Genetics 211 Genomics

Course Schedule - Winter 2014

Tues 1/7 Course Overview (30 minutes)
Lecture #1 -- Sherlock: Whole Genome Sequencing   [PDF]
Thurs 1/9 Discussion - Whole-Genome Sequence Assembly
Batzoglou, et al. (2002) ARACHNE: A Whole-Genome Shotgun Assembler. Genome Research, 12:177-189
Fri 1/10
Python - Data Types Python Examples PS0 - Due 1/10/2014 at 9:00AM: Problem Set 0
Tues 1/14 Lecture #2 -- Sherlock : Ultra-High Throughput Sequencing Technologies   [PDF]
Thurs 1/16 Discussion - TBA
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.;
Fri 1/17
Python - Loops & Logic Python Examples PS1 - Due 1/17/2014 at 9:00AM: Problem Set 1
Tues 1/21 Lecture #3 -- Sherlock: Ultra-High Throughput Sequencing Analysis    [PDF]
Thurs 1/23 Discussion - RNA-Seq
Mortazavi., A. et al. (2009). Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nature Methods 5, 621-8.
Fri 1/24
Python - Functions Python Examples PS2 - Part 1 Due 1/24/2014 at 9:00AM: Problem Set 2
Tues 1/28 Lecture #4 -- Cherry: Sequence Comparison   [PDF]
Thurs 1/30 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
Fri 1/31
Python - Pattern matching Python Examples PS2 - Part 2 Due 1/31/2014 at 9:00AM: Problem Set 2
Tues 2/4 Lecture #5 -- Sherlock: Expression Analysis    [PDF]
Thurs 2/6 Discussion - Expression Analysis
Hughes, et al (2000) Functional Discovery via a Compendium of Expression Profiles. Cell 102:109-126
Fri 2/7
Python - File I/O & Code Modules Python Examples PS3 - Part 1 Due 2/7/2014 at 9:00AM: Problem Set 3
Tues 2/11 Lecture #6 -- Snyder: Personal & Disease Genomics   [PDF]
Thurs 2/13 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
Fri 2/14
Python - Object-Oriented Python Python Examples PS3 - Part 2 Due 2/14/2014 at 9:00AM: Problem Set 3
Tues 2/18 Lecture #7 -- Cherry: Functional & Manual Annotation   [PDF]
Thurs 2/20 Discussion - Epigenome & Gene Regulation
Boyle, A.P.et al. (2008) High-resolution mapping and characterization of open chromatin across the genome. Cell 132:311-22.
Fri 2/21
Python - Introduction to Biopython
Python Examples PS4 - Part 1 Due 2/21/2014 at 9:00AM: Problem Set 4
----
Final Project Abstract - Due Monday 2/24/2014 at 9:00am: Final Project Abstract
Tues 2/25 Lecture #8 -- Snyder: Epigenomics   
Thurs 2/27 Discussion Cancelled, prospective grad student interviews
Fri 2/28
Python - Cancelled, prospective grad student interviews
Tues 3/4 Lecture #9 -- Snyder : Proteomics  
Thurs 3/6 Discussion - Transcriptome & Proteome Correlation
Geiger, T. et al. (2013) Initial quantitative proteomic map of 28 mouse tissues using the SILAC mouse. Molecular & Cellular Proteomics 12:1709-22
Fri 3/7
Python - cgi & urllib2 Python Examples PS4 - Part 2 Due 3/7/2014 at 9:00AM: Problem Set 4
Tues 3/11 Lecture #10 -- Cherry: Interactions and Networks   [PDF]
Thurs 3/13 Discussion - TBA
Zhu, et al. (2012) Stitching together multiple data dimensions reveals interacting metabolomic and transcriptomic networks that modulate cell regulation. PLoS Biology 10 doi:10.1371/journal.pbio.1001301
Fri 3/14
Python - Miscellaneous and Python 3 Python Examples Final Project - Due Sunday 3/16/2014 at noon

Stanford Medicine Resources:

Footer Links: