March 24
Lecture 1 - (ppt.) Class matters, general Introduction, model organims, orthologs and paralogs.
pre-quiz (pg. 1, pg. 2)
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 26
Lecture 2 - (ppt.) Informatics, (Internet handout) and BLAST, Conserved domains, refseq accessions.
Downloads: BioEdit and MEGA
Reading: Hartwell Chs. 5, 10, 11 and 21.

March 31 (ppt. link for lecture 3)
Lecture 3a - More informatics: proteomics, networks, gene ontologies, model organism web sites, etc..
Model organism web sites (link)
Homework 1 due. (Homework 1 answers)
Lecture 3b - Paper 1 background: C. elegans, miRNAs and RNAi
Readings:
- Hartwell Ref. C "Caenorhabditis elegans: Genetic Portrait of a Simple Multicellular Animal";
- 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.

April 2
Homework 2 due. (Homework 2 answers) Homework 3 due.
Lecture 4 (ppt. link for lecture 4)
a) Phylogeny:
Bauldof on phylogeny (PDF, PMID 12801728)
b)More genomics resources (EBI, Ensembl, GO) :
Informatics page 3
c) Molecular Biology and Genomics, including high throughput sequencing methods
Nature Biotechnology focus issue on next-generation sequencing (contents)
.
April 7
Paper 1 Parry, Xu and Ruvkun. "A Whole-Genome RNAi Screen for C. elegans miRNA Pathway Genes." Current Biology 17:2013-2022. (Current Biology , PMID 18023351, PDF, SOM). (Presentation ppt.)
Lecture 5 - Paper 2 background: Arabidopsis thaliana and plants (ppt. link for lecture 5)
Readings: Hartwell Ref. B

April 9
Lecture 6a - (a story) non-Mendelian inheritance in hothead? (ppt. link for lecture 6)
Homework 4 due.
Lolle et al. 2006 (Presentation PPT; paper: Nature, PMID 15785770, PDF) plus Brief Communications Arising (Sept. 1, Sept. 28).
Lecture 6b - genetic suppression and enhancement, redundancy and synthetic phenotypes

April 14
Paper 2 Pandey, Nelson and Assmann. "Two Novel GPCR-Type G Proteins are Abscisic Acid Receptors in Arabidopsis" Cell 136:136-148. (Cell , PMID 19135895, PDF).(Presentation ppt.)
Lecture 7 - Paper 3 background: Saccharomyces cerevisiae (ppt.)
Readings: Hartwell Reference A, Sherman

April 16 (lecture 8 ppt.)
Lecture 8a - Meiosis, tetrad analysis, gene replacement and DNA repair.
Lecture 8b - Begin networks (synthetic lethal and otherwise), genetic interactions and epistasis.

April 21
Paper 3 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. 2004 (first paper). (PMID 15525520, PDF)
Pan et al. 2007 (method) (PMID 17189863, Methods, PDF)
Quiz given April 21 (answers)
Lecture 9 - Paper 4 background: the Mouse, mammalian genomics, Transgenics, knock-outs. (ppt.)
Hartwell Appendix E on the Mouse (Ref. E)

April 23
Lecture 10 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)

April 28
Paper 4 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.) Quiz given April 28 (answers)
Lecture 11 - Paper 5 background: Drosophila melanogaster basics, nomenclature (ppt.).
Hartwell Ref. D, Drosophila handout

April 30
Lecture 12 - Drosophila melanogaster: the many uses of P elements, binary systems. (homework due) (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)

May 5
Paper 5 Metzstein and Krasnow. 2006. PLoS Genetics 2:180. "Functions of the nonsense-mediated mRNA decay pathway in Drosophila development." (PLoS, PMID 17196039, PDF). (Presentation ppt.).
quiz paper 5 answers

May 7
Lecture 13 - 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)
Chalfie "Is the traditional way of teaching three-factor mapping sufficient?" (PubMed ID 9066267 , TIGS, PDF)

May 12
Paper 6 (full time) -- Dog genome paper. 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.)