Genomic Informatics

GENOME 373
Department of Genome Sciences
University of Washington
Spring Quarter, 2009

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.

This year, the course will be taught in a new format. Rather than requiring that students enter the class knowing how to program, we will teach programming in Python. The course will be taught in a computer lab, mixing the teaching of computational methods with practical programming.

Instructional staff

Instructor: William Stafford Noble
Email: william-noble@u.washington.edu
Office: Foege S220B
Phone: (206) 543-8930
Office hours: Mon 10:30-11:30

Teaching assistant: Jeffrey Kidd
Email: kiddj@u.washington.edu
Office: Foege S040
Office hours: Fri 12:30-1:30

Meeting times and locations

Lectures: Monday, Wednesday and Friday, 9:30 - 10:20 am, Hitchcock 220.

Section: Tuesday 9:30 - 10:20 am, Hitchcock 220. For the first six weeks of the quarter, an optional programming practice session will be offered on Thursdays at the same time and place.

Prerequisites

GENOME 371, GENOME 351 or permission of instructor.

Course materials

Most of the reading material will be available via the web. For people who are learning Python, the following book is recommended: Learning Python by Lutz and Ascher. This is a gentle introduction to programming in Python.

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	Unit	Lecture topic	Programming topic	Reading	Homework
Week 1
Mon Mar 30	Noble	Sequences	Pairwise sequence comparison	Introduction to Python	Lutz, ch. 1-3
Tue Mar 31	Kidd	Sequences		Command line arguments and strings
Wed Apr 1	Noble	Sequences	Dynamic programming	Strings	(Eddy Nat Biotech 2004a); Lutz, ch. 7	HW1 assigned
Thu Apr 2	Kidd	Sequences	Python programming practice session (optional)
Fri Apr 3	Noble	Sequences	More dynamic programming	Lists and tuples	Lutz, ch. 4-5, 8
Week 2
Mon Apr 6	Noble	Sequences	Local alignment via dynamic programming	Numbers	(Eddy Nat Biotech 2004b); Wikipedia: Needleman-Wunsch
Tue Apr 7	Kidd	Sequences		File input and output	Lutz, ch. 9
Wed Apr 8	Noble	Sequences	Significance of similarity scores	if/then/else	(Thisted 1998); Lutz, ch. 10, 12	HW1 due HW2 assigned
Thu Apr 9	Kidd	Sequences	Python programming practice session (optional)
Fri Apr 10	Noble	Sequences	Multiple testing correction	for loops
Week 3
Mon Apr 13	Noble	Sequences	Sequence database search (PSI-BLAST)	more for loops	(Nicholas Biotechniques 2000); (Pertsemlidis Genome Biol 2001)
Tue Apr 14	Kidd	Sequences	while loops
Wed Apr 15	Noble	Sequences	Position-specific scoring matrices	more loops		HW2 due HW3 assigned
Thu Apr 16	Kidd	Sequences	Python programming practice session (optional)
Fri Apr 17	Noble	Sequences	Remote homology detection	Writing good programs	(Eddy Nat Biotech 2004c), (Noble Nat Biotech 2006), Lutz, ch. 14
Week 4
Mon Apr 20	Noble	Sequences	Motif search	Nested loops	(Stormo Bioinformatics 2000)
Tue Apr 21	Kidd	Sequences	PSSM p-values
Wed Apr 22	Noble	Sequences	Motif discovery	Dictionaries		HW3 due HW4 assigned
Thu Apr 23	Kidd	Sequences	Python programming practice session (optional)
Fri Apr 24	Noble	Networks	Intro to biological networks	Functions	(Barabasi & Oltvai Nature Rev Gen 2005), Lutz, ch. 15
Week 5
Mon Apr 27	Noble	Networks	Network motifs	Sorting
Tue Apr 28	Kidd	Networks		Dictionaries and functions
Wed Apr 29	Noble	Networks	Predicting protein-protein interactions and protein function	Representing networks in python		HW4 due HW5 assigned
Thu Apr 30	Kidd	Networks	Python programming practice session (optional) (Python summary)
Fri May 1	Noble	Networks	Network diffusion	Reading networks (read-network.py)	Lutz, ch. 22-23
Week 6
Mon May 4	Noble	Mass spec	Intro to mass spectrometry	Network formats (convert-matrix-format.py)	(Nesvizhskii Nat Biotech 2007)
Tue May 5	Noble	Mass spec	Midterm review
Wed May 6	Noble	Mass spec	Peptide identification	compare-spectra.py (observed.txt, theoretical.txt)		HW5 due
Fri May 8		Midterm exam
Week 7
Mon May 11	Noble	Mass spec	Post-processing peptide-spectrum matches	compute-fdr.py (target.txt, decoy.txt)
Tue May 12	Kidd	Mass spec
Wed May 13	Noble	Mass spec	Protein identification	do-tryptic-digest.py (proteins.txt)		HW6 assigned
Fri May 15	Noble	Microarrays	Identifying differentially expressed genes	compute-t.py
Week 8
Mon May 18	Noble	Microarrays	ANOVA and supervised learning	compute-t-statistics.py	(Pavlidis 2003)
Tue May 19	Kidd	Microarrays	Clustering
Wed May 20	Kidd	Microarrays	Array CGH	get-mean-log2.py (arrayCGH.txt)	(D'haeseleer Nat Biotech 2005)	HW6 due HW7 assigned
Fri May 22	Noble	Next gen	Intro to next-generation sequencing	find-unique-tags.py (genome.txt, tags.txt)	(Shendure Nat Biotech 2008)
Week 9
Mon May 25	Noble	Memorial Day, no class
Tue May 26	Kidd	Next gen	Phred quality scores
Wed May 27	Noble	Next gen	Mapping short reads	map-tags.py, map-tags2.py	(Trapnell & Salzberg Nat Biotech 2009)	HW7 due
Fri May 29	Noble	Phylogenetics	Inferring phylogenetic trees			HW8 assigned
Week 10
Mon Jun 1	Noble	Phylogenetics	Distance and maximum likelihood methods	read-tree.py (mytree.txt)
Tue Jun 2	Kidd		Final exam review
Wed Jun 3	Noble		The UCSC Genome Browser	Biopython (read-fasta.py, sample.fa)	(Zweig Genomics 2008) Biopython tutorial
Fri Jun 5	Noble		Practical computational biology		(Noble PLoS Comp Bio 2009)	HW8 due
Exam week
Wed Jun 10		Final exam, 8:30-10:20 am, Hitchcock 220

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