2007-2008 Publications

White, R., Nie, Q., Lander, A., and Schilling, T. (2007).
Complex regulation of cyp26a1 creates a robust retinoic acid gradient in the zebrafish embryo. PLoS Biol 5, e304. PMID: 18031199. doi.
Zhang, Y., Lander, A., and Nie, Q. (2007).
Computational analysis of bmp gradients in dorsal-ventral patterning of the zebrafish embryo. J Theor Biol 248, 579-589. PMID: 17673236. doi.
Chou, C., Nie, Q., and Yi, T. (2008).
Modeling robustness tradeoffs in yeast cell polarization induced by spatial gradients. PLoS One 3, e3103. PMID: 21267054. doi.
Chou, S., Zhao, S., Song, Y., Liu, H., and Nie, Q. (2008).
Fus3-triggered tec1 degradation modulates mating transcriptional output during the pheromone response. Mol Syst Biol 4, 212. PMID: 18682702. doi.
Hilioti, Z., SabbaghJr, W., Paliwal, S., Bergmann, A., Goncalves, M., Bardwell, L., and Levchenko, A. (2008).
Oscillatory phosphorylation of yeast fus3 map kinase controls periodic gene expression and morphogenesis. Curr Biol 18, 1700-1706. PMID: 18976914. doi.
Iron, D., Syed, A., Theisen, H., Lukacsovich, T., Naghibi, M., Marsh, L., Wan, F., and Nie, Q. (2008).
The role of feedback in the formation of morphogen territories. Math Biosci Eng 5, 277-298. PMID: 18613734. doi.
Macklin, P., and Lowengrub, J. (2008).
A new ghost cell/level set method for moving boundary problems: Application to tumor growth. J Sci Comput 35, 266-299. PMID: 21331304. doi.
Moore, T., Chou, C., Nie, Q., Jeon, N., and Yi, T. (2008).
Robust spatial sensing of mating pheromone gradients by yeast cells. PLoS One 3, e3865. PMID: 19052645. doi.
Nie, Q., Wan, F., Zhang, Y., and Liu, X. (2008).
Compact integration factor methods in high spatial dimensions. J Comput Phys 227, 5238-5255. PMID: 19809596. doi.
Sanabria, H., Digman, M., Gratton, E., and Waxham, M. (2008).
Spatial diffusivity and availability of intracellular calmodulin. Biophys J 95, 6002-6015. PMID: 18820232. doi.
White, R., and Schilling, T. (2008).
How degrading: Cyp26s in hindbrain development. Dev Dyn 237, 2775-2790. PMID: 18816852. doi.
Wise, S., Lowengrub, J., Frieboes, H., and Cristini, V. (2008).
Three-dimensional multispecies nonlinear tumor growth--i model and numerical method. J Theor Biol 253, 524-543. PMID: 18485374. doi.
Wu, J., Sieglaff, D., Gervin, J., and Xie, X. (2008).
Discovering regulatory motifs in the plasmodium genome using comparative genomics. Bioinformatics 24, 1843-1849. PMID: 18611947. doi. 

2009 Publications

Bardwell, A., Frankson, E., and Bardwell, L. (2009).
Selectivity of docking sites in mapk kinases. J Biol Chem 284, 13165-13173. PMID: 19196711. doi.
Barlow, L., and Calof, A. (2009).
Symposium overview: Stem cells in sensory epithelium development and regeneration. Ann N Y Acad Sci 1170, 5-6. PMID: 19686097. doi.
Bearer, E., Lowengrub, J., Frieboes, H., Chuang, Y., Jin, F., Wise, S., Ferrari, M., Agus, D., and Cristini, V. (2009).
Multiparameter computational modeling of tumor invasion. Cancer Res 69, 4493-4501. PMID: 19366801. doi.
Beites, C., Hollenbeck, P., Kim, J., Lovell-Badge, R., Lander, A., and Calof, A. (2009).
Follistatin modulates a bmp autoregulatory loop to control the size and patterning of sensory domains in the developing tongue. Development 136, 2187-2197. PMID: 19474151. doi.
Beites, C., Kawauchi, S., and Calof, A. (2009).
