Publications

For citation information, see Google Scholar.


Submitted

  • Immunoediting restricts clonal neoantigens in primary tumors
    ES Borden, D Castellano, A Hughes, T Ma, X Li, AR Mangold, RN Gutenkunst, BJ LaFleur, KH Buetow, MA Wilson, KT Hastings
    preprint
  • Modeling biases from low-pass genome sequencing to enable accurate population genetic inferences
    EM Fonseca, LN Tran, H Mendoza,  RN Gutenkunst
    preprint
  • dadi-cli: Automated and distributed population genetic model inference from allele frequency spectra
    X Huang, TJ Struck, SW Davey, RN Gutenkunst
    preprint
  • Non-hypermutator cancers access driver mutations through reversals in germline mutational bias
    MZ Tuffaha, D Castellano,  C Serrano Colomé, RN Gutenkunst, LM Wahl
    preprint
  • Detection of domestication signals through the analysis of the full distribution of fitness effects using forward simulations and polygenic adaptation
    I-T Vourlaki, D Castellano, RN Gutenkunst, SE Ramos-Onsins
    preprint

2024

  • Computationally efficient demographic history inference from allele frequencies with supervised machine learning
    LN Tran, CK Sun, TJ Struck, M Sajan, RN Gutenkunst
    Molecular Biology and Evolution 41:msae077 (2024); link; pdf

2023

  • Demographic history inference and the polyploid continuum
    PD Blischak, M Sajan, MS Barker, RN Gutenkunst
    Genetics 224:iyad107 (2023); link; pdf
    • Featured by the editors of Genetics
  • Expanding the stdpopsim species catalog, and lessons learned for realistic genome simulations
    ME Lauterbur, MIA Cavassim, AL Gladstein, G Gower, NS Pope, G Tsambos, J Adrion, S Belsare, A Biddanda, V Caudill, J Cury, I Echevarria, BC Haller, AR Hasan, X Huang, LNM Iasi, E Noskova, J Obšteter, VAC Pavinato, A Pearson, D Peede, MF Perez, MF Rodrigues, CCR Smith, JP Spence, A Teterina, S Tittes, P Unneberg, JM Vazquez, RK Waples, AW Wohns, Y Wong, F Baumdicker, RA Cartwright, G Gorjanc, Gutenkunst RN, J Kelleher, AD Kern, AP Ragsdale, PL Ralph, DR Schrider, I Gronau
    eLife 12:RP84874 (2023); link; pdf
  • Shifts in mutation bias promote mutators by altering the distribution of fitness effects
    M Tuffaha, S Varakunan, D Castellano, RN Gutenkunst, LM Wahl
    American Naturalist 202:503 (2023); link; pdf

2022

  • Demes: a standard format for demographic models
    G Gower, AP Ragsdale, G Bisschop, RN Gutenkunst, M Hartfield, E Noskova, S Schiffels, TJ Struck, J Kelleher, K Thornton
    Genetics 222:iyac131 (2022); link; pdf
  • On the prospect of achieving accurate joint estimation of selection with population history
    P Johri, A Eyre-Walker, RN Gutenkunst, KE Lohmueller, JD Jensen
    Genome Biology and Evolution 14:evac088 (2022); link; pdf
  • The genomic origins of the world’s first farmers
    N Marchi, L Winkelbach, I Schulz, M Brami, Z Hofmanová, J Blöcher, CS Reyna-Blanco, Y Diekmann, A Thiéry, A Kapopoulou, V Link, V Piuz, S Kreutzer, SM Figarska, E Ganiatsou, A Pukaj, TJ Struck, RN Gutenkunst, N Karul, F Gerritsen, J Pechtl, J Peters, A Zeeb-Lanz, E Lenneis, M Teschler-Nicola, S Triantaphyllou, S Stefanović, C Papageorgopoulou, D Wegmann, J Burger, L Excoffier
    Cell 185:1842 (2022); link; pdf
  • Deep connections: divergence histories with gene flow in mesophotic Agaricia corals
    KE Prata, C Riginos, RN Gutenkunst, K Latijnhouwers K, JA Sánchez, N Englebert, K Hay, P Bongaerts
    Molecular Ecology 31:2511 (2022); link; pdf
  • Genomic landscape of lymphatic malformations and durable complete response to the PI3Kα inhibitor Alpelisib
    MF Shaheen, JY Tse, ES Sokol, M Masterson, P Bansal, I Rabinowitz, CA Tarleton, AS Dobroff, TL Smith, TJ Bocklage, BK Mannakee, RN Gutenkunst, JE Bischoff, SA Ness, GM Riedlinger, R Groisberg, R Pasqualini, S Ganesan, W Arap
    eLife 11:e74510 (2022); link; pdf

