Preprints
  • J. R. Adrion et al. A community-maintained standard library of population genetic models. bioRxiv, 2019.
  • C. J. Battey, P. L. Ralph, A. D. Kern. Predicting Geographic Location from Genetic Variation with Deep Neural Networks. bioRxiv, 2019.
  • J. R. Adrion, J. G. Galloway, A. D. Kern. Inferring the landscape of recombination using recurrent neural networks. bioRxiv 662247, 2019.
  • C. J. Battey, P. L. Ralph, A. D. Kern. Space is the Place: Effects of Continuous Spatial Structure on Analysis of Population Genetic Data. bioRxiv 659235, 2019.
  • A. T. Xue, D. R. Schrider, A. D. Kern, and the Ag1000G Consortium. Discovery of ongoing selective sweeps within Anopheles mosquito populations using deep learning. bioRxiv, 589069, 2019.

Selected Publications
  • A. D. Kern and M. W. Hahn. Neutral theory in light of natural selection. Mol. Biol. Evol. 35(6): 1366-1371, 2018.
  • D. R. Schrider, J. Ayroles, D. R. Matute, and A. D. Kern. Supervised machine learning reveals introgressed loci in the genomes of Drosophila simulans and D. sechellia. PLoS Genetics, 14(4):e1007341. bioRxiv.
  • A. D. Kern and D. R. Schrider. diploS/HIC: an updated approach to classifying selective sweeps. G3, doi.org/10.1534/g3.118.200262. 2018 bioRxiv.
  • D. R. Schrider and A. D. Kern. Supervised machine learning for population genetics: a new paradigm. Trends Genet. 10.1016/j.tig.2017.12.005. 2018. bioRxiv.
  • The Anopheles gambiae 1000 Genomes Consortium. Genetic diversity in the malaria vector Anopheles gambiae. Nature, 552(7683):96-100. 2017. bioRxiv.
  • E. Lavington and A. D. Kern. The effect of common inversion polymorphisms In(2L)t and In(3R)Mo on patterns of transcriptional variation in Drosophila melanogaster. G3, doi.org/10.1534/g3.117.1133. 2017. bioRxiv.
  • A. D. Kern and J. Hey. Exact calculation of the joint allele frequency spectrum for generalized isolation with migration models. Genetics, 207(1):241-253, 2017. bioRxiv.
  • D. R. Schrider and A. D. Kern. Soft sweeps are the dominant mode of adaptation in the human genome. Mol. Biol. Evol, 34(8): 1863-1877, 2017. bioRxiv
  • D. R. Schrider†, A. G. Shanku†, and A. D. Kern. Effects of linked selective sweeps on demographic inference and model choice. Genetics, (3):1207-1223, 2016. bioRxiv. †these authors contributed equally
  • A. D. Kern and D. R. Schrider. discoal: flexible coalescent simulations with selection. Bioinformatics, doi:10.1093/bioinformatics/btw556, 2016. bioRxiv.
  • D. R. Schrider and A. D. Kern. S/HIC: Robust identification of soft and hard sweeps using machine learning. PLoS Genetics, 12(3):e1005928, 2016. bioRxiv.
  • D. R. Schrider and A. D. Kern. Inferring selective constraint from population genomic data suggests recent regulatory turnover in the human brain. Genome Biol. Evol. doi: 10.1093/gbe/evv228. 2015. arXiv.
  • D. R. Schrider, F. K. Mendes, M. W. Hahn, and A. D. Kern. Soft shoulders ahead: spurious signatures of soft and partial sweeps result from linked hard sweeps. Genetics 200: 276-284. 2015.
  • E. H. B. Hellen and A. D. Kern. The role of DNA insertions in phenotypic differentiation between humans and other primates. Genome Biol. Evol. 7(4): 1168-1178. 2015.
  • A. D. Kern, D. A. Barbash, J. C. Mell, D. Hupalo, and A. Jensen. Highly constrained intergenic Drosophila ultraconserved elements are candidate ncRNAs. Genome Biol. Evol. 7(3): 689-698. 2015.
