Publications by authors named "Andrew D Kern"

49Publications

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

Predicting geographic location from genetic variation with deep neural networks.

Elife 2020 Jun 8;9. Epub 2020 Jun 8.

University of Oregon, Institute of Ecology and Evolution, Eugene, United States.

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http://dx.doi.org/10.7554/eLife.54507DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7324158PMC
June 2020

Space is the Place: Effects of Continuous Spatial Structure on Analysis of Population Genetic Data.

Genetics 2020 05 24;215(1):193-214. Epub 2020 Mar 24.

Institute of Ecology Evolution, Department of Biology, University of Oregon, Eugene, Oregon.

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http://dx.doi.org/10.1534/genetics.120.303143DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7198281PMC
May 2020

Predicting the Landscape of Recombination Using Deep Learning.

Mol Biol Evol 2020 06;37(6):1790-1808

Institute of Ecology and Evolution, University of Oregon, Eugene, OR.

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http://dx.doi.org/10.1093/molbev/msaa038DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7253213PMC
June 2020

The Neutral Theory in Light of Natural Selection.

Mol Biol Evol 2018 06;35(6):1366-1371

Department of Biology and Department of Computer Science, Indiana University Bloomington, IN.

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http://dx.doi.org/10.1093/molbev/msy092DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5967545PMC
June 2018

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

The Effect of Common Inversion Polymorphisms and on Patterns of Transcriptional Variation in .

G3 (Bethesda) 2017 11 6;7(11):3659-3668. Epub 2017 Nov 6.

Department of Genetics, Rutgers University, Piscataway, New Jersey 08901.

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http://dx.doi.org/10.1534/g3.117.1133DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5677173PMC
November 2017

Exact Calculation of the Joint Allele Frequency Spectrum for Isolation with Migration Models.

Genetics 2017 09 10;207(1):241-253. Epub 2017 Jul 10.

Department of Biology, Temple University, Philadelphia, Pennsylvania 19122.

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http://www.genetics.org/lookup/doi/10.1534/genetics.116.1940
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http://dx.doi.org/10.1534/genetics.116.194019DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5586375PMC
September 2017

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

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

Myristoylated CIL-7 regulates ciliary extracellular vesicle biogenesis.

Mol Biol Cell 2015 Aug 3;26(15):2823-32. Epub 2015 Jun 3.

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

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http://dx.doi.org/10.1091/mbc.E15-01-0009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4571341PMC
August 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

The role of DNA insertions in phenotypic differentiation between humans and other primates.

Genome Biol Evol 2015 Jan 28;7(4):1168-78. Epub 2015 Jan 28.

Department of Genetics, Nelson Biolabs, Piscataway, NJ, USA.

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http://dx.doi.org/10.1093/gbe/evv012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4419785PMC
January 2015

Highly constrained intergenic Drosophila ultraconserved elements are candidate ncRNAs.

Genome Biol Evol 2015 Jan 23;7(3):689-98. Epub 2015 Jan 23.

Department of Biology, Dartmouth College, Hanover, New Hampshire.

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http://dx.doi.org/10.1093/gbe/evv011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5322558PMC
January 2015

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

Parallel geographic variation in Drosophila melanogaster.

Genetics 2014 May 7;197(1):361-73. Epub 2014 Mar 7.

Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599.

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http://dx.doi.org/10.1534/genetics.114.161463DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4012493PMC
May 2014

Conservation and functional element discovery in 20 angiosperm plant genomes.

Mol Biol Evol 2013 Jul 2;30(7):1729-44. Epub 2013 May 2.

Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire, USA.

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http://dx.doi.org/10.1093/molbev/mst082DOI Listing
July 2013

Functional Annotation and Comparative Analysis of a Zygopteran Transcriptome.

G3 (Bethesda) 2013 04 9;3(4):763-770. Epub 2013 Apr 9.

Rutgers, The State University of New Jersey, Department of Genetics, Piscataway, New Jersey 08854-8082.

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http://dx.doi.org/10.1534/g3.113.005637DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3618363PMC
April 2013

Computational analysis and characterization of UCE-like elements (ULEs) in plant genomes.

Genome Res 2012 Dec 17;22(12):2455-66. Epub 2012 Sep 17.