2021

  • Chromosome-scale inference of hybrid speciation and admixture with convolutional neural networks
    PD Blischak, MS Barker, RN Gutenkunst
    Molecular Ecology Resources 21:2676 (2021); link; pdf
  • dadi.CUDA: Accelerating population genetic inference with Graphics Processing Units
    RN Gutenkunst
    Molecular Biology and Evolution 38:2177 (2021); link; pdf
  • Inferring genome-wide correlations of mutation fitness effects between populations
    X Huang, AL Fortier, AJ Coffman, TJ Struck, JE James, MN Irby, JE Leon-Burguete, AP Ragsdale, RN Gutenkunst
    Molecular Biology and Evolution 38:4588 (2021); link; pdf

2020

  • A community-maintained standard library of population genetic models
    JR Adrion, CB Cole, N Dukler, JG Galloway, AL Gladstein, G Gower, CC Kyriazis, AP Ragsdale, G Tsambos, F Baumdicker, J Carlson, RA Cartwright, A Durvasula, BY Kim, P McKenzie, PW Messer, E Noskova, DO Vecchyo, F Racimo, TJ Struck, S Gravel, RN Gutenkunst, KE Lohmeuller, PL Ralph, DR Schrider, A Siepel, J Kelleher, AD Kern
    eLife 9:e54967 (2020); link; pdf
  • Inferring the demographic history of inbred species from genome-wide SNP frequency data
    PD Blischak, MS Barker, RN Gutenkunst
    Molecular Biology and Evolution 37:2124 (2020); link; pdf
  • BATCAVE: Calling somatic mutations with a tumor- and site-specific prior
    BK Mannakee, RN Gutenkunst
    NAR: Genomics and Bioinformatics 2:lqaa004 (2020); link; pdf

2018

  • Sensitive and specific post-call filtering of genetic variants in xenograft and primary tumors
    BK Mannakee, U Balaji, AK Witkiewicz, RN Gutenkunst, ES Knudsen
    Bioinformatics 34:1713 (2018); link; pdf
  • The impact of genome-wide association studies on biomedical research publications
    TJ Struck, BK Mannakee, RN Gutenkunst
    Human Genomics 12:38 (2018); link; pdf

2017

  • Exome sequencing provides evidence of polygenic adaptation to a fat-rich animal diet in indigenous Siberian populations
    P Hsieh, B Hallmark, J Watkins, TM Karafet, LP Osipova, RN Gutenkunst, MF Hammer
    Molecular Biology and Evolution 34:2913 (2017); link; pdf
    • Press release; pdf
  • Population genomics of Daphnia pulex
    M Lynch, R Gutenkunst, M Ackerman, K Spitze, Z Ye, T Maruki, Z Jia
    Genetics 206:315 (2017); link; pdf
  • Genomic inferences of domestication events are corroborated by written records in Brassica rapa
    XC Qi, H An, AP Ragsdale, TE Hall, RN Gutenkunst, JC Pires, MS Barker
    Molecular Ecology 26:3373 (2017); link; pdf
  • Inferring demographic history using two-locus statistics
    AP Ragsdale, RN Gutenkunst
    Genetics 206:1037 (2017); link; pdf

