PUBLICATIONS

McLelland BT, Lin B, Mathur A, Aramant RB, Thomas BB, Nistor G, Keirstead HS, Seiler MJ.
Transplanted hESC-Derived Retina Organoid Sheets Differentiate, Integrate, and Improve Visual Function in Retinal Degenerate Rats. Invest Ophthalmol Vis Sci. 2018 May 1;59(6):2586-2603. doi: 10.1167/iovs.17-23646. PMCID:PMC5968836

Kim SM, Nguyen TT, Ravi A, Kubiniok P, Finicle BT, Jayashankar V, Malacrida L, Hou J, Robertson J, Gao D, Chernoff J, Digman MA, Potma EO, Tromberg BJ, Thibault P, Edinger AL.
PTEN Deficiency and AMPK Activation Promote Nutrient Scavenging and Anabolism in Prostate Cancer Cells. Cancer Discov. 2018 Jul;8(7):866-883. doi: 10.1158/2159-8290.CD-17-1215. Epub 2018 Mar 23. PMCID:PMC6030497

Pham K, Turian E, Liu K, Li S, Lowengrub J.
Nonlinear studies of tumor morphological stability using a two-fluid flow model. J Math Biol. 2018 Mar 15. doi: 10.1007/s00285-018-1212-3.  PMID:29546457

Lei J, Nie Q, Chen DB.
A single-cell epigenetic model for paternal psychological stress-induced transgenerational reprogramming in offspring. Biol Reprod. 2018 Jun 1;98(6):846-855. doi: 10.1093/biolre/ioy050. PMCID:PMC5991201

Malacrida L, Rao E, Gratton E.
Comparison between iMSD and 2D-pCF analysis for molecular motion studies on in vivo cells: The case of the epidermal growth factor receptor. Methods. 2018 May 1;140-141:74-84. doi: 10.1016/j.ymeth.2018.01.010.  PMCID:PMC5999564

Yu P, Nie Q, Tang C, Zhang L.
Nanog induced intermediate state in regulating stem cell differentiation and reprogramming. BMC Syst Biol. 2018 Feb 27;12(1):22. doi: 10.1186/s12918-018-0552-3. PMID:29486740

Staaf E, Hedde PN, Bagawath Singh S, Piguet J, Gratton E, Johansson S. Educated natural killer cells show dynamic movement of the activating receptor NKp46 and confinement of the inhibitory receptor Ly49A. Sci Signal. 2018 Feb 13;11(517). pii: eaai9200. doi: 10.1126/scisignal.aai9200. PMCID:PMC5925740

Huang J, Chen L, Rui H.
Multigrid Methods for A Mixed Finite Element Method of The Darcy-Forchheimer Model. J Sci Comput. 2018 Jan;74(1):396-411. doi: 10.1007/s10915-017-0466-z.  PMCID:PMC5800874

Kobylkevich BM, Sarkar A, Carlberg BR, Huang L, Ranjit S, Graham DM, Messerli MA.
Reversing the direction of galvanotaxis with controlled increases in boundary layer viscosity. Phys Biol. 2018 Mar 9;15(3):036005. doi: 10.1088/1478-3975/aaad91. PMCID:PMC5970543

Mahlbacher G, Curtis LT, Lowengrub J, Frieboes HB.
Mathematical modeling of tumor-associated macrophage interactions with the cancer microenvironment. J Immunother Cancer. 2018 Jan 30;6(1):10. doi: 10.1186/s40425-017-0313-7. PMCID:PMC5791333

Gach JS, Bouzin M, Wong MP, Chromikova V, Gorlani A, Yu KT, Sharma B, Gratton E, Forthal DN.
Human immunodeficiency virus type-1 (HIV-1) evades antibody-dependent phagocytosis.PLoS Pathog. 2017 Dec 27;13(12):e1006793. doi: 10.1371/journal.ppat.1006793. eCollection 2017 Dec. PMCID:PMC5760106

Davey RJ, Digman MA, Gratton E, Moens PDJ.
Quantitative image mean squared displacement (iMSD) analysis of the dynamics of profilin 1 at the membrane of live cells. Methods. 2018 May 1;140-141:119-125. doi: 10.1016/j.ymeth.2017.12.002. Epub 2017 Dec 11. PMCID:PMC5995621

Konstorum A, Lowengrub JS.
Activation of the HGF/c-Met axis in the tumor microenvironment: A multispecies model. J Theor Biol. 2018 Feb 14;439:86-99. doi: 10.1016/j.jtbi.2017.11.025. Epub 2017 Dec 5. PMCID:PMC5799021