Olfactory neuron patterning and specification. Dev Neurobiol 7, 145-156. PMID: 24817923. doi.
Cai, A., Peng, Y., Wells, J., Dai, X., and Nie, Q. (2009).
Multi-scale modelling for threshold dependent differentiation. Math Model Nat Phenom 4, 103-117. PMID: 20622931. doi.
Caracciolo, G., Caminiti, R., Digman, M., Gratton, E., and Sanchez, S. (2009).
Efficient escape from endosomes determines the superior efficiency of multicomponent lipoplexes. J Phys Chem B 113, 4995-4997. PMID: 19301832. doi.
Christley, S., Nie, Q., and Xie, X. (2009).
Incorporating existing network information into gene network inference. PLoS One 4, e6799. PMID: 19710931. doi.
Cinquin, O. (2009).
Purpose and regulation of stem cells: A systems-biology view from the caenorhabditis elegans germ line. J Pathol 217, 186-198. PMID: 19065622. doi.
Cristini, V., Li, X., Lowengrub, J., and Wise, S. (2009).
Nonlinear simulations of solid tumor growth using a mixture model: Invasion and branching. J Math Biol 58, 723-763. PMID: 18787827. doi.
Digman, M., and Gratton, E. (2009).
Fluorescence correlation spectroscopy and fluorescence cross-correlation spectroscopy. Wiley Interdiscip Rev Syst Biol Med 1, 273-282. PMID: 20835996. doi.
Digman, M., and Gratton, E. (2009).
Imaging barriers to diffusion by pair correlation functions. Biophys J 97, 665-673. PMID: 19619481. doi.
Digman, M., and Gratton, E. (2009).
Analysis of diffusion and binding in cells using the rics approach. Microsc Res Tech 72, 323-332. PMID: 19067357. doi.
Digman, M., Wiseman, P., Choi, C., Horwitz, A., and Gratton, E. (2009).
Stoichiometry of molecular complexes at adhesions in living cells. Proc Natl Acad Sci U S A 106, 2170-2175. PMID: 19168634. doi.
Digman, M., Wiseman, P., Horwitz, A., and Gratton, E. (2009).
Detecting protein complexes in living cells from laser scanning confocal image sequences by the cross correlation raster image spectroscopy method. Biophys J 96, 707-716. PMID: 19167315. doi.
Jen, Y., Musacchio, M., and Lander, A. (2009).
Glypican-1 controls brain size through regulation of fibroblast growth factor signaling in early neurogenesis. Neural Dev 4, 33. PMID: 19732411. doi.
Kawauchi, S., Kim, J., Santos, R., Wu, H., Lander, A., and Calof, A. (2009).
Foxg1 promotes olfactory neurogenesis by antagonizing gdf11. Development 136, 1453-1464. PMID: 19297409. doi.
Kawauchi, S., Santos, R., Kim, J., Hollenbeck, P., Murray, R., and Calof, A. (2009).
The role of foxg1 in the development of neural stem cells of the olfactory epithelium. Ann N Y Acad Sci 1170, 21-27. PMID: 19686101. doi.
Kuchaiev, O., Wang, P., Nenadic, Z., and Przulj, N. (2009).
Structure of brain functional networks. Conf Proc IEEE Eng Med Biol Soc 2009, 4166-4170. PMID: 19964621. doi.
Lander, A. (2009).
The 'stem cell' concept: Is it holding us back? J Biol 8, 70. PMID: 19769787. doi.
Lander, A., Gokoffski, K., Wan, F., Nie, Q., and Calof, A. (2009).
Cell lineages and the logic of proliferative control. PLoS Biol 7, e15. PMID: 19166268. doi.
Lander, A., Lo, W., Nie, Q., and Wan, F. (2009).
The measure of success: Constraints, objectives, and tradeoffs in morphogen-mediated patterning. Cold Spring Harb Perspect Biol 1, a002022. PMID: 20066078. doi.
Lander, A., Nie, Q., Wan, F., and Zhang, Y. (2009).
Localized ectopic expression of dpp receptors in a drosophila embryo. Stud Appl Math 123, 175-214. PMID: 20160891. doi.
