2010 Publications

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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. 
2011 2010. Copyright © 2013. The Center for Complex Biological Systems, UC Irvine
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