? The human genome is remarkably variable and understanding this variation is a vital component of promised advances in human health. Publicly available human and model organism reference genomic sequences provide a foundation for revolutionary advances in population genomics, the genomic-scale detection of DNA sequence variants and investigation of their role in affecting disease risk. However, even as the first population genomic data emerge, solid paradigms of description and analysis have not yet appeared. For example, integration of population genomic polymorphism and associated phenotypic variation into genomic annotations is an essential goal yet a daunting assignment. To directly address the basic challenge of population genomics we are proposing to begin an effort to obtain the complete sequence of 50 Drosophila melanogaster genomes. The Drosophila strains and their associated genomic polymorphisms will become objects of intense and diverse functional analyses and annotation. The goals of this proposal are (1) to develop and validate an appropriate resequencing technology, (2) to establish a sustainable, high quality resequencing capacity, and (3) to provide preliminary results and analysis that demonstrate the high added value of genomic coverage of population polymorphism. ? ?
| Lack, Justin B; Cardeno, Charis M; Crepeau, Marc W et al. (2015) The Drosophila genome nexus: a population genomic resource of 623 Drosophila melanogaster genomes, including 197 from a single ancestral range population. Genetics 199:1229-41 |
| Kirkpatrick, Bonnie; Stevens, Kristian (2014) Perfect Phylogeny Problems with Missing Values. IEEE/ACM Trans Comput Biol Bioinform 11:928-41 |
| Langley, Sasha A; Karpen, Gary H; Langley, Charles H (2014) Nucleosomes shape DNA polymorphism and divergence. PLoS Genet 10:e1004457 |
| Lee, Yuh Chwen G; Langley, Charles H; Begun, David J (2014) Differential strengths of positive selection revealed by hitchhiking effects at small physical scales in Drosophila melanogaster. Mol Biol Evol 31:804-16 |
| Langley, Charles H; Stevens, Kristian; Cardeno, Charis et al. (2012) Genomic variation in natural populations of Drosophila melanogaster. Genetics 192:533-98 |
| Pool, John E; Corbett-Detig, Russell B; Sugino, Ryuichi P et al. (2012) Population Genomics of sub-saharan Drosophila melanogaster: African diversity and non-African admixture. PLoS Genet 8:e1003080 |
| Poh, Yu-Ping; Ting, Chau-Ti; Fu, Hua-Wen et al. (2012) Population genomic analysis of base composition evolution in Drosophila melanogaster. Genome Biol Evol 4:1245-55 |
| Corbett-Detig, Russell B; Cardeno, Charis; Langley, Charles H (2012) Sequence-based detection and breakpoint assembly of polymorphic inversions. Genetics 192:131-7 |
| Langley, Charles H; Crepeau, Marc; Cardeno, Charis et al. (2011) Circumventing heterozygosity: sequencing the amplified genome of a single haploid Drosophila melanogaster embryo. Genetics 188:239-46 |
| Lam, Fumei; Langley, Charles H; Song, Yun S (2011) On the genealogy of asexual diploids. J Comput Biol 18:415-28 |
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