Tags:

    Syllabus & Reading List: 3

    WEEK & DATE TOPIC REQUIRED READING SUGGESTED READING
    1A 1/19/10 Intro, phylogeny primer Delsuc et al. Nat Reviews Gen. 2005.Phylogenomics & the Reconstruction of the Tree of
    Life.
    Harrison & Langdale. A step by step guide to phylogeny
    reconstruction
    1B
    1/21/10
    Anatomy of a genome project Metzker.Nat Reviews Gen.
    2006.Sequencing technologies -
    the next generation.
    2A
    1/26/10
    PAPER DISCUSSION Clark et al. Nature. 2007. Evolution of genes and genomes on
    the Drosophila phylogeny.
    2B
    1/28/10
    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
    3A
    2/2/10
    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
    3B
    2/4/10
    PAPER DISCUSSION PAPER:Zhou et
    al. 2008, Genome Research
    Hittenger & Carroll. Nature. 2007.Gene duplication and the adaptive evolution of a classic
    genetic switch.
    4A
    2/9/10
    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.
    4B
    2/11/10
    PAPER DISCUSSION PAPER:
    Aury et al. Global trends of whole-genome duplications revealed by the
    ciliate Paramecium tetraurelia
    5A
    2/16/10
    Lateral gene transfer and the bacterial species concept
    (Nicole Perna, guest lecturer)
    tbd
    5B
    2/18/10
    PAPER DISCUSSION tbd
    6A
    2/23/10
    Molecular evolution - Part I Nielsen. Annu Rev Genet. 2005.
    Molecular signatures of natural selection.
    6B
    2/25/10
    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.
    7A
    3/2/10
    Molecular evolution - Part II:genome-wide scans Stinchcombe & Hoekstra.Heredity. 2007.
    Combining population genomics and quantitative genetics: finding the
    genes underlying ecologically important traits
    7B
    3/4/10
    PAPER DISCUSSION Sabeti et al. 2007.Nature.
    Genome-wide detection and characterization of positive selection in
    human populations
    8A
    3/9/10
    QTL mapping (Karl Broman, guest lecturer) tbd
    8B
    3/11/10
    PAPER DISCUSSION tbd
    9A
    3/16/10
    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.
    9B
    3/18/10
    PAPER DISCUSSION Denver et al. 2005.The transcriptional consequences of mutation and natural
    selection in Cenorhabditis elegans
    10A
    3/23/10
    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.
    10B
    3/25/10
    PAPER DISCUSSION Tirosh et al. Science 2009 A yeast hybrid provides
    insight into the evolution of gene expression regulation.
    11A
    4/6/10
    Evolution of cis-regulation - Part I Ludwig et al. Nature 2000.
    Evidence for stabilizing selection in a eukaryotic enhancer element.
    11B
    4/8/10
    PAPER DISCUSSION Kim et al. 2009. PLoS Gen. Evolution of Regulatory Sequences in 12
    Drosophila species
    Berman 2002 PNAS.
    12A
    4/13/10
    Evolution of cis-regulation - Part II
    12B
    4/15/10
    PAPER DISCUSSION Tsong Nature 2006. Evolution of alternative transcriptional
    circuits with identical logic.
    13A
    4/20/10
    Evolution of cis-regulation - Part III
    13B
    4/22/10
    PAPER DISCUSSION Rubin paper - mammalian stuff
    14A
    4/27/10
    Evolutionary proteomics & systems biology
    14B
    4/29/10
    PAPER DISCUSSION tbd
    15A
    5/4/10
    Final wrap-up, remaining questions
    15B
    5/6/10
    PAPER DISCUSSION Clark et al. Nature. 2007. Evolution of genes and genomes on
    the Drosophila phylogeny.