Website for a course: Genomics (260.605)
|This course begins Friday, October 21 2011. We meet in room W4013, School of Public Health, from 10:30 to 11:50. Use the Wolfe Street entrance (the room overlooks the Meyer building). Note: on Mondays, computer lab is held in room W3025. Contact me (email) if you have any questions. See you then!|
|1||Friday 10-21||13||ppt (2010) and 2011||Introduction to genomics and the tree of life (part 1)|
|2||Monday 10-24||13||Lab 1/7: NCBI, UCSC, Galaxy|
|Wed 10-26||13||ppt||Introduction to genomics and the tree of life (part 2)|
|3||Mon 10-31||15||doc (2010)||Lab 2/7: Viruses, bacteria, and archaea|
|Wed 11-2||15||ppt (2011)||Bacteria and archaea (Ecocyc paper, Keseler et al. 2011)|
|Fri 11-4||15||ppt||Egbert Hoiczyk discusses amazing bacteria (link to his movie files 1 and 2).|
|4||Mon 11-7||16||ppt||Lab 3/7: The eukaryotic chromosome (Chapter 16)|
|Wed 11-9||16||ppt||The eukaryotic chromosome (Chapter 16)|
|Fri 11-11||17||ppt (2009)||The fungi including the yeast S. cerevisiae|
|5||Mon 11-14||16||ppt (2011)||Lab 4/7: Molecular phylogeny (MEGA paper, website). The fungi.|
|Wed 11-16||18||Sarah Wheelan discusses next-generation sequencing technology|
|Fri 11-18||18||pdf (2010)||David Sullivan discusses parasite genomics|
|6||Mon 11-21||18||Lab 5/7: Next-generation sequencing|
|Wed 11-23||18||ppt (2010)||Eukaryotic genomes|
|Fri 11-25||### Thanksgiving break ###|
|7||Mon 11-28||16||Lab 6/7: The human genome; Asian; Yoruba|
|Wed 11-30||18||pdf (2010)||Al Scott discusses nematode genomics|
|Fri 12-2||18||George Dimopoulos discusses mosquito genomics|
|8||Mon 12-5||19||ppt 2009||Lab 7/7: The human genome. 6 primate mtDNA sequences as txt, mas, and meg files. Paper by Brown et al.|
|Wed 12-7||18||ppt (2010)||Eukaryotic genomes (part 2)|
|Fri 12-9||19||Dave Valle discusses the human genome|
|9||Mon 12-12||Projects (part 1)|
|Wed 12-14||Projects (part 2)|
|Fri 12-16||Projects (part 3); final exam due|
You are responsible for one written document by the end of the course (Friday, December 16, 2011). At the midpoint of the course (Thanksgiving break), I plan to post rough drafts of everyone’s projects for discussion. Choose one of these two projects.
Project 1: analyze a genome in depth
 Prepare a written document in which you describe it from the
five perspectives outlined in the course:
 Identify an outstanding research problem and how genomics approaches can be, or are being applied to solve it.
Project 2: analyze a gene in depth
 Perform a phylogenetic analysis. If your gene is conserved, use the sequence to make a tree of life. If it is protein-coding, analyze the substitution rate at different codon positions, describe ancestral sequences, provide evidence for neutral evolution or selection, etc.
 Describe specific cases in which the gene has duplicated (or been lost) across genomes. Provide evidence for duplication/deletion and date the occurrence(s).
 Describe conserved synteny for this gene across multiple genomes. Describe its neighboring genes.
 Describe regulatory regions controlling expression of this gene.