Publications

  1. Vijay Rajagopal*, W. R. Holmes*, Peter Vee Sin Lee, “Computational Modelling of Single Cell and Cytoskeletal Mechanobiology”, Accepted, WIREs Systems Biology and Medicine, 2017
  2. Anna A.W.M. Sanders, Kevin Chang, Xiaodong Zhu, Roslin J. Thoppil, W. R. Holmes*, Irina Kaverina*,”Non-random $\gamma$-TuNA-dependent spatial pattern of microtubule nucleation at the Golgi”, Accepted, MBoC, 2017
  3. J.S. Trueblood*, W.R. Holmes* et al. (7 others), “Investigating the Cognitive Processes Involved in Cancer Cell Image Identification”, Submitted, 2017
  4. J. Evans, W. R. Holmes*, Jennifer S. Trueblood*, “Comparing models of context effects in multi-attribute choice”, Submitted, 2017
  5. Gilles, Dutilh, et al. (W. R. Holmes 1 of 27 co-authors), “The Quality of Response Time Data Inference: A Blinded,Collaborative Approach to the Validity of Cognitive Models”, Submitted 2017
  6. W. R. Holmes*, JinSeok Park, Andre Levchenko, Leah Edelstein-Keshet, “A mathematical model coupling polarity signaling to cell adhesion explains diverse cell migration patterns”, PLoS Computational Biology 13 (5), e1005524, 2017
  7. JinSeok Park, W. R. Holmes, et. al., “A mechano-chemical feedback underlies co-existence of qualitatively distinct cell polarity patterns within diverse cell populations”, PNAS, 201700054, 2017
  8. W. R. Holmes*, J.S. Trueblood, “Bayesian Analysis of the Piecewise Diusion Decision Model”, Behavioral Research Methods, pp. 1-14, 2017
  9. W. R. Holmes, Nabora Soledad Reyes de Mochel, Qixian Wang, Huijing Du, Michael Chiang, Olivier Cinquin, Ken W.Y. Cho, Qing Nie,“Gene Expression Noise Enhances Robust Organization of the Early Mammalian Blastocyst.” , PLoS Computational Biology 13 (1), e1005320, 2017
  10. Qixuan Wang, W. R. Holmes, Julian Sosnik, Thomas Shilling, Qing Nie, “Cell sorting and noise induced cell plasticity coordinate to sharpen boundaries between gene expression domains”, PLoS Computational Biology 13 (1), e1005307, 2017
  11. W. R. Holmes*, Leah Edelstein-Keshet, “Analysis of a minimal Rho-GTPase circuit regulating cell shape”, Physical Biology (13), 046001, 2016 – PDF
  12. W. R. Holmes*, Adriana E. Golding, William M. Bement, Leah Edelstein-Keshet, “A mathematical model of GTPase pattern formation during single-cell wound repair”, J. of the Royal Soc. Interface Focus, 20160032, 2016 – PDF
  13. W. R. Holmes*, Jennifer S. Trueblood, Andrew Heathcoat, “A new framework for modeling decisions about changing information: The Piecewise Linear Ballistic Accumulator model”. Cognitive Psychology (85), 1-29, 2016 – PDF
  14. Darragh Walsh, Philipp Roth. W. R. Holmes, Kerry Landman, Tobias Merson, Barry Hughes, “Is cell migration or proliferation dominant in the formation of linear arrays of oligodendrocytes?”, J. Theor. Biol, (406), 17-30, 2016 – PDF
  15. W. R. Holmes, “A practical guide to the Probability Density Approximation (PDA) with improved implementation and error characterization” Journal of Mathematical Psychology (68), 13-24, 2015 – PDF
  16. W. R.  Holmes, Laura Liao, William Bement, Leah Edelstein-Keshet, “Modeling the roles of protein kinase C beta and eta in single cell wound repair”. Molecular Biology of the Cell, 26(22): 4100-4108, 2015 – PDF
  17. Huijing Du, Qing Nie, W. R. Holmes*, “The interplay between Wnt mediated expansion and negative regulation of growth promote robust intestinal crypt structure and homeostasis.”, PLoS Comput. Biol., 11(8): e1004285, 2015 – PDF
  18. W. R. Holmes*, May Anne Mata, Leah Edelstein-Keshet, “Local Perturbation Analysis: A computational tool for biophysical reaction-diffusion models.” Biophysical Journal, 108(2), pp. 230-236, 2015 – PDF
    • This article has associated tutorials for implementing this method in both XPPAuto and the MatLab based package MatCont.
  19. W. R. Holmes, Q. Nie, “Interactions and tradeoffs between cell recruitment, proliferation, and differentiation affect CNS regeneration”, Biophysical Journal, 106(7): 1528-1536, 2014 – PDF
  20. Alexander Gord*, W. R. Holmes*, Xing Dai, Qing Nie, “Computational modeling of epidermal stratification highlights the importance of asymmetric cell division for predictable and robust layer formation”, Journal of the Royal Society Interface, 11(99): 20140631, 2014 – PDF
  21. W. R. Holmes, “An excitable compass guides chemotaxis?”, Biophysical Journal, 106(5): 989, 2014 – PDF
  22. W. R. Holmes*, “A Local Non-linear Stability Analysis for Detecting Pattern Formation in Reaction Diffusion Systems”, Bulletin of Mathematical Biology, 76(1), pp. 157-183, 2013 – PDF
  23. L. Edelstein-Keshet, W. R. Holmes*, Mark Zajac, Meghan Dutot, “From simple to detailed models for cell polarization”, Philos T Royal Society B, 368: 20130003, 2013 – PDF
  24. M. Meta, M. Dudot, L. Edelstein-Keshet, W. R. Holmes*, “A model for intracellular actin waves explored by nonlinear local perturbation analysis”, Journal of Theoretical Biology, 334, pp. 149-161, 2013 – PDF
  25. B. Lin, W. R. Holmes, J. Wang, T. Ueno, A. Harwell, L. Edelstein-Keshet, T. Inoue, and A. Levchenko, “Synthetic graded Rac activation drives cell polarity and locomotion”, PNAS, 109(52), E3668-E3677, 2012 – PDF
  26. W. R. Holmes*, L. Edelstein-Keshet, “A Comparison of Computational Models for Eukaryotic Cell Shape and Motility”, PLoS Comput. Biol., 8(12), e1002793, 2012 – PDF
  27. W. R. Holmes*, A. Carlsson, and L. Edelstein-Keshet, “Regimes of Wave Type Patterning driven by Refractory Actin Feedback: Transition from Static Polarization to Dynamic Wave Behaviour”, Phys. Biol., 9(4), 046005, 2012 – PDF
  28. W. R. Holmes*, B. Lin, A. Levchenko, and L. Edelstein-Keshet, “Modelling cell polarization driven by synthetic spatially graded Rac activation”, PloS Comput. Biol., 8(6), e1002366, 2012 – PDF
  29. W. R. Holmes*, M.S. Jolly, and J. Rubinstein, “Hydro-elastic waves in a cochlear model: Numerical simulations and an analytically reduced model”, Confluentes Mathematici, Vol. 3, No. 3 pp. 523-541, 2011 – PDF
  30. Perkins T. A*., Holmes W. R.*, Weltzin J. F., “Multi-species interactions in competitive hierarchies: new methods and empirical test”. Journal of Vegetation Science: Vol. 18, No. 5 pp. 685-692, 2007 (nominated for annual editors award) – PDF

*Indicates corresponding, co-corresponding author, or equal contributions.

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