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Items: 39


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

Blischak PD, Barker MS, Gutenkunst RN.

Mol Biol Evol. 2020 Feb 18. pii: msaa042. doi: 10.1093/molbev/msaa042. [Epub ahead of print]


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

Mannakee BK, Gutenkunst RN.

NAR Genom Bioinform. 2020 Mar;2(1):lqaa004. doi: 10.1093/nargab/lqaa004. Epub 2020 Feb 6.


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

Struck TJ, Mannakee BK, Gutenkunst RN.

Hum Genomics. 2018 Aug 13;12(1):38. doi: 10.1186/s40246-018-0172-4.


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

Mannakee BK, Balaji U, Witkiewicz AK, Gutenkunst RN, Knudsen ES.

Bioinformatics. 2018 May 15;34(10):1713-1718. doi: 10.1093/bioinformatics/bty010.


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

Hsieh P, Hallmark B, Watkins J, Karafet TM, Osipova LP, Gutenkunst RN, Hammer MF.

Mol Biol Evol. 2017 Nov 1;34(11):2913-2926. doi: 10.1093/molbev/msx226.


Inferring Demographic History Using Two-Locus Statistics.

Ragsdale AP, Gutenkunst RN.

Genetics. 2017 Jun;206(2):1037-1048. doi: 10.1534/genetics.117.201251. Epub 2017 Apr 16.


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

Qi X, An H, Ragsdale AP, Hall TE, Gutenkunst RN, Chris Pires J, Barker MS.

Mol Ecol. 2017 Jul;26(13):3373-3388. doi: 10.1111/mec.14131. Epub 2017 May 5.


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

Mannakee BK, Gutenkunst RN.

PLoS Genet. 2016 Jul 5;12(7):e1006132. doi: 10.1371/journal.pgen.1006132. eCollection 2016 Jul.


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

Hsieh P, Woerner AE, Wall JD, Lachance J, Tishkoff SA, Gutenkunst RN, Hammer MF.

Genome Res. 2016 May;26(5):717.1. doi: 10.1101/gr.206524.116. No abstract available.


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

Ragsdale AP, Coffman AJ, Hsieh P, Struck TJ, Gutenkunst RN.

Genetics. 2016 May;203(1):513-23. doi: 10.1534/genetics.115.184812. Epub 2016 Mar 30.


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

Hsieh P, Woerner AE, Wall JD, Lachance J, Tishkoff SA, Gutenkunst RN, Hammer MF.

Genome Res. 2016 Mar;26(3):291-300. doi: 10.1101/gr.196634.115. Epub 2016 Feb 17. Erratum in: Genome Res. 2016 May;26(5):717.1.


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

Hsieh P, Veeramah KR, Lachance J, Tishkoff SA, Wall JD, Hammer MF, Gutenkunst RN.

Genome Res. 2016 Mar;26(3):279-90. doi: 10.1101/gr.192971.115. Epub 2016 Feb 17.


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

Edwards T, Tollis M, Hsieh P, Gutenkunst RN, Liu Z, Kusumi K, Culver M, Murphy RW.

Ecol Evol. 2016 Jan 7;6(2):379-96. doi: 10.1002/ece3.1865. eCollection 2016 Jan.


Computationally Efficient Composite Likelihood Statistics for Demographic Inference.

Coffman AJ, Hsieh PH, Gravel S, Gutenkunst RN.

Mol Biol Evol. 2016 Feb;33(2):591-3. doi: 10.1093/molbev/msv255. Epub 2015 Nov 5.


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

Hermansen RA, Mannakee BK, Knecht W, Liberles DA, Gutenkunst RN.

BMC Evol Biol. 2015 Oct 28;15:232. doi: 10.1186/s12862-015-0515-x.


Sampling strategies for frequency spectrum-based population genomic inference.

Robinson JD, Coffman AJ, Hickerson MJ, Gutenkunst RN.

BMC Evol Biol. 2014 Dec 4;14:254. doi: 10.1186/s12862-014-0254-4.