Lei, J., He, G., Liu, H., and Nie, Q. (2009).
A delay model for noise-induced bi-directional switching. Nonlinearity 22, 2845-2859. PMID: 20592956. doi.
Li, X., Lowengrub, J., Ratz, A., and Voigt, A. (2009).
Solving pdes in complex geometries: A diffuse domain approach. Commun Math Sci 7, 81-107. PMID: 21603084. doi.
Li, X., and Nie, Q. (2009).
A high-order boundary integral method for surface diffusions on elastically stressed axisymmetric rods. J Comput Phys 228, 4625-4637. PMID: 26487788. doi.
Linville, A., Radtke, K., Waxman, J., Yelon, D., and Schilling, T. (2009).
Combinatorial roles for zebrafish retinoic acid receptors in the hindbrain, limbs and pharyngeal arches. Dev Biol 325, 60-70. PMID: 18929555. doi.
Lo, W., Chou, C., Gokoffski, K., Wan, F., Lander, A., Calof, A., and Nie, Q. (2009).
Feedback regulation in multistage cell lineages. Math Biosci Eng 6, 59-82. PMID: 19292508. doi.
Lowengrub, J., Ratz, A., and Voigt, A. (2009).
Phase-field modeling of the dynamics of multicomponent vesicles: Spinodal decomposition, coarsening, budding, and fission. Phys Rev E Stat Nonlin Soft Matter Phys 79, 031926. PMID: 19391990. doi.
Macklin, P., McDougall, S., Anderson, A., Chaplain, M., Cristini, V., and Lowengrub, J. (2009).
Multiscale modelling and nonlinear simulation of vascular tumour growth. J Math Biol 58, 765-798. PMID: 18781303. doi.
Mitchell, B., Stubbs, J., Huisman, F., Taborek, P., Yu, C., and Kintner, C. (2009).
The pcp pathway instructs the planar orientation of ciliated cells in the xenopus larval skin. Curr Biol 19, 924-929. PMID: 19427216. doi.
Mjolsness, E., Orendorff, D., Chatelain, P., and Koumoutsakos, P. (2009).
An exact accelerated stochastic simulation algorithm. J Chem Phys 130, 144110. PMID: 19368432. doi.
Tanner, K., Ferris, D., Lanzano, L., Mandefro, B., Mantulin, W., Gardiner, D., Rugg, E., and Gratton, E. (2009).
Coherent movement of cell layers during wound healing by image correlation spectroscopy. Biophys J 97, 2098-2106. PMID: 19804742. doi.
Teigen, K., Li, X., Lowengrub, J., Wang, F., and Voigt, A. (2009).
A diffuse-interface approach for modeling transport, diffusion and adsorption/desorption of material quantities on a deformable interface. Commun Math Sci 4, 1009-1037. PMID: 21373370. doi.
Thalhauser, C., and Komarova, N. (2009).
Specificity and robustness of the mammalian mapk-ieg network. Biophys J 96, 3471-3482. PMID: 19413954. doi.
Wells, J., Lee, B., Cai, A., Karapetyan, A., Lee, W., Rugg, E., Sinha, S., Nie, Q., and Dai, X. (2009).
Ovol2 suppresses cell cycling and terminal differentiation of keratinocytes by directly repressing c-myc and notch1. J Biol Chem 284, 29125-29135. PMID: 19700410. doi.
Zhou, Y., He, J., and Nie, Q. (2009).
A comparative runtime analysis of heuristic algorithms for satisfiability problems. Artif Intell 173, 240-257. PMID: 20126510. doi 

2011 Publications

Azartash, K., Kwan, J., Paugh, J., Nguyen, A., Jester, J., and Gratton, E. (2011).
Pre-corneal tear film thickness in humans measured with a novel technique. Mol Vis 17, 756-767. PMID: 21527997. doi.
Bardwell, L. (2011).
Synthetic biology: Modulating the map kinase module. Curr Biol 21, R249-251. PMID: 21481758. doi.
Blaine, J., Lanzano, L., Giral, H., Caldas, Y., Levi, M., Gratton, E., Moldovan, R., and Lei, T. (2011).
