2015 Publications

Adu-Gyamfi, E., Johnson, K., Fraser, M., Scott, J., Soni, S., Jones, K., Digman, M., Gratton, E., Tessier, C., and Stahelin, R. (2015).
Host cell plasma membrane phosphatidylserine regulates the assembly and budding of ebola virus. J Virol 89, 9440-9453. PMID: 26136573. doi.
Aland, S., Hatzikirou, H., Lowengrub, J., and Voigt, A. (2015).
A mechanistic collective cell model for epithelial colony growth and contact inhibition. Biophys J 109, 1347-1357. PMID: 26445436. doi.
Annibale, P., Dvornikov, A., and Gratton, E. (2015).
Electrically tunable lens speeds up 3d orbital tracking. Biomed Opt Express 6, 2181-2190. PMID: 26114037. doi.
Anzalone, A., Gabriel, M., Estrada, L., and Gratton, E. (2015).
Spectral properties of single gold nanoparticles in close proximity to biological fluorophores excited by 2-photon excitation. PLoS One 10, e0124975. PMID: 25909648. doi.
Bardwell, A., and Bardwell, L. (2015).
Two hydrophobic residues can determine the specificity of mitogen-activated protein kinase docking interactions. J Biol Chem 290, 26661-26674. PMID: 26370088. doi.
Buzi, G., Lander, A., and Khammash, M. (2015).
Cell lineage branching as a strategy for proliferative control. BMC Biol 13, 122. PMID: 25784392. doi.
Chen, C., Wang, L., Plikus, M., Jiang, T., Murray, P., Ramos, R., Guerrero-Juarez, C., Hughes, M., Lee, O., Shi, S., et al. (2015).
Organ-level quorum sensing directs regeneration in hair stem cell populations. Cell 161, 277-290. PMID: 25860610. doi.
Chen, H., Gratton, E., and Digman, M. (2015).
Spectral properties and dynamics of gold nanorods revealed by emccd-based spectral phasor method. Microsc Res Tech 78, 283-293. PMID: 25684346. doi.
Chen, H., Holst, G., and Gratton, E. (2015).
Modulated cmos camera for fluorescence lifetime microscopy. Microsc Res Tech 78, 1075-1081. PMID: 26500051. doi.
Chen, L., Wang, M., and Zhong, L. (2015).
Convergence analysis of triangular mac schemes for two dimensional stokes equations. J Sci Comput 63, 716-744. PMID: 26041948. doi.
Chiang, M., Cinquin, A., Paz, A., Meeds, E., Price, C., Welling, M., and Cinquin, O. (2015).
Control of caenorhabditis elegans germ-line stem-cell cycling speed meets requirements of design to minimize mutation accumulation. BMC Biol 13, 51. PMID: 26187634. doi.
Chiang, M., Hallman, S., Cinquin, A., deMochel, N., Paz, A., Kawauchi, S., Calof, A., Cho, K., Fowlkes, C., and Cinquin, O. (2015).
Analysis of in vivo single cell behavior by high throughput, human-in-the-loop segmentation of three-dimensional images. BMC Bioinformatics 16, 397. PMID: 26607933. doi.
Chou, C., Moore, T., Nie, Q., and Yi, T. (2015).
Alternative cell polarity behaviours arise from changes in g-protein spatial dynamics. IET Syst Biol 9, 52-63. PMID: 26029251. doi.
Cinquin, A., Zheng, L., Taylor, P., Paz, A., Zhang, L., Chiang, M., Snow, J., Nie, Q., and Cinquin, O. (2015).
Semi-permeable diffusion barriers enhance patterning robustness in the c. Elegans germline. Dev Cell 35, 405-417. PMID: 26609956. doi.
Cox, G., and Lowengrub, J. (2015).
The effect of spontaneous curvature on a two-phase vesicle. Nonlinearity 28, 773-793. PMID: 26097287. doi.
Curtis, L., Wu, M., Lowengrub, J., Decuzzi, P., and Frieboes, H. (2015).
Computational modeling of tumor response to drug release from vasculature-bound nanoparticles. PLoS One 10, e0144888. PMID: 26660469. doi.
Datta, R., Alfonso-Garca, A., Cinco, R., and Gratton, E. (2015).
Fluorescence lifetime imaging of endogenous biomarker of oxidative stress. Sci Rep 5, 9848. PMID: 25993434. doi.
Du, H., Nie, Q., and Holmes, W. (2015).
