Tags:

    Syllabus & Reading List

    WEEK DATE

    TOPIC

    REQUIRED READING

    SUGGESTED READING

    Click for ppt & pdfs

    Week 1A 1/21/14




    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
    Week 1B
    1/23/14
    Anatomy of a genome project Metzker.Nat Reviews Gen. 2006.Sequencing technologies - the next generation.

    Week 2B
    1/30/14
    PAPER DISCUSSION Clark et al. Nature. 2007. Evolution of genes and genomes on the Drosophila phylogeny.

    Week 3A
    2/4/14
    Orthology, paralogy, and gene history Koonin.Annu Rev Gen. 2005. Orthologs, Paralogs, and Evolutionary Genomics Powell et al. 2014. NAR. eggNOG v4.0: nested orthology inference across 3686 organisms.
    Brigham et al. 2006. Evolution of hormone-receptor complexity by molecular exploitation.
    Week 3B
    2/6/14

    Evolution of new gene functions
    Zu & Wang. 2008;
    Lynch & Conery.Science 2000.The evolutionary fate and consequences of duplicate genes.
    Carvunis et al. Nature. 2012. Proto-genes and de novo gene birth.
    Week 4A
    2/11/14
    PAPER DISCUSSION


    Zhou et al. 2008. Genome Research. On the origin of new genes in Drosophila.

    Wu et al. 2011. PLoS Genetics. De novo origin of human protein-coding genes
    Week 4B
    2/13/14
    Bacterial Genomics
    Thomas & Nielsen. 2005. Nat Rev Micro. Mechanisms of, and barriers to, horizontal gene transfer between bacteria
    Mira et al. 2010. International Microbiology. The bacterial pan genome: a new paradigm in microbiology.


    Week 5A
    2/18/14




    PAPER DISCUSSION
    Smillie et al. Nature 2011. Ecology drives a global
    network of gene exchange connecting the
    human microbiome.


    Week 5B
    2/20/14



    Whole genome
    Duplication
    Semom & Wolfe.2007.Consequences of genome duplication
    Van de Peer.Nat. Reviews Gen. 2009.The evolutionary significance of ancient genome duplications.

    Week 6A
    2/25/14
    PAPER DISCUSSION Rodgers-Melnick et al. 2011. Contrasting patterns of evolution following whole genome versus tandem duplication events in Populus.


    Week 6B
    2/27/14
    Molecular evolution - Part I Nielsen. Annu Rev Genet. 2005.Molecular signatures of natural selection.

    Wagner. Nat Rev Gen. 2008. Neutralism and selectionism: a network-based reconciliation
    M. Nei. 2005. Mol Biol. Evo. Selectionism and Neutralism in Molecular Evolution

    Week 7A
    3/4/14
    PAPER DISCUSSION Fay, Wycoff, Wu.Nature. 2002. Testing the neutral theory of molecular evolution with genomic data from Drosophila.
    Gossman et al. Mol Biol Evol. 2010. Genome Wide Analyses Reveal Little Evidence for Adaptive Evolution in Many Plant Species

    Smith & Eyre-Walker.Nature. 2002.Adaptive protein evolution in Drosophila.
    Week7B
    3/6/14

    Molecular evolution - Part II:genome-wide scans Stinchcombe & Hoekstra.Heredity. 2007.
    Combining population genomics and
    quantitative genetics: finding the genes
    underlying ecologically important traits.

    Sabeti et al. 2002. Detecting recent positive
    selection in the human genome from haplotype structure

    Week 8A
    3/11/14

    PAPER DISCUSSION

    Sabeti et al. 2007.
    Nature.Genome-wide detection and characterization of positive selection in human populations


    Week 8B
    3/13/14
    QTL mapping & Genome-wide
    association (GWAS)
    Broman 2001. Review of Statistical Methods for QTL mapping in experimental crosses.

    MacKay et al. 2009. The Genetics of Quantitive Traits: Challenges and Prospects.


    3/17/14-3/21/14

    Week 9A
    3/25/14
    NO CLASS - SPRING BREAK

    PAPER DISCUSSION


    Schoenebeck et al. 2012. Variation of BMP3 contributes to dog breed skull diversity


    Shapiro et al. 2009. Current Biol. The genetic architecture of skeletal convergence and sex determination in ninespine sticklebacks.
    Week 9B
    3/27/14
    Evolution of gene expression

    Pall et al. Nat Gen Reviews 2006. An integrated view of protein evolution.
    Wray. 2007. Nat Gen Reviews. The evolutionary significance of cis-regulatory mutations.


    Week 10A
    4/1/14
    PAPER DISCUSSION


    Brawand et al. Nature 2011. The evolution of

    gene expression levels in mammalian organs.


    Week 10B
    4/3/14
    eQTL mapping & the cis-trans debate Rockman & Kruglyak. Nat Reviews Gen 2006. Genetics of global gene expression. 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 11A
    4/8/14
    PAPER DISCUSSION
    Zhang et al. Genome Research. 2011. Genetic
    architecture of regulatory variation in Arabidopsis
    thaliana.
    Bougas et al. Heredity. 2013. Linking transcriptomic and genomic variation to growth in brook charr hybrids ...
    Week 11B
    4/10/14

    Evolution of transcriptional motifs and regulation

    Wittkopp & Kalay. Nat Rev Genetics. 2012. Cis-regulatory elements: molecular mechanisms and evolutionary processes underlying divergence.

    Ludwig et al. Nature 2000.
    Evidence for stabilizing selection in a eukaryotic enhancer element.



    Schmidt et al. Science 2009. Five-Vertebrate ChIP-seq Reveals the Evolutionary Dynamics of Transcription Factor Binding




    Week 12A
    4/15/14
    PAPER DISCUSSION Stefflova et al. Cell 2013. Cooperativity and rapid evolution of cobound transcription factors in closely related mammals;


    Week 12B

    4/17/14


    Network evolution


    Wohlbach et al. 2009. From elements to modules: regulatory evolution in Ascomycota fungi.

    Lavoie et al. 2010. PLoS Bio. Evolutionary tinkering with conserved components of a transcriptional regulatory network.

    Borneman et al. 2007. Science. Divergence of Transcription Factor Binding Sites Across Related Yeast Species.

    Kasowski et al. 2010. Science. Variation in Transcription Factor Binding Among Humans
    .

    Week 13A
    4/22/14

    PAPER DISCUSSION


    Baker et al. Science. 2013. Following gene duplication, paralog interference constrains transcription circuit evolution.
    Booth et al. Nature. 2010. Intercalation of a new tier of transcription regulation into an ancient circuit.

    Week 13B
    4/24/14
    Evolutionary
    proteomics
    Yamada and Bork. Nat. Rev. 2009. Evolution of Biomolecular Networks - Lessons from Metabolic and Protein Interactions.
    Beltrao et al. 2009. PLoS Biology. Evolution of Phosphoregulation: Comparison of phosphorylation patterns across yeast species

    Week 14A
    4/29/14

    PAPER DISCUSSION

    Systematic Functional Prioritization of Protein Post-translational Modifications. Beltrao et al. Cell. 2012.


    Week 14B
    5/1/14

    Non-model organism
    Evolutionary Genomics
    & Final wrap-up
    Genome sequencing and population genomics in non-model organisms.
    Ellegren. 2014. T

    Week 15A
    5/6/14

    PAPER DISCUSSION
    Qia et al. Nature. 2012. The Yak genome and adaptation to life at high altitude.



    Week 15B
    5/8/14

    PAPER DISCUSSION Clark et al. Nature. 2007. Evolution of genes and genomes on the Drosophila phylogeny.