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

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Models, Molecular
K. Casey Huang and Wingreen, N. S., Min-protein oscillations in round bacteria., Phys Biol, vol. 1, no. 3-4, pp. 229-35, 2004.
M. L. Skoge, Endres, R. G., and Wingreen, N. S., Receptor-receptor coupling in bacterial chemotaxis: evidence for strongly coupled clusters., Biophys J, vol. 90, no. 12, pp. 4317-26, 2006.
L. Furchtgott, Wingreen, N. S., and Huang, K. Casey, Mechanisms for maintaining cell shape in rod-shaped Gram-negative bacteria., Mol Microbiol, vol. 81, no. 2, pp. 340-53, 2011.
J. Miller, Zeng, C., Wingreen, N. S., and Tang, C., Emergence of highly designable protein-backbone conformations in an off-lattice model., Proteins, vol. 47, no. 4, pp. 506-12, 2002.
W. Ndifon, Wingreen, N. S., and Levin, S. A., Differential neutralization efficiency of hemagglutinin epitopes, antibody interference, and the design of influenza vaccines., Proc Natl Acad Sci U S A, vol. 106, no. 21, pp. 8701-6, 2009.
W. - L. Ng, Wei, Y., Perez, L. J., Cong, J., Long, T., Koch, M., Semmelhack, M. F., Wingreen, N. S., and Bassler, B. L., Probing bacterial transmembrane histidine kinase receptor-ligand interactions with natural and synthetic molecules., Proc Natl Acad Sci U S A, vol. 107, no. 12, pp. 5575-80, 2010.
E. G. Emberly, Wingreen, N. S., and Tang, C., Designability of alpha-helical proteins., Proc Natl Acad Sci U S A, vol. 99, no. 17, pp. 11163-8, 2002.
R. G. Endres, Schulthess, T. C., and Wingreen, N. S., Toward an atomistic model for predicting transcription-factor binding sites., Proteins, vol. 57, no. 2, pp. 262-8, 2004.
R. Mukhopadhyay, Emberly, E., Tang, C., and Wingreen, N. S., Statistical mechanics of RNA folding: importance of alphabet size., Phys Rev E Stat Nonlin Soft Matter Phys, vol. 68, no. 4 Pt 1, p. 041904, 2003.
E. G. Emberly, Miller, J., Zeng, C., Wingreen, N. S., and Tang, C., Identifying proteins of high designability via surface-exposure patterns., Proteins, vol. 47, no. 3, pp. 295-304, 2002.
E. Kruus, Thumfort, P., Tang, C., and Wingreen, N. S., Gibbs sampling and helix-cap motifs., Nucleic Acids Res, vol. 33, no. 16, pp. 5343-53, 2005.
E. G. Emberly, Mukhopadhyay, R., Tang, C., and Wingreen, N. S., Flexibility of beta-sheets: principal component analysis of database protein structures., Proteins, vol. 55, no. 1, pp. 91-8, 2004.
E. G. Emberly, Mukhopadhyay, R., Wingreen, N. S., and Tang, C., Flexibility of alpha-helices: results of a statistical analysis of database protein structures., J Mol Biol, vol. 327, no. 1, pp. 229-37, 2003.
Models, Chemical
M. L. Skoge, Endres, R. G., and Wingreen, N. S., Receptor-receptor coupling in bacterial chemotaxis: evidence for strongly coupled clusters., Biophys J, vol. 90, no. 12, pp. 4317-26, 2006.
R. Mukhopadhyay, Huang, K. Casey, and Wingreen, N. S., Lipid localization in bacterial cells through curvature-mediated microphase separation., Biophys J, vol. 95, no. 3, pp. 1034-49, 2008.
R. V. Kulkarni, Huang, K. Casey, Kloster, M., and Wingreen, N. S., Pattern formation within Escherichia coli: diffusion, membrane attachment, and self-interaction of MinD molecules., Phys Rev Lett, vol. 93, no. 22, p. 228103, 2004.