The interplay between wnt mediated expansion and negative regulation of growth promotes robust intestinal crypt structure and homeostasis. PLoS Comput Biol 11, e1004285. PMID: 26288152. doi.
Golfetto, O., Hinde, E., and Gratton, E. (2015).
The laurdan spectral phasor method to explore membrane micro-heterogeneity and lipid domains in live cells. Methods Mol Biol 1232, 273-290. PMID: 25331141. doi.
Hedde, P., and Gratton, E. (2015).
Active focus stabilization for upright selective plane illumination microscopy. Opt Express 23, 14707-14714. PMID: 26072829. doi.
Hedde, P., Ranjit, S., and Gratton, E. (2015).
3d fluorescence anisotropy imaging using selective plane illumination microscopy. Opt Express 23, 22308-22317. PMID: 26368202. doi.
Hendrix, J., Baumgrtel, V., Schrimpf, W., Ivanchenko, S., Digman, M., Gratton, E., Krusslich, H., Mller, B., and Lamb, D. (2015).
Live-cell observation of cytosolic hiv-1 assembly onset reveals rna-interacting gag oligomers. J Cell Biol 210, 629-646. PMID: 26283800. doi.
Hinde, E., Cardarelli, F., and Gratton, E. (2015).
Spatiotemporal regulation of heterochromatin protein 1-alpha oligomerization and dynamics in live cells. Sci Rep 5, 12001. PMID: 26238434. doi.
Holmes, W., Mata, M., and Edelstein-Keshet, L. (2015).
Local perturbation analysis: A computational tool for biophysical reaction-diffusion models. Biophys J 108, 230-236. PMID: 25606671. doi.
Hong, T., Fung, E., Zhang, L., Huynh, G., Monuki, E., and Nie, Q. (2015).
Semi-adaptive response and noise attenuation in bone morphogenetic protein signalling. J R Soc Interface 12. PMID: 25972436. doi.
Hong, T., Watanabe, K., Ta, C., Villarreal-Ponce, A., Nie, Q., and Dai, X. (2015).
An ovol2-zeb1 mutual inhibitory circuit governs bidirectional and multi-step transition between epithelial and mesenchymal states. PLoS Comput Biol 11, e1004569. PMID: 26554584. doi.
Ito, A., Hong, C., Rong, X., Zhu, X., Tarling, E., Hedde, P., Gratton, E., Parks, J., and Tontonoz, P. (2015).
Lxrs link metabolism to inflammation through abca1-dependent regulation of membrane composition and tlr signaling. Elife 4, e08009. PMID: 26173179. doi.
Lakhani, V., Hinde, E., Gratton, E., and Elston, T. (2015).
Spatio-temporal regulation of rac1 mobility by actin islands. PLoS One 10, e0143753. PMID: 26606145. doi.
Lanzan, L., CotoHernndez, I., Castello, M., Gratton, E., Diaspro, A., and Vicidomini, G. (2015).
Encoding and decoding spatio-temporal information for super-resolution microscopy. Nat Commun 6, 6701. PMID: 25833391. doi.
Li, A., Lai, Y., Figueroa, S., Yang, T., Widelitz, R., Kobielak, K., Nie, Q., and Chuong, C. (2015).
Deciphering principles of morphogenesis from temporal and spatial patterns on the integument. Dev Dyn 244, 905-920. PMID: 25858668. doi.
Lo, W., Zhou, S., Wan, F., Lander, A., and Nie, Q. (2015).
Robust and precise morphogen-mediated patterning: Trade-offs, constraints and mechanisms. J R Soc Interface 12, 20141041. PMID: 25551154. doi.
Malacrida, L., Gratton, E., and Jameson, D. (2015).
Model-free methods to study membrane environmental probes: A comparison of the spectral phasor and generalized polarization approaches. Methods Appl Fluoresc 3. PMID: 27182438. doi.
Meeds, E., Chiang, M., Lee, M., Cinquin, O., Lowengrub, J., and Welling, M. (2015).
Pope: Post optimization posterior evaluation of likelihood free models. BMC Bioinformatics 16, 264. PMID: 26289041. doi.
Mieruszynski, S., Briggs, C., Digman, M., Gratton, E., and Jones, M. (2015).
Live cell characterization of DNA aggregation delivered through lipofection. Sci Rep 5, 10528. PMID: 26013547. doi.
Mieruszynski, S., Digman, M., Gratton, E., and Jones, M. (2015).
