Andrew D. Kern - Publications

Institute of Ecology and Evolution University of Oregon, Eugene, OR, United States 
Population and Comparative Genomics

62 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Rehmann CT, Ralph PL, Kern AD. Evaluating evidence for co-geography in the Anopheles Plasmodium host-parasite system. Biorxiv : the Preprint Server For Biology. PMID 37503196 DOI: 10.1101/2023.07.17.549405  0.522
2023 Lauterbur ME, Cavassim MIA, Gladstein AL, Gower G, Pope NS, Tsambos G, Adrion J, Belsare S, Biddanda A, Caudill V, Cury J, Echevarria I, Haller BC, Hasan AR, Huang X, ... ... Kern AD, et al. Expanding the stdpopsim species catalog, and lessons learned for realistic genome simulations. Elife. 12. PMID 37342968 DOI: 10.7554/eLife.84874  0.793
2023 Smith CCR, Tittes S, Ralph PL, Kern AD. Dispersal inference from population genetic variation using a convolutional neural network. Genetics. PMID 37052957 DOI: 10.1093/genetics/iyad068  0.566
2023 Small ST, Costantini C, Sagnon N, Guelbeogo MW, Emrich SJ, Kern AD, Fontaine MC, Besansky NJ. Standing genetic variation and chromosome differences drove rapid ecotype formation in a major malaria mosquito. Proceedings of the National Academy of Sciences of the United States of America. 120: e2219835120. PMID 36881629 DOI: 10.1073/pnas.2219835120  0.408
2023 Rodrigues MF, Kern AD, Ralph PL. Shared evolutionary processes shape landscapes of genomic variation in the great apes. Biorxiv : the Preprint Server For Biology. PMID 36798346 DOI: 10.1101/2023.02.07.527547  0.795
2022 Songco-Casey JO, Coffing GC, Piscopo DM, Pungor JR, Kern AD, Miller AC, Niell CM. Cell types and molecular architecture of the Octopus bimaculoides visual system. Current Biology : Cb. PMID 36318923 DOI: 10.1016/j.cub.2022.10.015  0.768
2021 Baumdicker F, Bisschop G, Goldstein D, Gower G, Ragsdale AP, Tsambos G, Zhu S, Eldon B, Ellerman EC, Galloway JG, Gladstein AL, Gorjanc G, Guo B, Jeffery B, Kretzschmar WW, ... ... Kern AD, et al. Efficient ancestry and mutation simulation with msprime 1.0. Genetics. PMID 34897427 DOI: 10.1093/genetics/iyab229  0.719
2021 Kasimatis KR, Abraham A, Ralph PL, Kern AD, Capra JA, Phillips PC. Evaluating human autosomal loci for sexually antagonistic viability selection in two large biobanks. Genetics. 217: 1-10. PMID 33683357 DOI: 10.1093/genetics/iyaa015  0.531
2021 Battey CJ, Coffing GC, Kern AD. Visualizing population structure with variational autoencoders. G3 (Bethesda, Md.). 11. PMID 33561250 DOI: 10.1093/g3journal/jkaa036  0.775
2020 Xue AT, Schrider DR, Kern AD. Discovery of ongoing selective sweeps within Anopheles mosquito populations using deep learning. Molecular Biology and Evolution. PMID 33022051 DOI: 10.1093/molbev/msaa259  0.836
2020 Adrion JR, Cole CB, Dukler N, Galloway JG, Gladstein AL, Gower G, Kyriazis CC, Ragsdale AP, Tsambos G, Baumdicker F, Carlson J, Cartwright RA, Durvasula A, Gronau I, Kim BY, ... ... Kern AD, et al. A community-maintained standard library of population genetic models. Elife. 9. PMID 32573438 DOI: 10.7554/Elife.54967  0.8
2020 Battey CJ, Ralph PL, Kern AD. Predicting geographic location from genetic variation with deep neural networks. Elife. 9. PMID 32511092 DOI: 10.7554/eLife.54507  0.829
2020 Battey CJ, Ralph PL, Kern AD. Space Is the Place: Effects of Continuous Spatial Structure on Analysis of Population Genetic Data. Genetics. PMID 32209569 DOI: 10.1534/genetics.120.303143  0.822
2020 Adrion JR, Galloway JG, Kern AD. Predicting the landscape of recombination using deep learning. Molecular Biology and Evolution. PMID 32077950 DOI: 10.1093/molbev/msaa038  0.842
