Publications by authors named "Daniel R Schrider"

32Publications

Discovery of ongoing selective sweeps within Anopheles mosquito populations using deep learning.

Mol Biol Evol 2020 Oct 6. Epub 2020 Oct 6.

Institute of Ecology and Evolution, 5289 University of Oregon, Onyx Bridge 272, Eugene, OR.

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http://dx.doi.org/10.1093/molbev/msaa259DOI Listing
October 2020

Background Selection Does Not Mimic the Patterns of Genetic Diversity Produced by Selective Sweeps.

Genetics 2020 Oct 26;216(2):499-519. Epub 2020 Aug 26.

Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27514

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http://dx.doi.org/10.1534/genetics.120.303469DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7536861PMC
October 2020

Accurate Inference of Tree Topologies from Multiple Sequence Alignments Using Deep Learning.

Syst Biol 2020 03;69(2):221-233

Biological and Biomedical Sciences Program, University of North Carolina at Chapel Hill, 130 Mason Farm Road, UNC-Chapel Hill Chapel Hill, NC 27599-7264, USA.

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http://dx.doi.org/10.1093/sysbio/syz060DOI Listing
March 2020

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

Mol Biol Evol 2019 02;36(2):220-238

Department of Genetics, University of North Carolina, Chapel Hill, NC.

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http://dx.doi.org/10.1093/molbev/msy224DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6367976PMC
February 2019

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

Proc Natl Acad Sci U S A 2018 05 23;115(19):5028-5033. Epub 2018 Apr 23.

Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO 80523.

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http://dx.doi.org/10.1073/pnas.1719998115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5948977PMC
May 2018

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

PLoS Genet 2018 04 23;14(4):e1007341. Epub 2018 Apr 23.

Department of Genetics, Rutgers University, Piscataway, New Jersey, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1007341DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5933812PMC
April 2018

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

G3 (Bethesda) 2018 05 31;8(6):1959-1970. Epub 2018 May 31.

Department of Genetics, Rutgers University, Piscataway, NJ 08854.

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http://dx.doi.org/10.1534/g3.118.200262DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5982824PMC
May 2018

Supervised Machine Learning for Population Genetics: A New Paradigm.

Trends Genet 2018 04 10;34(4):301-312. Epub 2018 Jan 10.

Department of Genetics, and Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08554, USA. Electronic address:

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http://dx.doi.org/10.1016/j.tig.2017.12.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5905713PMC
April 2018

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

Mol Biol Evol 2017 08;34(8):1863-1877

Department of Genetics, Rutgers University, Piscataway, NJ.

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http://dx.doi.org/10.1093/molbev/msx154DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5850737PMC
August 2017

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

Genetics 2016 11 7;204(3):1207-1223. Epub 2016 Sep 7.

Department of Genetics, Rutgers University, Piscataway, New Jersey 08854.

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http://dx.doi.org/10.1534/genetics.116.190223DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5105852PMC
November 2016

Discoal: flexible coalescent simulations with selection.

Bioinformatics 2016 12 24;32(24):3839-3841. Epub 2016 Aug 24.

Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08554, USA.

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http://dx.doi.org/10.1093/bioinformatics/btw556DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5167068PMC
December 2016

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

PLoS Genet 2016 Mar 15;12(3):e1005928. Epub 2016 Mar 15.

Department of Genetics, Rutgers University, Piscataway, New Jersey, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1005928DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4792382PMC
March 2016

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

Mol Biol Evol 2016 05 25;33(5):1308-16. Epub 2016 Jan 25.

Department of Evolution and Ecology, University of California, Davis.

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http://dx.doi.org/10.1093/molbev/msw014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4909135PMC
May 2016

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

G3 (Bethesda) 2016 04 7;6(4):793-803. Epub 2016 Apr 7.

Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, Colorado 80523.

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http://g3journal.org/lookup/doi/10.1534/g3.115.021279
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http://dx.doi.org/10.1534/g3.115.021279DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4825650PMC
April 2016

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

Genome Biol Evol 2015 Nov 19;7(12):3511-28. Epub 2015 Nov 19.

Department of Genetics, Rutgers University, Piscataway Human Genetics Institute of New Jersey, Piscataway, New Jersey.

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http://dx.doi.org/10.1093/gbe/evv228DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4700959PMC
November 2015

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

Genetics 2015 May 25;200(1):267-84. Epub 2015 Feb 25.

Department of Genetics, Rutgers University, Piscataway, New Jersey 08854 Human Genetics Institute of New Jersey, Piscataway, New Jersey 08854.

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http://www.genetics.org/cgi/doi/10.1534/genetics.115.174912
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http://dx.doi.org/10.1534/genetics.115.174912DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4423368PMC
May 2015

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

PLoS Comput Biol 2014 Dec 4;10(12):e1003998. Epub 2014 Dec 4.

