List of Faculty Publications

Below is a list of Faculty publications imported from PubMed or manually added. By default, publications are sorted by year with titles displayed in ascending alphabetical order.
Shortcuts: Wühr, Martin | Wingreen, Ned | Wieschaus, Eric | Troyanskaya, Olga | Tilghman, Shirley | Storey, John | Singh, Mona | Shvartsman, Stanislav | Shaevitz, Joshua | Rabinowitz, Joshua | Murphy, Coleen | Levine, Michael {Levine, Michael S.} | Gregor, Thomas | Botstein, David | Bialek, William | Ayroles, Julien | Andolfatto, Peter | Akey, Joshua

Filters: Keyword is Models, Theoretical  [Clear All Filters]
2015
B. P. Bratton and Shaevitz, J. W., “Simple Experimental Methods for Determining the Apparent Focal Shift in a Microscope System.”, PLoS One, vol. 10, no. 8, p. e0134616, 2015.
2014
W. Bialek, Cavagna, A., Giardina, I., Mora, T., Pohl, O., Silvestri, E., Viale, M., and Walczak, A. M., “Social interactions dominate speed control in poising natural flocks near criticality.”, Proc Natl Acad Sci U S A, vol. 111, no. 20, pp. 7212-7, 2014.
2013
G. J. Stephens, Mora, T., Tkačik, G., and Bialek, W., “Statistical thermodynamics of natural images.”, Phys Rev Lett, vol. 110, no. 1, p. 018701, 2013.
M. Osterfield, Du, X. X., Schüpbach, T., Wieschaus, E., and Shvartsman, S. Y., “Three-dimensional epithelial morphogenesis in the developing Drosophila egg.”, Dev Cell, vol. 24, no. 4, pp. 400-10, 2013.
2012
D. S. A. Simakov, Cheung, L. S., Pismen, L. M., and Shvartsman, S. Y., “EGFR-dependent network interactions that pattern Drosophila eggshell appendages.”, Development, vol. 139, no. 15, pp. 2814-20, 2012.
S. Y. Shvartsman and Baker, R. E., “Mathematical models of morphogen gradients and their effects on gene expression.”, Wiley Interdiscip Rev Dev Biol, vol. 1, no. 5, pp. 715-30, 2012.
U. Ober, Ayroles, J. F., Stone, E. A., Richards, S., Zhu, D., Gibbs, R. A., Stricker, C., Gianola, D., Schlather, M., Mackay, T. F. C., and Simianer, H., “Using whole-genome sequence data to predict quantitative trait phenotypes in Drosophila melanogaster.”, PLoS Genet, vol. 8, no. 5, p. e1002685, 2012.
2011
Y. Kim, Andreu, M. José, Lim, B., Chung, K., Terayama, M., Jiménez, G., Berg, C. A., Lu, H., and Shvartsman, S. Y., “Gene regulation by MAPK substrate competition.”, Dev Cell, vol. 20, no. 6, pp. 880-7, 2011.
2010
S. Neumann, Hansen, C. H., Wingreen, N. S., and Sourjik, V., “Differences in signalling by directly and indirectly binding ligands in bacterial chemotaxis.”, EMBO J, vol. 29, no. 20, pp. 3484-95, 2010.
G. J. Stephens and Bialek, W., “Statistical mechanics of letters in words.”, Phys Rev E Stat Nonlin Soft Matter Phys, vol. 81, no. 6 Pt 2, p. 066119, 2010.
2008
P. A. DiMaggio, McAllister, S. R., Floudas, C. A., Feng, X. - J., Rabinowitz, J. D., and Rabitz, H. A., “Biclustering via optimal re-ordering of data matrices in systems biology: rigorous methods and comparative studies.”, BMC Bioinformatics, vol. 9, p. 458, 2008.
J. D. Rabinowitz, Hsiao, J. J., Gryncel, K. R., Kantrowitz, E. R., Feng, X. - J., Li, G., and Rabitz, H., “Dissecting enzyme regulation by multiple allosteric effectors: nucleotide regulation of aspartate transcarbamoylase.”, Biochemistry, vol. 47, no. 21, pp. 5881-8, 2008.
2007
J. W. Shaevitz and Fletcher, D. A., “Load fluctuations drive actin network growth.”, Proc Natl Acad Sci U S A, vol. 104, no. 40, pp. 15688-92, 2007.
2006
A. M. Berezhkovskii, Monine, M. I., Muratov, C. B., and Shvartsman, S. Y., “Homogenization of boundary conditions for surfaces with regular arrays of traps.”, J Chem Phys, vol. 124, no. 3, p. 036103, 2006.
2005
M. I. Monine, Berezhkovskii, A. M., Joslin, E. J., H Wiley, S., Lauffenburger, D. A., and Shvartsman, S. Y., “Ligand accumulation in autocrine cell cultures.”, Biophys J, vol. 88, no. 4, pp. 2384-90, 2005.
E. Nabieva, Jim, K., Agarwal, A., Chazelle, B., and Singh, M., “Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps.”, Bioinformatics, vol. 21 Suppl 1, pp. i302-10, 2005.
2004
A. M. Berezhkovskii, Batsilas, L., and Shvartsman, S. Y., “Ligand trapping in epithelial layers and cell cultures.”, Biophys Chem, vol. 107, no. 3, pp. 221-7, 2004.
2003
E. Schneidman, Still, S., Berry, M. J., and Bialek, W., “Network information and connected correlations.”, Phys Rev Lett, vol. 91, no. 23, p. 238701, 2003.
M. Pribyl, Muratov, C. B., and Shvartsman, S. Y., “Transitions in the model of epithelial patterning.”, Dev Dyn, vol. 226, no. 1, pp. 155-9, 2003.
2002
H. Li, Tang, C., and Wingreen, N. S., “Designability of protein structures: a lattice-model study using the Miyazawa-Jernigan matrix.”, Proteins, vol. 49, no. 3, pp. 403-12, 2002.
S. Y. Shvartsman, Muratov, C. B., and Lauffenburger, D. A., “Modeling and computational analysis of EGF receptor-mediated cell communication in Drosophila oogenesis.”, Development, vol. 129, no. 11, pp. 2577-89, 2002.