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Items: 29


Accurate inference of tree topologies from multiple sequence alignments using deep learning.

Suvorov A, Hochuli J, Schrider DR.

Syst Biol. 2019 Sep 3. pii: syz060. doi: 10.1093/sysbio/syz060. [Epub ahead of print]


The Unreasonable Effectiveness of Convolutional Neural Networks in Population Genetic Inference.

Flagel L, Brandvain Y, Schrider DR.

Mol Biol Evol. 2019 Feb 1;36(2):220-238. doi: 10.1093/molbev/msy224.


Combining population genomics and fitness QTLs to identify the genetics of local adaptation in Arabidopsis thaliana.

Price N, Moyers BT, Lopez L, Lasky JR, Monroe JG, Mullen JL, Oakley CG, Lin J, Ågren J, Schrider DR, Kern AD, McKay JK.

Proc Natl Acad Sci U S A. 2018 May 8;115(19):5028-5033. doi: 10.1073/pnas.1719998115. Epub 2018 Apr 23.


Supervised machine learning reveals introgressed loci in the genomes of Drosophila simulans and D. sechellia.

Schrider DR, Ayroles J, Matute DR, Kern AD.

PLoS Genet. 2018 Apr 23;14(4):e1007341. doi: 10.1371/journal.pgen.1007341. eCollection 2018 Apr.


diploS/HIC: An Updated Approach to Classifying Selective Sweeps.

Kern AD, Schrider DR.

G3 (Bethesda). 2018 May 31;8(6):1959-1970. doi: 10.1534/g3.118.200262.


Supervised Machine Learning for Population Genetics: A New Paradigm.

Schrider DR, Kern AD.

Trends Genet. 2018 Apr;34(4):301-312. doi: 10.1016/j.tig.2017.12.005. Epub 2018 Jan 10. Review.


Soft Sweeps Are the Dominant Mode of Adaptation in the Human Genome.

Schrider DR, Kern AD.

Mol Biol Evol. 2017 Aug 1;34(8):1863-1877. doi: 10.1093/molbev/msx154.


Genome-Wide Estimates of Transposable Element Insertion and Deletion Rates in Drosophila Melanogaster.

Adrion JR, Song MJ, Schrider DR, Hahn MW, Schaack S.

Genome Biol Evol. 2017 May 1;9(5):1329-1340. doi: 10.1093/gbe/evx050.


Effects of Linked Selective Sweeps on Demographic Inference and Model Selection.

Schrider DR, Shanku AG, Kern AD.

Genetics. 2016 Nov;204(3):1207-1223. doi: 10.1534/genetics.116.190223. Epub 2016 Sep 7.


Discoal: flexible coalescent simulations with selection.

Kern AD, Schrider DR.

Bioinformatics. 2016 Dec 15;32(24):3839-3841. Epub 2016 Aug 24.


S/HIC: Robust Identification of Soft and Hard Sweeps Using Machine Learning.

Schrider DR, Kern AD.

PLoS Genet. 2016 Mar 15;12(3):e1005928. doi: 10.1371/journal.pgen.1005928. eCollection 2016 Mar.


Parallel Evolution of Copy-Number Variation across Continents in Drosophila melanogaster.

Schrider DR, Hahn MW, Begun DJ.

Mol Biol Evol. 2016 May;33(5):1308-16. doi: 10.1093/molbev/msw014. Epub 2016 Jan 25.


Identification of Polymorphisms Associated with Drought Adaptation QTL in Brassica napus by Resequencing.

Fletcher RS, Herrmann D, Mullen JL, Li Q, Schrider DR, Price N, Lin J, Grogan K, Kern A, McKay JK.

G3 (Bethesda). 2016 Apr 7;6(4):793-803. doi: 10.1534/g3.115.021279.


Inferring Selective Constraint from Population Genomic Data Suggests Recent Regulatory Turnover in the Human Brain.

Schrider DR, Kern AD.

Genome Biol Evol. 2015 Nov 19;7(12):3511-28. doi: 10.1093/gbe/evv228.


High mutational rates of large-scale duplication and deletion in Daphnia pulex.

Keith N, Tucker AE, Jackson CE, Sung W, Lucas Lledó JI, Schrider DR, Schaack S, Dudycha JL, Ackerman M, Younge AJ, Shaw JR, Lynch M.

Genome Res. 2016 Jan;26(1):60-9. doi: 10.1101/gr.191338.115. Epub 2015 Oct 30.


Soft shoulders ahead: spurious signatures of soft and partial selective sweeps result from linked hard sweeps.

Schrider DR, Mendes FK, Hahn MW, Kern AD.

