Dan Garrigan has provided this preliminary list for the Fall 2010 journal club:

1.  Pool et al. (2010) Population genetic inference from genomic sequence variation.  Genome Research 20: 291-300. [doi link]

2.  Mardis (2008) Next-generation DNA sequencing methods. Annual Review of Genomics and Human Genetics 9: 387-402. [doi link]

3.  Begun et al. (2007) Population genomics: whole-genome analysis of polymorphism and divergence in Drosophila simulans.  PLoS Biology 5: 2534-2559. [doi link]

4.  Liti et al. (2009) Population genomics of domestic and wild yeasts.  Nature 458: 337-341. [doi link]

5.  Neafsey et al. (2010) Population genomic sequencing of Coccidioides fungi reveals recent hybridization and transposon control. Genome Research 20: 938-946. [doi link]

6.  Xia et al. (2009) Complete resequencing of 40 genomes reveal domestication events and genes in silkworm (Bombyx). Science 326: 433-436. [doi link]

7.  Korbel et al. (2007) Paired-end mapping reveals extensive structural variation in the human genome.  Science 318: 420-426. [doi link]

8.  Ossowski et al. (2008) Sequencing of natural strains of Arabidopsis thaliana with short reads. Genome Research 18: 2024-2033. [doi link]

9.  Hellmann et al. (2008) Population genetic analysis of shotgun assemblies of genomic sequences from multiple individuals.  Genome Research 18: 1020-1029. [doi link]

10.  Cridland and Thornton (2010) Validation of rearrangement break points identified by paired-end sequencing in natural populations of Drosophila mealnogaster.  Genome Biology & Evolution 2: 83-101.

11.  Lynch (2009) Estimation of allele frequencies from high-coverage genome-sequencing projects. Genetics 182: 295-301. [doi link]

12.  Hahn (2006) Accurate inference and estimation in population genomics. Molecular Biology and Evolution 23: 911-918. [doi link]