2013 Publications

Adu-Gyamfi, E., Soni, S., Xue, Y., Digman, M., Gratton, E., and Stahelin, R. (2013).
The ebola virus matrix protein penetrates into the plasma membrane: A key step in viral protein 40 (vp40) oligomerization and viral egress. J Biol Chem 288, 5779-5789. PMID: 23297401. doi.
Altamore, I., Lanzano, L., and Gratton, E. (2013).
Dual channel detection of ultra low concentration of bacteria in real time by scanning fcs. Meas Sci Technol 24, 65702. PMID: 24039347. doi.
Andrews, L., Jones, M., Digman, M., and Gratton, E. (2013).
Detecting pyronin y labeled rna transcripts in live cell microenvironments by phasor-flim analysis. Methods Appl Fluoresc 1, 015001. PMID: 24563776. doi.
Andrews, L., Jones, M., Digman, M., and Gratton, E. (2013).
Spectral phasor analysis of pyronin y labeled rna microenvironments in living cells. Biomed Opt Express 4, 171-177. PMID: 23304656. doi.
Chen, H., and Gratton, E. (2013).
A practical implementation of multifrequency widefield frequency-domain fluorescence lifetime imaging microscopy. Microsc Res Tech 76, 282-289. PMID: 23296945. doi.
Chen, M., Wang, L., Liu, C., and Nie, Q. (2013).
Noise attenuation in the on and off states of biological switches. ACS Synth Biol 2, 587-593. PMID: 23768065. doi.
Chiu, C., Digman, M., and Gratton, E. (2013).
Measuring actin flow in 3d cell protrusions. Biophys J 105, 1746-1755. PMID: 24138850. doi.
Chiu, C., Digman, M., and Gratton, E. (2013).
Cell matrix remodeling ability shown by image spatial correlation. J Biophys 2013, 532030. PMID: 23935614. doi.
Chiu, C., and Gratton, E. (2013).
Axial super resolution topography of focal adhesion by confocal microscopy. Microsc Res Tech 76, 1070-1078. PMID: 23897846. doi.
Clemens, K., Bilanchone, V., Beliakova-Bethell, N., Larsen, L., Nguyen, K., and Sandmeyer, S. (2013).
Sequence requirements for localization and packaging of ty3 retroelement rna. Virus Res 171, 319-331. PMID: 23073180. doi.
Conway, D., Breckenridge, M., Hinde, E., Gratton, E., Chen, C., and Schwartz, M. (2013).
Fluid shear stress on endothelial cells modulates mechanical tension across ve-cadherin and pecam-1. Curr Biol 23, 1024-1030. PMID: 23684974. doi.
Coppola, S., Cardarelli, F., Pozzi, D., Estrada, L., Digman, M., Gratton, E., Bifone, A., Marianecci, C., and Caracciolo, G. (2013).
The role of cytoskeleton networks on lipid-mediated delivery of DNA. Ther Deliv 4, 191-202. PMID: 23343159. doi.
Coppola, S., Pozzi, D., DeSanctis, S., Digman, M., Gratton, E., and Caracciolo, G. (2013).
Quantitative measurement of intracellular transport of nanocarriers by spatio-temporal image correlation spectroscopy. Methods Appl Fluoresc 1. PMID: 24376913. doi.
Cutrale, F., Salih, A., and Gratton, E. (2013).
Spectral phasor approach for fingerprinting of photo-activatable fluorescent proteins dronpa, kaede and kikgr. Method Appl Fluoresc 1, 35001. PMID: 24040513. doi.
Diez, C., Gaut, B., Meca, E., Scheinvar, E., Montes-Hernandez, S., Eguiarte, L., and Tenaillon, M. (2013).
Genome size variation in wild and cultivated maize along altitudinal gradients. New Phytol 199, 264-276. PMID: 23550586. doi.
Digman, M., Stakic, M., and Gratton, E. (2013).
Raster image correlation spectroscopy and number and brightness analysis. Methods Enzymol 518, 121-144. PMID: 23276538. doi.
DiRienzo, C., Gratton, E., Beltram, F., and Cardarelli, F. (2013).
Fast spatiotemporal correlation spectroscopy to determine protein lateral diffusion laws in live cell membranes. Proc Natl Acad Sci U S A 110, 12307-12312. PMID: 23836651. doi.
Frieboes, H., Wu, M., Lowengrub, J., Decuzzi, P., and Cristini, V. (2013).
A computational model for predicting nanoparticle accumulation in tumor vasculature. PLoS One 8, e56876. PMID: 23468887. doi.
Golfetto, O., Hinde, E., and Gratton, E. (2013).
Laurdan fluorescence lifetime discriminates cholesterol content from changes in fluidity in living cell membranes. Biophys J 104, 1238-1247. PMID: 23528083. doi.
Gordon, E., Whisenant, T., Zeller, M., Kaake, R., Gordon, W., Krotee, P., Patel, V., Huang, L., Baldi, P., and Bardwell, L. (2013).
Combining docking site and phosphosite predictions to find new substrates: Identification of smoothelin-like-2 (smtnl2) as a c-jun n-terminal kinase (jnk) substrate. Cell Signal 25, 2518-2529. PMID: 23981301. doi.