Genetics. 2015 May;200(1):267-84. doi: 10.1534/genetics.115.174912. Epub 2015 Feb 25.


Extensive error in the number of genes inferred from draft genome assemblies.

Denton JF, Lugo-Martinez J, Tucker AE, Schrider DR, Warren WC, Hahn MW.

PLoS Comput Biol. 2014 Dec 4;10(12):e1003998. doi: 10.1371/journal.pcbi.1003998. eCollection 2014 Dec.


Discovering functional DNA elements using population genomic information: a proof of concept using human mtDNA.

Schrider DR, Kern AD.

Genome Biol Evol. 2014 Jun 9;6(7):1542-8. doi: 10.1093/gbe/evu116.


Rates and genomic consequences of spontaneous mutational events in Drosophila melanogaster.

Schrider DR, Houle D, Lynch M, Hahn MW.

Genetics. 2013 Aug;194(4):937-54. doi: 10.1534/genetics.113.151670. Epub 2013 Jun 3.


Gene copy-number polymorphism caused by retrotransposition in humans.

Schrider DR, Navarro FC, Galante PA, Parmigiani RB, Camargo AA, Hahn MW, de Souza SJ.

PLoS Genet. 2013;9(1):e1003242. doi: 10.1371/journal.pgen.1003242. Epub 2013 Jan 24.


Genomic variation in natural populations of Drosophila melanogaster.

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, Song YS, Hahn MW, Begun DJ.

Genetics. 2012 Oct;192(2):533-98. doi: 10.1534/genetics.112.142018. Epub 2012 Jun 5.


Genome-wide analysis of retrogene polymorphisms in Drosophila melanogaster.

Schrider DR, Stevens K, Cardeño CM, Langley CH, Hahn MW.

Genome Res. 2011 Dec;21(12):2087-95. doi: 10.1101/gr.116434.110.


Very few RNA and DNA sequence differences in the human transcriptome.

Schrider DR, Gout JF, Hahn MW.

PLoS One. 2011;6(10):e25842. doi: 10.1371/journal.pone.0025842. Epub 2011 Oct 12.


Pervasive multinucleotide mutational events in eukaryotes.

Schrider DR, Hourmozdi JN, Hahn MW.

Curr Biol. 2011 Jun 21;21(12):1051-4. doi: 10.1016/j.cub.2011.05.013.


Comparative and demographic analysis of orang-utan genomes.

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, Fulton LA, Fulton RS, Nelson JO, Magrini V, Pohl C, Graves TA, Markovic C, Cree A, Dinh HH, Hume J, Kovar CL, Fowler GR, Lunter G, Meader S, Heger A, Ponting CP, Marques-Bonet T, Alkan C, Chen L, Cheng Z, Kidd JM, Eichler EE, White S, Searle S, Vilella AJ, Chen Y, Flicek P, Ma J, Raney B, Suh B, Burhans R, Herrero J, Haussler D, Faria R, Fernando O, Darré F, Farré D, Gazave E, Oliva M, Navarro A, Roberto R, Capozzi O, Archidiacono N, Della Valle G, Purgato S, Rocchi M, Konkel MK, Walker JA, Ullmer B, Batzer MA, Smit AF, Hubley R, Casola C, Schrider DR, Hahn MW, Quesada V, Puente XS, Ordoñez GR, López-Otín C, Vinar T, Brejova B, Ratan A, Harris RS, Miller W, Kosiol C, Lawson HA, Taliwal V, Martins AL, Siepel A, Roychoudhury A, Ma X, Degenhardt J, Bustamante CD, Gutenkunst RN, Mailund T, Dutheil JY, Hobolth A, Schierup MH, Ryder OA, Yoshinaga Y, de Jong PJ, Weinstock GM, Rogers J, Mardis ER, Gibbs RA, Wilson RK.

Nature. 2011 Jan 27;469(7331):529-33. doi: 10.1038/nature09687.


Gene copy-number polymorphism in nature.

Schrider DR, Hahn MW.

Proc Biol Sci. 2010 Nov 7;277(1698):3213-21. doi: 10.1098/rspb.2010.1180. Epub 2010 Jun 30. Review.


All human-specific gene losses are present in the genome as pseudogenes.

Schrider DR, Costello JC, Hahn MW.

J Comput Biol. 2009 Oct;16(10):1419-27. doi: 10.1089/cmb.2009.0085.


Lower linkage disequilibrium at CNVs is due to both recurrent mutation and transposing duplications.

Schrider DR, Hahn MW.

Mol Biol Evol. 2010 Jan;27(1):103-11. doi: 10.1093/molbev/msp210.

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