1. W. R. Holmes, (2019) “Sub-diffusive dynamics lead to depleted particle densities near cellular borders”, Biophysical Journal, 116(8), pp 1538-1546, 2019 – Link – biorxiv Link
  2. Kai M Bracey, Kung-Hsien Ho, Dmitry Yampolsky, Guoqiang Gu, Irina Kaverina, William R Holmes, “Microtubules Regulate Spatial Localization and Avaliability of Insulin Granules in Pancreatic Beta Cells” (2019), Submitted, biorxiv Link
  3. Cole Zmurchok, William R. Holmes, “Modeling cell shape diversity arising from complex Rho GTPase dynamics” (2019), Submitted – biorxiv Link
  4. Zachary P Kipatrick, William R Holmes, Tahra L Eissa, Krešimir Josić, “Optimal Models of decision-making in dynamic environments” (2019), Current Opinion in Neurobiology, Accepted – ArXiv Link
  5. W. R. Holmes, J.S. Trueblood, N.J. Evans, A. Heathcote, (2019) “Urgency, Leakage, and the Relative Nature of Information Processing in Decision Making”, Submitted – biorxiv Link
  6. W. R. Holmes, J.S. Trueblood, N.J. Evans, A. Heathcote, (2019) “A Joint Deep Neural Network and Evidence Accumulation Modeling approach to Human Decision-making with Naturalistic Images.”, Computational Brain and Behavior, Accepted  (2019)
  7. N. J. Evans, W. R. Holmes*, Jennifer S. Trueblood*, “Response-time data provide critical constraints on dynamic models of multi-alternative, multi-attribute choice”, Psychonomic Bulletin and Review, 26(3), pp 901-933, 2019. – Link
  8. N. J. Evans, J.S. Trueblood, W.R. Holmes, “A parameter recovery assessment of time-variant models of decision-making.”, Behavioral Research Methods, pp. 1-14, 2019 – Link
  9. Y. Lin, A. Heathcote, W. R. Holmes (2019) “Parallel Probability Density Approximation”, Accepted in Behavioral Research Methods
  10. Vijay Rajagopal*, W. R. Holmes*, Peter Vee Sin Lee, “Computational Modelling of Single Cell and Cytoskeletal Mechanobiology”, WIREs Systems Biology and Medicine, 10(2), pp e1407, 2018 – Link
  11. W. R. Holmes, L. Edelstein-Keshet, “Editorial Overview: Mathematical Modeling Issue”, Current Opinion in Systems Biology”, Current Opinion in Systems Biology, 9, pp. iv-viii, 2018 – Link
  12. 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”, Molecular Biology of the Cell, 28(23), pp. 3181-3192, 2017 – Link
  13. J.S. Trueblood*, W.R. Holmes* et al. (7 others), “The impact of speed and bias on the cognitive processes of experts and novices in medical image decision-making”, Cognitive Research: Principles and Implications, 3(1), pp 28, 2018 – Link
  14. 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”, Psychological Bulletin and Review, pp 1-19, 2017 – Link
  15. 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 – Link
  16. 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 – Link
  17. W. R. Holmes*, J.S. Trueblood, “Bayesian Analysis of the Piecewise Diffusion Decision Model”, Behavioral Research Methods, pp. 1-14, 2017 – Link
  18. 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 – Link
  19. 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 – Link
  20. W. R. Holmes*, Leah Edelstein-Keshet, “Analysis of a minimal Rho-GTPase circuit regulating cell shape”, Physical Biology (13), 046001, 2016 – PDF
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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.
  28. 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
  29. 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
  30. W. R. Holmes, “An excitable compass guides chemotaxis?”, Biophysical Journal, 106(5): 989, 2014 – PDF
  31. 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
  32. 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
  33. 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
  34. 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
  35. 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
  36. 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
  37. 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
  38. 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
  39. 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