2014 Publications

Adu-Gyamfi, E., Soni, S., Jee, C., Digman, M., Gratton, E., and Stahelin, R. (2014).
A loop region in the n-terminal domain of ebola virus vp40 is important in viral assembly, budding, and egress. Viruses 6, 3837-3854. PMID: 25330123. doi.
Aland, S., Egerer, S., Lowengrub, J., and Voigt, A. (2014).
Diffuse interface models of locally inextensible vesicles in a viscous fluid. J Comput Phys 277, 32-47. PMID: 25246712. doi.
Annibale, P., and Gratton, E. (2014).
Advanced fluorescence microscopy methods for the real-time study of transcription and chromatin dynamics. Transcription 5. PMID: 24802848. doi.
Anzalone, A., Annibale, P., and Gratton, E. (2014).
3d orbital tracking in a modified two-photon microscope: An application to the tracking of intracellular vesicles. J Vis Exp, e51794. PMID: 25350070. doi.
Bachir, A., Zareno, J., Moissoglu, K., Plow, E., Gratton, E., and Horwitz, A. (2014).
Integrin-associated complexes form hierarchically with variable stoichiometry in nascent adhesions. Curr Biol 24, 1845-1853. PMID: 25088556. doi.
Bonaventura, G., Barcellona, M., Golfetto, O., Nourse, J., Flanagan, L., and Gratton, E. (2014).
Laurdan monitors different lipids content in eukaryotic membrane during embryonic neural development. Cell Biochem Biophys 70, 785-794. PMID: 24839062. doi.
Chen, Y., and Lowengrub, J. (2014).
Tumor growth in complex, evolving microenvironmental geometries: A diffuse domain approach. J Theor Biol 361, 14-30. PMID: 25014472. doi.
Chen, Y., Wise, S., Shenoy, V., and Lowengrub, J. (2014).
A stable scheme for a nonlinear, multiphase tumor growth model with an elastic membrane. Int J Numer Method Biomed Eng 30, 726-754. PMID: 24443369. doi.
Chiu, C., Aguilar, J., Tsai, C., Wu, G., Gratton, E., and Digman, M. (2014).
Nanoimaging of focal adhesion dynamics in 3d. PLoS One 9, e99896. PMID: 24959851. doi.
Conesa, A., and Mortazavi, A. (2014).
The common ground of genomics and systems biology. BMC Syst Biol 8 Suppl 2, S1. PMID: 25033072. doi.
Crosignani, V., Jahid, S., Dvornikov, A., and Gratton, E. (2014).
A deep tissue fluorescence imaging system with enhanced shg detection capabilities. Microsc Res Tech 77, 368-373. PMID: 24610799. doi.
Diez, C., Meca, E., Tenaillon, M., and Gaut, B. (2014).
Three groups of transposable elements with contrasting copy number dynamics and host responses in the maize (zea mays ssp. Mays) genome. PLoS Genet 10, e1004298. PMID: 24743518. doi.
DiRienzo, C., Gratton, E., Beltram, F., and Cardarelli, F. (2014).
From fast fluorescence imaging to molecular diffusion law on live cell membranes in a commercial microscope. J Vis Exp, e51994. PMID: 25350683. doi.
DiRienzo, C., Piazza, V., Gratton, E., Beltram, F., and Cardarelli, F. (2014).
Probing short-range protein brownian motion in the cytoplasm of living cells. Nat Commun 5, 5891. PMID: 25532887. doi.
Gord, A., Holmes, W., Dai, X., and Nie, Q. (2014).
Computational modelling of epidermal stratification highlights the importance of asymmetric cell division for predictable and robust layer formation. J R Soc Interface 11. PMID: 25100322. doi.
Hedde, P., Stakic, M., and Gratton, E. (2014).
Rapid measurement of molecular transport and interaction inside living cells using single plane illumination. Sci Rep 4, 7048. PMID: 25394360. doi.
Hinde, E., Kong, X., Yokomori, K., and Gratton, E. (2014).
Chromatin dynamics during DNA repair revealed by pair correlation analysis of molecular flow in the nucleus. Biophys J 107, 55-65. PMID: 24988341. doi.
Hinde, E., Yokomori, K., Gaus, K., Hahn, K., and Gratton, E. (2014).
Fluctuation-based imaging of nuclear rac1 activation by protein oligomerisation. Sci Rep 4, 4219. PMID: 24573109. doi.