School of Informatics and Computing, Indiana University, Bloomington, Indiana; Department of Biology, Indiana University, Bloomington, Indiana.

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http://dx.doi.org/10.1371/journal.pcbi.1003998DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4256071PMC
December 2014

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

Genome Biol Evol 2014 Jun 9;6(7):1542-8. Epub 2014 Jun 9.

Department of Genetics, Rutgers, The State University of New Jersey.

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http://dx.doi.org/10.1093/gbe/evu116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4122919PMC
June 2014

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

Genetics 2013 Aug 3;194(4):937-54. Epub 2013 Jun 3.

Department of Biology, Indiana University, Bloomington, IN 47405, USA.

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http://dx.doi.org/10.1534/genetics.113.151670DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3730921PMC
August 2013

Detecting highly differentiated copy-number variants from pooled population sequencing.

Pac Symp Biocomput 2013 :344-55

Department of Biology and School of Informatics and Computing, Indiana University, 1001 E Third St., Bloomington, IN 47405, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3587772PMC
December 2013

Genome-wide analysis of retrogene polymorphisms in Drosophila melanogaster.

Genome Res 2011 Dec;21(12):2087-95

Department of Biology, Indiana University, Bloomington, Indiana 47405, USA.

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http://dx.doi.org/10.1101/gr.116434.110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3227099PMC
December 2011

Pervasive multinucleotide mutational events in eukaryotes.

Curr Biol 2011 Jun;21(12):1051-4

Department of Biology, Indiana University Bloomington, Bloomington, IN 47405, USA.

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http://dx.doi.org/10.1016/j.cub.2011.05.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4744473PMC
June 2011

Comparative and demographic analysis of orang-utan genomes.

Authors:
Devin P Locke LaDeana W Hillier Wesley C Warren Kim C Worley Lynne V Nazareth Donna M Muzny Shiaw-Pyng Yang Zhengyuan Wang Asif T Chinwalla Pat Minx Makedonka Mitreva Lisa Cook Kim D Delehaunty Catrina Fronick Heather Schmidt Lucinda A Fulton Robert S Fulton Joanne O Nelson Vincent Magrini Craig Pohl Tina A Graves Chris Markovic Andy Cree Huyen H Dinh Jennifer Hume Christie L Kovar Gerald R Fowler Gerton Lunter Stephen Meader Andreas Heger Chris P Ponting Tomas Marques-Bonet Can Alkan Lin Chen Ze Cheng Jeffrey M Kidd Evan E Eichler Simon White Stephen Searle Albert J Vilella Yuan Chen Paul Flicek Jian Ma Brian Raney Bernard Suh Richard Burhans Javier Herrero David Haussler Rui Faria Olga Fernando Fleur Darré Domènec Farré Elodie Gazave Meritxell Oliva Arcadi Navarro Roberta Roberto Oronzo Capozzi Nicoletta Archidiacono Giuliano Della Valle Stefania Purgato Mariano Rocchi Miriam K Konkel Jerilyn A Walker Brygg Ullmer Mark A Batzer Arian F A Smit Robert Hubley Claudio Casola Daniel R Schrider Matthew W Hahn Victor Quesada Xose S Puente Gonzalo R Ordoñez Carlos López-Otín Tomas Vinar Brona Brejova Aakrosh Ratan Robert S Harris Webb Miller Carolin Kosiol Heather A Lawson Vikas Taliwal André L Martins Adam Siepel Arindam Roychoudhury Xin Ma Jeremiah Degenhardt Carlos D Bustamante Ryan N Gutenkunst Thomas Mailund Julien Y Dutheil Asger Hobolth Mikkel H Schierup Oliver A Ryder Yuko Yoshinaga Pieter J de Jong George M Weinstock Jeffrey Rogers Elaine R Mardis Richard A Gibbs Richard K Wilson

Nature 2011 Jan;469(7331):529-33

The Genome Center at Washington University, Washington University School of Medicine, 4444 Forest Park Avenue, Saint Louis, Missouri 63108, USA.

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http://dx.doi.org/10.1038/nature09687DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3060778PMC
January 2011

Gene copy-number polymorphism in nature.

Proc Biol Sci 2010 Nov 30;277(1698):3213-21. Epub 2010 Jun 30.

Department of Biology and School of Informatics and Computing, Indiana University, Bloomington, IN 47405, USA.

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http://dx.doi.org/10.1098/rspb.2010.1180DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2981937PMC
November 2010

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

J Comput Biol 2009 Oct;16(10):1419-27

Department of Biology and School of Informatics and Computing, Indiana University, Bloomington, IN 47405, USA.

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http://dx.doi.org/10.1089/cmb.2009.0085DOI Listing
October 2009

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

Mol Biol Evol 2010 Jan;27(1):103-11

Department of Biology, Indiana University, Bloomington, IN, USA.

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http://dx.doi.org/10.1093/molbev/msp210DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2877554PMC
January 2010