Dynamic imaging of the sodium phosphate cotransporters. Adv Chronic Kidney Dis 18, 145-150. PMID: 21406299. doi.
Cardarelli, F., Lanzano, L., and Gratton, E. (2011).
Fluorescence correlation spectroscopy of intact nuclear pore complexes. Biophys J 101, L27-29. PMID: 21843462. doi.
Chen, B., Estrada, L., Hellriegel, C., and Gratton, E. (2011).
Nanometer-scale optical imaging of collagen fibers using gold nanoparticles. Biomed Opt Express 2, 511-519. PMID: 21412457. doi.
Choi, C., Zareno, J., Digman, M., Gratton, E., and Horwitz, A. (2011).
Cross-correlated fluctuation analysis reveals phosphorylation-regulated paxillin-fak complexes in nascent adhesions. Biophys J 100, 583-592. PMID: 21281572. doi.
Chou, C., Bardwell, L., Nie, Q., and Yi, T. (2011).
Noise filtering tradeoffs in spatial gradient sensing and cell polarization response. BMC Syst Biol 5, 196. PMID: 22166067. doi.
Crosignani, V., Dvornikov, A., and Gratton, E. (2011).
Enhancement of imaging depth in turbid media using a wide area detector. J Biophotonics 4, 592-599. PMID: 21425242. doi.
Digman, M., and Gratton, E. (2011).
Lessons in fluctuation correlation spectroscopy. Annu Rev Phys Chem 62, 645-668. PMID: 21219151. doi.
Estrada, L., and Gratton, E. (2011).
3d nanometer images of biological fibers by directed motion of gold nanoparticles. Nano Lett 11, 4656-4660. PMID: 21919444. doi.
Giral, H., Lanzano, L., Caldas, Y., Blaine, J., Verlander, J., Lei, T., Gratton, E., and Levi, M. (2011).
Role of pdzk1 protein in apical membrane expression of renal sodium-coupled phosphate transporters. J Biol Chem 286, 15032-15042. PMID: 21388960. doi.
Gokoffski, K., Wu, H., Beites, C., Kim, J., Kim, E., Matzuk, M., Johnson, J., Lander, A., and Calof, A. (2011).
Activin and gdf11 collaborate in feedback control of neuroepithelial stem cell proliferation and fate. Development 138, 4131-4142. PMID: 21852401. doi.
Hetherington, A., and Bardwell, L. (2011).
Plant signalling pathways: A comparative evolutionary overview. Curr Biol 21, R317-319. PMID: 21549953. doi.
Hinde, E., Cardarelli, F., Digman, M., Kershner, A., Kimble, J., and Gratton, E. (2011).
The impact of mitotic versus interphase chromatin architecture on the molecular flow of egfp by pair correlation analysis. Biophys J 100, 1829-1836. PMID: 21463597. doi.
Itano, M., Neumann, A., Liu, P., Zhang, F., Gratton, E., Parak, W., Thompson, N., and Jacobson, K. (2011).
Dc-sign and influenza hemagglutinin dynamics in plasma membrane microdomains are markedly different. Biophys J 100, 2662-2670. PMID: 21641311. doi.
Lander, A. (2011).
Pattern, growth, and control. Cell 144, 955-969. PMID: 21414486. doi.
Lander, A. (2011).
The individuality of stem cells. BMC Biol 9, 40. PMID: 21649941. doi.
Lander, A., Nie, Q., Vargas, B., and Wan, F. (2011).
Size-normalized robustness of dpp gradient in drosophila wing imaginal disc. J Mech Mater Struct 6, 321-350. PMID: 21841941. doi.
Lanzano, L., Digman, M., Fwu, P., Giral, H., Levi, M., and Gratton, E. (2011).
Nanometer-scale imaging by the modulation tracking method. J Biophotonics 4, 415-424. PMID: 21462350. doi.
Lei, J., Wan, F., Lander, A., and Nie, Q. (2011).
Robustness of signaling gradient in drosophila wing imaginal disc. Discrete Continuous Dyn Syst Ser B 16, 835-866. PMID: 24098092. doi.
Lim, R., Suhalim, J., Miyazaki-Anzai, S., Miyazaki, M., Levi, M., Potma, E., and Tromberg, B. (2011).
