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    Syllabus & Reading List: 10

    WEEK & DATE TOPIC REQUIRED READING SUGGESTED READING
    Week 1A 1/19/10 Intro, phylogeny primer Delsuc et al. Nat Reviews Gen. 2005.Phylogenomics & the Reconstruction of the Tree of Life.
    Download file "Delsuc_Nature Reviews Genetics_2005.pdf"
    Harrison & Langdale. A step by step guide to phylogeny reconstruction
    Week 1B1/21/10 Anatomy of a genome project Metzker.Nat Reviews Gen. 2006.Sequencing technologies - the next generation.
    Download file "Metzker_Nature Reviews Genetics_2010.pdf"
    Week 2A1/26/10 PAPER DISCUSSION Clark et al. Nature. 2007. Evolution of genes and genomes on the Drosophila phylogeny.
    Week 2B1/28/10 Orthology, paralogy, and gene history Koonin.Annu Rev Gen. 2005. Orthologs, Paralogs, and Evolutionary Genomics
    Ortlund et al. 2007.Crystal structure of an ancient protein:evolution by conformational epistasis
    Week 3A2/2/10 Evolution of new gene functions Lynch & Conery.Science 2000.The evolutionary fate and consequences of duplicate genes. Bailey & Eichler. Nat Reviews Gen. 2006.Primate segmental duplications: crucibles of evolution, diversity and disease
    Week 3B2/4/10 PAPER DISCUSSION PAPER:Zhou et al. 2008, Genome Research Hittenger & Carroll. Nature. 2007.Gene duplication and the adaptive evolution of a classic genetic switch.
    Week 4A2/9/10 Whole genome duplication (Dana Wohlbach, guest lecturer) Semom & Wolfe.2007.Consequences of genome duplication. Van de Peer.Nat. Reviews Gen. 2009.The evolutionary significance of ancient genome duplications.
    Week 4B2/11/10 PAPER DISCUSSION PAPER:Aury et al. Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia
    Week 5A2/16/10 Lateral gene transfer and the bacterial species concept (Nicole Perna, guest lecturer) tbd
    Week 5B2/18/10 PAPER DISCUSSION tbd
    Week 6A2/23/10 Molecular evolution - Part I Nielsen. Annu Rev Genet. 2005.Molecular signatures of natural selection.
    Week 6B2/25/10 PAPER DISCUSSION Fay, Wycoff, Wu.Nature. 2002. Testing the neutral theory of molecular evolution with genomic data from Drosophila.
    Smith & Eyre-Walker.Nature. 2002.Adaptive protein evolution in Drosophila.
    Week 7A3/2/10 Molecular evolution - Part II:genome-wide scans Stinchcombe & Hoekstra.Heredity. 2007.Combining population genomics and quantitative genetics: finding the genes underlying ecologically important traits
    Week 7B3/4/10 PAPER DISCUSSION Sabeti et al. 2007.Nature.Genome-wide detection and characterization of positive selection in human populations
    Week 8A3/9/10 QTL mapping (Karl Broman, guest lecturer) tbd
    Week 8B3/11/10 PAPER DISCUSSION tbd
    Week 9A3/16/10 Evolution of gene expression Rifkin et al. 2003.Nat Gen. Evolution of gene expression in the Drosophila melanogaster subgroup Pall et al. Nat Gen Reviews 2006. An integrated view of protein evolution.
    Week 9B3/18/10 PAPER DISCUSSION Denver et al. 2005.The transcriptional consequences of mutation and natural selection in Cenorhabditis elegans
    Week 10A3/23/10 eQTL mapping & the cis-trans debate Rockman & Kruglyak. Nat Reviews Gen 2006. Genetics of global gene expression. ** OR ** Gilad eQTL review Brem et al. Science. 2002Genetic dissection of transcriptional regulation in budding yeast.
    Wittkopp et al. Nat Gen. 2008.Regulatory changes underlying expression differences within and between Drosophila species.
    Week 10B3/25/10 PAPER DISCUSSION Tirosh et al. Science 2009 A yeast hybrid provides insight into the evolution of gene expression regulation.
    Week 11A4/6/10 Evolution of cis-regulation - Part I Ludwig et al. Nature 2000.Evidence for stabilizing selection in a eukaryotic enhancer element.
    Week 11B4/8/10 PAPER DISCUSSION Kim et al. 2009. PLoS Gen. Evolution of Regulatory Sequences in 12 Drosophila species
    Berman 2002 PNAS.
    Week 12A4/13/10 Evolution of cis-regulation - Part II
    Week 12B4/15/10 PAPER DISCUSSION Tsong Nature 2006. Evolution of alternative transcriptional circuits with identical logic.
    Week 13A4/20/10 Evolution of cis-regulation - Part III
    Week 13B4/22/10 PAPER DISCUSSION Rubin paper - mammalian stuff
    Week 14A4/27/10 Evolutionary proteomics & systems biology
    Week 14B4/29/10 PAPER DISCUSSION tbd
    Week 15A5/4/10 Final wrap-up, remaining questions
    Week 15B5/6/10 PAPER DISCUSSION Clark et al. Nature. 2007. Evolution of genes and genomes on the Drosophila phylogeny.