Genetics 211– Genomics

Course Schedule - Winter 2012

Tuesday 1/10 Course Overview (30 minutes)
Lecture #1 -- Sherlock: Whole Genome Sequencing   [PDF]
Thursday 1/12 Discussion - Whole-Genome Sequence Assembly
Batzoglou, et al.. (2002) ARACHNE: A Whole-Genome Shotgun Assembler. Genome Research, 12:177-189
Friday 1/13
Perl - Data Types Perl Examples
PS0 - Due 1/13/2012 at 9:00AM:
Problem Set 0
Tuesday 1/17 Lecture #2 -- Cherry: Sequence Comparison   [PDF]
Thursday 1/19 Discussion - Sequence Alignment [** Two Papers **]
Notredame, C., et al. (2000) T-coffee: a novel method for fast and accurate multiple sequence alignment. J. Mol. Bio. 302:205-217
Henikoff, S. & Henikoff, J. (1992) Amino Acid substitution matrices from protein blocks. PNAS 89:10915-10919
Friday 1/20
Perl - Control Structures Perl Examples
PS1 - Due 1/20/2012 at 9:00AM: Problem Set 1
Tuesday 1/24 Lecture #3 -- Snyder : Personal Genomes & Disease   [PDF]
Thursday 1/26 Discussion - Personal Genomics
Ashley, E.U. et al. (2010). Clinical assessment incorporating a personal genome. Lancet 375, 1525-1535.
Friday 1/27
Perl - Pattern Matching Perl Examples
PS2 - Part 1 Due 1/27/2012 at 9:00AM: Problem Set 2
Tuesday 1/31 Lecture #4 -- Sherlock : Ultra-High Throughput Sequencing Technologies   [PDF]
Thursday 2/2 Discussion - Whole Exome Sequencing
Ng, S.B. et al (2009). Targeted capture and massively parallel sequencing of 12 human exomes. Nature 461, 272-6.; also review the supplemental material
Friday 2/3
Perl - IO (including system calls & libraries) Perl Examples
PS2 - Part 2 Due 2/3/2012 at 9:00AM: Problem Set 2
Tuesday 2/7 Lecture #5 -- Sherlock: Ultra-High Throughput Sequencing Analysis    [PDF]
Thursday 2/9 Discussion - RNA-Seq
Mortazavi., A. et al. (2009). Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nature Methods 5, 621-8.
Friday 2/10
Perl - Pointers, Name Spaces, & Modules Perl Examples
PS3 - Part 1 Due 2/10/2012 at 9:00AM: Problem Set 3
Tuesday 2/14 Lecture #6 -- Snyder: Proteomics and Interactions   [PDF]
Thursday 2/16 Discussion - Quantitative Proteomics
Gruhler, A. et al. (2005) Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway. Mol. Cell Proteommics Mar;4(3):310-27. Epub 2005 Jan 22.
For background see: Nita-Lazar, A. et al. (2008) Quantitative phosphoproteomics by mass spectrometry: Past, present, and future. Proteomics 8 4433-4443.
Friday 2/17
Perl - Objects Perl Examples
PS3 - Part 2 Due 2/17/2012 at 9:00AM: Problem Set 3
Tuesday 2/21 Lecture #7 -- Sherlock: Expression Analysis    [PDF]
Thursday 2/23 Discussion - Expression Analysis
Hughes, et al (2000) Functional Discovery via a Compendium of Expression Profiles. Cell 102:109-126
Friday 2/24
Perl - BioPerl #1 Perl Examples
PS4 - Part 1 Due 2/24/2012 at 9:00AM: Problem Set 4
Final Project Abstract - Due 2/27/2012 at 9:00am: Abstract for Final Details
Tuesday 2/28 Lecture #8 -- Snyder: Proteomics and Interactions II    [PDF]
Thursday 2/30 Discussion Cancelled, prospective grad student interviews
Friday 3/2
Perl - Cancelled, prospective grad student interviews
Tuesday 3/6 Lecture #9 -- Cherry: Functional & Manual Annotation   [PDF]
Thursday 3/8 Discussion : Drosophila Comparative Genomics
Stark A., et al. (2007) Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature 450:219-232
Friday 3/9
Perl - Miscellaneous Perl Resources Perl Examples
PS4 - Part 2 Due 3/9/2012 at 9:00AM: Problem Set 4
Tuesday 3/13 Lecture #10 -- Cherry: Interactions, ENCODE and Networks   [PDF]
Thursday 3/15 Discussion - Transcriptional Regulatory Networks
Balaji., et al. (2006) Comprehensive Analysis of Combinatorial Regulation using the Transcriptional Regulatory Network of Yeast. J. Mol. Biol. 360:213-227
Friday 3/16
Perl - LWP & CGI Perl Examples
Final Project - Due Sunday 3/18/2012 at 9:00AM:

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