Holmes, W. (2014).
An efficient, nonlinear stability analysis for detecting pattern formation in reaction diffusion systems. Bull Math Biol 76, 157-183. PMID: 24158538. doi.
Holmes, W., and Nie, Q. (2014).
Interactions and tradeoffs between cell recruitment, proliferation, and differentiation affect cns regeneration. Biophys J 106, 1528-1536. PMID: 24703314. doi.
James, N., Digman, M., Ross, J., Barylko, B., Wang, L., Li, J., Chen, Y., Mueller, J., Gratton, E., Albanesi, J., et al. (2014).
A mutation associated with centronuclear myopathy enhances the size and stability of dynamin 2 complexes in cells. Biochim Biophys Acta 1840, 315-321. PMID: 24016602. doi.
Kang, D., Ali, M., Zhang, K., Huang, S., Peterson, E., Digman, M., Gratton, E., and Zhao, W. (2014).
Rapid detection of single bacteria in unprocessed blood using integrated comprehensive droplet digital detection. Nat Commun 5, 5427. PMID: 25391809. doi.
Kim, M., Li, D., Pham, L., Wong, B., and Hui, E. (2014).
Microfabrication of high-resolution porous membranes for cell culture. J Memb Sci 452, 460-469. PMID: 24567663. doi.
Kushner, T., Simonyan, A., and Wan, F. (2014).
A new approach to feedback for robust signaling gradients. Stud Appl Math 133, 18-51. PMID: 25214676. doi.
Lander, A. (2014).
Making sense in biology: An appreciation of julian lewis. BMC Biol 12, 57. PMID: 25185109. doi.
Lanzan, L., and Gratton, E. (2014).
Orbital single particle tracking on a commercial confocal microscope using piezoelectric stage feedback. Methods Appl Fluoresc 2. PMID: 25419461. doi.
Lee, B., Villarreal-Ponce, A., Fallahi, M., Ovadia, J., Sun, P., Yu, Q., Ito, S., Sinha, S., Nie, Q., and Dai, X. (2014).
Transcriptional mechanisms link epithelial plasticity to adhesion and differentiation of epidermal progenitor cells. Dev Cell 29, 47-58. PMID: 24735878. doi.
Lei, J., Levin, S., and Nie, Q. (2014).
Mathematical model of adult stem cell regeneration with cross-talk between genetic and epigenetic regulation. Proc Natl Acad Sci U S A 111, E880-887. PMID: 24501127. doi.
Li, J., and Lowengrub, J. (2014).
The effects of cell compressibility, motility and contact inhibition on the growth of tumor cell clusters using the cellular potts model. J Theor Biol 343, 79-91. PMID: 24211749. doi.
Mattson-Hoss, M., Niitani, Y., Gordon, E., Jun, Y., Bardwell, L., Tomishige, M., and Gross, S. (2014).
Ck2 activates kinesin via induction of a conformational change. Proc Natl Acad Sci U S A 111, 7000-7005. PMID: 24782540. doi.
McHale, P., and Lander, A. (2014).
The protective role of symmetric stem cell division on the accumulation of heritable damage. PLoS Comput Biol 10, e1003802. PMID: 25121484. doi.
Muto, A., Ikeda, S., Lopez-Burks, M., Kikuchi, Y., Calof, A., Lander, A., and Schilling, T. (2014).
Nipbl and mediator cooperatively regulate gene expression to control limb development. PLoS Genet 10, e1004671. PMID: 25255084. doi.
Narayanareddy, B., Vartiainen, S., Hariri, N., D, O.D., and Gross, S. (2014).
A biophysical analysis of mitochondrial movement: Differences between transport in neuronal cell bodies versus processes. Traffic 15, 762-771. PMID: 24673933. doi.
Ovadia, J., and Nie, Q. (2014).
Numerical methods for two-dimensional stem cell tissue growth. J Sci Comput 58, 149-175. PMID: 24415847. doi.
Paladino, S., Lebreton, S., Tivodar, S., Formiggini, F., Ossato, G., Gratton, E., Tramier, M., Coppey-Moisan, M., and Zurzolo, C. (2014).
Golgi sorting regulates organization and activity of gpi proteins at apical membranes. Nat Chem Biol 10, 350-357. PMID: 24681536. doi.
Pate, K., Stringari, C., Sprowl-Tanio, S., Wang, K., TeSlaa, T., Hoverter, N., McQuade, M., Garner, C., Digman, M., Teitell, M., et al. (2014).
