2011 Syllabus
Lectures will be posted after presentation.
March 17
Lecture 1 - (ppt.: 2011) Class matters, general Introduction
Model organisms, orthologs and paralogs.
Summary of class survey.
Summary of pre-quiz.
Readings: Hartwell Chs. 1-2, 4 (pp.88-103), 5 (pp. 152-155), 19 (703-709), 9 (pp. 335-339), 22 (799-811)
Fitch 2001 on orthologs and paralongs (PDF, PMID 10782117)
March 29
Homework 1 due
Lecture 2- (ppts.: 2010, 2011) Informatics, (Internet handout) and BLAST, Conserved domains, refseq accessions.
Readings: Hartwell Chs. 5, 10, 11 and 21.
Readings:
- Hartwell Ref. C "Caenorhabditis elegans: Genetic Portrait of a Simple Multicellular Animal";
miRNAs and RNAi
- Nature Insight on RNA silencing (Jan. 22, 2009), especially Siomi and Siomi 2009, "On the road to reading the RNA-interference code." (Nature; PMID 19158785; PDF)
- Ambros 2008, "The evolution of our thinking about microRNAs" (Nature Medicine, PMID 18841144, PDF) 2008 Lasker Award.
March 31 April 5: Paper 1, April 7 - (2011 lecture) April 12/Paper 2 April 19/Paper 3 April 26/Paper 4
Homework 2 due; Homework 3 due
- (ppts.: 2011)
Lecture 3 -
More phylogeny; forward, reverse and parallel genetic analysis; general (informatics)
Parry, Xu and Ruvkun. 2007" A Whole-Genome RNAi Screen for C. elegans miRNA Pathway Genes." Current Biology 17:2013-2022. (Current Biology , PMID 18023351, PDF, SOM). (Presentation ppt.)
Readings: Hartwell Ref. B
Saccharomyces cerevisiae
Readings: Hartwell Reference A, Sherman
Meiosis, tetrad analysis, gene replacement and DNA repair.
Networks I (synthetic lethal and otherwise), genetic interactions and epistasis.
Pan et al. 2006. "A DNA Intergrity Network in the Yeast Saccharomyces cerevisiae" Cell 124:1069-1081. (Cell, PMID 16487579, PDF; SOMs, TableS1, TableS2, TableS3, TableS4, TableS5). (Presentation ppt.) Background papers:
Pan et al. 2007 (method) (PMID 17189863, Methods, PDF)
Arabidopsis thaliana and plants- (ppt.: 2011)
April 14
Types of allele and genetic interactions (epistasis) - (ppt.: 2011)
Lampard, Lukowitz, Ellis and Bergmann. 2009. " Novel and Expanded Roles for MAPK Signaling in Arabidopsis Stomatal Cell Fate Revealed by Cell Type-Specific Manipulations" Plant Cell 21:3506-3517. (Plant Cell , PMID 19897669, PDF). (Presentation ppt.; Presentation guide)
Background: Bergmann and Sack 2007. Ann. Rev. Plant Biol. 58:163-181. "Stomatal Development." (PDF)
the Mouse, mammalian genomics, Transgenics, knock-outs.(ppt.)
Hartwell Appendix E on the Mouse (Ref. E)
April 21
Complex traits, inbred strains, RILs, GWAS, etc..
(ppt.)
HMG II online (15.4, with box and Table)
Festing 2000 ("Mighty Mice" PDF, PMID 10786770), Peters 2007 (PDF, PMID 17173058)
Buchner et al. 2003. "SCNM1, a putative RNA splicing factor that modifies disease severity in mice." Science 301:967-969. (Science, PMID 12920299, PDF, SOM). (Presentation ppt.)
Drosophila melanogaster basics, nomenclature (ppt.).
Hartwell Ref. D, Drosophila handout
April 28
Drosophila melanogaster: the many uses of P elements, binary systems.(ppt.)
Background methods: Lee and Luo. 1999. "Mosaic analysis with a repressible cell marker for studies of gene function in neuronal morphogenesis." (Neuron, PubMed, PDF)
Informatics (see March 29)
May 3/Paper 5
Metzstein and Krasnow. 2006."Functions of the nonsense-mediated mRNA decay pathway in Drosophila development."PLoS Genetics 2:180. " (PLoS, PMID 17196039, PDF).
(Presentation ppt.)
Human/mammalian gene mapping and cloning; population genetics, complex traits and advanced mapping.(ppt.)
Readings:
Strachan and Read, "Genetic mapping of Mendelian Characters"
Strachan and Read: Ch. 12: Genetic mapping of complex characters
Hartwell Chs. 5, 10 and 11. Bovine Genome Project (Science issue 5926, Genome pdf, HapMap pdf)
May 5
Human/mammalian genetic continued.
1000 Genomes (PDF, PMID 20981092)
May 10/Paper 6
Lindblad-Toh et al. 2005"Genome sequence, comparative analysis and haplotype structure of the domestic dog."Nature 438: 803-19. (Nature, PubMed, PDF, Suppl-text, Suppl-figs; other papers on dogs) (Handout; Presentation ppt.)
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Last modified March 13, 2011