Identification of cholesterol crystals in plaques of atherosclerotic mice using hyperspectral cars imaging. J Lipid Res 52, 2177-2186. PMID: 21949051. doi.
Lu, Y., Su, C., Wang, A., and Liu, H. (2011).
Hyphal development in candida albicans requires two temporally linked changes in promoter chromatin for initiation and maintenance. PLoS Biol 9, e1001105. PMID: 21811397. doi.
Marchini, C., Pozzi, D., Montani, M., Alfonsi, C., Amici, A., CandeloroDeSanctis, S., Digman, M., Sanchez, S., Gratton, E., Amenitsch, H., et al. (2011).
Role of temperature-independent lipoplex-cell membrane interactions in the efficiency boost of multicomponent lipoplexes. Cancer Gene Ther 18, 543-552. PMID: 21394110. doi.
Nahmad, M., and Lander, A. (2011).
Spatiotemporal mechanisms of morphogen gradient interpretation. Curr Opin Genet Dev 21, 726-731. PMID: 22033220. doi.
Pham, K., Frieboes, H., Cristini, V., and Lowengrub, J. (2011).
Predictions of tumour morphological stability and evaluation against experimental observations. J R Soc Interface 8, 16-29. PMID: 20519213. doi.
Stafford, R., Hinde, E., Knight, M., Pennella, M., Ear, J., Digman, M., Gratton, E., and Bowie, J. (2011).
Tandem sam domain structure of human caskin1: A presynaptic, self-assembling scaffold for cask. Structure 19, 1826-1836. PMID: 22153505. doi.
Stevenson, J., and Liu, H. (2011).
Regulation of white and opaque cell-type formation in candida albicans by rtt109 and hst3. Mol Microbiol 81, 1078-1091. PMID: 21749487. doi.
Stringari, C., Cinquin, A., Cinquin, O., Digman, M., Donovan, P., 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. PMID: 21808026. doi.
Teigen, K., Song, P., Lowengrub, J., and Voigt, A. (2011).
A diffuse-interface method for two-phase flows with soluble surfactants. J Comput Phys 230, 375-393. PMID: 21218125. doi.
Vetri, V., Ossato, G., Militello, V., Digman, M., Leone, M., and Gratton, E. (2011).
Fluctuation methods to study protein aggregation in live cells: Concanavalin a oligomers formation. Biophys J 100, 774-783. PMID: 21281593. doi.
Wise, S., Lowengrub, J., and Cristini, V. (2011).
An adaptive multigrid algorithm for simulating solid tumor growth using mixture models. Math Comput Model 53, 1-20. PMID: 21076663. doi.
Zhao, S., Ovadia, J., Liu, X., Zhang, Y., and Nie, Q. (2011).
Operator splitting implicit integration factor methods for stiff reaction-diffusion-advection systems. J Comput Phys 230, 5996-6009. PMID: 21666863. doi.
Zheng, Z., Chou, C., Yi, T., and Nie, Q. (2011).
Mathematical analysis of steady-state solutions in compartment and continuum models of cell polarization. Math Biosci Eng 8, 1135-1168. PMID: 21936604. doi. 

2010 Publications

Aland, S., Lowengrub, J., and Voigt, A. (2010).
Two-phase flow in complex geometries: A diffuse domain approach. Comput Model Eng Sci 57, 77-106. PMID: 21918638. doi.
Cardarelli, F., and Gratton, E. (2010).
In vivo imaging of single-molecule translocation through nuclear pore complexes by pair correlation functions. PLoS One 5, e10475. PMID: 20454622. doi.
Celli, A., and Gratton, E. (2010).
Dynamics of lipid domain formation: Fluctuation analysis. Biochim Biophys Acta 1798, 1368-1376. PMID: 20025848. doi.
Celli, A., Sanchez, S., Behne, M., Hazlett, T., Gratton, E., and Mauro, T. (2010).
The epidermal ca(2+) gradient: Measurement using the phasor representation of fluorescent lifetime imaging. Biophys J 98, 911-921. PMID: 20197045. doi.