Wnt signaling directs a metabolic program of glycolysis and angiogenesis in colon cancer. Embo j 33, 1454-1473. PMID: 24825347. doi.
Patel, V., Eckel-Mahan, K., Sassone-Corsi, P., and Baldi, P. (2014).
How pervasive are circadian oscillations? Trends Cell Biol 24, 329-331. PMID: 24794425. doi.
Plotegher, N., Gratton, E., and Bubacco, L. (2014).
Number and brightness analysis of alpha-synuclein oligomerization and the associated mitochondrial morphology alterations in live cells. Biochim Biophys Acta 1840, 2014-2024. PMID: 24561157. doi.
Pozzi, D., Marchini, C., Cardarelli, F., Salomone, F., Coppola, S., Montani, M., Zabaleta, M., Digman, M., Gratton, E., Colapicchioni, V., et al. (2014).
Mechanistic evaluation of the transfection barriers involved in lipid-mediated gene delivery: Interplay between nanostructure and composition. Biochim Biophys Acta 1838, 957-967. PMID: 24296066. doi.
Quang, D., and Xie, X. (2014).
Extreme: An online em algorithm for motif discovery. Bioinformatics 30, 1667-1673. PMID: 24532725. doi.
Ranjit, S., Dvornikov, A., Holland, D., Reinhart, G., Jameson, D., and Gratton, E. (2014).
Application of three-photon excitation fcs to the study of protein oligomerization. J Phys Chem B 118, 14627-14631. PMID: 25438088. doi.
Ranjit, S., Lanzano, L., and Gratton, E. (2014).
Mapping diffusion in a living cell via the phasor approach. Biophys J 107, 2775-2785. PMID: 25517145. doi.
Sanchez-Tapia, C., and Wan, F. (2014).
Fastest time to cancer by loss of tumor suppressor genes. Bull Math Biol 76, 2737-2784. PMID: 25338553. doi.
Seiler, M., Aramant, R., Jones, M., Ferguson, D., Bryda, E., and Keirstead, H. (2014).
A new immunodeficient pigmented retinal degenerate rat strain to study transplantation of human cells without immunosuppression. Graefes Arch Clin Exp Ophthalmol 252, 1079-1092. PMID: 24817311. doi.
Sharma, H., Digman, M., Felsinger, N., Gratton, E., and Khine, M. (2014).
Enhanced emission of fluorophores on shrink-induced wrinkled composite structures. Opt Mater Express 4, 753-763. PMID: 25383253. doi.
Srinivasan, S., Hu, J., Currle, D., Fung, E., Hayes, W., Lander, A., and Monuki, E. (2014).
A bmp-fgf morphogen toggle switch drives the ultrasensitive expression of multiple genes in the developing forebrain. PLoS Comput Biol 10, e1003463. PMID: 24550718. doi.
Subashchandrabose, S., Krishnan, K., Gratton, E., Megharaj, M., and Naidu, R. (2014).
Potential of fluorescence imaging techniques to monitor mutagenic pah uptake by microalga. Environ Sci Technol 48, 9152-9160. PMID: 25020149. doi.
Wan, F. (2014).
Cell-surface bound nonreceptors and signaling morphogen gradients. Stud Appl Math 133, 151-181. PMID: 25232201. doi.
Wang, D., Zhang, L., and Nie, Q. (2014).
Array-representation integration factor method for high-dimensional systems. J Comput Phys 258. PMID: 24415797. doi.
Wu, M., Frieboes, H., Chaplain, M., McDougall, S., Cristini, V., and Lowengrub, J. (2014).
The effect of interstitial pressure on therapeutic agent transport: Coupling with the tumor blood and lymphatic vascular systems. J Theor Biol 355, 194-207. PMID: 24751927. doi.
Zheng, Z., Christley, S., Chiu, W., Blitz, I., Xie, X., Cho, K., and Nie, Q. (2014).
Inference of the xenopus tropicalis embryonic regulatory network and spatial gene expression patterns. BMC Syst Biol 8, 3. PMID: 24397936. doi.
Zhou, J., Hu, X., Zhong, L., Shu, S., and Chen, L. (2014).
Two-grid methods for maxwell eigenvalue problems. SIAM J Numer Anal 52, 2027-2047. PMID: 26190866. doi. 
2011 2014. Copyright © 2013. The Center for Complex Biological Systems, UC Irvine
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