2007-2008 Publications

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White, R., Nie, Q., Lander, A., and Schilling, T. (2007).
Complex regulation of cyp26a1 creates a robust retinoic acid gradient in the zebrafish embryo. PLoS Biol 5, e304. PMID: 18031199. doi.
Zhang, Y., Lander, A., and Nie, Q. (2007).
Computational analysis of bmp gradients in dorsal-ventral patterning of the zebrafish embryo. J Theor Biol 248, 579-589. PMID: 17673236. doi.
Chou, C., Nie, Q., and Yi, T. (2008).
Modeling robustness tradeoffs in yeast cell polarization induced by spatial gradients. PLoS One 3, e3103. PMID: 21267054. doi.
Chou, S., Zhao, S., Song, Y., Liu, H., and Nie, Q. (2008).
Fus3-triggered tec1 degradation modulates mating transcriptional output during the pheromone response. Mol Syst Biol 4, 212. PMID: 18682702. doi.
Hilioti, Z., SabbaghJr, W., Paliwal, S., Bergmann, A., Goncalves, M., Bardwell, L., and Levchenko, A. (2008).
Oscillatory phosphorylation of yeast fus3 map kinase controls periodic gene expression and morphogenesis. Curr Biol 18, 1700-1706. PMID: 18976914. doi.
Iron, D., Syed, A., Theisen, H., Lukacsovich, T., Naghibi, M., Marsh, L., Wan, F., and Nie, Q. (2008).
The role of feedback in the formation of morphogen territories. Math Biosci Eng 5, 277-298. PMID: 18613734. doi.
Macklin, P., and Lowengrub, J. (2008).
A new ghost cell/level set method for moving boundary problems: Application to tumor growth. J Sci Comput 35, 266-299. PMID: 21331304. doi.
Moore, T., Chou, C., Nie, Q., Jeon, N., and Yi, T. (2008).
Robust spatial sensing of mating pheromone gradients by yeast cells. PLoS One 3, e3865. PMID: 19052645. doi.
Nie, Q., Wan, F., Zhang, Y., and Liu, X. (2008).
Compact integration factor methods in high spatial dimensions. J Comput Phys 227, 5238-5255. PMID: 19809596. doi.
Sanabria, H., Digman, M., Gratton, E., and Waxham, M. (2008).
Spatial diffusivity and availability of intracellular calmodulin. Biophys J 95, 6002-6015. PMID: 18820232. doi.
White, R., and Schilling, T. (2008).
How degrading: Cyp26s in hindbrain development. Dev Dyn 237, 2775-2790. PMID: 18816852. doi.
Wise, S., Lowengrub, J., Frieboes, H., and Cristini, V. (2008).
Three-dimensional multispecies nonlinear tumor growth--i model and numerical method. J Theor Biol 253, 524-543. PMID: 18485374. doi.
Wu, J., Sieglaff, D., Gervin, J., and Xie, X. (2008).
Discovering regulatory motifs in the plasmodium genome using comparative genomics. Bioinformatics 24, 1843-1849. PMID: 18611947. doi. 
2011 2007-8. Copyright © 2013. The Center for Complex Biological Systems, UC Irvine
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