Daniel R. Schrider, Ph.D. - Publications

Biology|Informatics and Computing Indiana University, Bloomington, Bloomington, IN, United States 
Evolutionary Genetics

45 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 Booker WW, Schrider DR. The genetic consequences of range expansion and its influence on diploidization in polyploids. Biorxiv : the Preprint Server For Biology. PMID 37905020 DOI: 10.1101/2023.10.18.562992  0.336
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, ... ... Schrider DR, et al. Expanding the stdpopsim species catalog, and lessons learned for realistic genome simulations. Elife. 12. PMID 37342968 DOI: 10.7554/eLife.84874  0.763
2023 Whitehouse LS, Schrider DR. Timesweeper: Accurately Identifying Selective Sweeps Using Population Genomic Time Series. Genetics. PMID 37157914 DOI: 10.1093/genetics/iyad084  0.491
2023 Booker WW, Ray DD, Schrider DR. This population does not exist: learning the distribution of evolutionary histories with generative adversarial networks. Genetics. PMID 37067864 DOI: 10.1093/genetics/iyad063  0.383
2023 Love RR, Sikder JR, Vivero RJ, Matute DR, Schrider DR. Strong positive selection in Aedes aegypti and the rapid evolution of insecticide resistance. Molecular Biology and Evolution. PMID 36971242 DOI: 10.1093/molbev/msad072  0.692
2023 Hamid I, Korunes KL, Schrider DR, Goldberg A. Localizing post-admixture adaptive variants with object detection on ancestry-painted chromosomes. Molecular Biology and Evolution. PMID 36947126 DOI: 10.1093/molbev/msad074  0.505
2023 Ray DD, Flagel L, Schrider DR. IntroUNET: identifying introgressed alleles via semantic segmentation. Biorxiv : the Preprint Server For Biology. PMID 36865105 DOI: 10.1101/2023.02.07.527435  0.475
2022 Sun Q, Yang Y, Rosen JD, Jiang MZ, Chen J, Liu W, Wen J, Raffield LM, Pace RG, Zhou YH, Wright FA, Blackman SM, Bamshad MJ, Gibson RL, Cutting GR, ... ... Schrider DR, et al. MagicalRsq: Machine-learning-based genotype imputation quality calibration. American Journal of Human Genetics. PMID 36198314 DOI: 10.1016/j.ajhg.2022.09.009  0.366
2022 Locke DP, Hillier LW, Warren WC, Worley KC, Nazareth LV, Muzny DM, Yang SP, Wang Z, Chinwalla AT, Minx P, Mitreva M, Cook L, Delehaunty KD, Fronick C, Schmidt H, ... ... Schrider DR, et al. Author Correction: Comparative and demographic analysis of orang-utan genomes. Nature. PMID 35962045 DOI: 10.1038/s41586-022-04799-7  0.673
2021 Suvorov A, Kim BY, Wang J, Armstrong EE, Peede D, D'Agostino ERR, Price DK, Waddell P, Lang M, Courtier-Orgogozo V, David JR, Petrov D, Matute DR, Schrider DR, Comeault AA. Widespread introgression across a phylogeny of 155 Drosophila genomes. Current Biology : Cb. PMID 34788634 DOI: 10.1016/j.cub.2021.10.052  0.821
2021 Suvorov A, Scornavacca C, Fujimoto MS, Bodily P, Clement M, Crandall KA, Whiting MF, Schrider DR, Bybee SM. Deep ancestral introgression shapes evolutionary history of dragonflies and damselflies. Systematic Biology. PMID 34324671 DOI: 10.1093/sysbio/syab063  0.778
2020 Schrider DR. Background Selection Does Not Mimic the Patterns of Genetic Diversity Produced by Selective Sweeps. Genetics. 216: 499-519. PMID 33954603 DOI: 10.1534/genetics.120.303469  0.404
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  0.825
2020 Schrider DR. Background Selection Does Not Mimic the Patterns of Genetic Diversity Produced by Selective Sweeps. Genetics. PMID 32847814 DOI: 10.1534/genetics.120.303469  0.4
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, ... ... Schrider DR, et al. A community-maintained standard library of population genetic models. Elife. 9. PMID 32573438 DOI: 10.7554/Elife.54967  0.797
2019 Suvorov A, Hochuli J, Schrider DR. Accurate inference of tree topologies from multiple sequence alignments using deep learning. Systematic Biology. PMID 31504938 DOI: 10.1093/Sysbio/Syz060  0.723
2018 Flagel L, Brandvain Y, Schrider DR. The Unreasonable Effectiveness of Convolutional Neural Networks in Population Genetic Inference. Molecular Biology and Evolution. PMID 30517664 DOI: 10.1093/Molbev/Msy224  0.464
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  0.749
