Publications by authors named "Ryan N Gutenkunst"

39Publications

Inferring the Demographic History of Inbred Species from Genome-Wide SNP Frequency Data.

Mol Biol Evol 2020 07;37(7):2124-2136

Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ.

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July 2020

BATCAVE: calling somatic mutations with a tumor- and site-specific prior.

NAR Genom Bioinform 2020 Mar 6;2(1):lqaa004. Epub 2020 Feb 6.

Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85721, USA.

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March 2020

The impact of genome-wide association studies on biomedical research publications.

Hum Genomics 2018 08 13;12(1):38. Epub 2018 Aug 13.

Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, USA.

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August 2018

Sensitive and specific post-call filtering of genetic variants in xenograft and primary tumors.

Bioinformatics 2018 05;34(10):1713-1718

University of Arizona Cancer Center, University of Arizona, Tucson, AZ 85721, USA.

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May 2018

Inferring Demographic History Using Two-Locus Statistics.

Genetics 2017 06 16;206(2):1037-1048. Epub 2017 Apr 16.

Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721

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June 2017

Genomic inferences of domestication events are corroborated by written records in Brassica rapa.

Mol Ecol 2017 Jul 5;26(13):3373-3388. Epub 2017 May 5.

Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, AZ, USA.

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July 2017

Selection on Network Dynamics Drives Differential Rates of Protein Domain Evolution.

PLoS Genet 2016 07 5;12(7):e1006132. Epub 2016 Jul 5.

Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona, United States of America.

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July 2016

Triallelic Population Genomics for Inferring Correlated Fitness Effects of Same Site Nonsynonymous Mutations.

Genetics 2016 05 30;203(1):513-23. Epub 2016 Mar 30.

Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721

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May 2016

Model-based analyses of whole-genome data reveal a complex evolutionary history involving archaic introgression in Central African Pygmies.

Genome Res 2016 Mar 17;26(3):291-300. Epub 2016 Feb 17.

Arizona Research Laboratories Division of Biotechnology, University of Arizona, Tucson, Arizona 85721, USA;

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March 2016

Whole-genome sequence analyses of Western Central African Pygmy hunter-gatherers reveal a complex demographic history and identify candidate genes under positive natural selection.

Genome Res 2016 Mar 17;26(3):279-90. Epub 2016 Feb 17.

Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA; Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721, USA.

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March 2016

Assessing models of speciation under different biogeographic scenarios; an empirical study using multi-locus and RNA-seq analyses.

Ecol Evol 2016 01 7;6(2):379-96. Epub 2016 Jan 7.

State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming 650223 China; Centre for Biodiversity and Conservation Biology Royal Ontario Museum Toronto ON Canada.

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January 2016

Computationally Efficient Composite Likelihood Statistics for Demographic Inference.

Mol Biol Evol 2016 Feb 5;33(2):591-3. Epub 2015 Nov 5.

Department of Molecular and Cellular Biology, University of Arizona

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February 2016

Characterizing selective pressures on the pathway for de novo biosynthesis of pyrimidines in yeast.

BMC Evol Biol 2015 Oct 28;15:232. Epub 2015 Oct 28.

Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, 85721, USA.

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October 2015

Sampling strategies for frequency spectrum-based population genomic inference.

BMC Evol Biol 2014 Dec 4;14:254. Epub 2014 Dec 4.

Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, 85721, USA.

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December 2014

Testing whether metazoan tyrosine loss was driven by selection against promiscuous phosphorylation.

Mol Biol Evol 2015 Jan 13;32(1):144-52. Epub 2014 Oct 13.

Department of Molecular and Cellular Biology, University of Arizona

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January 2015

Loss of amino-terminal acetylation suppresses a prion phenotype by modulating global protein folding.

Nat Commun 2014 Jul 15;5:4383. Epub 2014 Jul 15.

1] Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, 185 Meeting Street, Providence, Rhode Island 02912, USA [2].

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July 2014

Evidence for increased levels of positive and negative selection on the X chromosome versus autosomes in humans.

Mol Biol Evol 2014 Sep 15;31(9):2267-82. Epub 2014 May 15.

Arizona Research Laboratories Division of Biotechnology, University of Arizona

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September 2014

Effect of dedifferentiation on time to mutation acquisition in stem cell-driven cancers.

PLoS Comput Biol 2014 Mar 6;10(3):e1003481. Epub 2014 Mar 6.

Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona, United States of America.

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March 2014

Kinetics of coinfection with influenza A virus and Streptococcus pneumoniae.

PLoS Pathog 2013 Mar 21;9(3):e1003238. Epub 2013 Mar 21.

Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America.

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March 2013

Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes.

Nat Biotechnol 2011 Dec 11;30(1):105-11. Epub 2011 Dec 11.

CAS-Max Planck Junior Research Group on Evolutionary Genomics, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, China.

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December 2011

Demographic history and rare allele sharing among human populations.

Proc Natl Acad Sci U S A 2011 Jul 5;108(29):11983-8. Epub 2011 Jul 5.

Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305-5120, USA.

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July 2011

Guidelines for visualizing and annotating rule-based models.

Mol Biosyst 2011 Oct 7;7(10):2779-95. Epub 2011 Jun 7.

Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.

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October 2011

A biophysical model of cell adhesion mediated by immunoadhesin drugs and antibodies.

PLoS One 2011 18;6(5):e19701. Epub 2011 May 18.

Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona, United States of America.

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September 2011

Effect of 1918 PB1-F2 expression on influenza A virus infection kinetics.

PLoS Comput Biol 2011 Feb 17;7(2):e1001081. Epub 2011 Feb 17.

Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America.

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February 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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January 2011

RuleMonkey: software for stochastic simulation of rule-based models.

BMC Bioinformatics 2010 Jul 30;11:404. Epub 2010 Jul 30.

Clinical Translational Research Division, Translational Genomics Research Institute, Phoenix, AZ 85004, USA.

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July 2010

Inferring the joint demographic history of multiple populations from multidimensional SNP frequency data.

PLoS Genet 2009 Oct 23;5(10):e1000695. Epub 2009 Oct 23.

Theoretical Biology and Biophysics and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico, USA.

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October 2009

Variational method for estimating the rate of convergence of Markov-chain Monte Carlo algorithms.

Phys Rev E Stat Nonlin Soft Matter Phys 2008 Oct 20;78(4 Pt 2):046704. Epub 2008 Oct 20.

Complex and Adaptive Systems Laboratory, University College Dublin, Dublin 4, Ireland.

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October 2008

Sloppiness, robustness, and evolvability in systems biology.

Curr Opin Biotechnol 2008 Aug 25;19(4):389-95. Epub 2008 Jul 25.

Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, NY, USA.

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August 2008

Extracting falsifiable predictions from sloppy models.

Ann N Y Acad Sci 2007 Dec 9;1115:203-11. Epub 2007 Oct 9.

Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, NY 14853, USA.

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December 2007

Universally sloppy parameter sensitivities in systems biology models.

PLoS Comput Biol 2007 Oct 15;3(10):1871-78. Epub 2007 Aug 15.

Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, New York, USA.

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October 2007

Sloppy-model universality class and the Vandermonde matrix.

Phys Rev Lett 2006 Oct 12;97(15):150601. Epub 2006 Oct 12.

Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, New York 14853, USA.

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October 2006