Chou, C., Lo, W., Gokoffski, K., Zhang, Y., Wan, F., Lander, A., Calof, A., and Nie, Q. (2010).
Spatial dynamics of multistage cell lineages in tissue stratification. Biophys J 99, 3145-3154. PMID: 21081061. doi.
Christley, S., Lee, B., Dai, X., and Nie, Q. (2010).
Integrative multicellular biological modeling: A case study of 3d epidermal development using gpu algorithms. BMC Syst Biol 4, 107. PMID: 20696053. doi.
Cinquin, O., Crittenden, S., Morgan, D., and Kimble, J. (2010).
Progression from a stem cell-like state to early differentiation in the c. Elegans germ line. Proc Natl Acad Sci U S A 107, 2048-2053. PMID: 20080700. doi.
Compani, B., Su, T., Chang, I., Cheng, J., Shah, K., Whisenant, T., Dou, Y., Bergmann, A., Cheong, R., Wold, B., et al. (2010).
A scalable and integrative system for pathway bioinformatics and systems biology. Adv Exp Med Biol 680, 523-534. PMID: 20865537. doi.
Daily, K., Rigor, P., Christley, S., Xie, X., and Baldi, P. (2010).
Data structures and compression algorithms for high-throughput sequencing technologies. BMC Bioinformatics 11, 514. PMID: 20946637. doi.
Frieboes, H., Jin, F., Chuang, Y., Wise, S., Lowengrub, J., and Cristini, V. (2010).
Three-dimensional multispecies nonlinear tumor growth-ii: Tumor invasion and angiogenesis. J Theor Biol 264, 1254-1278. PMID: 20303982. doi.
Haney, S., Bardwell, L., and Nie, Q. (2010).
Ultrasensitive responses and specificity in cell signaling. BMC Syst Biol 4, 119. PMID: 20735856. doi.
Hinde, E., Cardarelli, F., Digman, M., 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. PMID: 20823232. doi.
Janes, M., Limon, J., So, L., Chen, J., Lim, R., Chavez, M., Vu, C., Lilly, M., Mallya, S., Ong, S., et al. (2010).
Effective and selective targeting of leukemia cells using a torc1/2 kinase inhibitor. Nat Med 16, 205-213. PMID: 20072130. doi.
Kim, S., Sanabria, H., Digman, M., Gratton, E., Schwille, P., Zipfel, W., and Waxham, M. (2010).
Quantifying translational mobility in neurons: Comparison between current optical techniques. J Neurosci 30, 16409-16416. PMID: 21147979. doi.
Kuo, W., Digman, M., and Lander, A. (2010).
Heparan sulfate acts as a bone morphogenetic protein coreceptor by facilitating ligand-induced receptor hetero-oligomerization. Mol Biol Cell 21, 4028-4041. PMID: 20861306. doi.
Lander, A. (2010).
The edges of understanding. BMC Biol 8, 40. PMID: 20385033. doi.
Liu, Q., Lin, K., Andersen, B., Smyth, P., and Ihler, A. (2010).
Estimating replicate time shifts using gaussian process regression. Bioinformatics 26, 770-776. PMID: 20147305. doi.
Liu, X., Bardwell, L., and Nie, Q. (2010).
A combination of multisite phosphorylation and substrate sequestration produces switchlike responses. Biophys J 98, 1396-1407. PMID: 20409458. doi.
Liu, X., and Nie, Q. (2010).
Compact integration factor methods for complex domains and adaptive mesh refinement. J Comput Phys 229, 5692-5706. PMID: 20543883. doi.
Lowengrub, J., Frieboes, H., Jin, F., Chuang, Y., Li, X., Macklin, P., Wise, S., and Cristini, V. (2010).
Nonlinear modelling of cancer: Bridging the gap between cells and tumours. Nonlinearity 23, R1-r9. PMID: 20808719. doi.
Milenkovic, T., Memisevic, V., Ganesan, A., and Przulj, N. (2010).
Systems-level cancer gene identification from protein interaction network topology applied to melanogenesis-related functional genomics data. J R Soc Interface 7, 423-437. PMID: 19625303. doi.
