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. |
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. |
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Week 2A1/26/10 |
PAPER DISCUSSION |
Clark et al. Nature. 2007. Evolution of genes and genomes on
the Drosophila phylogeny. |
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Week 2B1/28/10 |
Orthology, paralogy, and gene history |
Koonin.Annu Rev Gen. 2005.
Orthologs, Paralogs, and Evolutionary Genomics |
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Ortlund et al. 2007.Crystal
structure of an ancient protein:evolution by conformational epistasis |
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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. |
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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 |
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Week 5A2/16/10 |
Lateral gene transfer and the bacterial species concept
(Nicole Perna, guest lecturer) |
tbd |
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Week 5B2/18/10 |
PAPER DISCUSSION |
tbd |
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Week 6A2/23/10 |
Molecular evolution - Part I |
Nielsen. Annu Rev Genet. 2005.Molecular signatures of natural selection. |
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Week 6B2/25/10 |
PAPER DISCUSSION |
Fay, Wycoff, Wu.Nature. 2002. Testing the neutral theory of molecular
evolution with genomic data from Drosophila. |
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Smith & Eyre-Walker.Nature. 2002.Adaptive
protein evolution in Drosophila. |
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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 |
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Week 8A3/9/10 |
QTL mapping (Karl Broman, guest lecturer) |
tbd |
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Week 8B3/11/10 |
PAPER DISCUSSION |
tbd |
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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 |
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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. |
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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. |
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Week 11A4/6/10 |
Evolution of cis-regulation - Part I |
Ludwig et al. Nature 2000.Evidence for stabilizing selection in a eukaryotic enhancer element. |
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Week 11B4/8/10 |
PAPER DISCUSSION |
Kim et al. 2009. PLoS Gen. Evolution of Regulatory Sequences in 12
Drosophila species |
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Berman 2002 PNAS. |
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Week 12A4/13/10 |
Evolution of cis-regulation - Part II |
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Week 12B4/15/10 |
PAPER DISCUSSION |
Tsong Nature 2006. Evolution of alternative transcriptional
circuits with identical logic. |
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Week 13A4/20/10 |
Evolution of cis-regulation - Part III |
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Week 13B4/22/10 |
PAPER DISCUSSION |
Rubin paper - mammalian stuff |
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Week 14A4/27/10 |
Evolutionary proteomics & systems biology |
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Week 14B4/29/10 |
PAPER DISCUSSION |
tbd |
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Week 15A5/4/10 |
Final wrap-up, remaining questions |
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Week 15B5/6/10 |
PAPER DISCUSSION |
Clark et al. Nature. 2007. Evolution of genes and genomes on
the Drosophila phylogeny. |
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