Institute of Plant Biology & Zürich-Basel Plant Science Center, University Zürich, CH-8008 Zürich, Switzerland.

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http://dx.doi.org/10.1101/gr.129346.111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3514675PMC
December 2012

Recurrent adaptation in RNA interference genes across the Drosophila phylogeny.

Mol Biol Evol 2011 Feb 22;28(2):1033-42. Epub 2010 Oct 22.

Department of Biological Sciences, Dartmouth College, NH, USA.

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http://dx.doi.org/10.1093/molbev/msq284DOI Listing
February 2011

GC-biased evolution near human accelerated regions.

PLoS Genet 2010 May 20;6(5):e1000960. Epub 2010 May 20.

Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1000960DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2873926PMC
May 2010

A population genetic hidden Markov model for detecting genomic regions under selection.

Mol Biol Evol 2010 Jul 25;27(7):1673-85. Epub 2010 Feb 25.

Department of Biological Sciences, Dartmouth College, Hanover, NH, USA.

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http://dx.doi.org/10.1093/molbev/msq053DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2912474PMC
July 2010

Correcting the site frequency spectrum for divergence-based ascertainment.

Authors:
Andrew D Kern

PLoS One 2009 16;4(4):e5152. Epub 2009 Apr 16.

Department of Biological Sciences, Dartmouth College, Hanover, NH, USA.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0005152PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2666160PMC
July 2009

Recurrent deletion and gene presence/absence polymorphism: telomere dynamics dominate evolution at the tip of 3L in Drosophila melanogaster and D. simulans.

Genetics 2008 Jun 27;179(2):1021-7. Epub 2008 May 27.

Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California 95060, USA.

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http://dx.doi.org/10.1534/genetics.107.078345DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2429855PMC
June 2008

Human genome ultraconserved elements are ultraselected.

Science 2007 Aug;317(5840):915

Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, USA.

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http://dx.doi.org/10.1126/science.1142430DOI Listing
August 2007