2018 Kern AD, Hahn MW. The neutral theory in light of natural selection. Molecular Biology and Evolution. PMID 29722831 DOI: 10.1093/molbev/msy092  0.535
2018 Price N, Moyers BT, Lopez L, Lasky JR, Monroe JG, Mullen JL, Oakley CG, Lin J, Ågren J, Schrider DR, Kern AD, McKay JK. Combining population genomics and fitness QTLs to identify the genetics of local adaptation in . Proceedings of the National Academy of Sciences of the United States of America. PMID 29686078 DOI: 10.1073/Pnas.1719998115  0.779
2018 Schrider DR, Ayroles J, Matute DR, Kern AD. Supervised machine learning reveals introgressed loci in the genomes of Drosophila simulans and D. sechellia. Plos Genetics. 14: e1007341. PMID 29684059 DOI: 10.1371/Journal.Pgen.1007341  0.784
2018 Kern AD, Schrider DR. diploS/HIC: An Updated Approach to Classifying Selective Sweeps. G3 (Bethesda, Md.). PMID 29626082 DOI: 10.1534/G3.118.200262  0.777
2018 Schrider DR, Kern AD. Supervised Machine Learning for Population Genetics: A New Paradigm. Trends in Genetics : Tig. PMID 29331490 DOI: 10.1016/J.Tig.2017.12.005  0.769
2017 Miles A, Harding NJ, Bottà G, Clarkson CS, Antão T, Kozak K, Schrider DR, Kern AD, Redmond S, Sharakhov I, Pearson RD, Bergey C, Fontaine MC, Donnelly MJ, Lawniczak MKN, et al. Genetic diversity of the African malaria vector Anopheles gambiae. Nature. 552: 96-100. PMID 29186111 DOI: 10.1038/Nature24995  0.813
2017 Lavington E, Kern AD. The Effect of Common Inversion Polymorphisms In(2L)t and In(3R)Mo on Patterns of Transcriptional Variation in Drosophila melanogaster. G3 (Bethesda, Md.). PMID 28916647 DOI: 10.1534/g3.117.1133  0.479
2017 Kern AD, Hey J. Exact Calculation of the Joint Allele Frequency Spectrum for Isolation with Migration Models. Genetics. PMID 28696217 DOI: 10.1534/genetics.116.194019  0.421
2017 Schrider DR, Kern AD. Soft sweeps are the dominant mode of adaptation in the human genome. Molecular Biology and Evolution. PMID 28482049 DOI: 10.1093/Molbev/Msx154  0.758
2016 Schrider DR, Shanku AG, Kern AD. Effects of Linked Selective Sweeps on Demographic Inference and Model Selection. Genetics. PMID 27605051 DOI: 10.1534/Genetics.116.190223  0.81
2016 Kern AD, Schrider DR. discoal: flexible coalescent simulations with selection. Bioinformatics (Oxford, England). PMID 27559153 DOI: 10.1093/Bioinformatics/Btw556  0.725
2016 Schrider DR, Kern AD. S/HIC: Robust Identification of Soft and Hard Sweeps Using Machine Learning. Plos Genetics. 12: e1005928. PMID 26977894 DOI: 10.1371/Journal.Pgen.1005928  0.766
2016 Fletcher RS, Herrmann D, Mullen JL, Li Q, Schrider DR, Price N, Lin J, Grogan K, Kern A, McKay JK. Identification of Polymorphisms Associated with Drought Adaptation QTL in Brassica napus by Resequencing. G3 (Bethesda, Md.). PMID 26801646 DOI: 10.1534/G3.115.021279  0.768
2015 Schrider DR, Kern AD. Inferring selective constraint from population genomic data suggests recent regulatory turnover in the human brain. Genome Biology and Evolution. PMID 26590212 DOI: 10.1093/Gbe/Evv228  0.792
2015 Maguire JE, Silva M, Nguyen KC, Hellen E, Kern AD, Hall DH, Barr MM. Myristoylated CIL-7 Regulates Ciliary Extracellular Vesicle Biogenesis. Molecular Biology of the Cell. PMID 26041936 DOI: 10.1091/Mbc.E15-01-0009  0.765
2015 Schrider DR, Mendes FK, Hahn MW, Kern AD. Soft shoulders ahead: spurious signatures of soft and partial selective sweeps result from linked hard sweeps. Genetics. 200: 267-84. PMID 25716978 DOI: 10.1534/Genetics.115.174912  0.811
2015 Hellen EH, Kern AD. The role of DNA insertions in phenotypic differentiation between humans and other primates. Genome Biology and Evolution. 7: 1168-78. PMID 25635043 DOI: 10.1093/Gbe/Evv012  0.818
