Bioinformatics and Functional Genomics

(second edition)

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Website for a course: Genomics (260.605)

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!

Week Date Chapter Ppt Lecturer, topic
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)
  Fri 10-28 14 ppt Viruses
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

Genomics project

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

[1] Select any genome. Let me know your choice, preferably within the first two weeks of the course.

[2] Prepare a written document in which you describe it from the five perspectives outlined in the course:
1) Catalog genomic information (genome size; number of chromosomes; GC content; isochores; number of genes; repetitive DNA; unique features)
2) Catalog comparative genomic information (ladder-and-constellation approach;
orthologs and paralogs; COGs; lateral gene transfer)
3) Mechanisms of evolution (how genome size is regulated; polyploidization; birth and death of genes; neutral theory of evolution; positive and negative selection; speciation)
4) Human disease relevance
5) Computational biology aspects (algorithms, databases, websites)

[3] 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

[1] Select a single protein, RNA, or DNA sequence. Unless you have a particular gene of interest, select one that is conserved across the three domains of life. Obtain a large number of homologous sequences (e.g. 100) in the fasta format.

[2] 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.

[3] Describe specific cases in which the gene has duplicated (or been lost) across genomes. Provide evidence for duplication/deletion and date the occurrence(s).

[4] Describe conserved synteny for this gene across multiple genomes. Describe its neighboring genes.

[5] Describe regulatory regions controlling expression of this gene.


©2008-2009 Dr. Jonathan Pevsner