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Ryan Gutenkunst (CV) received his Ph.D. in physics from Cornell University, where he worked with Jim Sethna on unveiling universal “sloppy” parameter sensitivities in systems biology models and on modeling their evolutionary implications. He then did a postdoc with Carlos Bustamante, where he developed ∂a∂i, a powerful method for inferring population histories from genomic data. His second postdoc was with Byron Goldstein at Los Alamos National Lab, where Ryan modeled aspects of immune signaling in mast cells. Ryan joined the faculty in Molecular and Cellular Biology at the University of Arizona in Fall 2010. He is also a member of the BIO5 Institute, the Departments of Ecology and Evolutionary Biology and Epidemiology and Biostatistics, and the Graduate Programs in Applied Biosciences, Applied Mathematics, Genetics, and Statistics. He continues to work on both systems biology and population genetics, with a focus on understanding the evolution of biomolecular networks. Outside of work, Ryan’s interests include his family, triathlon, skiing, and photography.

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Courses
  • REE
    Research in Ecology and Evolution

  • BDMBB
    Big Data in Molecular Biology and Biomedicine

  • IBI
    Introductory Biology I

  • KCQB
    Key Concepts in Quantitative Biology

  • CS
    Cell Systems

  • QB
    Quantitative Biology

  • SC
    Scientific Communication

Grants
  • Funding agency logo
    Population Genomic Inferences of History and Selection Across Populations and Time

    Principal Investigator (PI)

    2023

    $151.6K
    Active
  • Funding agency logo
    Joint Inferences of Natural Selection Between Sites and Populations

    Principal Investigator (PI)

    2019

    $1.6M
    Active
  • Funding agency logo
    Joint Inferences of Natural Selection between Sites and Populations

    Principal Investigator (PI)

    2019

    $199.7K
    Active
  • Funding agency logo
    Reach: Reading and Assembling Contextual and Holistic Mechanisms From Text

    Co-Investigator (COI)

    2014

    $3.6M
  • Funding agency logo
    Demographic History Inference from Genomic Linkage and Allele Frequency Spectra

    Principal Investigator (PI)

    2012

    $552.0K
News
  • Students Earn NSF Graduate Research Fellowships

    2018

  • Four Questions With the Class of 2018 (Part 2)

    2018

  • Raising Computers to Be Good Scientists

    2015

  • First Analysis of Orangutan Genome Yields Surprises

    2011

Publications (52)
Recent
  • Deep connections: Divergence histories with gene flow in mesophotic Agaricia corals

    2022

  • Genomic Landscape of Lymphatic Malformations: A Case Series and Response to the PI3Kα Inhibitor Alpelisib in an N-of-One Clinical Trial

    2022

  • Demogenomic modeling of the timing and the processes of early European farmers differentiation

    2021

  • Inferring Genome-Wide Correlations of Mutation Fitness Effects between Populations

    2021

  • Chromosome-scale inference of hybrid speciation and admixture with convolutional neural networks

    2021

  • dadi.CUDA: Accelerating Population Genetics Inference with Graphics Processing Units

    2021

  • A community-maintained standard library of population genetic models

    2020

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

    2020

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

    2020

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

    2018

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

    2018

  • Genome wide analyses of diverse Brassica rapa cultivars reveal significant genetic structure and corroborate historical record of domestication

    2017

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

    2017

  • Population Genomics of Daphnia pulex

    2017

  • Exome sequencing provides evidence of polygenic adaptation to a fat-rich animal diet in indigenous Siberian populations

    2017

  • Inferring Demographic History Using Two-Locus Statistics

    2017

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

    2016

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

    2016

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

    2016

  • Computationally Efficient Composite Likelihood Statistics for Demographic Inference

    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

    2016

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

    2016

  • Testing whether Metazoan Tyrosine Loss Was Driven by Selection against Promiscuous Phosphorylation

    2015

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

    2015

  • Sampling strategies for frequency spectrum-based population genomic inference

    2014

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

    2014

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

    2014

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

    2014

  • Kinetics of coinfection with influenza A virus and Streptococcus pneumoniae

    2013

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

    2013

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

    2011

  • Effect of 1918 PB1-F2 expression on influenza a virus infection kinetics

    2011

  • Demographic history and rare allele sharing among human populations

    2011

  • Comparative and demographic analysis of orang-utan genomes

    2011

  • Guidelines for visualizing and annotating rule-based models

    2011

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

    2011

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

    2011

  • A map of human genome variation from population-scale sequencing

    2010

  • RuleMonkey: Software for stochastic simulation of rule-based models

    2010

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

    2009

  • Darwinian and demographic forces affecting human protein coding genes

    2009

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

    2009

  • Targets of balancing selection in the human genome

    2009

  • Sloppiness, robustness, and evolvability in systems biology

    2008

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

    2008

  • Universally sloppy parameter sensitivities in systems biology models

    2007

  • Inferring resource distributions from Atlantic bluefin tuna movements: an analysis based on net displacement and length of track

    2007

  • Python unleashed on systems biology

    2007

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

    2007

  • Extracting falsifiable predictions from sloppy models

    2007

  • Sloppy-model universality class and the Vandermonde matrix

    2006

  • An introduction to signal extraction in interferometric gravitational wave detectors

    2003

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