Ryan Gutenkunst

Associate Department Head, Molecular and Cellular Biology
Associate Professor, Molecular and Cellular Biology
Associate Professor, Ecology and Evolutionary Biology
Associate Professor, BIO5 Institute
Associate Professor, Applied BioSciences - GIDP
Associate Professor, Applied Mathematics - GIDP
Associate Professor, Genetics - GIDP
Associate Professor, Statistics-GIDP
Associate Professor, Public Health

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.

 

 

Publications

2021

Gutenkunst, R. N., "dadi.CUDA: Accelerating Population Genetics Inference with Graphics Processing Units.", Mol Biol Evol, 2021 Jan 22. PMID: 33480999

2020

Blischak, P. D., M. S. Barker, and R. N. Gutenkunst, "Inferring the Demographic History of Inbred Species from Genome-Wide SNP Frequency Data.", Mol Biol Evol, vol. 37, issue 7, pp. 2124-2136, 2020 07 01. PMID: 32068861
Mannakee, B. K., and R. N. Gutenkunst, "BATCAVE: calling somatic mutations with a tumor- and site-specific prior.", NAR Genom Bioinform, vol. 2, issue 1, pp. lqaa004, 2020 Mar. PMCID: PMC7003682 PMID: 32051931
Adrion, J. R., C. B. Cole, N. Dukler, J. G. Galloway, A. L. Gladstein, G. Gower, C. C. Kyriazis, A. P. Ragsdale, G. Tsambos, F. Baumdicker, et al., "A community-maintained standard library of population genetic models.", Elife, vol. 9, 2020 06 23. PMCID: PMC7438115 PMID: 32573438

2018

Mannakee, B. K., U. Balaji, A. K. Witkiewicz, R. N. Gutenkunst, and E. S. Knudsen, "Sensitive and specific post-call filtering of genetic variants in xenograft and primary tumors.", Bioinformatics, vol. 34, issue 10, pp. 1713-1718, 2018 05 15. PMCID: PMC5946891 PMID: 29325072
Struck, T. J., B. K. Mannakee, and R. N. Gutenkunst, "The impact of genome-wide association studies on biomedical research publications.", Hum Genomics, vol. 12, issue 1, pp. 38, 2018 08 13. PMCID: PMC6090631 PMID: 30103832

2017

Lynch, M., R. Gutenkunst, M. Ackerman, K. Spitze, Z. Ye, T. Maruki, and Z. Jia, "Population Genomics of .", Genetics, vol. 206, issue 1, pp. 315-332, 2017 05. PMCID: PMC5419477 PMID: 27932545
Hsieh, PH., B. Hallmark, J. Watkins, T. M. Karafet, L. P. Osipova, R. N. Gutenkunst, and M. F. Hammer, "Exome Sequencing Provides Evidence of Polygenic Adaptation to a Fat-Rich Animal Diet in Indigenous Siberian Populations.", Mol Biol Evol, vol. 34, issue 11, pp. 2913-2926, 2017 Nov 01. PMID: 28962010
Qi, X., H. An, A. P. Ragsdale, T. E. Hall, R. N. Gutenkunst, C. J Pires, and M. S. Barker, "Genomic inferences of domestication events are corroborated by written records in Brassica rapa.", Mol Ecol, vol. 26, issue 13, pp. 3373-3388, 2017 Jul. PMID: 28371014
Ragsdale, A. P., and R. N. Gutenkunst, "Inferring Demographic History Using Two-Locus Statistics.", Genetics, vol. 206, issue 2, pp. 1037-1048, 2017 06. PMCID: PMC5499162 PMID: 28413158

2016

Hsieh, PH., K. R. Veeramah, J. Lachance, S. A. Tishkoff, J. D. Wall, M. F. Hammer, and R. N. Gutenkunst, "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, vol. 26, issue 3, pp. 279-90, 2016 Mar. PMCID: PMC4772011 PMID: 26888263
Coffman, A. J., P. Hsun Hsieh, S. Gravel, and R. N. Gutenkunst, "Computationally Efficient Composite Likelihood Statistics for Demographic Inference.", Mol Biol Evol, vol. 33, issue 2, pp. 591-3, 2016 Feb. PMCID: PMC5854098 PMID: 26545922
Mannakee, B. K., and R. N. Gutenkunst, "Selection on Network Dynamics Drives Differential Rates of Protein Domain Evolution.", PLoS Genet, vol. 12, issue 7, pp. e1006132, 2016 07. PMCID: PMC4933380 PMID: 27380265
Edwards, T., M. Tollis, PH. Hsieh, R. N. Gutenkunst, Z. Liu, K. Kusumi, M. Culver, and R. W. Murphy, "Assessing models of speciation under different biogeographic scenarios; an empirical study using multi-locus and RNA-seq analyses.", Ecol Evol, vol. 6, issue 2, pp. 379-96, 2016 01. PMCID: PMC4729248 PMID: 26843925
Ragsdale, A. P., A. J. Coffman, PH. Hsieh, T. J. Struck, and R. N. Gutenkunst, "Triallelic Population Genomics for Inferring Correlated Fitness Effects of Same Site Nonsynonymous Mutations.", Genetics, vol. 203, issue 1, pp. 513-23, 2016 05. PMCID: PMC4858796 PMID: 27029732

2015

Hermansen, R. A., B. K. Mannakee, W. Knecht, D. A. Liberles, and R. N. Gutenkunst, "Characterizing selective pressures on the pathway for de novo biosynthesis of pyrimidines in yeast.", BMC Evol Biol, vol. 15, pp. 232, 2015 Oct 28. PMCID: PMC4625875 PMID: 26511837
Pandya, S., T. J. Struck, B. K. Mannakee, M. Paniscus, and R. N. Gutenkunst, "Testing whether metazoan tyrosine loss was driven by selection against promiscuous phosphorylation.", Mol Biol Evol, vol. 32, issue 1, pp. 144-52, 2015 Jan. PMCID: PMC4271526 PMID: 25312910

2014

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
Robinson, J. D., A. J. Coffman, M. J. Hickerson, and R. N. Gutenkunst, "Sampling strategies for frequency spectrum-based population genomic inference.", BMC Evol Biol, vol. 14, pp. 254, 2014 Dec 04. PMCID: PMC4269862 PMID: 25471595

2013

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

2011

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

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