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 - 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
- Optimization in the demographic simulation software dadi
K Cunningham, Honors BS in Molecular & Cellular Biology, 2013 - Modeling selection bias on recombination rates inferred through linkage disequilibrium
A Fan, Honors BS in Statistics & Data Science, 2023 - Inferring the demographic history and joint distribution of fitness effects in the wild house mouse, Mus musculus domesticus
O Fernflores, Honors BS in Molecular & Cellular Biology, 2024 - Improving the robustness of dominance and selection inference
AL Fortier, Honors BS in Molecular & Cellular Biology, 2018 - Model-based population genetics in indigenous humans: Inferences of demographic history, adaptive selection, and African archaic admixture using whole-genome/exome sequencing data
P Hsieh, PhD in Ecology and Evolutionary Biology, 2016 - The joint distribution of fitness effects of wild tomatoes and a brief introduction to linkage in DFE inference
MN Irby, Honors BS in Molecular & Cellular Biology and Mathematics, 2020 - Evolutionary rate covariation of domain families
B Jernigan, BS in Chemical and Environmental Engineering, 2017 - Evolutionary rate at the protein domain level is constraint by importance to network dynamics
BK Mannakee, Honors BS in Biochemistry, 2012 - Statistical methods for improving low frequency variant calling in cancer genomics
BK Mannakee, PhD in Biostatistics, 2019 - Directional selection on tyrosine frequencies in eukaryotes versus solvent accessibility
S Pandya, Honors BS in Biochemistry, 2013 - Multi-allele population genomics for inference of demography and natural selection
AP Ragsdale, PhD in Applied Mathematics, 2016 - Computationally efficient, cost-effective, and interpretable machine learning methods for population genomic inference
LN Tran, PhD in Genetics, 2024