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

Pandya S, Struck TJ, Mannakee BK, Paniscus M, Gutenkunst RN.

Mol Biol Evol. 2015 Jan;32(1):144-52. doi: 10.1093/molbev/msu284. Epub 2014 Oct 13.


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

Holmes WM, Mannakee BK, Gutenkunst RN, Serio TR.

Nat Commun. 2014 Jul 15;5:4383. doi: 10.1038/ncomms5383.


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

Veeramah KR, Gutenkunst RN, Woerner AE, Watkins JC, Hammer MF.

Mol Biol Evol. 2014 Sep;31(9):2267-82. doi: 10.1093/molbev/msu166. Epub 2014 May 15.


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

Jilkine A, Gutenkunst RN.

PLoS Comput Biol. 2014 Mar 6;10(3):e1003481. doi: 10.1371/journal.pcbi.1003481. eCollection 2014 Mar.


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

Ma X, Kelley JL, Eilertson K, Musharoff S, Degenhardt JD, Martins AL, Vinar T, Kosiol C, Siepel A, Gutenkunst RN, Bustamante CD.

PLoS One. 2013 Oct 23;8(10):e77175. doi: 10.1371/journal.pone.0077175. eCollection 2013.


Kinetics of coinfection with influenza A virus and Streptococcus pneumoniae.

Smith AM, Adler FR, Ribeiro RM, Gutenkunst RN, McAuley JL, McCullers JA, Perelson AS.

PLoS Pathog. 2013 Mar;9(3):e1003238. doi: 10.1371/journal.ppat.1003238. Epub 2013 Mar 21.


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

Xu X, Liu X, Ge S, Jensen JD, Hu F, Li X, Dong Y, Gutenkunst RN, Fang L, Huang L, Li J, He W, Zhang G, Zheng X, Zhang F, Li Y, Yu C, Kristiansen K, Zhang X, Wang J, Wright M, McCouch S, Nielsen R, Wang J, Wang W.

Nat Biotechnol. 2011 Dec 11;30(1):105-11. doi: 10.1038/nbt.2050.


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

Skar H, Gutenkunst RN, Wilbe Ramsay K, Alaeus A, Albert J, Leitner T.

PLoS One. 2011;6(8):e21747. doi: 10.1371/journal.pone.0021747. Epub 2011 Aug 2.


Demographic history and rare allele sharing among human populations.

Gravel S, Henn BM, Gutenkunst RN, Indap AR, Marth GT, Clark AG, Yu F, Gibbs RA; 1000 Genomes Project, Bustamante CD.

Proc Natl Acad Sci U S A. 2011 Jul 19;108(29):11983-8. doi: 10.1073/pnas.1019276108. Epub 2011 Jul 5.


Guidelines for visualizing and annotating rule-based models.

Chylek LA, Hu B, Blinov ML, Emonet T, Faeder JR, Goldstein B, Gutenkunst RN, Haugh JM, Lipniacki T, Posner RG, Yang J, Hlavacek WS.

Mol Biosyst. 2011 Oct;7(10):2779-95. doi: 10.1039/c1mb05077j. Epub 2011 Jun 7.


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

Gutenkunst RN, Coombs D, Starr T, Dustin ML, Goldstein B.

PLoS One. 2011;6(5):e19701. doi: 10.1371/journal.pone.0019701. Epub 2011 May 18.


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

Smith AM, Adler FR, McAuley JL, Gutenkunst RN, Ribeiro RM, McCullers JA, Perelson AS.

PLoS Comput Biol. 2011 Feb;7(2):e1001081. doi: 10.1371/journal.pcbi.1001081. Epub 2011 Feb 17.


Comparative and demographic analysis of orang-utan genomes.