2015 Kern AD, Barbash DA, Chang Mell J, Hupalo D, Jensen A. Highly constrained intergenic Drosophila ultraconserved elements are candidate ncRNAs. Genome Biology and Evolution. 7: 689-98. PMID 25618141 DOI: 10.1093/Gbe/Evv011  0.804
2014 Schrider DR, Kern AD. Discovering functional DNA elements using population genomic information: a proof of concept using human mtDNA. Genome Biology and Evolution. 6: 1542-8. PMID 24916662 DOI: 10.1093/Gbe/Evu116  0.798
2014 Reinhardt JA, Kolaczkowski B, Jones CD, Begun DJ, Kern AD. Parallel geographic variation in Drosophila melanogaster. Genetics. 197: 361-73. PMID 24610860 DOI: 10.1534/Genetics.114.161463  0.835
2013 Hupalo D, Kern AD. Conservation and functional element discovery in 20 angiosperm plant genomes. Molecular Biology and Evolution. 30: 1729-44. PMID 23640124 DOI: 10.1093/Molbev/Mst082  0.818
2013 Shanku AG, McPeek MA, Kern AD. Functional Annotation and Comparative Analysis of a Zygopteran Transcriptome. G3 (Bethesda, Md.). PMID 23550132 DOI: 10.1534/G3.113.005637  0.787
2013 Duryea MC, Kern AD, Cox RM, Calsbeek R. A novel application of Approximate Bayesian Computation for detecting male reproductive advantages due to mating order Behavioral Ecology and Sociobiology. 67: 1867-1875. DOI: 10.1007/S00265-013-1612-8  0.301
2012 Kritsas K, Wuest SE, Hupalo D, Kern AD, Wicker T, Grossniklaus U. Computational analysis and characterization of UCE-like elements (ULEs) in plant genomes. Genome Research. 22: 2455-66. PMID 22987666 DOI: 10.1101/Gr.129346.111  0.82
2012 Langley CH, Stevens K, Cardeno C, Lee YC, Schrider DR, Pool JE, Langley SA, Suarez C, Corbett-Detig RB, Kolaczkowski B, Fang S, Nista PM, Holloway AK, Kern AD, Dewey CN, et al. Genomic variation in natural populations of Drosophila melanogaster. Genetics. 192: 533-98. PMID 22673804 DOI: 10.1534/Genetics.112.142018  0.836
2012 Kirkpatrick M, Kern A. Where's the money? Inversions, genes, and the hunt for genomic targets of selection. Genetics. 190: 1153-5. PMID 22491888 DOI: 10.1534/Genetics.112.139899  0.485
2011 Kolaczkowski B, Kern AD, Holloway AK, Begun DJ. Genomic differentiation between temperate and tropical Australian populations of Drosophila melanogaster. Genetics. 187: 245-60. PMID 21059887 DOI: 10.1534/Genetics.110.123059  0.836
2011 Kolaczkowski B, Hupalo DN, Kern AD. Recurrent adaptation in RNA interference genes across the Drosophila phylogeny. Molecular Biology and Evolution. 28: 1033-42. PMID 20971974 DOI: 10.1093/Molbev/Msq284  0.801
2010 Gasc A, Duryea MC, Cox RM, Kern A, Calsbeek R. Invasive predators deplete genetic diversity of island lizards. Plos One. 5: e12061. PMID 20706576 DOI: 10.1371/Journal.Pone.0012061  0.402
2010 Katzman S, Kern AD, Pollard KS, Salama SR, Haussler D. GC-biased evolution near human accelerated regions. Plos Genetics. 6: e1000960. PMID 20502635 DOI: 10.1371/Journal.Pgen.1000960  0.798
2010 Kern AD, Haussler D. A population genetic hidden Markov model for detecting genomic regions under selection. Molecular Biology and Evolution. 27: 1673-85. PMID 20185453 DOI: 10.1093/Molbev/Msq053  0.665
2009 Kern AD. Correcting the site frequency spectrum for divergence-based ascertainment. Plos One. 4: e5152. PMID 19370150 DOI: 10.1371/journal.pone.0005152  0.468
2008 Kern AD, Begun DJ. Recurrent deletion and gene presence/absence polymorphism: telomere dynamics dominate evolution at the tip of 3L in Drosophila melanogaster and D. simulans. Genetics. 179: 1021-7. PMID 18505885 DOI: 10.1534/genetics.107.078345  0.645
2007 Begun DJ, Holloway AK, Stevens K, Hillier LW, Poh YP, Hahn MW, Nista PM, Jones CD, Kern AD, Dewey CN, Pachter L, Myers E, Langley CH. Population genomics: whole-genome analysis of polymorphism and divergence in Drosophila simulans. Plos Biology. 5: e310. PMID 17988176 DOI: 10.1371/Journal.Pbio.0050310  0.847
