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.

 

 

Publications

2022

Prata, K. E., C. Riginos, R. N. Gutenkunst, K. R. W. Latijnhouwers, J. A. Sánchez, N. Englebert, K. B. Hay, and P. Bongaerts, "Deep connections: Divergence histories with gene flow in mesophotic Agaricia corals.", Mol Ecol, vol. 31, issue 9, pp. 2511-2527, 2022 May. PMCID: PMC9303685 PMID: 35152496
Shaheen, M. F., J. Y. Tse, E. S. Sokol, M. Masterson, P. Bansal, I. Rabinowitz, C. A. Tarleton, A. S. Dobroff, T. L. Smith, T. J. Bocklage, et al., "Genomic landscape of lymphatic malformations: a case series and response to the PI3Kα inhibitor alpelisib in an -of-1 clinical trial.", Elife, vol. 11, 2022 Jul 05. PMCID: PMC9255965 PMID: 35787784
Johri, P., A. Eyre-Walker, R. N. Gutenkunst, K. E. Lohmueller, and J. D. Jensen, "On the prospect of achieving accurate joint estimation of selection with population history.", Genome Biol Evol, vol. 14, issue 7, 2022 Jul 02. PMCID: PMC9254643 PMID: 35675379
Marchi, N., L. Winkelbach, I. Schulz, M. Brami, Z. Hofmanová, J. Blöcher, C. S. Reyna-Blanco, Y. Diekmann, A. Thiéry, A. Kapopoulou, et al., "The genomic origins of the world's first farmers.", Cell, vol. 185, issue 11, pp. 1842-1859.e18, 2022 May 26. PMCID: PMC9166250 PMID: 35561686
Gower, G., A. P. Ragsdale, G. Bisschop, R. N. Gutenkunst, M. Hartfield, E. Noskova, S. Schiffels, T. J. Struck, J. Kelleher, and K. R. Thornton, "Demes: a standard format for demographic models.", Genetics, vol. 222, issue 3, 2022 Nov 01. PMCID: PMC9630982 PMID: 36173327

2021

Blischak, P. D., M. S. Barker, and R. N. Gutenkunst, "Chromosome-scale inference of hybrid speciation and admixture with convolutional neural networks.", Mol Ecol Resour, vol. 21, issue 8, pp. 2676-2688, 2021 Nov. PMCID: PMC8675098 PMID: 33682305
Gutenkunst, R. N., "dadi.CUDA: Accelerating Population Genetics Inference with Graphics Processing Units.", Mol Biol Evol, 2021 Jan 22. PMID: 33480999
Huang, X., A. Lyn Fortier, A. J. Coffman, T. J. Struck, M. N. Irby, J. E. James, J. E. León-Burguete, A. P. Ragsdale, and R. N. Gutenkunst, "Inferring Genome-Wide Correlations of Mutation Fitness Effects between Populations.", Mol Biol Evol, vol. 38, issue 10, pp. 4588-4602, 2021 Sep 27. PMCID: PMC8476148 PMID: 34043790

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

Pages

Supervising

Justin Conover
Travis Struck