2016

  • Computationally efficient composite likelihood statistics for demographic inference
    AJ Coffman, P Hsieh, S Gravel, RN Gutenkunst
    Molecular Biology and Evolution 33:591 (2016); link; pdf
  • Assessing models of speciation under different biogeographic scenarios; an empirical study using multi-locus and RNA-seq analyses
    T Edwards, M Tollis, P Hsieh, RN Gutenkunst, Z Liu, K Kusumi, M Culver, RW Murphy
    Ecology and Evolution 6:379 (2016); link; pdf
  • Whole-genome sequence analyses of Western Central African Pygmy hunter-gatherers reveal a complex demographic history and identify candidate genes under positive natural selection
    P Hsieh, KR Veeramah, J Lachance, SA Tishkoff, JD Wall, MF Hammer, RN Gutenkunst
    Genome Research 26:279 (2016); link; pdf
    • Featured in the Arizona Daily Star; pdf
  • Model-based analyses of whole genome data reveal a complex evolutionary history involving archaic introgression in Central African Pygmies
    P Hsieh, AE Woerner, JD Wall, J Lachance, SA Tishkoff, RN Gutenkunst, MF Hammer
    Genome Research 26:291 (2016); link; pdf
  • Selection on network dynamics drives differential rates of protein domain evolution
    BK Mannakee, RN Gutenkunst
    PLoS Genetics 12:e1006132 (2016); link; pdf
  • Sloppiness and the geometry of parameter space
    BK Mannakee, AP Ragsdale, MK Transtrum, RN Gutenkunst
    in D Gomez-Cabrero and L Geris, editors, Uncertainty in Biology: a Computational Modeling Approach, Springer International (2016); link; pdf
  • Triallelic population genomics for inferring correlated fitness effects of same site nonsynonymous mutations
    AP Ragsdale, AJ Coffman, P Hsieh, TJ Struck, RN Gutenkunst
    Genetics 203:513 (2016); link; pdf
    • Highlighted by the editors of Genetics; pdf

2015

  • Characterizing selective pressures on the pathway for de novo biosynthesis of pyrimidines in yeast
    RA Hermansen*, BK Mannakee*, W Knecht, DA Liberles, RN Gutenkunst
    BMC Evolutionary Biology 15:232 (2015); link; pdf
  • Testing whether metazoan tyrosine loss was driven by selection against promiscuous phosphorylation
    S Pandya, TJ Struck, BK Mannakee, M Paniscus, RN Gutenkunst
    Molecular Biology and Evolution 32:144 (2015); link; pdf

2014

  • Loss of N-terminal acetylation suppresses a prion phenotype by modulating global protein folding
    WM Holmes, BK Mannakee, RN Gutenkunst, TR Serio
    Nature Communications 5:4383 (2014); link; pdf
  • Effect of dedifferentiation on time to mutation acquisition in stem cell-driven cancers
    A Jilkine, RN Gutenkunst
    PLoS Computational Biology 10:e1003481 (2014); link; pdf
  • Sampling strategies for frequency spectrum-based population genomic inference
    JD Robinson, AJ Coffman, MJ Hickerson, RN Gutenkunst
    BMC Evolutionary Biology 14:254 (2014); link; pdf
  • Evidence for increased levels of positive and negative selection on the X chromosome versus autosomes in humans
    K Veeramah, RN Gutenkunst, A Woerner, J Watkins, M Hammer
    Molecular Biology and Evolution 31:2267 (2014); link; pdf

2013

  • Mathematical tools for evolutionary systems biology
    Loewe L, Swain P, Gutenkunst R
    Banff International Research Station meeting report; link; pdf
  • Population genomic analysis of ten genomes reveals a rich speciation and demographic history of orang-utans (Pongo pygmaeus and Pongo abelii)
    X Ma, JL Kelley, K Eilertson, S Musharoff, JD Degenhardt, AL Martins, T Vinar, C Kosiol, A Siepel, RN Gutenkunst, CD Bustamante
    PLoS ONE 8:e77175 (2013); link; pdf
  • Kinetics of coinfection with influenza A virus and Streptococcus pneumoniae
    AM Smith, FR Adler, RM Ribeiro, RN Gutenkunst, JL McAuley, JA McCullers, AS Perelson
    PLoS Pathogens 9:e1003238 (2013); link; pdf

2012

  • Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes
    X Xu*, X Liu*, S Ge*, JD Jensen*, F Hu*, X Li*, Y Dong*, RN Gutenkunst, L Fang, L Huang, J Li, W He, G Zhang, X Zheng, F Zhang, Y Li, C Yu, K Kristiansen, X Zhang, J Wang, M Wright, S McCouch, R Nielsen, J Wang, W Wang
    Nature Biotechnology 30:105 (2012); link; pdf

