Publications

Names of Thornton lab members are in bold face. The names of students and postdocs from other labs are UCI labs are in italics.

2022

• Gower, G., A. P. Ragsdale, G. Bisschop, R. N. Gutenkunst, M. Hartfield, E. Noskova, S. Schiffels, T. J. Struck, J. Kelleher, K. R. Thornton (2022) Demes: a standard format for demographic models. Genetics 222 (3):iyac131 DOI

  • This was a featured article in the November 2022 issue of Genetics
  • Blog post

• Baumdicker et al. 2022. Efficient ancestry and mutation simulation with msprime 1.0. Genetics 220(3):iyab229 DOI

  • This was a featured article in the March 2022 issue of Genetics

2020

• Ralph, P., K. Thornton, and J. Kelleher 2020. Efficiently summarizing relationships in large samples: a general duality between statistics of genealogies and genomes. Genetics 215: 779-797 DOI

2019

• Thornton, Kevin R. 2019. Polygenic Adaptation to an Environmental Shift: Temporal Dynamics of Variation under Gaussian Stabilizing Selection and Additive Effects on a Single Trait. Genetics 213: 1513-1530 DOI

2018

• Stetter, M. G., K. R. Thornton, and J. Ross-Ibarra (2018) Genetic architecture and selective sweeps after polygenic adaptation to distant trait optima. PLoS Genetics DOI

• Kelleher, J., K. Thornton, J. Ashander, and P. Ralph (2018) Efficient pedigree recording for fast population genetics simulation. PLoS Computational Biology DOI BioRxiv GitHub Repo 1 GitHub Repo 2 GitHub Repo 3

• Gruning et al. (2018) Bioconda: sustainable and comprehensive software distribution for the life sciences. Nature Methods 15, pages475–476

• Sanjak, J.S., J. Sidorenko, M.R. Robinson, K.R. Thornton, and P.M. Visscher (2018). Evidence of Directional and Stabilizing Selection in Contemporary Humans. PNAS 115 151–56. Paper

2017

• Rogers, R.R., L. Shao, and K.R. Thornton (2017) Tandem duplications lead to novel expression patterns through exon shuffling in Drosophila yakuba. PLoS Genetics 13 (5): e1006795 Paper

• Sanjak, J.S., A.D. Long, and K.R. Thornton (2017) A Model of Compound Heterozygous, Loss-of-Function Alleles Is Broadly Consistent with Observations from Complex-Disease GWAS Datasets. PLoS Genetics 13 (1): e1006573. PMID: 28103232 Paper

2016

• Sanjak, J.S., A.D. Long and K. R. Thornton (2016) Efficient Software for Multi-marker, Region-Based Analysis of GWAS Data. G3: Genes, Genomes, Genetics. ABSTRACT PMID: 26865700 DOI: 10.1534/g3.115.026013

2015

• Rogers, R.L, J.M. Cridland, L. Shao, T. Hu, P. Andolfatto, and K. R. Thornton (2015) Tandem Duplications and the Limits of Natural Selection in Drosophila yakuba and Drosophila simulans. PMID: 26176952 PLoS One. DOI:10.1371/journal.pone.0132184

• Cridland, J. M., K. R. Thornton and A. D. Long (2015) Gene expression variation in Drosophila melanogaster due to rare transposable element insertion alleles of large effect. Genetics 199: 85-93. PMID: 25335504 ABSTRACT. This article was chosen as an issue highlight.

2014

• Rogers, R. L., L. Shao, J. Sanjak, P. Andolfatto and K. R. Thornton (2014) Sex-biased expression in the Drosophila melanogaster group. G3: Genes, Genomes, Genetics. 4: 2345-2351 PMID: 25273863 ABSTRACT GFF files. This article has been chosen for the upcoming 2014 G3 “Spotlight” issue.

