| Year |
Citation |
Score |
| 2024 |
Smith CCR, Patterson G, Ralph PL, Kern AD. Estimation of spatial demographic maps from polymorphism data using a neural network. Molecular Ecology Resources. e14005. PMID 39152666 DOI: 10.1111/1755-0998.14005 |
0.558 |
|
| 2024 |
Chevy ET, Min J, Caudill V, Champer SE, Haller BC, Rehmann CT, Smith CCR, Tittes S, Messer PW, Kern AD, Ramachandran S, Ralph PL. Population genetics meets ecology: a guide to individual-based simulations in continuous landscapes. Biorxiv : the Preprint Server For Biology. PMID 39091875 DOI: 10.1101/2024.07.24.604988 |
0.539 |
|
| 2024 |
Smith CCR, Patterson G, Ralph PL, Kern AD. Estimation of spatial demographic maps from polymorphism data using a neural network. Biorxiv : the Preprint Server For Biology. PMID 38559192 DOI: 10.1101/2024.03.15.585300 |
0.557 |
|
| 2024 |
Buffalo V, Kern AD. A quantitative genetic model of background selection in humans. Plos Genetics. 20: e1011144. PMID 38507461 DOI: 10.1371/journal.pgen.1011144 |
0.82 |
|
| 2024 |
Coffing GC, Tittes S, Small ST, Songco-Casey JO, Piscopo DM, Pungor JR, Miller AC, Niell CM, Kern AD. Cephalopod Sex Determination and its Ancient Evolutionary Origin Revealed by Chromosome-level Assembly of the California Two-Spot Octopus. Biorxiv : the Preprint Server For Biology. PMID 38463997 DOI: 10.1101/2024.02.21.581452 |
0.773 |
|
| 2024 |
Rodrigues MF, Kern AD, Ralph PL. Shared evolutionary processes shape landscapes of genomic variation in the great apes. Genetics. PMID 38242701 DOI: 10.1093/genetics/iyae006 |
0.787 |
|
| 2024 |
Rehmann CT, Ralph PL, Kern AD. Evaluating evidence for co-geography in the Anopheles-Plasmodium host-parasite system. G3 (Bethesda, Md.). PMID 38230808 DOI: 10.1093/g3journal/jkae008 |
0.782 |
|
| 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 |
0.788 |
|
| 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 |
0.796 |
|
| 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 |
0.57 |
|
| 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 |
0.418 |
|
| 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 |
0.794 |
|
| 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 |
0.769 |
|
| 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 |
0.714 |
|
| 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 |
0.528 |
|
| 2021 |
Battey CJ, Coffing GC, Kern AD. Visualizing population structure with variational autoencoders. G3 (Bethesda, Md.). 11. PMID 33561250 DOI: 10.1093/g3journal/jkaa036 |
0.782 |
|
| 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 |
0.834 |
|
| 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 |
0.803 |
|
| 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 |
0.835 |
|
| 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 |
0.827 |
|
| 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 |
0.839 |
|
| 2018 |
Kern AD, Hahn MW. The neutral theory in light of natural selection. Molecular Biology and Evolution. PMID 29722831 DOI: 10.1093/molbev/msy092 |
0.532 |
|
| 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 |
0.767 |
|
| 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 |
0.77 |
|
| 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 |
0.763 |
|
| 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 |
0.753 |
|
| 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 |
0.807 |
|
| 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 |
0.474 |
|
| 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 |
0.413 |
|
| 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 |
0.744 |
|
| 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 |
0.813 |
|
| 2016 |
Kern AD, Schrider DR. discoal: flexible coalescent simulations with selection. Bioinformatics (Oxford, England). PMID 27559153 DOI: 10.1093/Bioinformatics/Btw556 |
0.711 |
|
| 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 |
0.751 |
|
| 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 |
0.753 |
|
| 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 |
0.772 |
|
| 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 |
0.766 |
|
| 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 |
0.801 |
|
| 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 |
0.816 |
|
| 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 |
0.786 |
|
| 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 |
0.785 |
|
| 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 |
0.836 |
|
| 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 |
0.797 |
|
| 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 |
0.31 |
|
| 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 |
0.8 |
|
| 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 |
0.837 |
|
| 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 |
0.469 |
|
| 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 |
0.835 |
|
| 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 |
0.802 |
|
| 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 |
0.411 |
|
| 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 |
0.791 |
|
| 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 |
0.653 |
|
| 2009 |
Kern AD. Correcting the site frequency spectrum for divergence-based ascertainment. Plos One. 4: e5152. PMID 19370150 DOI: 10.1371/journal.pone.0005152 |
0.459 |
|
| 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 |
0.639 |
|
| 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 |
0.845 |
|
| 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 |
0.753 |
|
| 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 |
0.82 |
|
| 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 |
0.699 |
|
| 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 |
0.833 |
|
| 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 |
0.681 |
|
| 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 |
0.748 |
|
| 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 |
0.823 |
|
| 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 |
0.818 |
|
| 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 |
0.793 |
|
| 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 |
0.508 |
|
| 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 |
0.609 |
|
| 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 |
0.738 |
|
| 2002 |
Kern AD, Jones CD, Begun DJ. Genomic effects of nucleotide substitutions in Drosophila simulans. Genetics. 162: 1753-61. PMID 12524346 |
0.714 |
|
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