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

Authors:
Ewan Birney John A Stamatoyannopoulos Anindya Dutta Roderic Guigó Thomas R Gingeras Elliott H Margulies Zhiping Weng Michael Snyder Emmanouil T Dermitzakis Robert E Thurman Michael S Kuehn Christopher M Taylor Shane Neph Christoph M Koch Saurabh Asthana Ankit Malhotra Ivan Adzhubei Jason A Greenbaum Robert M Andrews Paul Flicek Patrick J Boyle Hua Cao Nigel P Carter Gayle K Clelland Sean Davis Nathan Day Pawandeep Dhami Shane C Dillon Michael O Dorschner Heike Fiegler Paul G Giresi Jeff Goldy Michael Hawrylycz Andrew Haydock Richard Humbert Keith D James Brett E Johnson Ericka M Johnson Tristan T Frum Elizabeth R Rosenzweig Neerja Karnani Kirsten Lee Gregory C Lefebvre Patrick A Navas Fidencio Neri Stephen C J Parker Peter J Sabo Richard Sandstrom Anthony Shafer David Vetrie Molly Weaver Sarah Wilcox Man Yu Francis S Collins Job Dekker Jason D Lieb Thomas D Tullius Gregory E Crawford Shamil Sunyaev William S Noble Ian Dunham France Denoeud Alexandre Reymond Philipp Kapranov Joel Rozowsky Deyou Zheng Robert Castelo Adam Frankish Jennifer Harrow Srinka Ghosh Albin Sandelin Ivo L Hofacker Robert Baertsch Damian Keefe Sujit Dike Jill Cheng Heather A Hirsch Edward A Sekinger Julien Lagarde Josep F Abril Atif Shahab Christoph Flamm Claudia Fried Jörg Hackermüller Jana Hertel Manja Lindemeyer Kristin Missal Andrea Tanzer Stefan Washietl Jan Korbel Olof Emanuelsson Jakob S Pedersen Nancy Holroyd Ruth Taylor David Swarbreck Nicholas Matthews Mark C Dickson Daryl J Thomas Matthew T Weirauch James Gilbert Jorg Drenkow Ian Bell XiaoDong Zhao K G Srinivasan Wing-Kin Sung Hong Sain Ooi Kuo Ping Chiu Sylvain Foissac Tyler Alioto Michael Brent Lior Pachter Michael L Tress Alfonso Valencia Siew Woh Choo Chiou Yu Choo Catherine Ucla Caroline Manzano Carine Wyss Evelyn Cheung Taane G Clark James B Brown Madhavan Ganesh Sandeep Patel Hari Tammana Jacqueline Chrast Charlotte N Henrichsen Chikatoshi Kai Jun Kawai Ugrappa Nagalakshmi Jiaqian Wu Zheng Lian Jin Lian Peter Newburger Xueqing Zhang Peter Bickel John S Mattick Piero Carninci Yoshihide Hayashizaki Sherman Weissman Tim Hubbard Richard M Myers Jane Rogers Peter F Stadler Todd M Lowe Chia-Lin Wei Yijun Ruan Kevin Struhl Mark Gerstein Stylianos E Antonarakis Yutao Fu Eric D Green Ulaş Karaöz Adam Siepel James Taylor Laura A Liefer Kris A Wetterstrand Peter J Good Elise A Feingold Mark S Guyer Gregory M Cooper George Asimenos Colin N Dewey Minmei Hou Sergey Nikolaev Juan I Montoya-Burgos Ari Löytynoja Simon Whelan Fabio Pardi Tim Massingham Haiyan Huang Nancy R Zhang Ian Holmes James C Mullikin Abel Ureta-Vidal Benedict Paten Michael Seringhaus Deanna Church Kate Rosenbloom W James Kent Eric A Stone Serafim Batzoglou Nick Goldman Ross C Hardison David Haussler Webb Miller Arend Sidow Nathan D Trinklein Zhengdong D Zhang Leah Barrera Rhona Stuart David C King Adam Ameur Stefan Enroth Mark C Bieda Jonghwan Kim Akshay A Bhinge Nan Jiang Jun Liu Fei Yao Vinsensius B Vega Charlie W H Lee Patrick Ng Atif Shahab Annie Yang Zarmik Moqtaderi Zhou Zhu Xiaoqin Xu Sharon Squazzo Matthew J Oberley David Inman Michael A Singer Todd A Richmond Kyle J Munn Alvaro Rada-Iglesias Ola Wallerman Jan Komorowski Joanna C Fowler Phillippe Couttet Alexander W Bruce Oliver M Dovey Peter D Ellis Cordelia F Langford David A Nix Ghia Euskirchen Stephen Hartman Alexander E Urban Peter Kraus Sara Van Calcar Nate Heintzman Tae Hoon Kim Kun Wang Chunxu Qu Gary Hon Rosa Luna Christopher K Glass M Geoff Rosenfeld Shelley Force Aldred Sara J Cooper Anason Halees Jane M Lin Hennady P Shulha Xiaoling Zhang Mousheng Xu Jaafar N S Haidar Yong Yu Yijun Ruan Vishwanath R Iyer Roland D Green Claes Wadelius Peggy J Farnham Bing Ren Rachel A Harte Angie S Hinrichs Heather Trumbower Hiram Clawson Jennifer Hillman-Jackson Ann S Zweig Kayla Smith Archana Thakkapallayil Galt Barber Robert M Kuhn Donna Karolchik Lluis Armengol Christine P Bird Paul I W de Bakker Andrew D Kern Nuria Lopez-Bigas Joel D Martin Barbara E Stranger Abigail Woodroffe Eugene Davydov Antigone Dimas Eduardo Eyras Ingileif B Hallgrímsdóttir Julian Huppert Michael C Zody Gonçalo R Abecasis Xavier Estivill Gerard G Bouffard Xiaobin Guan Nancy F Hansen Jacquelyn R Idol Valerie V B Maduro Baishali Maskeri Jennifer C McDowell Morgan Park Pamela J Thomas Alice C Young Robert W Blakesley Donna M Muzny Erica Sodergren David A Wheeler Kim C Worley Huaiyang Jiang George M Weinstock Richard A Gibbs Tina Graves Robert Fulton Elaine R Mardis Richard K Wilson Michele Clamp James Cuff Sante Gnerre David B Jaffe Jean L Chang Kerstin Lindblad-Toh Eric S Lander Maxim Koriabine Mikhail Nefedov Kazutoyo Osoegawa Yuko Yoshinaga Baoli Zhu Pieter J de Jong
June 2007

Evidence for de novo evolution of testis-expressed genes in the Drosophila yakuba/Drosophila erecta clade.

