2012 Publications

Adu-Gyamfi, E., Digman, M., Gratton, E., and Stahelin, R. (2012).
Single-particle tracking demonstrates that actin coordinates the movement of the ebola virus matrix protein. Biophys J 103, L41-43. PMID: 23199932. doi.
Adu-Gyamfi, E., Digman, M., Gratton, E., and Stahelin, R. (2012).
Investigation of ebola vp40 assembly and oligomerization in live cells using number and brightness analysis. Biophys J 102, 2517-2525. PMID: 22713567. doi.
Aland, S., Lowengrub, J., and Voigt, A. (2012).
Particles at fluid-fluid interfaces: A new navier-stokes-cahn-hilliard surface- phase-field-crystal model. Phys Rev E Stat Nonlin Soft Matter Phys 86, 046321. PMID: 23214691. doi.
Battisti, A., Digman, M., Gratton, E., Storti, B., Beltram, F., and Bizzarri, R. (2012).
Intracellular ph measurements made simple by fluorescent protein probes and the phasor approach to fluorescence lifetime imaging. Chem Commun (Camb) 48, 5127-5129. PMID: 22517076. doi.
Cai, A., Radtke, K., Linville, A., Lander, A., Nie, Q., and Schilling, T. (2012).
Cellular retinoic acid-binding proteins are essential for hindbrain patterning and signal robustness in zebrafish. Development 139, 2150-2155. PMID: 22619388. doi.
Cao, Y., Liang, C., Naveed, H., Li, Y., Chen, M., and Nie, Q. (2012).
Modeling spatial population dynamics of stem cell lineage in tissue growth. Conf Proc IEEE Eng Med Biol Soc 2012, 5502-5505. PMID: 23367175. doi.
Cardarelli, F., Lanzano, L., and Gratton, E. (2012).
Capturing directed molecular motion in the nuclear pore complex of live cells. Proc Natl Acad Sci U S A 109, 9863-9868. PMID: 22665783. doi.
Chan, C., Liu, X., Wang, L., Bardwell, L., Nie, Q., and Enciso, G. (2012).
Protein scaffolds can enhance the bistability of multisite phosphorylation systems. PLoS Comput Biol 8, e1002551. PMID: 22737061. doi.
Chou, C., Moore, T., Chang, S., Nie, Q., and Yi, T. (2012).
Signaling regulated endocytosis and exocytosis lead to mating pheromone concentration dependent morphologies in yeast. FEBS Lett 586, 4208-4214. PMID: 23108052. doi.
Coppola, S., Estrada, L., Digman, M., Pozzi, D., Cardarelli, F., Gratton, E., and Caracciolo, G. (2012).
Intracellular trafficking of cationic liposome-DNA complexes in living cells. Soft Matter 8, 7919-7927. PMID: 25152766. doi.
Crosignani, V., Dvornikov, A., Aguilar, J., Stringari, C., Edwards, R., Mantulin, W., and Gratton, E. (2012).
Deep tissue fluorescence imaging and in vivo biological applications. J Biomed Opt 17, 116023. PMID: 23214184. doi.
Cutrale, F., and Gratton, E. (2012).
Inclined selective plane illumination microscopy adaptor for conventional microscopes. Microsc Res Tech 75, 1461-1466. PMID: 22736488. doi.
Digman, M., and Gratton, E. (2012).
Scanning image correlation spectroscopy. Bioessays 34, 377-385. PMID: 22415853. doi.
Giral, H., Cranston, D., Lanzano, L., Caldas, Y., Sutherland, E., Rachelson, J., Dobrinskikh, E., Weinman, E., Doctor, R., Gratton, E., et al. (2012).
Nhe3 regulatory factor 1 (nherf1) modulates intestinal sodium-dependent phosphate transporter (napi-2b) expression in apical microvilli. J Biol Chem 287, 35047-35056. PMID: 22904329. doi.
Hinde, E., Cardarelli, F., Chen, A., Khine, M., and Gratton, E. (2012).
