Ryan Gutenkunst

Department Head, Molecular and Cellular Biology
Professor, Molecular and Cellular Biology
Professor, Ecology and Evolutionary Biology

Our research group integrates computational systems biology and population genetics to understand the function and evolution of the complex molecular networks that underlie life. We build and analyze mathematical simulations of protein networks to probe deeper into their function than experiments can. We also analyze genomic data to undercover signatures of population history and natural selection, with an emphasis on humans. Recent projects include studying how protein network dynamics constrain protein domain evolution, testing the hypothesis that selection against signaling crosstalk shapes protein amino acid composition, and searching for signatures of natural selection in human Pygmy populations.

Watch Dr. Gutenkunst talk about his research and what drew him to science - and still does!

Dr. Gutenkunst explains why his lab is a dry lab.

Dr. Gutenkunst talks about The Gutenkunst Group's research.

Dr. Gutenkunst talks about the backgrounds of PhD students in his lab.





Veeramah, K. R., R. N. Gutenkunst, A. E. Woerner, J. C. Watkins, and M. F. Hammer, "Evidence for increased levels of positive and negative selection on the X chromosome versus autosomes in humans.", Mol Biol Evol, vol. 31, issue 9, pp. 2267-82, 2014 Sep. PMCID: PMC4137703 PMID: 24830675
Holmes, W. M., B. K. Mannakee, R. N. Gutenkunst, and T. R. Serio, "Loss of amino-terminal acetylation suppresses a prion phenotype by modulating global protein folding.", Nat Commun, vol. 5, pp. 4383, 2014 Jul 15. PMCID: PMC4140192 PMID: 25023910
Jilkine, A., and R. N. Gutenkunst, "Effect of dedifferentiation on time to mutation acquisition in stem cell-driven cancers.", PLoS Comput Biol, vol. 10, issue 3, pp. e1003481, 2014 Mar. PMCID: PMC3945168 PMID: 24603301


Ma, X., J. L. Kelley, K. Eilertson, S. Musharoff, J. D. Degenhardt, A. L. Martins, T. Vinar, C. Kosiol, A. Siepel, R. N. Gutenkunst, et al., "Population genomic analysis reveals a rich speciation and demographic history of orang-utans (Pongo pygmaeus and Pongo abelii).", PLoS One, vol. 8, issue 10, pp. e77175, 2013. PMCID: PMC3806739 PMID: 24194868
Smith, A. M., F. R. Adler, R. M. Ribeiro, R. N. Gutenkunst, J. L. McAuley, J. A. McCullers, and A. S. Perelson, "Kinetics of coinfection with influenza A virus and Streptococcus pneumoniae.", PLoS Pathog, vol. 9, issue 3, pp. e1003238, 2013 Mar. PMCID: PMC3605146 PMID: 23555251


Gutenkunst, R. N., D. Coombs, T. Starr, M. L. Dustin, and B. Goldstein, "A biophysical model of cell adhesion mediated by immunoadhesin drugs and antibodies.", PLoS One, vol. 6, issue 5, pp. e19701, 2011. PMCID: PMC3100730 PMID: 21629715
Chylek, L. A., B. Hu, M. L. Blinov, T. Emonet, J. R. Faeder, B. Goldstein, R. N. Gutenkunst, J. M. Haugh, T. Lipniacki, R. G. Posner, et al., "Guidelines for visualizing and annotating rule-based models.", Mol Biosyst, vol. 7, issue 10, pp. 2779-95, 2011 Oct. PMCID: PMC3168731 PMID: 21647530
Locke, D. P., LD. W. Hillier, W. C. Warren, K. C. Worley, L. V. Nazareth, D. M. Muzny, S-P. Yang, Z. Wang, A. T. Chinwalla, P. Minx, et al., "Comparative and demographic analysis of orang-utan genomes.", Nature, vol. 469, issue 7331, pp. 529-33, 2011 Jan 27. PMCID: PMC3060778 PMID: 21270892
Skar, H., R. N. Gutenkunst, K. Wilbe Ramsay, A. Alaeus, J. Albert, and T. Leitner, "Daily sampling of an HIV-1 patient with slowly progressing disease displays persistence of multiple env subpopulations consistent with neutrality.", PLoS One, vol. 6, issue 8, pp. e21747, 2011. PMCID: PMC3149046 PMID: 21829600
Gravel, S., B. M. Henn, R. N. Gutenkunst, A. R. Indap, G. T. Marth, A. G. Clark, F. Yu, R. A. Gibbs, and C. D. Bustamante, "Demographic history and rare allele sharing among human populations.", Proc Natl Acad Sci U S A, vol. 108, issue 29, pp. 11983-8, 2011 Jul 19. PMCID: PMC3142009 PMID: 21730125
Xu, X., X. Liu, S. Ge, J. D. Jensen, F. Hu, X. Li, Y. Dong, R. N. Gutenkunst, L. Fang, L. Huang, et al., "Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes.", Nat Biotechnol, vol. 30, issue 1, pp. 105-11, 2011 Dec 11. PMID: 22158310