Wang XX, Wang D, Luo Y, Myakala K, Dobrinskikh E, Rosenberg AZ, Levi J, Kopp JB, Field A, Hill A, Lucia S, Qiu L, Jiang T, Peng Y, Orlicky D, Garcia G, Herman-Edelstein M, D'Agati V, Henriksen K, Adorini L, Pruzanski M, Xie C, et al.
FXR/TGR5 Dual Agonist Prevents Progression of Nephropathy in Diabetes and Obesity. J Am Soc Nephrol. 2018 Jan;29(1):118-137. doi: 10.1681/ASN.2017020222. Epub 2017 Oct 31. PMCID:PMC5748904

Yan H, Konstorum A, Lowengrub JS.
Three-Dimensional Spatiotemporal Modeling of Colon Cancer Organoids Reveals that Multimodal Control of Stem Cell Self-Renewal is a Critical Determinant of Size and Shape in Early Stages of Tumor Growth. Bull Math Biol. 2018 May;80(5):1404-1433. doi: 10.1007/s11538-017-0294-1. Epub 2017 Jul 5. PMCID:PMC5756149

Gach JS, Bouzin M, Wong MP, Chromikova V, Gorlani A, Yu KT, Sharma B, Gratton E, Forthal DN.
Human immunodeficiency virus type-1 (HIV-1) evades antibody-dependent phagocytosis. PLoS Pathog. 2017 Dec 27;13(12):e1006793. doi: 10.1371/journal.ppat.1006793. eCollection 2017 Dec. PMCID:PMC5760106

Digiacomo L, Cardarelli F, Pozzi D, Palchetti S, Digman MA, Gratton E, Capriotti AL, Mahmoudi M, Caracciolo G.
An apolipoprotein-enriched biomolecular corona switches the cellular uptake mechanism and trafficking pathway of lipid nanoparticles. Nanoscale. 2017 Nov 16;9(44):17254-17262. doi: 10.1039/c7nr06437c. PMCID:PMC5700750

Westerhof TM, Cox-Muranami WA, Li GP, Bachman M, Fan H, Nelson EL.
Highly efficient cellular cloning using Ferro-core Micropallet Arrays. Sci Rep. 2017 Oct 12;7(1):13081. doi: 10.1038/s41598-017-13242-1. PMCID:PMC5638909

Wan FYM, Enciso GA.
Optimal Proliferation and Differentiation of Chlamydia Trachomatis. Stud Appl Math. 2017 Jul;139(1):129-178. doi: 10.1111/sapm.12175. Epub 2017 May 30. PMCID:PMC5627525

Bohorquez-Hernandez A, Gratton E, Pacheco J, Asanov A, Vaca L.
Cholesterol modulates the cellular localization of Orai1 channels and its disposition among membrane domains. Biochim Biophys Acta. 2017 Dec;1862(12):1481-1490. doi: 10.1016/j.bbalip.2017.09.005. Epub 2017 Sep 13. PMCID:PMC5902182

Malacrida L, Jameson DM, Gratton E.
A multidimensional phasor approach reveals LAURDAN photophysics in NIH-3T3 cell membranes. Sci Rep. 2017 Aug 23;7(1):9215. doi: 10.1038/s41598-017-08564-z. PMCID:PMC5569084

Stortz M, Presman DM, Bruno L, Annibale P, Dansey MV, Burton G, Gratton E, Pecci A, Levi V.
Mapping the Dynamics of the Glucocorticoid Receptor within the Nuclear Landscape. Sci Rep. 2017 Jul 24;7(1):6219. doi: 10.1038/s41598-017-06676-0. PMCID:PMC5524710

Wang Q, Oh JW, Lee HL, Dhar A, Peng T, Ramos R, Guerrero-Juarez CF, Wang X, Zhao R, Cao X, Le J, Fuentes MA, Jocoy SC, Rossi AR, Vu B, Pham K, Wang X, Mali NM, Park JM, Choi JH, Lee H, Legrand JMD, et al.
A multi-scale model for hair follicles reveals heterogeneous domains driving rapid spatiotemporal hair growth patterning. Elife. 2017 Jul 11;6. pii: e22772. doi: 10.7554/eLife.22772. PMCID:PMC5610035

Bhattacharjee A, Datta R, Gratton E, Hochbaum AI.
Metabolic fingerprinting of bacteria by fluorescence lifetime imaging microscopy. Sci Rep. 2017 Jun 16;7(1):3743. doi: 10.1038/s41598-017-04032-w. PMCID:PMC5473825

Yan H, Romero-López M, Benitez LI, Di K, Frieboes HB, Hughes CCW, Bota DA, Lowengrub JS.
3D Mathematical Modeling of Glioblastoma Suggests That Transdifferentiated Vascular Endothelial Cells Mediate Resistance to Current Standard-of-Care Therapy. Cancer Res. 2017 Aug 1;77(15):4171-4184. doi: 10.1158/0008-5472.CAN-16-3094. Epub 2017 May 23. PMCID:PMC5540807