2011

  • Guidelines for visualizing and annotating rule-based models
    LA Chylek, H Bin, ML Blinov, T Emonet, JR Faeder, B Goldstein, RN Gutenkunst, JM Haugh, T Lipniacki, RG Posner, J Yang, WS Hlavacek
    Molecular BioSystems 7:2779 (2011); link; pdf
  • Demographic history and rare allele sharing among human populations
    S Gravel, BM Henn, RN Gutenkunst, AR Indap, GT Marth, AG Clark, The 1000 Genomes consortium, CD Bustamante
    Proceedings of the National Academy of Sciences USA 108:11983 (2011); link; pdf;abstract
    • Featured in the New York Times; pdf
  • A biophysical model of cell adhesion mediated by immunoadhesin drugs and antibodies
    RN Gutenkunst, D Coombs, T Starr, ML Dustin, B Goldstein
    PLoS ONE 6:e19701 (2011); link; pdf
  • Comparative and demographic analysis of orang-utan genomes
    DP Locke, LW Hillier, WC Warren, KC Worley, LV Nazareth, DM Muzny, SP Yang, Z Wang, AT Chinwalla, P Minx, M Mitreva, L Cook, KD Delehaunty, C Fronick, H Schmidt, LA Fulton, RS Fulton, JO Nelson, V Magrini, C Pohl, TA Graves, C Markovic, A Cree, HH Dinh, J Hume, CL Kovar, GR Fowler, G Lunter, S Meader, A Heger, CP Ponting, T Marques-Bonet, C Alkan, L Chen, Z Cheng, JM Kidd, EE Eichler, S White, S Searle, AJ Vilella, Y Chen, P Flicek, J Ma, B Raney, B Suh, R Burhans, J Herrero, D Haussler, R Faria, O Fernando, F Darré, D Farré, E Gazave, M Oliva, A Navarro, R Roberto, O Capozzi, N Archidiacono, G Della Valle, S Purgato, M Rocchi, MK Konkel, JA Walker, B Ullmer, MA Batzer, AFA Smit, R Hubley, C Casola,DR Schrider, MW Hahn, V Quesada, XS Puente, GR Ordoñez, C López-Otín, T Vinar, B Brejova, A Ratan, RS Harris, W Miller, C Kosiol, HA Lawson, V Taliwal, AL Martins, A Siepel, A Roychoudhury, X Ma, J Degenhardt, CD Bustamante, RN Gutenkunst, T Mailund, JY Dutheil, A Hobolth, MH Schierup, OA Ryder, Y Yoshinaga, PJ de Jong, GM Weinstock, J Rogers, ER Mardis, RA Gibbs, RK Wilson
    Nature 469:529 (2011); link; pdf
    • Featured in UANews; pdf
  • Daily sampling of an HIV-1 patient with slowly progressing disease displays persistence of multiple env subpopulations consistent with neutrality
    H Skar*, RN Gutenkunst*, KW Ramsay, A Alaeus, J Albert, T Leitner
    PLoS ONE 6:e21747 (2011); link; pdf
  • Effect of 1918 PB1-F2 expression on influenza A virus infection kinetics
    AM Smith, FR Adler, JL McAuley, RN Gutenkunst, RM Ribeiro, JA McCullers, AS Perelson
    PLoS Computational Biology 7:e1001081 (2011); link; pdf
  • Discussion of “Riemannian manifold Langevin and Hamiltonian Monte Carlo methods” by Girolami and Calderhead
    MK Transtrum, RN Gutenkunst, Y Chen, BB Machta, JP Sethna
    Journal of the Royal Statistical Society: Series B 73:199 (2011); link; pdf

2010

  • A map of human genome variation from population scale sequencing
    The 1000 Genomes Project Consortium
    Nature 467:1061 (2010); link; pdf
  • RuleMonkey: Software for stochastic simulation of rule-based models
    J Colvin, MI Monine, RN Gutenkunst, WS Hlavacek, DD Von Hoff, RG Posner
    BMC Bioinformatics 11:404 (2010); link; pdf
  • Genetics and genomics of human population structure
    S Ramachandran, H Tang, RN Gutenkunst, CD Bustamante
    in M Speicher et al., editors, Vogel and Motulsky’s Human Genetics: Problems and Approaches, Springer Verlag (2010); link; pdf

