See Google scholar for the most up-to-date (free) information on publications, as the list below may not be current.

If you are interested in the latest from the lab, we are (slowly) starting to share slides from our talks on slideshare:

Kevin Thornton on slideshare.net. (There may be nothing there yet...)

Names in bold-faced red text are current or former members of the Thornton Lab at UC Irvine.

  1. Baldwin-Brown, J., A. D. Long, and K. R. Thornton (in press) The Power to Detect Quantitative Trait Loci Using Resequenced, Experimentally Evolved Populations of Diploid, Sexual Organisms. The accepted manuscript is online here.
  2. Cridland, J.M., S.J. MacDonald, A.D. Long, and K.R Thornton (2013) Abundance and Distribution of Transposable Elements in Two Drosophila QTL Mapping Resources. Molecular Biology and Evolution. The open-access manuscript is available here.
  3. Thornton, K.R., A. J. Foran, and A. D. Long (2013) Properties and Modeling of GWAS when Complex Disease Risk is due to non-complementing, deleterious mutations in genes of large effect. PLoS Genetics 9: e1003258. The simulation code and output used for the main results in the paper are available here. The paper can be found here.
  4. Hu, T., M. B. Eisen, K. R. Thornton, and P. Andolfatto (2013) A second generation assembly of the Drosophila simulans genome provides new insights into patterns of lineage-specific divergence. Genome Research 23: 89-98
  5. Garrigan, G., S. B. Kingan, A. J. Geneva, P. Andolfatto, A. G. Clark, K. R. Thornton, and D. C. Presgraves (2012) Genome sequencing reveals complex speciation in the Drosophila simulans clade. Genome Research 22: 1499-1511
  6. Mackay, T. F. C., S. Richards, E. A. Stone, A. Barbadilla, J. F. Ayroles, D. Zhu, S. Casillas, Y. Han, M. M. Magwire, J. M. Cridland, M. F. Richardson, R. R. H. Anholt, M. Barrón,C. Bess K. P. Blankenburg, M. A. Carbone, D. Castellano, L. Chaboub, L. Duncan, Z. Harris, M. Javaid, J. C. Jayaseelan, S. N. Jhangiani, K. W. Jordan, F. Lara, F. Lawrence, S. L. Lee, P. Librado, R. S. Linheiro, R. F. Lyman, A. J. Mackey, M. Munidasa, D. M. Muzny, L. Nazareth, I. Newsham, L. Perales, L.-L. Pu, C. Qu, M. Ràmia, J. G. Reid, S. M. Rollmann, J. Rozas, N. Saada, L. Turlapati, K. C. Worley, Y.-Q. Wu, A. Yamamoto, Y. Zhu, C. M. Bergman, K. R. Thornton, D. Mittelman and R. A. Gibbs (2012) The Drosophila melanogaster genetic reference panel. Nature 482: 173-178
  7. Cridland, J.M. and K.R Thornton (2010) Validation of rearrangement breakpoints identified by paired-end sequencing in natural populations of Drosophila melanogaster. Genome Biology and Evolution. 2010: 83-101
  8. Burke, M. K., J. P. Dunham, P. Shahrestani, K. R. Thornton, M. R. Rose, and A. D. Long (2010) Genome-wide analysis of a long-term evolution experiment with Drosophila. Nature 467, 587–590
  9. Sainudiin, R., K. Thornton, J. Harlow, J. Booth, M. Stillman, R. Yoshida, R. Griffiths, G. McVean, and P. Donnelly. (2010) Experiments with the site-frequency spectrum. Bulletin of Mathematical Biology, Algebraic Biology Special Edition, 0092-8240, p.1-44
  10. Gilad, Y., J. K. Prichard, and K. Thornton (2009) Characterizing natural variation using next-generation sequencing technologies. Trends in Genetics 25: 463-471
  11. Thornton, K. (2009) Automating approximate Bayesian computation by local linear regression. BMC Genetics 10:35. PAPER SOFTWARE
  12. Jensen, J. D. , K. R. Thornton and P. Andolfatto (2008) An approximate Bayesian estimator suggests strong, recurrent selective sweeps in Drosophila. PLoS Genetics 4: e1000198 The paper is here.
  13. Jensen, J. D., K. R. Thornton, and C. F. Aquadro (2008) Inferring selection in partially-sequenced regions. MBE 25: 438-446