Tracking the mechanical dynamics of human embryonic stem cell chromatin. Epigenetics Chromatin 5, 20. PMID: 23259580. doi.
Hinde, E., Cardarelli, F., Digman, M., and Gratton, E. (2012).
Changes in chromatin compaction during the cell cycle revealed by micrometer-scale measurement of molecular flow in the nucleus. Biophys J 102, 691-697. PMID: 22325293. doi.
Hinde, E., Digman, M., Welch, C., Hahn, K., and Gratton, E. (2012).
Biosensor forster resonance energy transfer detection by the phasor approach to fluorescence lifetime imaging microscopy. Microsc Res Tech 75, 271-281. PMID: 21858900. doi.
Kavousanakis, M., Liu, P., Boudouvis, A., Lowengrub, J., and Kevrekidis, I. (2012).
Efficient coarse simulation of a growing avascular tumor. Phys Rev E Stat Nonlin Soft Matter Phys 85, 031912. PMID: 22587128. doi.
Kniazeva, E., Weidling, J., Singh, R., Botvinick, E., Digman, M., Gratton, E., and Putnam, A. (2012).
Quantification of local matrix deformations and mechanical properties during capillary morphogenesis in 3d. Integr Biol (Camb) 4, 431-439. PMID: 22281872. doi.
Lander, A., Kimble, J., Clevers, H., Fuchs, E., Montarras, D., Buckingham, M., Calof, A., Trumpp, A., and Oskarsson, T. (2012).
What does the concept of the stem cell niche really mean today? BMC Biol 10, 19. PMID: 22405133. doi.
Lo, W., Chen, L., Wang, M., and Nie, Q. (2012).
A robust and efficient method for steady state patterns in reaction-diffusion systems. J Comput Phys 231, 5062-5077. PMID: 22773849. doi.
Lu, Y., Su, C., and Liu, H. (2012).
A gata transcription factor recruits hda1 in response to reduced tor1 signaling to establish a hyphal chromatin state in candida albicans. PLoS Pathog 8, e1002663. PMID: 22536157. doi.
Nagawa, S., Xu, T., Lin, D., Dhonukshe, P., Zhang, X., Friml, J., Scheres, B., Fu, Y., and Yang, Z. (2012).
Rop gtpase-dependent actin microfilaments promote pin1 polarization by localized inhibition of clathrin-dependent endocytosis. PLoS Biol 10, e1001299. PMID: 22509133. doi.
Orendorff, D., and Mjolsness, E. (2012).
A hierarchical exact accelerated stochastic simulation algorithm. J Chem Phys 137, 214104. PMID: 23231214. doi.
Palmer, R., McGeary, J., Francazio, S., Raphael, B., Lander, A., Heath, A., and Knopik, V. (2012).
The genetics of alcohol dependence: Advancing towards systems-based approaches. Drug Alcohol Depend 125, 179-191. PMID: 22854292. doi.
Park, E., Williams, B., Wold, B., and Mortazavi, A. (2012).
Rna editing in the human encode rna-seq data. Genome Res 22, 1626-1633. PMID: 22955975. doi.
Pham, K., Chauviere, A., Hatzikirou, H., Li, X., Byrne, H., Cristini, V., and Lowengrub, J. (2012).
Density-dependent quiescence in glioma invasion: Instability in a simple reaction-diffusion model for the migration/proliferation dichotomy. J Biol Dyn 6 Suppl 1, 54-71. PMID: 22873675. doi.
Sanchez, S., Tricerri, M., and Gratton, E. (2012).
Laurdan generalized polarization fluctuations measures membrane packing micro-heterogeneity in vivo. Proc Natl Acad Sci U S A 109, 7314-7319. PMID: 22529342. doi.
Santos, R., Wu, J., Hamilton, J., Pinter, R., Hindges, R., and Calof, A. (2012).
Restoration of retinal development in vsx2 deficient mice by reduction of gdf11 levels. Adv Exp Med Biol 723, 671-677. PMID: 22183392. doi.
Schilling, T., Nie, Q., and Lander, A. (2012).