• Thornton, K. R. (2014) A C++ template library for efficient forward-time population genetic simulation of large populations. Genetics 98:157-166 PMID: 24950894, Manuscript, Software

• Rogers, R. L., J. M. Cridland, L. Shao, T. T. Hu, P. Andolfatto and K. R. Thornton (2014) Landscape of standing variation for tandem duplications in Drosophila yakuba and Drosophila simulans. Molecular Biology and Evolution 31: 1750-1766 PMID 24710518, Manuscript Data

• Baldwin-Brown, J., A. D. Long, and K. R. Thornton (2014) The Power to Detect Quantitative Trait Loci Using Resequenced, Experimentally Evolved Populations of Diploid, Sexual Organisms. Molecular Biology and Evolution 31: 1040-1055. PMID 24441104, Manuscript Code

2013

• 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 30: 2311-2327. PMID 23883524 Manuscript

• 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. PMID 23437004, Manuscript, Data Code (Note: this code link is for archival purposes and there is a better version of this simulation distributed with fwdpp.)

• 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. PMID 22936249, Manuscript

2012

• 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. PMID 22534282, Manuscript

• 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. PMID 22318601

2010

• 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, 0092-8 240, p.1-44. PMID: 21181503

• 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. PMID 20844486

• 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. PMID 20333226, Manuscript

2009

• Gilad, Y., J. K. Pritchard, and K. Thornton (2009) Characterizing natural variation using next-generation sequencing technologies. Trends in Genetics 25: 463-471 Manuscript

• K. R. Thornton (2009) Automating approximate Bayesian computation by local linear regression. BMC Genetics 10:35. PMID 19583871, Manuscript, Software

2008

• 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. PMID 18802463, Manuscript

• Jensen, J. D., K. R. Thornton and C. F. Aquadro (2008) Inferring selection in partially sequenced regions. Molecular Biology and Evolution 25: 438-446. PMID 18165259, Manuscript

2007

• K. R. Thornton (2007) The neutral coalescent process for recent gene duplications and copy number variants. Genetics 177: 987-1000. PMID 17720930

• 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

• 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. PMID 17579516

• Thornton, K. R. and J. D. Jensen (2007) Controlling the false positive rate in multilocus genome scans for selection. Genetics 175: 737-750 PMID 17110489

• 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. PMID 17473869

2006

• Thornton, K., and P. Andolfatto (2006) Approximate Bayesian inference reveals evidence for a recent strong bottleneck in non-African populations of Drosophila melanogaster Genetics 172: 1607-1619 PMID 16299396

• 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 Manuscript

• D. Bachtrog, 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

• G.M. Wilson, S. Flibotte, P.I. Missirlis, M.A. Marra, S. Jones, K. Thornton, A.G. Clark, and R.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 PMID: 16365383

2005

• Thornton, K. (2005) Recombination and the properties of Tajima’s D in the context of approximate likelihood calculation. Genetics 171: 2143-2148.

• 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

• 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

• 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

2004

• Wang, W., K. Thornton, J.J. Emerson, and M. Long (2004) Nucleotide variation and recombination along the fourth chromosome in Drosophila simulans. Genetics 166: 1783-1794

2003

• Thornton, K. (2003) libsequence, a C++ class library for evolutionary genetic analysis. Bioinformatics 19(17): 2325-2327 PMID 14630667 Manuscript, Software

• Long, M., E. Betran, K. Thornton, and W. Wang. (2003) Origin of new genes: Glimpses from the young and old. Nature Reviews Genetics 4: 865-875

2002

• Betran, E., K. Thornton, and M. Long (2002) Retroposed new genes out of the X in Drosophila. Genome Research 12: 1854-1859.

• Thornton, K. and M. Long (2002) Rapid Divergence of Gene Duplicates on the Drosophila melanogaster X chromosome. Molecular Biology and Evolution 19:918-925.

• Wang, W., K. Thornton, A. Berry and M. Long (2002) Nucleotide variation along the Drosophila melanogaster fourth chromosome. Science 295: 134-137.

2001

• Long, M. and K. Thornton. (2001) Techincal Comment: Gene Duplication and Evolution. Science 293: 1551a.

1998

• Wimberger, P.H., R.E. Reis, and K.R. Thornton (1998) Mitochondrial phylogenetics, biogeography, and evolution of parental care and mating systems in Gymnogeophagus (Percoformes: Cichlidae). In Malabara, LR et al. (eds) Phylogeny and Classification of Neotropical Fishes. EDIPUCRS, Porto Alegre, Brasil.

Written on: Nov 16 2022