Ryan N Gutenkunst

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.

View Article and Find Full Text PDF

March 2016

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

Authors:

Taylor Edwards Marc Tollis PingHsun Hsieh Ryan N Gutenkunst Zhen Liu Kenro Kusumi Melanie Culver Robert W Murphy

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.

View Article and Find Full Text PDF

January 2016

Computationally Efficient Composite Likelihood Statistics for Demographic Inference.

Authors:

Alec J Coffman Ping Hsun Hsieh Simon Gravel Ryan N Gutenkunst

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

Department of Molecular and Cellular Biology, University of Arizona

View Article and Find Full Text PDF

February 2016

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

Authors:

Russell A Hermansen Brian K Mannakee Wolfgang Knecht David A Liberles Ryan N Gutenkunst

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.

View Article and Find Full Text PDF

October 2015

Sampling strategies for frequency spectrum-based population genomic inference.

Authors:

John D Robinson Alec J Coffman Michael J Hickerson Ryan N Gutenkunst

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.

View Article and Find Full Text PDF

December 2014

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

Authors:

Siddharth Pandya Travis J Struck Brian K Mannakee Mary Paniscus Ryan N Gutenkunst

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

Department of Molecular and Cellular Biology, University of Arizona

View Article and Find Full Text PDF

January 2015

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

Authors:

William M Holmes Brian K Mannakee Ryan N Gutenkunst Tricia R Serio

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].

View Article and Find Full Text PDF

July 2014

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

Authors:

Krishna R Veeramah Ryan N Gutenkunst August E Woerner Joseph C Watkins Michael F Hammer

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

Arizona Research Laboratories Division of Biotechnology, University of Arizona

View Article and Find Full Text PDF

September 2014

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

Authors:

Alexandra Jilkine Ryan N Gutenkunst

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.

View Article and Find Full Text PDF

March 2014

Population genomic analysis reveals a rich speciation and demographic history of orang-utans (Pongo pygmaeus and Pongo abelii).

Authors:

Xin Ma Joanna L Kelley Kirsten Eilertson Shaila Musharoff Jeremiah D Degenhardt André L Martins Tomas Vinar Carolin Kosiol Adam Siepel Ryan N Gutenkunst Carlos D Bustamante

PLoS One 2013 23;8(10):e77175. Epub 2013 Oct 23.

Department of Statistics, Stanford University, Stanford, California, United States of America.

View Article and Find Full Text PDF

February 2015

Kinetics of coinfection with influenza A virus and Streptococcus pneumoniae.

Authors:

Amber M Smith Frederick R Adler Ruy M Ribeiro Ryan N Gutenkunst Julie L McAuley Jonathan A McCullers Alan S Perelson

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.

View Article and Find Full Text PDF

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.

View Article and Find Full Text PDF

December 2011

Daily sampling of an HIV-1 patient with slowly progressing disease displays persistence of multiple env subpopulations consistent with neutrality.

Authors:

Helena Skar Ryan N Gutenkunst Karin Wilbe Ramsay Annette Alaeus Jan Albert Thomas Leitner

PLoS One 2011 2;6(8):e21747. Epub 2011 Aug 2.

Department of Virology, Swedish Institute for Infectious Disease Control, Solna, Sweden.

View Article and Find Full Text PDF

December 2011

Demographic history and rare allele sharing among human populations.

Authors:

Simon Gravel Brenna M Henn Ryan N Gutenkunst Amit R Indap Gabor T Marth Andrew G Clark Fuli Yu Richard A Gibbs Carlos D Bustamante

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.

View Article and Find Full Text PDF

July 2011

Guidelines for visualizing and annotating rule-based models.

Authors:

Lily A Chylek Bin Hu Michael L Blinov Thierry Emonet James R Faeder Byron Goldstein Ryan N Gutenkunst Jason M Haugh Tomasz Lipniacki Richard G Posner Jin Yang William S Hlavacek

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.

View Article and Find Full Text PDF

October 2011

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

Authors:

Ryan N Gutenkunst Daniel Coombs Toby Starr Michael L Dustin Byron Goldstein

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.

View Article and Find Full Text PDF

September 2011

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

Authors:

Amber M Smith Frederick R Adler Julie L McAuley Ryan N Gutenkunst Ruy M Ribeiro Jonathan A McCullers Alan S Perelson

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.

View Article and Find Full Text PDF

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.

View Article and Find Full Text PDF

January 2011

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

Authors:

Joshua Colvin Michael I Monine Ryan N Gutenkunst William S Hlavacek Daniel D Von Hoff Richard G Posner

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

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

View Article and Find Full Text PDF

July 2010

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

Authors:

Ryan N Gutenkunst Ryan D Hernandez Scott H Williamson Carlos D Bustamante

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.

View Article and Find Full Text PDF

October 2009

Targets of balancing selection in the human genome.

Authors:

Aida M Andrés Melissa J Hubisz Amit Indap Dara G Torgerson Jeremiah D Degenhardt Adam R Boyko Ryan N Gutenkunst Thomas J White Eric D Green Carlos D Bustamante Andrew G Clark Rasmus Nielsen

Mol Biol Evol 2009 Dec 27;26(12):2755-64. Epub 2009 Aug 27.

Department of Molecular Biology and Genetics, Cornell University, USA.

View Article and Find Full Text PDF

December 2009

Global distribution of genomic diversity underscores rich complex history of continental human populations.

Authors:

Adam Auton Katarzyna Bryc Adam R Boyko Kirk E Lohmueller John Novembre Andy Reynolds Amit Indap Mark H Wright Jeremiah D Degenhardt Ryan N Gutenkunst Karen S King Matthew R Nelson Carlos D Bustamante

Genome Res 2009 May 13;19(5):795-803. Epub 2009 Feb 13.

Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853-2601, USA.

View Article and Find Full Text PDF

May 2009

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

Authors:

Fergal P Casey Joshua J Waterfall Ryan N Gutenkunst Christopher R Myers James P Sethna

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.

View Article and Find Full Text PDF

October 2008

Sloppiness, robustness, and evolvability in systems biology.

Authors:

Bryan C Daniels Yan-Jiun Chen James P Sethna Ryan N Gutenkunst Christopher R Myers

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.

View Article and Find Full Text PDF

August 2008

Extracting falsifiable predictions from sloppy models.

Authors:

Ryan N Gutenkunst Fergal P Casey Joshua J Waterfall Christopher R Myers James P Sethna

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.

View Article and Find Full Text PDF

December 2007

Universally sloppy parameter sensitivities in systems biology models.

Authors:

Ryan N Gutenkunst Joshua J Waterfall Fergal P Casey Kevin S Brown Christopher R Myers James P Sethna

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.

View Article and Find Full Text PDF

October 2007

Sloppy-model universality class and the Vandermonde matrix.

Authors:

Joshua J Waterfall Fergal P Casey Ryan N Gutenkunst Kevin S Brown Christopher R Myers Piet W Brouwer Veit Elser James P Sethna

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.

View Article and Find Full Text PDF

October 2006

Publications by authors named "Ryan N Gutenkunst"

Authors:

Authors:

Authors:

Authors:

Authors:

Authors:

Authors:

Authors:

Authors:

Authors:

Authors:

Authors:

Authors:

Authors:

Authors:

Authors:

Authors:

Authors:

Authors:

Authors:

Authors:

Authors:

Authors:

Authors:

Authors:

Authors:

Authors:

Authors:

Authors:

Authors:

Authors:

Authors:

Authors:

Authors:

Authors:

Authors:

Authors:

Authors:

Authors: