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. 

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 

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. 

Publication Highlights

 
1. Cai, A.Q., Radtke, K., Linville, A., Lander, A.D., Nie, Q., and Schilling, T.F. (2012). Cellular retinoic acid-binding proteins are essential for hindbrain patterning and signal robustness in zebrafish. Development 139, 2150-2155. PMCID 3357909. This work combines experiments and modeling to reveal the regulatory roles played by cellular retinoic acid binding proteins during development.
 
2. Cardarelli, F., Lanzano, L., and Gratton, E. (2012). Capturing directed molecular motion in the nuclear pore complex of live cells. Proc Natl Acad Sci U S A 109, 9863-9868. PMCID 3382504. This work leverages fluorescence dynamics to elucidate that paths and rates of motion of molecules as they go through nuclear pores.
 
3. Chan, C., Liu, X., Wang, L., Bardwell, L., Nie, Q., and Enciso, G. (2012). Protein scaffolds can enhance the bistability of multisite phosphorylation systems. PLoS Comput Biol 8, e1002551. PMCID 3380838. This work elucidates how scaffolds and compartments contribute to signaling specificity within cells.

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

5. Gordon, E.A., Whisenant, T.C., Zeller, M., Kaake, R.M., Gordon, W.M., Krotee, P., Patel, V., Huang, L., Baldi, P., and Bardwell, L. (2013). Combining docking site and phosphosite predictions to find new substrates: identification of smoothelin-like-2 (SMTNL2) as a c-Jun N-terminal kinase (JNK) substrate. Cell Signal 25, 2518-2529. NIHMSID 526352. This work, a collaboration between Cell Biology and Computer Science groups, used computational techniques to identify and validate new MAP kinase substrates.

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

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

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

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

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

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

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

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

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

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

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

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

18. Zhang, L., Lander, A.D., and Nie, Q. (2012). A reaction-diffusion mechanism influences cell lineage progression as a basis for formation, regeneration, and stability of intestinal crypts. BMC Syst Biol 6, 93. PMCID 3434027. This work shows how feedback interactions in cell lineage progression drive morphogenesis in the intestine.

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

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