Genomic Informatics

GENOME 373
Department of Genome Sciences
University of Washington
Spring Quarter, 2007

Course description

This course is intended to introduce students to the breadth of problems and methods in computational analysis of genomes, arguably the single most important new area in biological research. The specific subjects will include large-scale comparative genome structure, sequence alignment and search methods, gene prediction, evolutionary relationships among genes, and microarray analysis. Dr. Noble is trained in statistics and computer science, whereas Dr. Thomas is trained in genetics and molecular genetics. They collaborate in teaching the course to provide an inter-disciplinary view of this inter-disciplinary field. Teaching will alternate blocks of application to problems in biology with theoretical and algorithmic methods.

Instructional staff

Instructor: James Thomas
Email: jht@u.washington.edu
Office: Foege S333C
Phone: (206) 543-7877
Office hours: Wed 12:30-1:30

Instructor: William Stafford Noble
Email: noble@gs.washington.edu
Office: Foege S220B
Phone: (206) 543-8930
Office hours: Tue 12:30-1:30

Teaching assistant: Aaron Klammer
Email: aklammer@u.washington.edu
Office: Foege S220
Office hours: Mon 2-3 pm in the Foege cafeteria (a.k.a., Vista Cafe)

Meeting times and locations

Lectures: Monday, Wednesday and Friday, 9:30 - 10:20 am, Foege S110.

Review and homework discussion section: Tuesday 9:30 - 10:20 am, Foege S040.

Prerequisites

GENOME 371, GENOME 351 or permission of instructor.

Previously, this course had as a prerequisite the ability to write computer programs for data analysis. Starting this year, we will provide introductory programming tutorials for students who do not have background in programming.

Course materials

Required: Bioinformatics: Sequence and Genome Analysis by Mount. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 2004. Second edition. Paperback, ~$89.

Recommended:

Some of the homework assignments will include programming. You are welcome to use any language that you are comfortable with (i.e., C, C++, Java, Perl, Python, Matlab). For those without programming background, we will be providing introductory tutorials in Python. Here are some useful Python books:

• Learning Python by Lutz and Ascher. This is a gentle introduction to programming in Python.
• Python in a Nutshell by Martelli. This is a Python reference for people who plan to program in the language regularly.

Homework

Homework is assigned each Wednesday and is due at the beginning of class the following Wednesday.

Examinations

• Midterm exam in class, Friday, May 4.
• Final exam, Wednesday, June 6.

Course grade

• 50% homework
• 20% midterm
• 30% final exam

  The final exam covers the entire semester, with emphasis on the latter half.

Home page

The course home page can be found at http://www.gs.washington.edu/~noble/genome373.

Additional web-based resources related to this class are listed on this page.

Class schedule

Date	Instructor	Topic	Reading	Homework
Week 1
Mon Mar 26	Noble	Introduction to Computational Genomics
Tue Mar 27	Klammer	Introduction to Python programming 1 (Python quick reference)
Wed Mar 28	Noble	The UCSC Genome Browser and the ENCODE Consortium	pp. 8-22, 30-58	HW1 assigned
Thu Mar 29	Klammer	Python programming practice session (optional)
Fri Mar 30	Thomas	Introduction to pairwise sequence alignment algorithms	pp. 227-280
Week 2
Mon Apr 2	Thomas	Introduction to pairwise sequence alignment algorithms	pp. 65-94
Tue Apr 3	Klammer	Introduction to Python programming 2
Wed Apr 4	Thomas	Sequence alignment applications and dot plots (A, B, C, D, E)	pp. 94-111	HW1 due HW2 assigned
Thu Apr 5	Klammer	Python programming practice session (optional)
Fri Apr 6	Noble	Introduction to dynamic programming	pp. 227-240, 248-259
Week 3
Mon Apr 9	Noble	More dynamic programming
Tue Apr 10	Klammer	Introduction to Python programming 3
Wed Apr 11	Thomas	Collecting and analyzing a gene family (part 1)	pp. 42-47, 215-217, 292-294, 419-428	HW2 due HW3 assigned
Thu Apr 12	Klammer	Python programming practice session (optional)
Fri Apr 13	Thomas	Collecting and analyzing a gene family (part 2)
Week 4
Mon Apr 16	Noble	PSI-BLAST and position-specific scoring matrices	pp. 204-215, 269-270
Tue Apr 17	Klammer	Substitution matrices
Wed Apr 18	Noble	Statistical significance of sequence similarity scores	pp. 129-147	HW3 due HW4 (Part 1) assigned
Thu Apr 19	Klammer	Python programming practice session (optional)
Fri Apr 20	Noble	Significance of sequence search results: multiple testing correction and E-values		HW4 (Part 2) assigned
Week 5
Mon Apr 23	Thomas	Introduction to Trees	pp. 282-293
Tue Apr 24		No section this week
Wed Apr 25	Thomas	Computing distance trees	pp. 294-321
Thu Apr 28	Klammer	Python programming practice session (optional)
Fri Apr 27	Thomas	Applications of trees
Week 6
Mon April 30	Noble	Inferring phylogenetic trees: parsimony and distance methods	pp. 282-305	HW4 due
Tue May 1	Klammer	Midterm review
Wed May 2	Noble	Inferring phylogenetic trees: distance and maximum likelihood methods	pp. 305-322
Fri May 4		Midterm exam
Week 7
Mon May 7	Thomas	Gene structure and experimental validation	pp. 361-378
Tue May 8	Klammer	Tree enumeration and topologies
Wed May 9	Thomas	Gene prediction utility and overview	pp. 379-382	HW5 assigned (Dotter)
Fri May 11	Thomas	Gene prediction utility and overview (continued)
Week 8
Mon May 14	Noble	Gene prediction	pp. 362-394
Tue May 15	Klammer	Profile hidden Markov models
Wed May 16	Noble	Gene prediction: parsing algorithms		HW5 due HW6 assigned
Fri May 18	Noble	Gene prediction: More complex HMMs
Week 9
Mon May 21	Thomas	Introduction to microarrays
Tue May 22	Klammer
Wed May 23	Thomas	Gene clustering with microarrays
Fri May 25	Thomas	Microarray CGH		HW6 due
Week 10
Mon May 28		Memorial Day, no class
Tue May 29	Klammer
Wed May 30	Noble	Microarray analysis: Identifying differentially regulated genes	pp. 612-619, 628-631
Fri Jun 1	Noble	Microarray analysis: ANOVA and multiple testing correction	pp. 622-628, 631-646
Exam week
Wed Jun 6		Final exam, 8:30-10:20 am, Foege S110