  • D. R. Schrider and A. D. Kern. Discovering functional DNA elements using population genomic information: A proof of concept using human mtDNA. Genome Biol. Evol. 6(7): 1542-1548. 2014. arXiv.
  • J. A. Reinhardt, B. Kolaczkowski, C. D. Jones, D. J. Begun, and A. D. Kern. Parallel geographic variation in Drosophila melanogaster. Genetics 197(1): 361-373. 2014.
  • D. Hupalo and A.D. Kern. Conservation and Functional Element Discovery in 20 Angiosperm Genomes. Mol. Biol. Evol. 30(7): 1729-1744. 2013.
  • A.G. Shanku, M.A. McPeek, A.D. Kern. Functional Annotation and Comparative Analysis of a Zygopteran Transcriptome. G3 3(4): 763-770. 2013.
  • K. Kristas, S.E. Wuest, D. Hupalo, A.D. Kern, T. Wicker, U. Grossniklaus. Computational analysis and characterization of UCE-like elements (ULEs) in plant genomes. Genome Res. 22(12): 2455-2466. 2012.
  • C. H. Langley, K. Stevens, C. Cardeno, Y. C. Lee, D. R. Schrider, J. E. Pool, S.A. Langley, C. Suarez, R. B. Corbett-Detig, B. Kolaczkowski, S. Fang, P.M. Nista, A. K. Halloway, A. D. Kern, C. N. Dewey, Y. S. Song, M. W. Hahn, D. J. Begun. Genomic variation in natural populations of Drosophila melanogaster. Genetics. 2012 Oct;192(2):533-98.
  • M. Kirkpatrick and A. Kern. Where's the money? Inversions, genes, and the hunt for genomic targets of selection. Genetics. 190: 1153-1155. 2012.
  • B. Kolaczkowski †, A. D. Kern†, A. K. Holloway, D. J. Begun. Genomic differentiation between temperate and tropical Australian populations of Drosophila melanogaster. Genetics,187(1):245-260. 2011†these authors contributed equally
  • B. Kolaczkowski, D. N. Hupalo, and A. D. Kern. Recurrent adaptation in RNA-interference genes across the Drosophila phylogeny. Mol. Biol. Evol. 28(2):1033-1042. 2011.
  • The 1000 Genomes Consortium. A map of human genome variation from population-scale sequencing. Nature 467(7319):1061-73. 2010.
  • A. D. Kern and D. Haussler. A Population Genetic Hidden Markov Model for Detecting Genomic Regions Under Selection. Mol. Biol. Evol. 27(7):1673-1685, 2010.
  • S. Katzman, A. D. Kern, K. Pollard, S. Salama, D. Haussler. GC-biased evolution near human accelerated regions. PLoS Genetics, May 20;6(5):e1000960, 2010.
  • B. Kolaczkowski and A. D. Kern. On the power of comparative genomics: does conservation imply function? In M.A. Bell, D. J. Futuyma, W.F. Eanes, and J. S. Levinton (eds.), Evolution Since Darwin: The First 150 Years, Sinauer, Sunderland, 2010.
  • A. Gasc, M.C. Duryea, R.M. Cox, A. Kern, R. Calsbeek. Invasive predators deplete genetic diversity of island lizzards. PLoS One, 5(8):e12061, 2010.
  • A. D. Kern. Correcting the site frequency spectrum for divergence-based ascertainment bias. PLoS One, 4(4):e5152, 2009.
  • A. D. Kern and D. J. Begun. Recurrent deletion and gene presence/absence polymorphism: telomere dynamics dominate DNA evolution at the tip of 3L in Drosophila. Genetics, 179(2):1021- 1027, 2008.
  • D. J. Begun, A. K. Holloway, K. Stevens, L. W. Hillier, Y. P. Poh, M. W. Hahn, P. M. Nista, C. D. Jones, A. D. Kern, C. N. Dewey, L. Pachter, E. Myers, C. H. Langley. Population genomics: whole genome analysis of polymorphism and divergence in Drosophila simulans. PLoS Biology, 5(11): e310, 2007.
