Ryan Gutenkunst

Theoretical Biology and Biophysics & Center for Nonlinear Studies
Los Alamos National Laboratory

ryang@lanl.gov
ryan@gutenkunst.org

Peer reviewed publications

  1. Genome variation of rice under domestication
    X Xu°, S Ge°, JD Jensen°, RN Gutenkunst°, J Li°, X Li°, L Fang, L Huang, K Ye, W He, G Zhang, X Zheng, F Zhang, F Hu, Y Li, C Yu, Y Guo, D Li, K Kristiansen, X Zhang, J Wang, R Nielsen, J Wang, W Wang
    °contributed equally
    submitted; LA-UR 09-07280
  2. Proteins with greater influence on network dynamics evolve slower but are not more essential
    RN Gutenkunst
    submitted; arXiv:0909.2889; LA-UR 09-05782
  3. Adaptive mutation in a geometrical model of chemotype evolution
    RN Gutenkunst, JP Sethna
    submitted; arXiv:0712.3240
  4. Human population genetics and genomics
    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 (in press); LA-UR 09-05785
  5. 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 (in press), publisher copy
  6. Inferring the joint demographic history of multiple populations from multidimensional SNP data
    RN Gutenkunst, RD Hernandez, SH Williamson, CD Bustamante
    PLoS Genetics 5(10):e1000695 (2009); arXiv:0909.0925; publisher copy; local copy; local supporting info; LA-UR: 09-03343
  7. 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 19:838-849 (2009); publisher copy; local copy
  8. 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); publisher copy; local copy
  9. Sloppiness, robustness, and evolvability in systems biology
    BC Daniels, YJ Chen, JP Sethna, RN Gutenkunst, CR Myers
    Current Opinion in Biotechnology 19:389-395 (2008); arXiv:0805.2628; publisher copy; local copy; local supporting info
  10. 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); arXiv:physics/0609001; publisher copy; local copy
  11. Universally sloppy parameter sensitivities in systems biology
    RN Gutenkunst, JJ Waterfall, FP Casey, KS Brown, CR Myers, JP Sethna
    PLoS Computational Biology 3(10):e189 (2007); arXiv:q-bio.QM/0701039; publisher copy; local copy; local supporting info
    • Featured in a one-page article: A Dance, "Sloppy" Systems Biology, Biomedical Computation Review Winter:2 (2007/08); publisher copy; local copy
    • "Exceptional" evaluation on Faculty of 1000: Biology.
  12. 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 1115:203-211 (2007); arXiv:0704.3049; publisher copy; local copy
  13. 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(3):190-202 (2007); arXiv:q-bio.MN/0610024; publisher copy; local copy
  14. Python unleashed on systems biology
    CR Myers, RN Gutenkunst, JP Sethna
    Computing in Science and Engineering 9(3):34-37 (2007); arXiv:0704.3259; publisher copy; local copy
  15. 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(2):243-257 (2007); publisher copy; local copy
  16. 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); arXiv:cond-mat/0605387; publisher copy; local copy
  17. An introduction to signal extraction in interferometric gravitational wave detectors
    ED Black, RN Gutenkunst
    American Journal of Physics 71(4):365-378 (2003); publisher copy; local copy
  18. Extracting light from water: Sonoluminescence
    R Gutenkunst
    Caltech Undergraduate Research Journal 2(1):16-22 (2002); local copy

Software

Other science publications

  1. Sloppiness, Modeling, and Evolution in Biochemical Networks
    RN Gutenkunst
    Ph.D. thesis, Cornell University (2007); university copy; hyperlinked local copy

Selected presentations

Photography publications

  1. Los Gatos Holds 52nd Parade
    A Dallas, R Gutenkunst (photographer)
    Los Gatos Observer December 9 (2008); link
  2. Black Tusk: Črna gora v Britanski Kolumbiji
    M Željko, R Gutenkunst (photographer)
    Planinski Vestnik May:22 (2004); local copy (sadly, poor photo quality in pdf)

Contact