C. L. Vizcarra, Zhang, N., Marshall, S. A., Wingreen, N. S., Zeng, C., and Mayo, S. L., An improved pairwise decomposable finite-difference Poisson-Boltzmann method for computational protein design., J Comput Chem, vol. 29, no. 7, pp. 1153-62, 2008.
E. Emberly and Wingreen, N. S., Hourglass model for a protein-based circadian oscillator., Phys Rev Lett, vol. 96, no. 3, p. 038303, 2006.
S. Wang and Wingreen, N. S., Cell shape can mediate the spatial organization of the bacterial cytoskeleton., Biophys J, vol. 104, no. 3, pp. 541-52, 2013.
E. G. Emberly, Mukhopadhyay, R., Wingreen, N. S., and Tang, C., Flexibility of alpha-helices: results of a statistical analysis of database protein structures., J Mol Biol, vol. 327, no. 1, pp. 229-37, 2003.
P. B. Kidd and Wingreen, N. S., Modeling the role of covalent enzyme modification in Escherichia coli nitrogen metabolism., Phys Biol, vol. 7, no. 1, p. 016006, 2010.
Models, Biological
S. - W. Teng, Schaffer, J. N., Tu, K. C., Mehta, P., Lu, W., Ong, N. P., Bassler, B. L., and Wingreen, N. S., Active regulation of receptor ratios controls integration of quorum-sensing signals in Vibrio harveyi., Mol Syst Biol, vol. 7, p. 491, 2011.
V. Sourjik and Wingreen, N. S., Responding to chemical gradients: bacterial chemotaxis., Curr Opin Cell Biol, vol. 24, no. 2, pp. 262-8, 2012.
M. L. Skoge, Endres, R. G., and Wingreen, N. S., Receptor-receptor coupling in bacterial chemotaxis: evidence for strongly coupled clusters., Biophys J, vol. 90, no. 12, pp. 4317-26, 2006.
D. Swanson and Wingreen, N. S., Active biopolymers confer fast reorganization kinetics., Phys Rev Lett, vol. 107, no. 21, p. 218103, 2011.
R. M. Cooper, Wingreen, N. S., and Cox, E. C., An excitable cortex and memory model successfully predicts new pseudopod dynamics., PLoS One, vol. 7, no. 3, p. e33528, 2012.
S. Goyal, Yuan, J., Chen, T., Rabinowitz, J. D., and Wingreen, N. S., Achieving optimal growth through product feedback inhibition in metabolism., PLoS Comput Biol, vol. 6, no. 6, p. e1000802, 2010.
R. G. Endres and Wingreen, N. S., Accuracy of direct gradient sensing by single cells., Proc Natl Acad Sci U S A, vol. 105, no. 41, pp. 15749-54, 2008.
R. G. Endres and Wingreen, N. S., Accuracy of direct gradient sensing by cell-surface receptors., Prog Biophys Mol Biol, vol. 100, no. 1-3, pp. 33-9, 2009.
C. H. Hansen, Sourjik, V., and Wingreen, N. S., A dynamic-signaling-team model for chemotaxis receptors in Escherichia coli., Proc Natl Acad Sci U S A, vol. 107, no. 40, pp. 17170-5, 2010.
K. E. Daly, Huang, K. Casey, Wingreen, N. S., and Mukhopadhyay, R., Mechanics of membrane bulging during cell-wall disruption in gram-negative bacteria., Phys Rev E Stat Nonlin Soft Matter Phys, vol. 83, no. 4 Pt 1, p. 041922, 2011.
M. Skoge, Meir, Y., and Wingreen, N. S., Dynamics of cooperativity in chemical sensing among cell-surface receptors., Phys Rev Lett, vol. 107, no. 17, p. 178101, 2011.