Genetics 2007 Jun 15;176(2):1131-7. Epub 2007 Apr 15.

Section of Evolution and Ecology, University of California, Davis, California 95616, USA.

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http://dx.doi.org/10.1534/genetics.106.069245DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1894579PMC
June 2007

Variation resources at UC Santa Cruz.

Nucleic Acids Res 2007 Jan 6;35(Database issue):D716-20. Epub 2006 Dec 6.

Department of Biomolecular Engineering, University of California at Santa Cruz, Santa Cruz, CA, USA.

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http://dx.doi.org/10.1093/nar/gkl953DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1781230PMC
January 2007

Forces shaping the fastest evolving regions in the human genome.

PLoS Genet 2006 Oct 23;2(10):e168. Epub 2006 Aug 23.

Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.0020168DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1599772PMC
October 2006

An RNA gene expressed during cortical development evolved rapidly in humans.

Nature 2006 Sep 16;443(7108):167-72. Epub 2006 Aug 16.

Center for Biomolecular Science & Engineering, Department of Molecular, Cell & Developmental Biology, University of California, Santa Cruz, California 95064, USA.

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http://dx.doi.org/10.1038/nature05113DOI Listing
September 2006

Novel genes derived from noncoding DNA in Drosophila melanogaster are frequently X-linked and exhibit testis-biased expression.

Proc Natl Acad Sci U S A 2006 Jun 15;103(26):9935-9. Epub 2006 Jun 15.

Center for Population Biology, University of California-Davis, Davis, CA 95616, USA.

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http://www.pnas.org/cgi/doi/10.1073/pnas.0509809103
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http://dx.doi.org/10.1073/pnas.0509809103DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1502557PMC
June 2006

Evolutionary genomics: codon bias and selection on single genomes.

Nature 2005 Jan;433(7023):E5-6; discussion E7-8

Center for Population Biology and Section of Evolution and Ecology, University of California, Davis, California 95616, USA.

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http://dx.doi.org/10.1038/nature03221DOI Listing
January 2005

Comparative genomics of centrality and essentiality in three eukaryotic protein-interaction networks.

Mol Biol Evol 2005 Apr 22;22(4):803-6. Epub 2004 Dec 22.

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http://dx.doi.org/10.1093/molbev/msi072DOI Listing
April 2005

Mechanisms and convergence of compensatory evolution in mammalian mitochondrial tRNAs.

Nat Genet 2004 Nov 24;36(11):1207-12. Epub 2004 Oct 24.

Center for Population Biology, Section of Evolution and Ecology, University of California at Davis, Davis, California 95616, USA.

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http://dx.doi.org/10.1038/ng1451DOI Listing
November 2004

Patterns of polymorphism and divergence from noncoding sequences of Drosophila melanogaster and D. simulans: evidence for nonequilibrium processes.

Mol Biol Evol 2005 Jan 29;22(1):51-62. Epub 2004 Sep 29.

Center for Population Biology, University of California, Davis, USA.

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http://dx.doi.org/10.1093/molbev/msh269DOI Listing
January 2005

Molecular population genetics of male accessory gland proteins in the Drosophila simulans complex.

Genetics 2004 Jun;167(2):725-35

Center for Population Biology, University of California, Davis, 95616, USA.

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http://dx.doi.org/10.1534/genetics.103.020883DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1470896PMC
June 2004

Genomic effects of nucleotide substitutions in Drosophila simulans.

Genetics 2002 Dec;162(4):1753-61

Center for Population Biology, University of California, Davis, California 95616, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1462383PMC
December 2002

The crystal structure of YdcE, a 4-oxalocrotonate tautomerase homologue from Escherichia coli, confirms the structural basis for oligomer diversity.

Biochemistry 2002 Oct;41(40):12010-24

Department of Chemistry and Biochemistry, Division of Medicinal Chemistry, College of Pharmacy, The University of Texas, Austin, TX 78712-1071, USA.

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http://dx.doi.org/10.1021/bi020271hDOI Listing
October 2002