2009 Publications

Bardwell, A., Frankson, E., and Bardwell, L. (2009).
Selectivity of docking sites in mapk kinases. J Biol Chem 284, 13165-13173. PMID: 19196711. doi.
Barlow, L., and Calof, A. (2009).
Symposium overview: Stem cells in sensory epithelium development and regeneration. Ann N Y Acad Sci 1170, 5-6. PMID: 19686097. doi.
Bearer, E., Lowengrub, J., Frieboes, H., Chuang, Y., Jin, F., Wise, S., Ferrari, M., Agus, D., and Cristini, V. (2009).
Multiparameter computational modeling of tumor invasion. Cancer Res 69, 4493-4501. PMID: 19366801. doi.
Beites, C., Hollenbeck, P., Kim, J., Lovell-Badge, R., Lander, A., and Calof, A. (2009).
Follistatin modulates a bmp autoregulatory loop to control the size and patterning of sensory domains in the developing tongue. Development 136, 2187-2197. PMID: 19474151. doi.
Beites, C., Kawauchi, S., and Calof, A. (2009).
Olfactory neuron patterning and specification. Dev Neurobiol 7, 145-156. PMID: 24817923. doi.
Cai, A., Peng, Y., Wells, J., Dai, X., and Nie, Q. (2009).
Multi-scale modelling for threshold dependent differentiation. Math Model Nat Phenom 4, 103-117. PMID: 20622931. doi.
Caracciolo, G., Caminiti, R., Digman, M., Gratton, E., and Sanchez, S. (2009).
Efficient escape from endosomes determines the superior efficiency of multicomponent lipoplexes. J Phys Chem B 113, 4995-4997. PMID: 19301832. doi.
Christley, S., Nie, Q., and Xie, X. (2009).
Incorporating existing network information into gene network inference. PLoS One 4, e6799. PMID: 19710931. doi.
Cinquin, O. (2009).
Purpose and regulation of stem cells: A systems-biology view from the caenorhabditis elegans germ line. J Pathol 217, 186-198. PMID: 19065622. doi.
Cristini, V., Li, X., Lowengrub, J., and Wise, S. (2009).
Nonlinear simulations of solid tumor growth using a mixture model: Invasion and branching. J Math Biol 58, 723-763. PMID: 18787827. doi.
Digman, M., and Gratton, E. (2009).
Fluorescence correlation spectroscopy and fluorescence cross-correlation spectroscopy. Wiley Interdiscip Rev Syst Biol Med 1, 273-282. PMID: 20835996. doi.
Digman, M., and Gratton, E. (2009).
Imaging barriers to diffusion by pair correlation functions. Biophys J 97, 665-673. PMID: 19619481. doi.
Digman, M., and Gratton, E. (2009).
Analysis of diffusion and binding in cells using the rics approach. Microsc Res Tech 72, 323-332. PMID: 19067357. doi.
Digman, M., Wiseman, P., Choi, C., Horwitz, A., and Gratton, E. (2009).
Stoichiometry of molecular complexes at adhesions in living cells. Proc Natl Acad Sci U S A 106, 2170-2175. PMID: 19168634. doi.
Digman, M., Wiseman, P., Horwitz, A., and Gratton, E. (2009).
Detecting protein complexes in living cells from laser scanning confocal image sequences by the cross correlation raster image spectroscopy method. Biophys J 96, 707-716. PMID: 19167315. doi.
Jen, Y., Musacchio, M., and Lander, A. (2009).
Glypican-1 controls brain size through regulation of fibroblast growth factor signaling in early neurogenesis. Neural Dev 4, 33. PMID: 19732411. doi.
Kawauchi, S., Kim, J., Santos, R., Wu, H., Lander, A., and Calof, A. (2009).
Foxg1 promotes olfactory neurogenesis by antagonizing gdf11. Development 136, 1453-1464. PMID: 19297409. doi.
Kawauchi, S., Santos, R., Kim, J., Hollenbeck, P., Murray, R., and Calof, A. (2009).
The role of foxg1 in the development of neural stem cells of the olfactory epithelium. Ann N Y Acad Sci 1170, 21-27. PMID: 19686101. doi.
Kuchaiev, O., Wang, P., Nenadic, Z., and Przulj, N. (2009).
Structure of brain functional networks. Conf Proc IEEE Eng Med Biol Soc 2009, 4166-4170. PMID: 19964621. doi.
Lander, A. (2009).