Mironova, V., Omelyanchuk, N., Yosiphon, G., Fadeev, S., Kolchanov, N., Mjolsness, E., and Likhoshvai, V. (2010).
A plausible mechanism for auxin patterning along the developing root. BMC Syst Biol 4, 98. PMID: 20663170. doi.
Ossato, G., Digman, M., Aiken, C., Lukacsovich, T., Marsh, J., and Gratton, E. (2010).
A two-step path to inclusion formation of huntingtin peptides revealed by number and brightness analysis. Biophys J 98, 3078-3085. PMID: 20550921. doi.
Potkin, S., Macciardi, F., Guffanti, G., Fallon, J., Wang, Q., Turner, J., Lakatos, A., Miles, M., Lander, A., Vawter, M., et al. (2010).
Identifying gene regulatory networks in schizophrenia. Neuroimage 53, 839-847. PMID: 20600988. doi.
Rossow, M., Sasaki, J., Digman, M., and Gratton, E. (2010).
Raster image correlation spectroscopy in live cells. Nat Protoc 5, 1761-1774. PMID: 21030952. doi.
Sanchez, S., Tricerri, M., Ossato, G., and Gratton, E. (2010).
Lipid packing determines protein-membrane interactions: Challenges for apolipoprotein a-i and high density lipoproteins. Biochim Biophys Acta 1798, 1399-1408. PMID: 20347719. doi.
Seiler, M., Aramant, R., Thomas, B., Peng, Q., Sadda, S., and Keirstead, H. (2010).
Visual restoration and transplant connectivity in degenerate rats implanted with retinal progenitor sheets. Eur J Neurosci 31, 508-520. PMID: 20105230. doi.
Sohn, J., Tseng, Y., Li, S., Voigt, A., and Lowengrub, J. (2010).
Dynamics of multicomponent vesicles in a viscous fluid. J Comput Phys 229, 119-144. PMID: 20808718. doi.
Tanaka, H., and Yi, T. (2010).
The effects of replacing sst2 with the heterologous rgs4 on polarization and mating in yeast. Biophys J 99, 1007-1017. PMID: 20712983. doi.
Thalhauser, C., and Komarova, N. (2010).
Signal response sensitivity in the yeast mitogen-activated protein kinase cascade. PLoS One 5, e11568. PMID: 20668519. doi.
Thalhauser, C., Lowengrub, J., Stupack, D., and Komarova, N. (2010).
Selection in spatial stochastic models of cancer: Migration as a key modulator of fitness. Biol Direct 5, 21. PMID: 20406439. doi.
Wang, L., Nie, Q., and Enciso, G. (2010).
Nonessential sites improve phosphorylation switch. Biophys J 99, L41-43. PMID: 20858409. doi.
Wang, L., Xin, J., and Nie, Q. (2010).
A critical quantity for noise attenuation in feedback systems. PLoS Comput Biol 6, e1000764. PMID: 20442870. doi.
Wang, Y., Christley, S., Mjolsness, E., and Xie, X. (2010).
Parameter inference for discretely observed stochastic kinetic models using stochastic gradient descent. BMC Syst Biol 4, 99. PMID: 20663171. doi.
Whisenant, T., Ho, D., Benz, R., Rogers, J., Kaake, R., Gordon, E., Huang, L., Baldi, P., and Bardwell, L. (2010).
Computational prediction and experimental verification of new map kinase docking sites and substrates including gli transcription factors. PLoS Comput Biol 6. PMID: 20865152. doi.
Wolkenhauer, O., Auffray, C., Baltrusch, S., Blthgen, N., Byrne, H., Cascante, M., Ciliberto, A., Dale, T., Drasdo, D., Fell, D., et al. (2010).
Systems biologists seek fuller integration of systems biology approaches in new cancer research programs. Cancer Res 70, 12-13. PMID: 20028868. doi.
Yang, P., Seiler, M., Aramant, R., Yan, F., Mahoney, M., Kitzes, L., and Keirstead, H. (2010).
Trophic factors gdnf and bdnf improve function of retinal sheet transplants. Exp Eye Res 91, 727-738. PMID: 20804751. 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. 
2011 Research. Copyright © 2013. The Center for Complex Biological Systems, UC Irvine
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