- 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. (Submitted, Dec. 2015, ~20 pages)
- W. R. Holmes, Nabora Soledad Reyes de Mochel, Qixian Wang, Huijing Du, Michael Chiang, Olivier Cinquin, Ken W.Y. Cho, Qing Nie, “Intracellular noise has a significant, positive role in development of early embryonic structures.” Nature Communications (Under review, Dec. 2015, ~20 pages + 16 page SM)
- W. R. Holmes*, May Anne Mata, Leah Edelstein-Keshet, “Local Perturbation Analysis: A computational tool for biophysical reaction-diffusion models.” Biophysical Journal (In Press, Sept. 2015) - Preprint
- This article has associated tutorials for implementing this method in both XPPAuto and the MatLab based package MatCont.
- W. R. Holmes*, “A spectral, non-parametric approximate Bayesian computation algorithm for parameter inference: Theory and practice.” Journal of Mathematical Psychology (Currently being revised for second round review, Sept. 2014 -28 pages) - Preprint
- W. R. Holmes*, Jennifer S. Trueblood, Andrew Heathcoat, “Asymmetric updating and hysteresis in perceptual decision-making with changing information”. PLoS Comput. Biol. (Submitted, Aug. 2014 - 26 pages)
- W. R. Holmes, Q. Nie, ``Interactions and tradeoffs between cell recruitment, proliferation, and differentiation affect CNS regeneration", Biophys. Journal, 106(7): 1528-1536, 2014 - PDF
- 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, (To appear Oct. 2014) - PDF
- AG and WRH contributed equaly to this work.
- W. R. Holmes*, ``An excitable compass guides chemotaxis?", Submitted to the Biophys. Journal, 106(5): 989, 2014
- W. R. Holmes*, ``A Local Non-linear Stability Analysis for Detecting Pattern Formation in Reaction Diffusion Systems'', Bulletin of Mathematical Biology, Online First (October 2013) - PDF
- 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
- 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, In Press June 2013 - PDF
- WRH conceived, designed, and supervised this work.
- 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
- 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
- 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
- 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
- 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
- Perkins T. A.a, Holmes W. R.a, 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 (a equal contributions, nominated for annual editors award) - PDF
* Indicates corresponding author
In Preparation
- W. R. Holmes, Jinseok Park, Andre Levchenko, Leah Edelstein-Keshet, “Modeling polar and oscillatory
transitions in melanoma cell morphology”.
- A second companion manuscript to this is also in preparation.
- Qixuan Wang, W. R. Holmes, Qing Nie “Noise mediated plasticity and cell sorting jointly specify gene expression domains in the developing zebrafish hindbrain transitions in melanoma cell morphology”.
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