Colvin, J., M. I. Monine, R. N. Gutenkunst, W. S. Hlavacek, D. D. Von Hoff, and R. G. Posner, "RuleMonkey: software for stochastic simulation of rule-based models.", BMC Bioinformatics, vol. 11, pp. 404, 2010 Jul 30. PMCID: PMC2921409 PMID: 20673321
Abecasis, G. R., D. Altshuler, A. Auton, L. D. Brooks, R. M. Durbin, R. A. Gibbs, M. E. Hurles, and G. A. McVean, "A map of human genome variation from population-scale sequencing.", Nature, vol. 467, issue 7319, pp. 1061-73, 2010 Oct 28. PMCID: PMC3042601 PMID: 20981092


Nielsen, R., M. J. Hubisz, I. Hellmann, D. Torgerson, A. M. Andrés, A. Albrechtsen, R. Gutenkunst, M. D. Adams, M. Cargill, A. Boyko, et al., "Darwinian and demographic forces affecting human protein coding genes.", Genome Res, vol. 19, issue 5, pp. 838-49, 2009 May. PMCID: PMC2675972 PMID: 19279335
Auton, A., K. Bryc, A. R. Boyko, K. E. Lohmueller, J. Novembre, A. Reynolds, A. Indap, M. H. Wright, J. D. Degenhardt, R. N. Gutenkunst, et al., "Global distribution of genomic diversity underscores rich complex history of continental human populations.", Genome Res, vol. 19, issue 5, pp. 795-803, 2009 May. PMCID: PMC2675968 PMID: 19218534
Andrés, A. M., M. J. Hubisz, A. Indap, D. G. Torgerson, J. D. Degenhardt, A. R. Boyko, R. N. Gutenkunst, T. J. White, E. D. Green, C. D. Bustamante, et al., "Targets of balancing selection in the human genome.", Mol Biol Evol, vol. 26, issue 12, pp. 2755-64, 2009 Dec. PMCID: PMC2782326 PMID: 19713326
Gutenkunst, R. N., R. D. Hernandez, S. H. Williamson, and C. D. Bustamante, "Inferring the joint demographic history of multiple populations from multidimensional SNP frequency data.", PLoS Genet, vol. 5, issue 10, pp. e1000695, 2009 Oct. PMCID: PMC2760211 PMID: 19851460


Casey, F. P., J. J. Waterfall, R. N. Gutenkunst, C. R. Myers, and J. P. Sethna, "Variational method for estimating the rate of convergence of Markov-chain Monte Carlo algorithms.", Phys Rev E Stat Nonlin Soft Matter Phys, vol. 78, issue 4 Pt 2, pp. 046704, 2008 Oct. PMID: 18999558
Daniels, B. C., Y-J. Chen, J. P. Sethna, R. N. Gutenkunst, and C. R. Myers, "Sloppiness, robustness, and evolvability in systems biology.", Curr Opin Biotechnol, vol. 19, issue 4, pp. 389-95, 2008 Aug. PMID: 18620054


Gutenkunst, R., N. Newlands, M. Lutcavage, and L. Edelstein-Keshet, "Inferring resource distributions from Atlantic bluefin tuna movements: an analysis based on net displacement and length of track.", J Theor Biol, vol. 245, issue 2, pp. 243-57, 2007 Mar 21. PMID: 17140603
Gutenkunst, R. N., F. P. Casey, J. J. Waterfall, C. R. Myers, and J. P. Sethna, "Extracting falsifiable predictions from sloppy models.", Ann N Y Acad Sci, vol. 1115, pp. 203-11, 2007 Dec. PMID: 17925353
Gutenkunst, R. N., J. J. Waterfall, F. P. Casey, K. S. Brown, C. R. Myers, and J. P. Sethna, "Universally sloppy parameter sensitivities in systems biology models.", PLoS Comput Biol, vol. 3, issue 10, pp. 1871-78, 2007 Oct. PMCID: PMC2000971 PMID: 17922568
Casey, F. P., D. Baird, Q. Feng, R. N. Gutenkunst, J. J. Waterfall, C. R. Myers, K. S. Brown, R. A. Cerione, and J. P. Sethna, "Optimal experimental design in an epidermal growth factor receptor signalling and down-regulation model.", IET Syst Biol, vol. 1, issue 3, pp. 190-202, 2007 May. PMID: 17591178


Waterfall, J. J., F. P. Casey, R. N. Gutenkunst, K. S. Brown, C. R. Myers, P. W. Brouwer, V. Elser, and J. P. Sethna, "Sloppy-model universality class and the Vandermonde matrix.", Phys Rev Lett, vol. 97, issue 15, pp. 150601, 2006 Oct 13. PMID: 17155311