Dan Davison

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I use population genetic data to study population structure, speciation and 'species-level' systematics. I was a postdoc in Peter Donnelly's research group in the Statistics Department at Oxford University, and the Wellcome Trust Centre for Human Genetics, during 2006-2010. I'm currently working on analyses of large data sets of SNP genotypes of humans in the UK and continental Europe. I did my Ph.D. in the Committee on Evolutionary Biology at the University of Chicago, working in Jonathan Pritchard's group and in the Bird Division of the Field Museum of Natural History in Chicago with Shannon Hackett and John Bates. During 2008-2010 I worked with Peter Andolfatto's research group in the Ecology and Evolutionary Biology Department at Princeton University.

Selected Publications

  • D Davison, J Pritchard and G Coop (2009) An approximate likelihood for genetic data under a model with recombination and population splitting. Theoretical Population Biology 75(4):331-345
  • S Myles, D Davison, J Barrett, M Stoneking and N Timpson (2008) Worldwide population differentiation at disease-associated SNPs BMC Medical Genomics 1(1):22
  • Wellcome Trust Case Control Consortium (2007) Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature 447:661-678

In prep

  • D Davison. Variational Bayes and parallel algorithms for fitting mixture models to large genotype data sets. in prep.
  • P Andolfatto, D Davison, D Erezyilmaz, T T Hu, J Mast, T Morita and D L Stern. Multiplexed Shotgun Genotyping for Rapid and Efficient Genetic Mapping. in prep.

Population genetics software

shellfish

PCA for very large data sets of SNP genotypes. Computations are automatically performed in parallel on a computing cluster, and on a single multi-processor machine.

psi

Parallel implementation of the Pritchard et al. (2000) "Admixture Model" (EM, MCMC or VB)

Other software

Org-babel

A new software environment for reproducible research and literate programming. Developed in collaboration with Eric Schulte and Carsten Dominik.

lines and slice

Rapid extraction of lines and columns from tabular text files. Especially useful for large files, such as genome-wide genotype data.

Etc

plant photos

Taxonomically organised flower photographs

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Whip Spider (Amblypygi sp.) Floresta Nacional do Tapajós, Pará, Brasil