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  0.819
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  0.76
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  0.748
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  0.79
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  0.725
2017 Adrion JR, Song MJ, Schrider DR, Hahn MW, Schaack S. Genome-wide estimates of transposable element insertion and deletion rates in Drosophila melanogaster. Genome Biology and Evolution. PMID 28338986 DOI: 10.1093/Gbe/Evx050  0.795
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  0.774
2016 Kern AD, Schrider DR. discoal: flexible coalescent simulations with selection. Bioinformatics (Oxford, England). PMID 27559153 DOI: 10.1093/Bioinformatics/Btw556  0.697
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  0.744
2016 Schrider DR, Hahn MW, Begun DJ. Parallel evolution of copy-number variation across continents in Drosophila melanogaster. Molecular Biology and Evolution. PMID 26809315 DOI: 10.1093/Molbev/Msw014  0.753
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  0.736
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  0.755
2015 Keith N, Tucker AE, Jackson CE, Sung W, Lledó JI, Schrider DR, Schaack S, Dudycha JL, Ackerman MS, Younge AJ, Shaw JR, Lynch M. High mutational rates of large-scale duplication and deletion in Daphnia pulex. Genome Research. PMID 26518480 DOI: 10.1101/Gr.191338.115  0.466
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  0.792
2014 Denton JF, Lugo-Martinez J, Tucker AE, Schrider DR, Warren WC, Hahn MW. Extensive error in the number of genes inferred from draft genome assemblies. Plos Computational Biology. 10: e1003998. PMID 25474019 DOI: 10.1371/Journal.Pcbi.1003998  0.636
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  0.766
2013 Schrider DR, Houle D, Lynch M, Hahn MW. Rates and genomic consequences of spontaneous mutational events in Drosophila melanogaster. Genetics. 194: 937-54. PMID 23733788 DOI: 10.1534/Genetics.113.151670  0.593
2013 Schrider DR, Begun DJ, Hahn MW. Detecting highly differentiated copy-number variants from pooled population sequencing. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 344-55. PMID 23424139  0.717
2013 Schrider DR, Navarro FC, Galante PA, Parmigiani RB, Camargo AA, Hahn MW, de Souza SJ. Gene copy-number polymorphism caused by retrotransposition in humans. Plos Genetics. 9: e1003242. PMID 23359205 DOI: 10.1371/Journal.Pgen.1003242  0.652
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  0.825
2011 Schrider DR, Stevens K, Cardeño CM, Langley CH, Hahn MW. Genome-wide analysis of retrogene polymorphisms in Drosophila melanogaster. Genome Research. 21: 2087-95. PMID 22135405 DOI: 10.1101/Gr.116434.110  0.644
2011 Schrider DR, Gout JF, Hahn MW. Very few RNA and DNA sequence differences in the human transcriptome. Plos One. 6: e25842. PMID 22022455 DOI: 10.1371/Journal.Pone.0025842  0.541
2011 Schrider DR, Hourmozdi JN, Hahn MW. Pervasive multinucleotide mutational events in eukaryotes. Current Biology : Cb. 21: 1051-4. PMID 21636278 DOI: 10.1016/J.Cub.2011.05.013  0.548
2011 Locke DP, Hillier LW, Warren WC, Worley KC, Nazareth LV, Muzny DM, Yang SP, Wang Z, Chinwalla AT, Minx P, Mitreva M, Cook L, Delehaunty KD, Fronick C, Schmidt H, ... ... Schrider DR, et al. Comparative and demographic analysis of orang-utan genomes. Nature. 469: 529-33. PMID 21270892 DOI: 10.1038/Nature09687  0.767
2010 Schrider DR, Hahn MW. Gene copy-number polymorphism in nature. Proceedings. Biological Sciences / the Royal Society. 277: 3213-21. PMID 20591863 DOI: 10.1098/Rspb.2010.1180  0.652
2010 Schrider DR, Hahn MW. Lower linkage disequilibrium at CNVs is due to both recurrent mutation and transposing duplications. Molecular Biology and Evolution. 27: 103-11. PMID 19745000 DOI: 10.1093/Molbev/Msp210  0.594
2009 Schrider DR, Costello JC, Hahn MW. All human-specific gene losses are present in the genome as pseudogenes. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 16: 1419-27. PMID 19754271 DOI: 10.1089/Cmb.2009.0085  0.578
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