Genetics 211
Home Page

Genomics
Genetics 211
Winter, 2007

Class Schedule
Tuesday 1/9 Course Overview (30 minutes)
Lecture #1 : Sherlock: Introduction to Microarrays [Lecture 1 PDF]
Thursday 1/11 Discussion - Testing Genome Annotation
Reboul, J., et al. (2003) C. elegans ORFeome version 1.1: experimental verification of the genome annotation and resource from proteome-scale protein expression. Nature Genetics 34:35-41
Friday 1/12
Perl - Data Types Perl Examples Due 1/12/2007: Problem Set 0
Tuesday 1/16 Lecture #2 : Sherlock: Expression Analysis [Lecture 2 PDF]
Thursday 1/18 Discussion - Systematic Genome Analysis
Hughes, et al (2000) Functional Discovery via a Compendium of Expression Profiles. Cell 102:109-126
Friday 1/19/
Perl - Control Structures Perl Examples Due 1/19/2007: Problem Set 1
Tuesday 1/23 Lecture #3 -- Sherlock: Data Analysis II / Applications of microarray technology [Lecture 3 PDF]
Thursday 1/25 Discussion - Epistatic Miniarray Profile
Schuldiner et al. (2005) Exploration of the Function and Organization of the Yeast Early Secretory Pathway through an Epistatic Miniaarray Profile. Cell 123:507-519
Friday 1/26
Perl - Pattern Matching Perl Examples Due 1/26/2007: Problem Set 2 (part 1)
Tuesday 1/30 Lecture #4 -- Myers: Functional Genomic Elements [Lecture 4 PDF]
Thursday 2/1 Discussion - Gene Control and snoRNA identification
Crawford, et al. (2006) Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS). Genome Research 16:123-131.
Friday 2/2
Perl - IO (including system calls & libraries) Perl Examples Due 2/2/2007: Problem Set 2 (part 2)
Tuesday 2/6 Lecture #5 -- Myers: DNA Sequencing and Assembly [Lecture 5 PDF]
Thursday 2/8 Discussion - Whole-Genome Sequence Assembly
Batzoglou, et al.. (2002) ARACHNE: A Whole-Genome Shotgun Assembler. Genome Research, 12:177-189
Friday 2/9
Perl - Pointers, Name Spaces, & Modules Perl Examples
Tuesday 2/13 Lecture #6 -- Cherry: Pairwise Sequence Alignment & Database Searches [Lecture 6 PDF]
Thursday 2/15 Discussion - Mouse Genome
Mouse Genome Sequencing Consortium. (2002) Initial sequencing and comparative analysis of the mouse genome. Nature 420:520-562
Friday 2/16
Perl - Objects Perl Examples Due 2/16/2007: Problem Set 3
Tuesday 2/20 Lecture #7 -- Cherry: Genome Annotation [Lecture 7 PDF]
Thursday 2/22 Discussion - Multiple Sequence Comparison
Notredame, Higgins & Heringa (2000) T-Coffee: A Novel Method for Fast and Accurate Multiple Sequence Alignment. JMB 302:205-217
Friday 2/23
Perl - BioPerl #1 Perl Examples Due 2/23/2007: Abstract for Final
Tuesday 2/27 Lecture #8a -- Cherry: Annotation Tools & Resources [Lecture 8a PDF]
Lecture #8b -- Sidow: Models of Sequence Evolution and Phylogenetic Inference
Thursday 3/1 Discussion CANCELLED, prospective grad student interviews
Friday 3/2
Perl - CANCELLED, prospective grad student interviews
Due 3/2/2007: Problem Set 4
Tuesday 3/6 Lecture #9 -- Sidow: Tree of Life & Comparative Genomics II
Thursday 3/8 Discussion - Saccharomyces Comparative Genomics
Kellis, et al. (2003) Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423:241-254
Friday 3/9
Perl - Miscellaneous Perl Resources Perl Examples
Tuesday 3/13 Lecture #10 -- Sidow: Comparative Genomics III
Thursday 3/15 Discussion - Evolution
Siepel, et al. (2005) Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Research 15:1034-1050
Friday 3/16
Perl - LWP & CGI Perl Examples Due 3/18/2007: Final Project
Last modified: Tue Mar 13 09:00:30 PDT 2007