  14. Thornton, K.R. (2007) The neutral coalescent process for recent gene duplications and copy-number variants. Genetics 177: 987-1000
  15. Tang, K., K. R. Thornton, and M. Stoneking (2007) A new approach for using genome scans to detect recent positive selection in the human genome. PLoS Biology, 5: e171 The paper is here.
  16. Thornton, K. R. and J. D. Jensen (2007) Controlling the false positive rate in multilocus genome scans for selection. Genetics 175: 737-750.
  17. Thornton, K. R., J. D. Jensen, C. Becquet, and P. Andolfatto (2007) Progress and prospects in mapping recent selection in the genome. Heredity 98: 340-348
  18. Jensen, J. D., K. R. Thornton, C. D. Bustamante, and C. F. Aquadro (2007). On the utility of linkage disequilibrium as a statistic for identifying targets of positive selection in non-equilibrium populations. Genetics 176: 2371-2379.
  19. Thornton, K., D. Bachtrog, and P. Andolfatto (2006) X chromosomes and autosomes evolve at similar rates in Drosophila: No evidence for faster-X protein evolution. Genome Research 16: 498-504.
  20. Thornton, K.R. and P. Andolfatto (2006) Approximate Bayesian Inference reveals evidence for a recent, severe, bottleneck in a Netherlands population of Drosophila melanogaster. Genetics 172: 1607-1619
  21. Gary M. Wilson, Stephane Flibotte, Perseus I. Missirlis, Marco A. Marra, Steven Jones, Kevin Thornton, Andrew G. Clark, and Robert A. Holt (2006) Identification by full-coverage array CGH of human DNA copy number increases relative to chimpanzee and gorilla. Genome Research 16: 173-181
  22. Bachtrog, D., K. Thornton, A. Clark, and P. Andolfatto (2006) Extensive introgression of mitochondrial DNA relative to nuclear genes in the Drosophila yakuba species group. Evolution 60: 292-302
  23. Thornton, K. and M. Long (2005) Excess of amino acid substitutions relative to polymorphism between X-linked duplications in Drosophila melanogaster. Molecular Biology and Evolution 22:273-284
  24. Haddrill, P., K.R. Thornton, B. Charlesworth, and P. Andolfatto. (2005) Multilocus patterns of nucleotide variability and the demographic and selection history of Drosophila melanogaster populations. Genome Research 15: 790-799
  25. Richards, S., Y. Liu, B. R. Bettencourt., P. Hradecky, S. Letovsky, R. Nielsen., K. Thornton, and 43 coauthors. (2005) Comparative genome sequencing of Drosophila pseudoobscura: Chromosomal, gene, and cis-element evolution. Genome Research 15:1-18
  26. Thornton, K. (2005) Recombination and the properties of Tajima's D in the context of approximate likelihood calculation. Genetics 171: 2143-2148
  27. Wang, W., K. Thornton, J.J. Emerson, M. Long (2004) Nucleotide variation and recombination along the fourth chromosome in Drosophila simulans. Genetics 166: 1783-1794 (Wang and Thornton contributed equally to this work)
  28. Thornton, K. (2003) libsequence: a C++ class library for evolutionary genetic analysis. Bioinformatics 19(17): 2325-2327
  29. Long, M., E. Betran, K. Thornton, and W. Wang (2003) The origin of new genes: glimpses from the youg and old. Nature Reviews Genetics 4:865-875
  30. Thornton, K. and M. Long (2002) Rapid Divergence of Gene Duplicates on the Drosophila melanogaster X chromosome. Molecular Biology and Evolution 19:918-925.
  31. Betran, E., K. Thornton, and M. Long (2002) Retroposed new genes out of the X in Drosophila. Genome Research 12: 1854-1859.
  32. Wang, W., K. Thornton, A. Berry and M. Long (2002) Nucleotide variation along the Drosophila melanogaster fourth chromosome. Science 295: 134-137.
  33. Long, M. and K. Thornton. (2001) Techincal Comment: Gene Duplication and Evolution. Science 2001 August 31; 293: 1551a.