2007 Katzman S, Kern AD, Bejerano G, Fewell G, Fulton L, Wilson RK, Salama SR, Haussler D. Human genome ultraconserved elements are ultraselected. Science (New York, N.Y.). 317: 915. PMID 17702936 DOI: 10.1126/Science.1142430  0.767
2007 Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, ... ... Kern AD, et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 447: 799-816. PMID 17571346 DOI: 10.1038/Nature05874  0.824
2007 Begun DJ, Lindfors HA, Kern AD, Jones CD. Evidence for de novo evolution of testis-expressed genes in the Drosophila yakuba/Drosophila erecta clade. Genetics. 176: 1131-7. PMID 17435230 DOI: 10.1534/genetics.106.069245  0.705
2007 Gibbs RA, Rogers J, Katze MG, Bumgarner R, Weinstock GM, Mardis ER, Remington KA, Strausberg RL, Venter JC, Wilson RK, Batzer MA, Bustamante CD, Eichler EE, Hahn MW, ... ... Kern AD, et al. Evolutionary and biomedical insights from the rhesus macaque genome. Science (New York, N.Y.). 316: 222-34. PMID 17431167 DOI: 10.1126/Science.1139247  0.834
2007 Giardine B, Riemer C, Hefferon T, Thomas D, Hsu F, Zielenski J, Sang Y, Elnitski L, Cutting G, Trumbower H, Kern A, Kuhn R, Patrinos GP, Hughes J, Higgs D, et al. PhenCode: connecting ENCODE data with mutations and phenotype. Human Mutation. 28: 554-62. PMID 17326095 DOI: 10.1002/Humu.20484  0.691
2007 Thomas DJ, Trumbower H, Kern AD, Rhead BL, Kuhn RM, Haussler D, Kent WJ. Variation resources at UC Santa Cruz. Nucleic Acids Research. 35: D716-20. PMID 17151077 DOI: 10.1093/Nar/Gkl953  0.759
2006 Pollard KS, Salama SR, King B, Kern AD, Dreszer T, Katzman S, Siepel A, Pedersen JS, Bejerano G, Baertsch R, Rosenbloom KR, Kent J, Haussler D. Forces shaping the fastest evolving regions in the human genome. Plos Genetics. 2: e168. PMID 17040131 DOI: 10.1371/Journal.Pgen.0020168  0.826
2006 Pollard KS, Salama SR, Lambert N, Lambot MA, Coppens S, Pedersen JS, Katzman S, King B, Onodera C, Siepel A, Kern AD, Dehay C, Igel H, Ares M, Vanderhaeghen P, et al. An RNA gene expressed during cortical development evolved rapidly in humans. Nature. 443: 167-72. PMID 16915236 DOI: 10.1038/Nature05113  0.794
2006 Levine MT, Jones CD, Kern AD, Lindfors HA, Begun DJ. Novel genes derived from noncoding DNA in Drosophila melanogaster are frequently X-linked and exhibit testis-biased expression. Proceedings of the National Academy of Sciences of the United States of America. 103: 9935-9. PMID 16777968 DOI: 10.1073/Pnas.0509809103  0.82
2005 Hahn MW, Mezey JG, Begun DJ, Gillespie JH, Kern AD, Langley CH, Moyle LC. Evolutionary genomics: codon bias and selection on single genomes. Nature. 433: E5-6; discussion E7-. PMID 15662370 DOI: 10.1038/Nature03221  0.801
2005 Hahn MW, Kern AD. Comparative genomics of centrality and essentiality in three eukaryotic protein-interaction networks. Molecular Biology and Evolution. 22: 803-6. PMID 15616139 DOI: 10.1093/molbev/msi072  0.511
2005 Kern AD, Begun DJ. Patterns of polymorphism and divergence from noncoding sequences of Drosophila melanogaster and D. simulans: evidence for nonequilibrium processes. Molecular Biology and Evolution. 22: 51-62. PMID 15456897 DOI: 10.1093/molbev/msh269  0.615
2004 Kern AD, Jones CD, Begun DJ. Molecular population genetics of male accessory gland proteins in the Drosophila simulans complex. Genetics. 167: 725-35. PMID 15238524 DOI: 10.1534/genetics.103.020883  0.741
2002 Kern AD, Jones CD, Begun DJ. Genomic effects of nucleotide substitutions in Drosophila simulans. Genetics. 162: 1753-61. PMID 12524346  0.721
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