  • S. Katzman† , A. D. Kern† , G. Bejerano, G. Fewell, L. Fulton, R. Wilson, D. Haussler. Human genome ultraconserved elements are ultraselected. Science, 317:915, 2007. † these authors contributed equally
  • The ENCODE consortium. The ENCODE pilot pro ject: functional annotation of 1% of the human genome. Nature, 447: 799-816, 2007.
  • D. J. Begun, H. A. Lindfors, A. D. Kern, C. D. Jones. Evidence for de novo evolution of testis-expressed genes in the Drosophila yakuba/Drosophila erecta clade. Genetics, 176: 1131-1137, 2007.
  • Rhesus Macaque Genome Sequencing and Analysis Consortium. Evolutionary and biomedical insights from the rhesus macaque genome. Science, 13: 222-234, 2007.
  • B. Giardine, C. Riemer, T. Hefferon, D. Thomas, F. Hsu, J. Zielenski, Y. Sang, L. Elnitski, G. Cutting, H. Trumbower, A. Kern, R. Kuhn, G. P. Patrinos, J. Hughes, D. Higgs, D. Chui, C. Scriver, M. Phommarinh, S. K. Patnaik, O. Blumenfeld, B. Gottlieb, J. Kent, W. Miller, R. C. Hardison. PhenCode: Connecting ENCODE Data with Mutations and Phenotype. Hum. Mut., 28: 554-562, 2007.
  • D. J. Thomas, H. Trumbower, A. D. Kern, B. Rhead, R. M. Kuhn, D. Haussler, W. J. Kent. Variation resources at UC Santa Cruz. Nucleic Acids Res. 316: 716-720, 2007.
  • K.S. Pollard, S. R. Salama, N. Lambert, M. A. Lambot, S. Coppens, J. S. Pedersen, S. Katzman, C. Onodera, A. Siepel, A. D. Kern, C. Dehay, H. Igel, M. Ares, P. Vanderhaeghen, and D. Haussler. An RNA gene expressed during cortical development evolved rapidly in humans. Nature 443: 167- 172, 2006.
  • K. S. Pollard, S. R. Salama, B. King, A. D. Kern, T. Dreszer, R. Beartsch, A. Siepel, G. Bejerano, K. Rosenbloom, J. Kent, and D. Haussler. Forces shaping the fastest evolving regions in the human genome. PLoS Genetics, 2:e168, 2006.
  • M. T. Levine, C. D. Jones, A. D. Kern, H. A. Lindfors, and D. J. Begun. Novel genes derived from noncoding DNA in Drosophila melanogaster. Proc. Natl. Acad. Sci USA 103:9935-9939, 2006.
  • M. W. Hahn, J. G. Mezey, D. J. Begun, J. H. Gillespie, A. D. Kern, C. H. Langley, and L. C. Moyle. Evolutionary Genomics: Codon Bias and Natural Selection on Single Genomes. Nature, 433: E5–7, 20005.
  • M. W. Hahn and A. D. Kern. Comparing Centrality and Essentiality in Three Eukaryotic Protein- Interaction Networks. Mol. Biol. Evol.22: 803–806, 2005.
  • A. D. Kern and D. J. Begun. Patterns of polymorphism and divergence from non-coding sequences of D. melanogaster and D. simulans: evidence for non-equilibrium processes Mol. Biol. Evol. 22:51– 62, 2005.
  • A. D. Kern and F. A. Kondrashov. Mechanisms and Convergence of Compensatory Evolution in mammalian tRNAs. Nature Genetics 36:1207–1212, 2004.
  • A. D. Kern, C. D. Jones, and D. J. Begun. Molecular population genetics of male accessory gland proteins in the Drosophila simulans complex. Genetics 164:725–735, 2004.
  • A. D. Kern, C. D. Jones, and D. J. Begun. Genomic effects of nucleotide substitution in Drosophila simulans. Genetics 162:1753–1761, 2002.