Genetics 211– Genomics

Course Schedule - Winter 2013

Tuesday 1/8 Course Overview (30 minutes)
Lecture #1 -- Sherlock: Whole Genome Sequencing   [PDF]
Thursday 1/10 Discussion - Whole-Genome Sequence Assembly
Batzoglou, et al. (2002) ARACHNE: A Whole-Genome Shotgun Assembler. Genome Research, 12:177-189
Friday 1/11
Perl - Data Types Perl Examples
PS0 - Due 1/11/2013 at 9:00AM: Problem Set 0
Tuesday 1/15 Lecture #2 -- Sherlock : Ultra-High Throughput Sequencing Technologies   [PDF]
Thursday 1/17 Discussion - Haplotype-resolved Genome Sequencing
1. Ng, S. B. et al (2009). Targeted capture and massively parallel sequencing of 12 human exomes. Nature 461, 272-278.;
2. Kitzman, J. O. et al (2011). Haplotype-resolved genome sequencing of a Gujarati Indian individual. Nature Biotech 29, 59-64.;
Friday 1/18
Perl - Control Structures Perl Examples
PS1 - Due 1/18/2013 at 9:00AM: Problem Set 1
Tuesday 1/22 Lecture #3 -- Sherlock: Ultra-High Throughput Sequencing Analysis    [PDF]
Thursday 1/24 Discussion - RNA-Seq
Mortazavi., A. et al. (2009). Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nature Methods 5, 621-8.
Friday 1/25
Perl - Pattern Matching Perl Examples
PS2 - Part 1 Due 1/25/2013 at 9:00AM: Problem Set 2
Tuesday 1/29 Lecture #4 -- Sherlock: Expression Analysis    [PDF]
Thursday 1/31 Discussion - Expression Analysis
Hughes, et al (2000) Functional Discovery via a Compendium of Expression Profiles. Cell 102:109-126
Friday 2/1
Perl - IO (including system calls & libraries) Perl Examples
PS2 - Part 2 Due 2/1/2013 at 9:00AM: Problem Set 2
Tuesday 2/5 Lecture #5 -- Snyder: Personal & Disease Genomics   [PDF]
Thursday 2/7 Discussion - Disease Genomics
Dewey, F.E. et al. (2011) Phased Whole-Genome Genetic Risk in a Family Quartet Using a Major Allele Reference Sequence. PLoS Genet 7(9): e1002280. doi:10.1371/journal.pgen.1002280
Friday 2/8
Perl - Pointers, Name Spaces, & Modules Perl Examples
PS3 - Part 1 Due 2/8/2013 at 9:00AM: Problem Set 3
Tuesday 2/12 Lecture #6 -- Snyder: Epigenomics    [PDF]
Thursday 2/14 Discussion - Epigenome & Gene Regulation
Wu, H.et al. (2011) Genome-wide analysis of 5-hydroxymethylcytosine distribution reveals its dual function in transcriptional regulation in mouse embryonic stem cells. Genes Dev. 25:679-684.
Friday 2/15
Perl - Objects Perl Examples
PS3 - Part 2 Due 2/15/2013 at 9:00AM: Problem Set 3
Tuesday 2/19 Lecture #7 -- Snyder : Proteomics   [PDF]
Thursday 2/21 Discussion - Transcriptome & Proteome Correlation
Lundberg, E., et al. (2010) Defining the transcriptome and proteome in three functionally different human cell lines. Molecular Systems Biology 6:450
Friday 2/22
Perl - BioPerl #1 Perl Examples
PS4 - Part 1 Due 2/22/2013 at 9:00AM: Problem Set 4
Final Project Abstract - Due 2/25/2013 at 9:00am: Abstract for Final Details
Tuesday 2/26 Lecture #8 -- Cherry: Sequence Comparison   [PDF]
Thursday 2/28 Discussion Cancelled, prospective grad student interviews
Friday 3/1
Perl - Cancelled, prospective grad student interviews
Tuesday 3/5 Lecture #9 -- Cherry: Functional & Manual Annotation   [PDF]
Thursday 3/7 Discussion : Multiple Sequence Alignment
Notredame, Higgins & Heringa (2000) T-Coffee: A Novel Method for Fast and Accurate Multiple Sequence Alignment. JMB 302:205-217
Henikoff, S. & Henikoff, J. (1992) Amino Acid substitution matrices from protein blocks. PNAS 89:10915-10919
Friday 3/8
Perl - Miscellaneous Perl Resources Perl Examples
PS4 - Part 2 Due 3/8/2013 at 9:00AM: Problem Set 4
Tuesday 3/12 Lecture #10 -- Cherry: Interactions and Networks   [PDF]
Thursday 3/14 Discussion - Centromere Evolution
Melters, et al. (2013) Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution. Genome Biolog 14:R10 doi:10.1186/gb-2013-14-1-r10
Friday 3/15
Perl - LWP & CGI Perl Examples
Final Project - Due Sunday 3/17/2013 at 9:00AM:

Stanford Medicine Resources:

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