2016 Publications

 
Alfonso-Garca, A., Smith, T., Datta, R., Luu, T., Gratton, E., Potma, E., and Liu, W. (2016).
Label-free identification of macrophage phenotype by fluorescence lifetime imaging microscopy. J Biomed Opt 21, 46005. PMID: 27086689. doi.
Annibale, P., Dvornikov, A., and Gratton, E. (2016).
Optical measurement of focal offset in tunable lenses. Opt Express 24, 1031-1036. PMID: 26832485. doi.
Brenner, M., Zhou, R., Conway, D., Lanzano, L., Gratton, E., Schwartz, M., and Ha, T. (2016).
Spider silk peptide is a compact, linear nanospring ideal for intracellular tension sensing. Nano Lett 16, 2096-2102. PMID: 26824190. doi.
Cinquin, A., Chiang, M., Paz, A., Hallman, S., Yuan, O., Vysniauskaite, I., Fowlkes, C., and Cinquin, O. (2016).
Intermittent stem cell cycling balances self-renewal and senescence of the c. Elegans germ line. PLoS Genet 12, e1005985. PMID: 27077385. doi.
Clark, N., Hinde, E., Winter, C., Fisher, A., Crosti, G., Blilou, I., Gratton, E., Benfey, P., and Sozzani, R. (2016).
Tracking transcription factor mobility and interaction in arabidopsis roots with fluorescence correlation spectroscopy. Elife 5. PMID: 27288545. doi.
Cox-Muranami, W., Nelson, E., Li, G., and Bachman, M. (2016).
Large area magnetic micropallet arrays for cell colony sorting. Lab Chip 16, 172-181. PMID: 26606460. doi.
Curtis, L., England, C., Wu, M., Lowengrub, J., and Frieboes, H. (2016).
An interdisciplinary computational/experimental approach to evaluate drug-loaded gold nanoparticle tumor cytotoxicity. Nanomedicine (Lond) 11, 197-216. PMID: 26829163. doi.
Datta, R., Heylman, C., George, S., and Gratton, E. (2016).
Label-free imaging of metabolism and oxidative stress in human induced pluripotent stem cell-derived cardiomyocytes. Biomed Opt Express 7, 1690-1701. PMID: 27231614. doi.
Hinde, E., Pandi, E., Yang, Z., Ng, I., Jans, D., Bogoyevitch, M., Gratton, E., and Gaus, K. (2016).
Quantifying the dynamics of the oligomeric transcription factor stat3 by pair correlation of molecular brightness. Nat Commun 7, 11047. PMID: 27009358. doi.
Holmes, W., Trueblood, J., and Heathcote, A. (2016).
A new framework for modeling decisions about changing information: The piecewise linear ballistic accumulator model. Cogn Psychol 85, 1-29. PMID: 26760448. doi.
Hu, Y., and Lowengrub, J. (2016).
Collective properties of a transcription initiation model under varying environment. J Comput Biol 23, 56-66. PMID: 26645781. doi.
Kawauchi, S., Santos, R., Muto, A., Lopez-Burks, M., Schilling, T., Lander, A., and Calof, A. (2016).
Using mouse and zebrafish models to understand the etiology of developmental defects in cornelia de lange syndrome. Am J Med Genet C Semin Med Genet 172, 138-145. PMID: 27120001. doi.
Konstorum, A., Hillen, T., and Lowengrub, J. (2016).
Feedback regulation in a cancer stem cell model can cause an allee effect. Bull Math Biol 78, 754-785. PMID: 27113934. doi.
Kunche, S., Yan, H., Calof, A., Lowengrub, J., and Lander, A. (2016).
Feedback, lineages and self-organizing morphogenesis. PLoS Comput Biol 12, e1004814. PMID: 26989903. doi.
Li, C., Hong, T., and Nie, Q. (2016).
Quantifying the landscape and kinetic paths for epithelial-mesenchymal transition from a core circuit. Phys Chem Chem Phys 18, 17949-17956. PMID: 27328302. doi.
Lin, S., Hedde, P., Venugopalan, V., Gratton, E., and Khine, M. (2016).
Multi-scale silica structures for improved hiv-1 capsid (p24) antigen detection. Analyst 141, 4181-4188. PMID: 27163263. doi.
Liu, K., Hamilton, C., Allard, J., Lowengrub, J., and Li, S. (2016).
Wrinkling dynamics of fluctuating vesicles in time-dependent viscous flow. Soft Matter 12, 5663-5675. PMID: 27136977. doi.
Lopez-Burks, M., Santos, R., Kawauchi, S., Calof, A., and Lander, A. (2016).
Genetic enhancement of limb defects in a mouse model of cornelia de lange syndrome. Am J Med Genet C Semin Med Genet 172, 146-154. PMID: 27120109. doi.
Lowengrub, J., Allard, J., and Aland, S. (2016).
Numerical simulation of endocytosis: Viscous flow driven by membranes with non-uniformly distributed curvature-inducing molecules. J Comput Phys 309, 112-128. PMID: 26869729. doi.
Sosnik, J., Zheng, L., Rackauckas, C., Digman, M., Gratton, E., Nie, Q., and Schilling, T. (2016).
Noise modulation in retinoic acid signaling sharpens segmental boundaries of gene expression in the embryonic zebrafish hindbrain. Elife 5, e14034. PMID: 27067377. doi.
Szymanska, A., Heylman, C., Datta, R., Gratton, E., and Nenadic, Z. (2016).
Automated detection and analysis of depolarization events in human cardiomyocytes using madec. Comput Biol Med 75, 109-117. PMID: 27281718. doi.
Wang, B., Rong, X., Duerr, M., Hermanson, D., Hedde, P., Wong, J., Vallim, T., Cravatt, B., Gratton, E., Ford, D., et al. (2016).
Intestinal phospholipid remodeling is required for dietary-lipid uptake and survival on a high-fat diet. Cell Metab 23, 492-504. PMID: 26833026. doi.
Wang, W., Chen, L., and Zhou, J. (2016).
Postprocessing mixed finite element methods for solving cahn-hilliard equation: Methods and error analysis. J Sci Comput 67, 724-746. PMID: 27110063. doi.
Westerhof, T., Li, G., Bachman, M., and Nelson, E. (2016).
Multicolor immunofluorescent imaging of complex cellular mixtures on micropallet arrays enables the identification of single cells of defined phenotype. Adv Healthc Mater 5, 767-771. PMID: 26924570. doi.
Xie, J., Xiang, C., Ma, J., Tan, J., Wen, T., Lei, J., and Nie, Q. (2016).
An adaptive hybrid algorithm for global network alignment. IEEE/ACM Trans Comput Biol Bioinform 13, 483-493. PMID: 27295633. doi. 

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. 

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. 

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. 

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. 
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