Research

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. 

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. 

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. 

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. 

Publication Highlights

 
1. Cai, A.Q., Radtke, K., Linville, A., Lander, A.D., Nie, Q., and Schilling, T.F. (2012). Cellular retinoic acid-binding proteins are essential for hindbrain patterning and signal robustness in zebrafish. Development 139, 2150-2155. PMCID 3357909. This work combines experiments and modeling to reveal the regulatory roles played by cellular retinoic acid binding proteins during development.
 
2. 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. PMCID 3382504. This work leverages fluorescence dynamics to elucidate that paths and rates of motion of molecules as they go through nuclear pores.
 
3. 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. PMCID 3380838. This work elucidates how scaffolds and compartments contribute to signaling specificity within cells.

4. Gokoffski, K.K., Wu, H.H., Beites, C.L., Kim, J., Kim, E.J., Matzuk, M.M., Johnson, J.E., Lander, A.D., and Calof, A.L. (2011). Activin and GDF11 collaborate in feedback control of neuroepithelial stem cell proliferation and fate. Development 138, 4131-4142. PMCID:3171217. This work shows how two secreted feedback factors control lineage branching in a neural epithelium.

5. Gordon, E.A., Whisenant, T.C., Zeller, M., Kaake, R.M., Gordon, W.M., 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. NIHMSID 526352. This work, a collaboration between Cell Biology and Computer Science groups, used computational techniques to identify and validate new MAP kinase substrates.

6. Hinde, E., Cardarelli, F., Digman, M.A., and Gratton, E. (2010). In vivo pair correlation analysis of EGFP intranuclear diffusion reveals DNA-dependent molecular flow. Proc Natl Acad Sci U S A 107, 16560-16565. PMCID:2944750. This work uses a novel fluorescence fluctuation-based technique to track the flow of molecules in and around chromatin.

7. Lander, A.D., Gokoffski, K.K., Wan, F.Y., Nie, Q., and Calof, A.L. (2009). Cell lineages and the logic of proliferative control. PLoS Biol 7, e15. PMCID 2628408. This work shows how feedback circuits tightly control cell proliferation to allow organs to grow to and maintain proper sizes.

8. Lander, A.D., Lo, W.C., Nie, Q., and Wan, F.Y. (2009b). The measure of success: constraints, objectives, and tradeoffs in morphogen-mediated patterning. Cold Spring Harb Perspect Biol 1, a002022. PMCID:2742077. This work uses modeling to reveal the tradeoffs that exist among mechanisms for achieving robustness and noise-tolerance in morphogen gradients.

9. Lee, B., Villarreal-Ponce, A., Fallahi, M., Ovadia, J., Sun, P., Yu, Q.C., Ito, S., Sinha, S., Nie, Q., and Dai, X. (2014). Transcriptional mechanisms link epithelial plasticity to adhesion and differentiation of epidermal progenitor cells. Developmental Cell 29, 47-58. This work involved a collaboration between a lab in Biochemistry and one in Mathematics to investigate transcriptional mechanisms in epidermal development.

10. McHale, P.T., and Lander, A.D. (2014). The Protective Role of Symmetric Stem Cell Division on the Accumulation of Heritable Damage. PLoS Comput Biol. DOI: 10.1371/journal.pcbi.1003802. This manuscript presents mathematical theory that shows that symmetric patterns of stem cell division significantly lower the risk of accumulation of mutations, provided that early mutations increase the probability of later ones (as occurs frequently in the development of cancer).

11. Mjolsness, E., Orendorff, D., Chatelain, P., and Koumoutsakos, P. (2009). An exact accelerated stochastic simulation algorithm. J Chem Phys 130, 144110. PMCID:2852436. The authors of this work develop a novel algorithm for fast stochastic simulation that substantially outperforms other algorithms on a class of hard problems.

12. Park, E., Williams, B., Wold, B.J., and Mortazavi, A. (2012). RNA editing in the human ENCODE RNA-seq data. Genome Res 22, 1626-1633. PMCID 3431480. This work reveals the extent and nature of RNA editing throughout the human genome.

13. Srinivasan, S., Hu, J.S., Currle, D.S., Fung, E.S., Hayes, W.B., Lander, A.D., and Monuki, E.S. (2014). A BMP-FGF morphogen toggle switch drives the ultrasensitive expression of multiple genes in the developing forebrain. PLoS Comput Biol 10, e1003463. PMCID 3923663. This manuscript uses a combination of experimental and mathematical methods to identify the gene regulatory logic underlying the formation of sharp spatial boundaries in forebrain development.

14. Stringari, C., Cinquin, A., Cinquin, O., Digman, M.A., Donovan, P.J., and Gratton, E. (2011). Phasor approach to fluorescence lifetime microscopy distinguishes different metabolic states of germ cells in a live tissue. Proc Natl Acad Sci U S A 108, 13582-13587. PMCID:3158156. This work uses the technique of fluorescence lifetime imaging to visualize metabolic states in cells within living tissues.

15. Wang, L., Nie, Q., and Enciso, G. (2010a). Nonessential sites improve phosphorylation switch. Biophys J 99, L41-43. PMCID:2941022. This work reveals a novel role for the large numbers of seemingly redundant phosphorylation sites that occur on many proteins.

16. Wang, L., Xin, J., and Nie, Q. (2010). A critical quantity for noise attenuation in feedback systems. PLoS Comput Biol 6, e1000764. PMCID 2861702. This work explores the mathematics behind the feedback strategies that biological systems use to filter noise, and resolves confusion about what kinds of feedback, and how many feedback loops, are most effective.

17. Xu, J., Reddy, B.J., Anand, P., Shu, Z., Cermelli, S., Mattson, M.K., Tripathy, S.K., Hoss, M.T., James, N.S., King, S.J., et al. (2012). Casein kinase 2 reverses tail-independent inactivation of kinesin-1. Nat Commun 3, 754. PMCID 3574636. This work shows that the motor protein, kinesin, self-inactivatives by a previously unknown mechanism, and reveals a non-enzymatic role for Casein kinase 2 in its re-activation. This work reveals a novel pathway for regulating the activity of cargo-bound kinesin.

18. Zhang, L., Lander, A.D., 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. PMCID 3434027. This work shows how feedback interactions in cell lineage progression drive morphogenesis in the intestine.

19. Zhang, L., Radtke, K., Zheng, L., Cai, A.Q., Schilling, T.F., and Nie, Q. (2012). Noise drives sharpening of gene expression boundaries in the zebrafish hindbrain. Mol Syst Biol 8, 613. PMCID 3472692. This paper elucidates the positive role of gene expression noise in making tissue patterning boundaries more precise.

20. Zhou, S., Lo, W.C., Suhalim, J.L., Digman, M.A., Gratton, E., Nie, Q., and Lander, A.D. (2012). Free extracellular diffusion creates the Dpp morphogen gradient of the Drosophila wing disc. Curr Biol 22, 668-675. PMCID 3338872. This work uses genetics, modeling, and fluorescence dynamics measurements to elucidate how molecular gradients set up patterns in organs and tissues.
 
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