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High-throughput (a.k.a. "next-gen") sequencing:
3. 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
2. 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
1. Gilad, Y., J. K. Prichard, and K. Thornton (2009) Characterizing natural variation using next-generation sequencing technologies. Trends in Genetics 25: 463-471
Gene duplications:
7. Thornton, K.R. (2007) The neutral coalescent process for recent gene duplications and copy-number variants. Genetics 177: 987-1000
6. 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
5. 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
4. 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
3. Betran, E., K. Thornton, and M. Long (2002) Retroposed new genes out of the X in Drosophila. Genome Research 12: 1854-1859.
2. Thornton, K. and M. Long (2002) Rapid Divergence of Gene Duplicates on the Drosophila melanogaster X chromosome. Molecular Biology and Evolution 19:918-925.
1. Long, M. and K. Thornton. (2001) Techincal Comment: Gene Duplication and Evolution. Science 2001 August 31; 293: 1551a.
Drosophila population genetics:
6. 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
5. 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
4. 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
3. 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
2. 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)
1. Wang, W., K. Thornton, A. Berry and M. Long (2002) Nucleotide variation along the Drosophila melanogaster fourth chromosome. Science 295: 134-137.
Human population genetics:
1. 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
General population genetics:
6. 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.
5. Jensen, J. D., K. R. Thornton, and C. F. Aquadro (2008) Inferring selection in partially-sequenced regions. MBE 25: 438-446
4. 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.
3. 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
2. Thornton, K. R. and J. D. Jensen (2007) Controlling the false positive rate in multilocus genome scans for selection. Genetics 175: 737-750.
1. Thornton, K. (2005) Recombination and the properties of Tajima's D in the context of approximate likelihood calculation. Genetics 171: 2143-2148
Comparative genomics of Drosophila:
2. 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.
1. 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-elelement evolution. Genome Research 15:1-18
Software development:
2. Thornton, K. (2009) Automating approximate Bayesian computation by local linear regression. BMC Genetics 10:35. PAPER SOFTWARE
1. Thornton, K. (2003) libsequence: a C++ class library for evolutionary genetic analysis. Bioinformatics 19(17): 2325-2327