Genetics 211 Genomics

Course Schedule - Winter 2014

Tues 1/6 Course Overview (30 minutes)
Lecture #1 -- Sherlock: Genome Sequencing   [Lecture PDF]
Thurs 1/8 Discussion - Whole-Genome Sequence Assembly
Batzoglou, et al. (2002) ARACHNE: A Whole-Genome Shotgun Assembler. Genome Research, 12:177-189
Fri 1/9
Python - Data Types Python Examples PS0 - Due 1/9/2015 at 9:00AM: Problem Set 0
Tues 1/13 Lecture #2 -- Sherlock : Short Read Genome (Re)sequencing       [PDF]
Thurs 1/15 Discussion - Exon Sequencing and Capturing Haplotype Information
1. Ng, S. B. et al (2009). Targeted capture and massively parallel sequencing of 12 human exomes. Nature 461, 272-278
2. Amini, S. et al (2014). Haplotype-resolved whole-genome sequencing by contiguity-preserving transposition and combinatorial indexing. Nature Genetics 46, 1343-1349
Fri 1/16
Python - Loops & Logic Python Examples PS1 - Due 1/16/2015 at 9:00AM: Problem Set 1
Tues 1/20 Lecture #3 -- Sherlock: Functional Genomics         [PDF]
Thurs 1/22 Discussion - Super-Enhancers
Whyte, W.A. et al. (2013). Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes. Cell 153, 307-319.
Fri 1/23
Python - Functions Python Examples PS2 - Part 1 Due 1/23/2015 at 9:00AM: Problem Set 2
Tues 1/27 Lecture #4 -- Salzman: RNA-seq    [PDF]
Thurs 1/29 Discussion : Transcriptome-wide Regulation of mRNA
Wang et al. (2012) Transcriptome-wide Regulation of Pre-mRNA Splicing and mRNA Localization by Muscleblind Proteins. Cell 150:710-724
Fri 1/30
Python - Pattern matching Python Examples PS2 - Part 2 Due 1/30/2015 at 9:00AM: Problem Set 2
Tues 2/3 Lecture #5 -- Snyder: Application of Genome Sequencing: Disease and Health    [PDF]
Thurs 2/5 Discussion - Phased Personal Genomes
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 2/6
Python - File I/O & Code Modules Python Examples PS3 - Part 1 Due 2/6/2015 at 9:00AM: Problem Set 3
Tues 2/10 Lecture #6 -- Snyder: Microbiome and Epigenomics   [PDF]
Thurs 2/12 Discussion - DNA Methylation
Okae, et al (2014) Genome-Wide Analysis of DNA Methylation Dynamics during Early Human Development. PLoS Genetics 10(12): e1004868
Fri 2/13
Python - Object-Oriented Python Python Examples PS3 - Part 2 Due 2/13/2015 at 9:00AM: Problem Set 3
Tues 2/17 Lecture #7 -- Cherry: Sequence Comparison   [PDF]
Thurs 2/19 Discussion - TBA
Henikoff, S. & Henikoff, J. (1992) Amino Acid substitution matrices from protein blocks. PNAS 89:10915-10919
Fri 2/20
Python - Introduction to Biopython
Python Examples PS4 - Part 1 Due 2/20/2015 at 9:00AM: Problem Set 4, part 1
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Final Project Abstract - Due Monday 2/23/2015 at 9:00am: Final Project Abstract
Tues 2/24 Lecture #8 -- Snyder: Proteomics   
Thurs 2/26 Discussion - TBA
Guruharsha, K.G.et al. (2011) A Protein Complex Network of Drosophila melanogaster. Cell 147:690-703.
Fri 2/27
Python - cgi & urllib2 Python Examples PS4 - Part 2 Due 2/27/2015 at 9:00AM: Problem Set 4-2
Tues 3/3 Lecture #9 -- Cherry : Functional & Manual Annotation   [PDF]
Thurs 3/5 Discussion Cancelled, prospective grad student interviews
Fri 3/6
Python - Cancelled, prospective grad student interviews
Tues 3/10 Lecture #10 -- Cherry: TBA  
Thurs 3/12 Discussion - TBA
Yosef, N.et al. (2013) Dynamic regulatory network controlling Th17 cell differentiation. Nature 496:461-470
Fri 3/13
Python - Miscellaneous Python Examples Final Project - Due Sunday 3/15/2015 at noon

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