2009

  • Targets of balancing selection in the human genome
    AM Andrés, MJ Hubisz, A Indap, D Torgerson, J Degenhardt, AR Boyko, RN Gutenkunst, TJ White, ED Green, CD Bustamante, AG Clark, R Nielsen
    Molecular Biology and Evolution 26:2755 (2009); link; pdf
  • Global distribution of genomic diversity underscores rich complex history of continental human populations
    A Auton, K Bryc, AR Boyko, KE Lohmueller, J Novembre, A Reynolds, A Indap, MH Wright, J Degenhardt, RN Gutenkunst, KS King, MR Nelson, CD Bustamante
    Genome Research 19:795-803 (2009); link; pdf
  • Inferring the joint demographic history of multiple populations from multidimensional SNP data
    RN Gutenkunst, RD Hernandez, SH Williamson, CD Bustamante
    PLoS Genetics 5:e1000695 (2009); link; pdf
  • Darwinian and demographic forces affecting human protein coding genes
    R Nielsen, MJ Hubisz, I Hellmann, D Torgerson, AM Andrés, A Albrechtsen, R Gutenkunst, MD Adams, M Cargill, X Hu, A Boyko, A Indap, CD Bustamante, AG Clark
    Genome Research 19:838 (2009); link; pdf

2008

  • Variational method for estimating the rate of convergence of Markov Chain Monte Carlo algorithms
    FP Casey, JJ Waterfall, RN Gutenkunst, CR Myers, JP Sethna
    Physical Review E 78:046704 (2008); link; pdf
  • Sloppiness, robustness, and evolvability in systems biology
    BC Daniels, YJ Chen, JP Sethna, RN Gutenkunst, CR Myers
    Current Opinion in Biotechnology 19:389 (2008); link; pdf
  • Sloppiness, Modeling, and Evolution in Biochemical Networks
    RN Gutenkunst
    Ph.D. dissertation, Cornell University (2008); link; pdf

2007

  • Optimal experimental design in an epidermal growth factor receptor signalling and down-regulation model
    FP Casey, D Baird, Q Feng, RN Gutenkunst, JJ Waterfall, CR Myers, KS Brown, RA Cerione, JP Sethna
    IET Systems Biology 1:190 (2007); link; pdf
  • Extracting falsifiable predictions from sloppy models
    RN Gutenkunst, FP Casey, JJ Waterfall, CR Myers, JP Sethna
    in G. Stolovitsky, A. Califano, J. Collins, editors, Reverse Engineering Biological Networks: Opportunities and Challenges in Computational Methods for Pathway Inference
    Annals of the New York Academy of Sciences 1115:203 (2007); link; pdf
  • Inferring resource distributions from Atlantic bluefin tuna movements: an analysis based on net displacement and length of track
    R Gutenkunst, N Newlands, M Lutcavage, L Edelstein-Keshet
    Journal of Theoretical Biology 245:243 (2007); link; pdf
  • Universally sloppy parameter sensitivities in systems biology
    RN Gutenkunst, JJ Waterfall, FP Casey, KS Brown, CR Myers, JP Sethna
    PLoS Computational Biology 3:e189 (2007); link; pdf
    • Featured in Biomedical Computation Review; pdf
    • “Exceptional” evaluation on Faculty of 1000: Biology
  • Adaptive mutation in a geometrical model of chemotype evolution
    RN Gutenkunst, JP Sethna
    arXiv:0712.3240 (2007); link; pdf
  • Python unleashed on systems biology
    CR Myers, RN Gutenkunst, JP Sethna
    Computing in Science and Engineering 9:34 (2007); link; pdf

2006

  • Sloppy-model universality class and the Vandermonde matrix
    JJ Waterfall, FP Casey, RN Gutenkunst, KS Brown, CR Myers, PW Brouwer, V Elser, JP Sethna
    Physical Review Letters 97:150601 (2006); link; pdf

2003

  • An introduction to signal extraction in interferometric gravitational wave detectors
    ED Black, RN Gutenkunst
    American Journal of Physics 71:365 (2003); link; pdf

2002

  • Extracting light from water: sonoluminescence
    R Gutenkunst
    Caltech Undergraduate Research Journal 2:16 (2002); pdf

Dissertations and Theses