Dynamics and precision in retinoic acid morphogen gradients. Curr Opin Genet Dev 22, 562-569. PMID: 23266215. doi.
Stringari, C., Edwards, R., Pate, K., Waterman, M., Donovan, P., and Gratton, E. (2012).
Metabolic trajectory of cellular differentiation in small intestine by phasor fluorescence lifetime microscopy of nadh. Sci Rep 2, 568. PMID: 22891156. doi.
Stringari, C., Nourse, J., Flanagan, L., and Gratton, E. (2012).
Phasor fluorescence lifetime microscopy of free and protein-bound nadh reveals neural stem cell differentiation potential. PLoS One 7, e48014. PMID: 23144844. doi.
Stringari, C., Sierra, R., Donovan, P., and Gratton, E. (2012).
Label-free separation of human embryonic stem cells and their differentiating progenies by phasor fluorescence lifetime microscopy. J Biomed Opt 17, 046012. PMID: 22559690. doi.
Suhalim, J., Chung, C., Lilledahl, M., Lim, R., Levi, M., Tromberg, B., and Potma, E. (2012).
Characterization of cholesterol crystals in atherosclerotic plaques using stimulated raman scattering and second-harmonic generation microscopy. Biophys J 102, 1988-1995. PMID: 22768956. doi.
Sun, Z., and Komarova, N. (2012).
Stochastic modeling of stem-cell dynamics with control. Math Biosci 240, 231-240. PMID: 22960597. doi.
Whiteside, M., Digman, M., Gratton, E., and Treseder, K. (2012).
Organic nitrogen uptake by arbuscular mycorrhizal fungi in a boreal forest. Soil Biol Biochem 55. PMID: 24371363. doi.
Wright, B., Andrews, L., Jones, M., Stringari, C., Digman, M., and Gratton, E. (2012).
Phasor-flim analysis of nadh distribution and localization in the nucleus of live progenitor myoblast cells. Microsc Res Tech 75, 1717-1722. PMID: 23019116. doi.
Wright, B., Andrews, L., Markham, J., Jones, M., Stringari, C., Digman, M., and Gratton, E. (2012).
Nadh distribution in live progenitor stem cells by phasor-fluorescence lifetime image microscopy. Biophys J 103, L7-9. PMID: 22828352. doi.
Xu, J., Reddy, B., Anand, P., Shu, Z., Cermelli, S., Mattson, M., Tripathy, S., Hoss, M., James, N., King, S., et al. (2012).
Casein kinase 2 reverses tail-independent inactivation of kinesin-1. Nat Commun 3, 754. PMID: 22453827. doi.
Youssefpour, H., Li, X., Lander, A., and Lowengrub, J. (2012).
Multispecies model of cell lineages and feedback control in solid tumors. J Theor Biol 304, 39-59. PMID: 22554945. doi.
Zeng, W., and Mortazavi, A. (2012).
Technical considerations for functional sequencing assays. Nat Immunol 13, 802-807. PMID: 22910383. doi.
Zhang, L., Lander, A., and Nie, Q. (2012).
A reaction-diffusion mechanism influences cell lineage progression as a basis for formation, regeneration, and stability of intestinal crypts. BMC Syst Biol 6, 93. PMID: 22849824. doi.
Zhang, L., Radtke, K., Zheng, L., Cai, A., Schilling, T., and Nie, Q. (2012).
Noise drives sharpening of gene expression boundaries in the zebrafish hindbrain. Mol Syst Biol 8, 613. PMID: 23010996. doi.
Zhou, S., Lo, W., Suhalim, J., Digman, M., Gratton, E., Nie, Q., and Lander, A. (2012).
Free extracellular diffusion creates the dpp morphogen gradient of the drosophila wing disc. Curr Biol 22, 668-675. PMID: 22445299. doi.
Zhu, X., Welling, M., Jin, F., and Lowengrub, J. (2012).
Predicting simulation parameters of biological systems using a gaussian process model. Stat Anal Data Min 5, 509-522. PMID: 23482410. doi. 
2011 2012. Copyright © 2013. The Center for Complex Biological Systems, UC Irvine
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