Ryan N Gutenkunst

Ryan N Gutenkunst

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Ryan N Gutenkunst

Publications by authors named "Ryan N Gutenkunst"

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36Publications

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

Authors:
Travis J Struck Brian K Mannakee Ryan N Gutenkunst

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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http://dx.doi.org/10.1186/s40246-018-0172-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6090631PMC
August 2018

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

Authors:
Brian K Mannakee Uthra Balaji Agnieszka K Witkiewicz Ryan N Gutenkunst Erik S Knudsen

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

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

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http://dx.doi.org/10.1093/bioinformatics/bty010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5946891PMC
May 2018

Exome Sequencing Provides Evidence of Polygenic Adaptation to a Fat-Rich Animal Diet in Indigenous Siberian Populations.

Authors:
PingHsun Hsieh Brian Hallmark Joseph Watkins Tatiana M Karafet Ludmila P Osipova Ryan N Gutenkunst Michael F Hammer

Mol Biol Evol 2017 Nov;34(11):2913-2926

Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ.

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http://dx.doi.org/10.1093/molbev/msx226DOI Listing
November 2017

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

Authors:
Xinshuai Qi Hong An Aaron P Ragsdale Tara E Hall Ryan N Gutenkunst J Chris Pires Michael S Barker

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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http://dx.doi.org/10.1111/mec.14131DOI Listing
July 2017

Inferring Demographic History Using Two-Locus Statistics.

Authors:
Aaron P Ragsdale Ryan N Gutenkunst

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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http://dx.doi.org/10.1534/genetics.117.201251DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5499162PMC
June 2017

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

Authors:
Brian K Mannakee Ryan N Gutenkunst

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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http://dx.doi.org/10.1371/journal.pgen.1006132DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4933380PMC
July 2016

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

Authors:
Aaron P Ragsdale Alec J Coffman PingHsun Hsieh Travis J Struck Ryan N Gutenkunst

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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http://dx.doi.org/10.1534/genetics.115.184812DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4858796PMC
May 2016

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

Authors:
PingHsun Hsieh August E Woerner Jeffrey D Wall Joseph Lachance Sarah A Tishkoff Ryan N Gutenkunst Michael F Hammer

Genome Res 2016 05;26(5):717.1

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http://dx.doi.org/10.1101/gr.206524.116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4864460PMC
May 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.

Authors:
PingHsun Hsieh Krishna R Veeramah Joseph Lachance Sarah A Tishkoff Jeffrey D Wall Michael F Hammer Ryan N Gutenkunst

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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http://dx.doi.org/10.1101/gr.192971.115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4772011PMC
March 2016

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

Authors:
PingHsun Hsieh August E Woerner Jeffrey D Wall Joseph Lachance Sarah A Tishkoff Ryan N Gutenkunst Michael F Hammer

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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http://dx.doi.org/10.1101/gr.196634.115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4772012PMC
March 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

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http://dx.doi.org/10.1093/molbev/msv255DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5854098PMC
February 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.

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http://dx.doi.org/10.1002/ece3.1865DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4729248PMC
January 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.

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http://dx.doi.org/10.1186/s12862-015-0515-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4625875PMC
October 2015

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.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0077175PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3806739PMC
February 2015

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

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http://dx.doi.org/10.1093/molbev/msu284DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4271526PMC
January 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.

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http://dx.doi.org/10.1186/s12862-014-0254-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4269862PMC
December 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

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http://dx.doi.org/10.1093/molbev/msu166DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4137703PMC
September 2014

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].

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http://dx.doi.org/10.1038/ncomms5383DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4140192PMC
July 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.

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http://gutengroup.mcb.arizona.edu/Publications/Jilkine2014.p
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http://dx.plos.org/10.1371/journal.pcbi.1003481
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http://dx.doi.org/10.1371/journal.pcbi.1003481DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3945168PMC
March 2014

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.

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http://dx.doi.org/10.1371/journal.ppat.1003238DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3605146PMC
March 2013

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.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0021747PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3149046PMC
December 2011

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

Authors:
Xun Xu Xin Liu Song Ge Jeffrey D Jensen Fengyi Hu Xin Li Yang Dong Ryan N Gutenkunst Lin Fang Lei Huang Jingxiang Li Weiming He Guojie Zhang Xiaoming Zheng Fumin Zhang Yingrui Li Chang Yu Karsten Kristiansen Xiuqing Zhang Jian Wang Mark Wright Susan McCouch Rasmus Nielsen Jun Wang Wen Wang

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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http://dx.doi.org/10.1038/nbt.2050DOI Listing
December 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.

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http://dx.doi.org/10.1039/c1mb05077jDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3168731PMC
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.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0019701PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3100730PMC
September 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.

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http://dx.doi.org/10.1073/pnas.1019276108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3142009PMC
July 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.

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http://dx.doi.org/10.1371/journal.pcbi.1001081DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3040654PMC
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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http://dx.doi.org/10.1038/nature09687DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3060778PMC
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.

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http://dx.doi.org/10.1186/1471-2105-11-404DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2921409PMC
July 2010

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.

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http://dx.doi.org/10.1093/molbev/msp190DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2782326PMC
December 2009

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.

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https://dx.plos.org/10.1371/journal.pgen.1000695
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http://dx.doi.org/10.1371/journal.pgen.1000695DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2760211PMC
October 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.

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http://dx.doi.org/10.1101/gr.088898.108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2675968PMC
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.

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http://dx.doi.org/10.1103/PhysRevE.78.046704DOI Listing
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.

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https://cbsu.tc.cornell.edu/staff/myers/papers/Daniels2008_s
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http://linkinghub.elsevier.com/retrieve/pii/S095816690800078
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http://dx.doi.org/10.1016/j.copbio.2008.06.008DOI Listing
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.

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http://dx.doi.org/10.1196/annals.1407.003DOI Listing
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.

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http://dx.doi.org/10.1371/journal.pcbi.0030189DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2000971PMC
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.

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https://link.aps.org/doi/10.1103/PhysRevLett.97.150601
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http://dx.doi.org/10.1103/PhysRevLett.97.150601DOI Listing
October 2006