Hinde, E., Digman, M., Hahn, K., and Gratton, E. (2013).
Millisecond spatiotemporal dynamics of fret biosensors by the pair correlation function and the phasor approach to flim. Proc Natl Acad Sci U S A 110, 135-140. PMID: 23248275. doi.
Konstorum, A., Sprowl, S., Waterman, M., Lander, A., and Lowengrub, J. (2013).
Predicting mechanism of biphasic growth factor action on tumor growth using a multi-species model with feedback control. J Coupled Syst Multiscale Dyn 1, 459-467. PMID: 25075381. doi.
Krasieva, T., Stringari, C., Liu, F., Sun, C., Kong, Y., Balu, M., Meyskens, F., Gratton, E., and Tromberg, B. (2013).
Two-photon excited fluorescence lifetime imaging and spectroscopy of melanins in vitro and in vivo. J Biomed Opt 18, 31107. PMID: 23235925. doi.
Lander, A. (2013).
How cells know where they are. Science 339, 923-927. PMID: 23430648. doi.
Lei, J., Wang, D., Song, Y., Nie, Q., and Wan, F. (2013).
Robustness of morphogen gradients with "bucket brigade" transport through membrane-associated non-receptors. Discrete Continuous Dyn Syst Ser B 18. PMID: 24244111. doi.
Li, A., Chen, M., Jiang, T., Wu, P., Nie, Q., Widelitz, R., and Chuong, C. (2013).
Shaping organs by a wingless-int/notch/nonmuscle myosin module which orients feather bud elongation. Proc Natl Acad Sci U S A 110, E1452-1461. PMID: 23576731. doi.
Li, K., Markosyan, R., Zheng, Y., Golfetto, O., Bungart, B., Li, M., Ding, S., He, Y., Liang, C., Lee, J., et al. (2013).
Ifitm proteins restrict viral membrane hemifusion. PLoS Pathog 9, e1003124. PMID: 23358889. doi.
Liu, X., Johnson, S., Liu, S., Kanojia, D., Yue, W., Singh, U., Singn, U., Wang, Q., Wang, Q., Nie, Q., et al. (2013).
Nonlinear growth kinetics of breast cancer stem cells: Implications for cancer stem cell targeted therapy. Sci Rep 3, 2473. PMID: 23959163. doi.
Mata, M., Dutot, M., Edelstein-Keshet, L., and Holmes, W. (2013).
A model for intracellular actin waves explored by nonlinear local perturbation analysis. J Theor Biol 334, 149-161. PMID: 23831272. doi.
Mjolsness, E. (2013).
Time-ordered product expansions for computational stochastic system biology. Phys Biol 10, 035009. PMID: 23735739. doi.
Mjolsness, E., and Prasad, U. (2013).
Mathematics of small stochastic reaction networks: A boundary layer theory for eigenstate analysis. J Chem Phys 138, 104111. PMID: 23514469. doi.
Moore, T., Tanaka, H., Kim, H., Jeon, N., and Yi, T. (2013).
Yeast g-proteins mediate directional sensing and polarization behaviors in response to changes in pheromone gradient direction. Mol Biol Cell 24, 521-534. PMID: 23242998. doi.
Ovadia, J., and Nie, Q. (2013).
Stem cell niche structure as an inherent cause of undulating epithelial morphologies. Biophys J 104, 237-246. PMID: 23332076. doi.
Skinner, J., Swift, K., Ruan, Q., Perfetto, S., Gratton, E., and Tetin, S. (2013).
Simplified confocal microscope for counting particles at low concentrations. Rev Sci Instrum 84, 074301. PMID: 23902088. doi.
Wong, B., Paz, A., Corrado, M., Ramos, B., Cinquin, A., Cinquin, O., and Hui, E. (2013).
Live imaging reveals active infiltration of mitotic zone by its stem cell niche. Integr Biol (Camb) 5, 976-982. PMID: 23695198. doi.
Wu, B., Piloto, S., Zeng, W., Hoverter, N., Schilling, T., and Waterman, M. (2013).
Ring finger protein 14 is a new regulator of tcf/beta-catenin-mediated transcription and colon cancer cell survival. EMBO Rep 14, 347-355. PMID: 23449499. doi.
Wu, M., Frieboes, H., McDougall, S., Chaplain, M., Cristini, V., and Lowengrub, J. (2013).
The effect of interstitial pressure on tumor growth: Coupling with the blood and lymphatic vascular systems. J Theor Biol 320, 131-151. PMID: 23220211. doi.
Ye, G., Tang, M., Cai, J., Nie, Q., and Xie, X. (2013).
Low-rank regularization for learning gene expression programs. PLoS One 8, e82146. PMID: 24358148. doi.
Zhang, J., Nie, Q., He, M., and Zhou, T. (2013).
An effective method for computing the noise in biochemical networks. J Chem Phys 138, 084106. PMID: 23464139. doi.
Zhou, B., Konstorum, A., Duong, T., Tieu, K., Wells, W., Brown, G., Stern, H., and Shahbaba, B. (2013).
A hierarchical modeling approach to data analysis and study design in a multi-site experimental fmri study. Psychometrika 78, 260-278. PMID: 25107616. doi. 
2011 2013. Copyright © 2013. The Center for Complex Biological Systems, UC Irvine
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