Characterization of exogenous DNA mobility in live cells through fluctuation correlation spectroscopy. Sci Rep 5, 13848. PMID: 26354725. doi.
Moens, P., Digman, M., and Gratton, E. (2015).
Modes of diffusion of cholera toxin bound to gm1 on live cell membrane by image mean square displacement analysis. Biophys J 108, 1448-1458. PMID: 25809257. doi.
Olivera-Couto, A., Salzman, V., Mailhos, M., Digman, M., Gratton, E., and Aguilar, P. (2015).
Eisosomes are dynamic plasma membrane domains showing pil1-lsp1 heteroligomer binding equilibrium. Biophys J 108, 1633-1644. PMID: 25863055. doi.
Patel, V., Ceglia, N., Zeller, M., Eckel-Mahan, K., Sassone-Corsi, P., and Baldi, P. (2015).
The pervasiveness and plasticity of circadian oscillations: The coupled circadian-oscillators framework. Bioinformatics 31, 3181-3188. PMID: 26049162. doi.
Perumal, V., Krishnan, K., Gratton, E., Dharmarajan, A., and Fox, S. (2015).
Number and brightness analysis of sfrp4 domains in live cells demonstrates vesicle association signal of the nld domain and dynamic intracellular responses to wnt3a. Int J Biochem Cell Biol 64, 91-96. PMID: 25805505. doi.
Plotegher, N., Stringari, C., Jahid, S., Veronesi, M., Girotto, S., Gratton, E., and Bubacco, L. (2015).
Nadh fluorescence lifetime is an endogenous reporter of î±-synuclein aggregation in live cells. Faseb j 29, 2484-2494. PMID: 25713058. doi.
Quang, D., Chen, Y., and Xie, X. (2015).
Dann: A deep learning approach for annotating the pathogenicity of genetic variants. Bioinformatics 31, 761-763. PMID: 25338716. doi.
Ranjit, S., Dvornikov, A., Stakic, M., Hong, S., Levi, M., Evans, R., and Gratton, E. (2015).
Imaging fibrosis and separating collagens using second harmonic generation and phasor approach to fluorescence lifetime imaging. Sci Rep 5, 13378. PMID: 26293987. doi.
Rong, X., Wang, B., Dunham, M., Hedde, P., Wong, J., Gratton, E., Young, S., Ford, D., and Tontonoz, P. (2015).
Lpcat3-dependent production of arachidonoyl phospholipids is a key determinant of triglyceride secretion. Elife 4. PMID: 25806685. doi.
Shapiro, B., Tobin, C., Mjolsness, E., and Meyerowitz, E. (2015).
Analysis of cell division patterns in the arabidopsis shoot apical meristem. Proc Natl Acad Sci U S A 112, 4815-4820. PMID: 25825722. doi.
Stringari, C., Wang, H., Geyfman, M., Crosignani, V., Kumar, V., Takahashi, J., Andersen, B., and Gratton, E. (2015).
In vivo single-cell detection of metabolic oscillations in stem cells. Cell Rep 10, 1-7. PMID: 25543138. doi.
Sun, Z., and Komarova, N. (2015).
Stochastic control of proliferation and differentiation in stem cell dynamics. J Math Biol 71, 883-901. PMID: 25319118. doi.
Ta, C., Wang, D., and Nie, Q. (2015).
An integration factor method for stochastic and stiff reaction-diffusion systems. J Comput Phys 295, 505-522. PMID: 25983341. doi.
Tan, Z., Dai, W., vanErp, T., Overman, J., Demuro, A., Digman, M., Hatami, A., Albay, R., Sontag, E., Potkin, K., et al. (2015).
Huntington's disease cerebrospinal fluid seeds aggregation of mutant huntingtin. Mol Psychiatry 20, 1286-1293. PMID: 26100538. doi.
Wang, D., Chen, W., and Nie, Q. (2015).
Semi-implicit integration factor methods on sparse grids for high-dimensional systems. J Comput Phys 292, 43-55. PMID: 25897178. doi.
Zhang, K., Kang, D., Ali, M., Liu, L., Labanieh, L., Lu, M., Riazifar, H., Nguyen, T., Zell, J., Digman, M., et al. (2015).
Digital quantification of mirna directly in plasma using integrated comprehensive droplet digital detection. Lab Chip 15, 4217-4226. PMID: 26387763. doi. 
2011 2015. Copyright © 2013. The Center for Complex Biological Systems, UC Irvine
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