2017 Affine gap penalties; Intro to Markov Models   [PDF]
09/14/2017 Hidden Markov Models Hw #3 out, due 9/28 [PDF] [PDF]
09/19/2017 Hidden Markov Models (Forward and Viterbi algorithms)   [PDF]
09/21/2017 Gene finding in practice (using IMMs and HMMs)   [PDF]
09/26/2017 intro to whole genome alignment   [PDF]
09/28/2017 suffix trees and suffix arrays   [PDF]
10/03/2017 midterm review, genome alignments and assembly   [PDF]
10/05/2017 In-class midterm    
10/10/2017 Genome assembly: hands on examples Hw #4 out, due 10/31 [PDF]
[ref FASTA] [AMOS AFG]
[PDF]
10/12/2017 Assembly validation   [PDF]
Midterm Break!
10/24/2017 Intro to phylogenetic analysis   [PDF]
10/26/2017 Phylogenetic trees: distance   [PDF]
10/31/2017 Phylogenetic analysis: distance vs. parsimony Hw #5 out, due 11/16 [PDF]
[large file FASTA][large file phylip]
[PDF]
11/02/2017 Other approaches for determining trees, intro to metagenomics   [PDF]
11/07/2017 Guest lecture: eDNA sequencing    
11/09/2017 Made up later (course proj)    
11/14/2017 Galaxy and Outsourcing Analysis   [PDF]
11/16/2017 Multiple sequence alignment Group update #1 due [PDF]
11/21/2017 Project-linked topic #1    
Happy Thanksgiving!
11/28/2017 Project-linked topic #2    
11/30/2017 Special topic: min hash sketching Group update #2 due  
12/05/2017 Special topic: Genomics in the news    
12/07/2017 Project presentations    

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.