Herrington KA, Trinh AL, Dang C, O'Shaughnessy E, Hahn KM, Gratton E, Digman MA, Sutterlin C.
Spatial analysis of Cdc42 activity reveals a role for plasma membrane-associated Cdc42 in centrosome regulation. Mol Biol Cell. 2017 Jul 15;28(15):2135-2145. doi: 10.1091/mbc.E16-09-0665. Epub 2017 May 24. PMCID:PMC5509425

Peng T, Liu L, MacLean AL, Wong CW, Zhao W, Nie Q.
A mathematical model of mechanotransduction reveals how mechanical memory regulates mesenchymal stem cell fate decisions. BMC Syst Biol. 2017 May 16;11(1):55. doi: 10.1186/s12918-017-0429-x. PMCID:PMC5434622

Ceccarelli A, Di Venere A, Nicolai E, De Luca A, Rosato N, Gratton E, Mei G, Caccuri AM.
New insight into the interaction of TRAF2 C-terminal domain with lipid raft microdomains. Biochim Biophys Acta. 2017 Sep;1862(9):813-822. doi: 10.1016/j.bbalip.2017.05.003. Epub 2017 May 9. PMCID:PMC5562040

Liu K, Marple GR, Allard J, Li S, Veerapaneni S, Lowengrub J. Dynamics of a multicomponent vesicle in shear flow. Soft Matter. 2017 May 21;13(19):3521-3531. doi: 10.1039/c6sm02452a. Epub 2017 Apr 25. PMCID:PMC5505236

Bardwell AJ, Lagunes L, Zebarjedi R, Bardwell L.
The WW domain of the scaffolding protein IQGAP1 is neither necessary nor sufficient for binding to the MAPKs ERK1 and ERK2. J Biol Chem. 2017 May 26;292(21):8750-8761. doi: 10.1074/jbc.M116.767087. Epub 2017 Apr 10. PMCID:PMC5448102

Li CJ, Hong T, Tung YT, Yen YP, Hsu HC, Lu YL, Chang M, Nie Q, Chen JA. MicroRNA filters Hox temporal transcription noise to confer boundary formation in the spinal cord. Nat Commun. 2017 Mar 24;8:14685. doi: 10.1038/ncomms14685. PMCID:PMC5376671

Kline AD, Krantz ID, Deardorff MA, Shirahige K, Dorsett D, Gerton JL, Wu M, Mehta D, Mills JA, Carrico CS, Noon S, Herrera PS, Horsfield JA, Bettale C, Morgan J, Huisman SA, Moss J, McCleery J, Grados M, Hansen BD, Srivastava S, Taylor-Snell E, et al.

Cornelia de Lange syndrome and molecular implications of the cohesin complex: Abstracts from the 7th biennial scientific and educational symposium 2016. Am J Med Genet A. 2017 May;173(5):1172-1185. doi: 10.1002/ajmg.a.38161. Epub 2017 Feb 12. PMCID:PMC5758041  

Lee M, Chen GT, Puttock E, Wang K, Edwards RA, Waterman ML, Lowengrub J. Mathematical modeling links Wnt signaling to emergent patterns of metabolism in colon cancer. Mol Syst Biol. 2017 Feb 9;13(2):912. doi: 10.15252/msb.20167386. PMCID:PMC5327728

Rackauckas C, Nie Q.
ADAPTIVE METHODS FOR STOCHASTIC DIFFERENTIAL EQUATIONS VIA NATURAL EMBEDDINGS AND REJECTION SAMPLING WITH MEMORY. Discrete Continuous Dyn Syst Ser B. 2017;22(7):2731-2761. doi: 10.3934/dcdsb.2017133. PMCID:PMC5844583

Romero-López M, Trinh AL, Sobrino A, Hatch MM, Keating MT, Fimbres C, Lewis DE, Gershon PD, Botvinick EL, Digman M, Lowengrub JS, Hughes CC. Recapitulating the human tumor microenvironment: Colon tumor-derived extracellular matrix promotes angiogenesis and tumor cell growth. Biomaterials. 2017 Feb;116:118-129. doi: 10.1016/j.biomaterials.2016.11.034. Epub 2016 Nov 24. PMCID:PMC5226635

Yan H, Romero-Lopez M, Frieboes HB, Hughes CC, Lowengrub JS.
Multiscale Modeling of Glioblastoma Suggests that the Partial Disruption of Vessel/Cancer Stem Cell Crosstalk Can Promote Tumor Regression Without Increasing Invasiveness. IEEE Trans Biomed Eng. 2017 Mar;64(3):538-548. doi: 10.1109/TBME.2016.2615566. Epub 2016 Oct 7. PMCID:PMC5501302

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. 

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. 

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. 

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. 

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. 

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. 

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. 

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. do 

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 

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. 

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.