Locke DP, Hillier LW, Warren WC, Worley KC, Nazareth LV, Muzny DM, Yang SP, Wang Z, Chinwalla AT, Minx P, Mitreva M, Cook L, Delehaunty KD, Fronick C, Schmidt H, Fulton LA, Fulton RS, Nelson JO, Magrini V, Pohl C, Graves TA, Markovic C, Cree A, Dinh HH, Hume J, Kovar CL, Fowler GR, Lunter G, Meader S, Heger A, Ponting CP, Marques-Bonet T, Alkan C, Chen L, Cheng Z, Kidd JM, Eichler EE, White S, Searle S, Vilella AJ, Chen Y, Flicek P, Ma J, Raney B, Suh B, Burhans R, Herrero J, Haussler D, Faria R, Fernando O, Darré F, Farré D, Gazave E, Oliva M, Navarro A, Roberto R, Capozzi O, Archidiacono N, Della Valle G, Purgato S, Rocchi M, Konkel MK, Walker JA, Ullmer B, Batzer MA, Smit AF, Hubley R, Casola C, Schrider DR, Hahn MW, Quesada V, Puente XS, Ordoñez GR, López-Otín C, Vinar T, Brejova B, Ratan A, Harris RS, Miller W, Kosiol C, Lawson HA, Taliwal V, Martins AL, Siepel A, Roychoudhury A, Ma X, Degenhardt J, Bustamante CD, Gutenkunst RN, Mailund T, Dutheil JY, Hobolth A, Schierup MH, Ryder OA, Yoshinaga Y, de Jong PJ, Weinstock GM, Rogers J, Mardis ER, Gibbs RA, Wilson RK.

Nature. 2011 Jan 27;469(7331):529-33. doi: 10.1038/nature09687.


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

Colvin J, Monine MI, Gutenkunst RN, Hlavacek WS, Von Hoff DD, Posner RG.

BMC Bioinformatics. 2010 Jul 30;11:404. doi: 10.1186/1471-2105-11-404.


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

Gutenkunst RN, Hernandez RD, Williamson SH, Bustamante CD.

PLoS Genet. 2009 Oct;5(10):e1000695. doi: 10.1371/journal.pgen.1000695. Epub 2009 Oct 23.


Targets of balancing selection in the human genome.

Andrés AM, Hubisz MJ, Indap A, Torgerson DG, Degenhardt JD, Boyko AR, Gutenkunst RN, White TJ, Green ED, Bustamante CD, Clark AG, Nielsen R.

Mol Biol Evol. 2009 Dec;26(12):2755-64. doi: 10.1093/molbev/msp190. Epub 2009 Aug 27.


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

Auton A, Bryc K, Boyko AR, Lohmueller KE, Novembre J, Reynolds A, Indap A, Wright MH, Degenhardt JD, Gutenkunst RN, King KS, Nelson MR, Bustamante CD.

Genome Res. 2009 May;19(5):795-803. doi: 10.1101/gr.088898.108. Epub 2009 Feb 13.


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

Casey FP, Waterfall JJ, Gutenkunst RN, Myers CR, Sethna JP.

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


Sloppiness, robustness, and evolvability in systems biology.

Daniels BC, Chen YJ, Sethna JP, Gutenkunst RN, Myers CR.

Curr Opin Biotechnol. 2008 Aug;19(4):389-95. doi: 10.1016/j.copbio.2008.06.008. Epub 2008 Jul 25. Review.


Extracting falsifiable predictions from sloppy models.

Gutenkunst RN, Casey FP, Waterfall JJ, Myers CR, Sethna JP.

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


Universally sloppy parameter sensitivities in systems biology models.

Gutenkunst RN, Waterfall JJ, Casey FP, Brown KS, Myers CR, Sethna JP.

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


Optimal experimental design in an epidermal growth factor receptor signalling and down-regulation model.

Casey FP, Baird D, Feng Q, Gutenkunst RN, Waterfall JJ, Myers CR, Brown KS, Cerione RA, Sethna JP.

IET Syst Biol. 2007 May;1(3):190-202.


Sloppy-model universality class and the Vandermonde matrix.

Waterfall JJ, Casey FP, Gutenkunst RN, Brown KS, Myers CR, Brouwer PW, Elser V, Sethna JP.

Phys Rev Lett. 2006 Oct 13;97(15):150601. Epub 2006 Oct 12.


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