The 'stem cell' concept: Is it holding us back? J Biol 8, 70. PMID: 19769787. doi.
Lander, A., Gokoffski, K., Wan, F., Nie, Q., and Calof, A. (2009).
Cell lineages and the logic of proliferative control. PLoS Biol 7, e15. PMID: 19166268. doi.
Lander, A., Lo, W., Nie, Q., and Wan, F. (2009).
The measure of success: Constraints, objectives, and tradeoffs in morphogen-mediated patterning. Cold Spring Harb Perspect Biol 1, a002022. PMID: 20066078. doi.
Lander, A., Nie, Q., Wan, F., and Zhang, Y. (2009).
Localized ectopic expression of dpp receptors in a drosophila embryo. Stud Appl Math 123, 175-214. PMID: 20160891. doi.
Lei, J., He, G., Liu, H., and Nie, Q. (2009).
A delay model for noise-induced bi-directional switching. Nonlinearity 22, 2845-2859. PMID: 20592956. doi.
Li, X., Lowengrub, J., Ratz, A., and Voigt, A. (2009).
Solving pdes in complex geometries: A diffuse domain approach. Commun Math Sci 7, 81-107. PMID: 21603084. doi.
Li, X., and Nie, Q. (2009).
A high-order boundary integral method for surface diffusions on elastically stressed axisymmetric rods. J Comput Phys 228, 4625-4637. PMID: 26487788. doi.
Linville, A., Radtke, K., Waxman, J., Yelon, D., and Schilling, T. (2009).
Combinatorial roles for zebrafish retinoic acid receptors in the hindbrain, limbs and pharyngeal arches. Dev Biol 325, 60-70. PMID: 18929555. doi.
Lo, W., Chou, C., Gokoffski, K., Wan, F., Lander, A., Calof, A., and Nie, Q. (2009).
Feedback regulation in multistage cell lineages. Math Biosci Eng 6, 59-82. PMID: 19292508. doi.
Lowengrub, J., Ratz, A., and Voigt, A. (2009).
Phase-field modeling of the dynamics of multicomponent vesicles: Spinodal decomposition, coarsening, budding, and fission. Phys Rev E Stat Nonlin Soft Matter Phys 79, 031926. PMID: 19391990. doi.
Macklin, P., McDougall, S., Anderson, A., Chaplain, M., Cristini, V., and Lowengrub, J. (2009).
Multiscale modelling and nonlinear simulation of vascular tumour growth. J Math Biol 58, 765-798. PMID: 18781303. doi.
Mitchell, B., Stubbs, J., Huisman, F., Taborek, P., Yu, C., and Kintner, C. (2009).
The pcp pathway instructs the planar orientation of ciliated cells in the xenopus larval skin. Curr Biol 19, 924-929. PMID: 19427216. doi.
Mjolsness, E., Orendorff, D., Chatelain, P., and Koumoutsakos, P. (2009).
An exact accelerated stochastic simulation algorithm. J Chem Phys 130, 144110. PMID: 19368432. doi.
Tanner, K., Ferris, D., Lanzano, L., Mandefro, B., Mantulin, W., Gardiner, D., Rugg, E., and Gratton, E. (2009).
Coherent movement of cell layers during wound healing by image correlation spectroscopy. Biophys J 97, 2098-2106. PMID: 19804742. doi.
Teigen, K., Li, X., Lowengrub, J., Wang, F., and Voigt, A. (2009).
A diffuse-interface approach for modeling transport, diffusion and adsorption/desorption of material quantities on a deformable interface. Commun Math Sci 4, 1009-1037. PMID: 21373370. doi.
Thalhauser, C., and Komarova, N. (2009).
Specificity and robustness of the mammalian mapk-ieg network. Biophys J 96, 3471-3482. PMID: 19413954. doi.
Wells, J., Lee, B., Cai, A., Karapetyan, A., Lee, W., Rugg, E., Sinha, S., Nie, Q., and Dai, X. (2009).
Ovol2 suppresses cell cycling and terminal differentiation of keratinocytes by directly repressing c-myc and notch1. J Biol Chem 284, 29125-29135. PMID: 19700410. doi.
Zhou, Y., He, J., and Nie, Q. (2009).
A comparative runtime analysis of heuristic algorithms for satisfiability problems. Artif Intell 173, 240-257. PMID: 20126510. doi 
2011 2009. Copyright © 2013. The Center for Complex Biological Systems, UC Irvine
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