S. R McIsaac, Huang, K. Casey, Sengupta, A., and Wingreen, N. S., Does the potential for chaos constrain the embryonic cell-cycle oscillator?, PLoS Comput Biol, vol. 7, no. 7, p. e1002109, 2011.
R. G. Endres and Wingreen, N. S., Maximum likelihood and the single receptor., Phys Rev Lett, vol. 103, no. 15, p. 158101, 2009.
R. Mukhopadhyay, Huang, K. Casey, and Wingreen, N. S., Lipid localization in bacterial cells through curvature-mediated microphase separation., Biophys J, vol. 95, no. 3, pp. 1034-49, 2008.
R. G. Endres, Oleksiuk, O., Hansen, C. H., Meir, Y., Sourjik, V., and Wingreen, N. S., Variable sizes of Escherichia coli chemoreceptor signaling teams., Mol Syst Biol, vol. 4, p. 211, 2008.
Y. Meir, Jakovljevic, V., Oleksiuk, O., Sourjik, V., and Wingreen, N. S., Precision and kinetics of adaptation in bacterial chemotaxis., Biophys J, vol. 99, no. 9, pp. 2766-74, 2010.
T. Mora and Wingreen, N. S., Limits of sensing temporal concentration changes by single cells., Phys Rev Lett, vol. 104, no. 24, p. 248101, 2010.
R. G. Endres and Wingreen, N. S., Precise adaptation in bacterial chemotaxis through "assistance neighborhoods"., Proc Natl Acad Sci U S A, vol. 103, no. 35, pp. 13040-4, 2006.
T. Mora, Yu, H., Sowa, Y., and Wingreen, N. S., Steps in the bacterial flagellar motor., PLoS Comput Biol, vol. 5, no. 10, p. e1000540, 2009.
K. Casey Huang, Mukhopadhyay, R., and Wingreen, N. S., A curvature-mediated mechanism for localization of lipids to bacterial poles., PLoS Comput Biol, vol. 2, no. 11, p. e151, 2006.
A. R. Ureta, Endres, R. G., Wingreen, N. S., and Silhavy, T. J., Kinetic analysis of the assembly of the outer membrane protein LamB in Escherichia coli mutants each lacking a secretion or targeting factor in a different cellular compartment., J Bacteriol, vol. 189, no. 2, pp. 446-54, 2007.
R. V. Kulkarni, Huang, K. Casey, Kloster, M., and Wingreen, N. S., Pattern formation within Escherichia coli: diffusion, membrane attachment, and self-interaction of MinD molecules., Phys Rev Lett, vol. 93, no. 22, p. 228103, 2004.
R. Mukhopadhyay and Wingreen, N. S., Curvature and shape determination of growing bacteria., Phys Rev E Stat Nonlin Soft Matter Phys, vol. 80, no. 6 Pt 1, p. 062901, 2009.
N. S. Wingreen and Levin, S. A., Cooperation among microorganisms., PLoS Biol, vol. 4, no. 9, p. e299, 2006.
D. H. Lenz, Mok, K. C., Lilley, B. N., Kulkarni, R. V., Wingreen, N. S., and Bassler, B. L., The small RNA chaperone Hfq and multiple small RNAs control quorum sensing in Vibrio harveyi and Vibrio cholerae., Cell, vol. 118, no. 1, pp. 69-82, 2004.
D. Bruce Borenstein, Meir, Y., Shaevitz, J. W., and Wingreen, N. S., Non-local interaction via diffusible resource prevents coexistence of cooperators and cheaters in a lattice model., PLoS One, vol. 8, no. 5, p. e63304, 2013.
R. G. Endres, Falke, J. J., and Wingreen, N. S., Chemotaxis receptor complexes: from signaling to assembly., PLoS Comput Biol, vol. 3, no. 7, p. e150, 2007.
C. H. Hansen, Endres, R. G., and Wingreen, N. S., Chemotaxis in Escherichia coli: a molecular model for robust precise adaptation., PLoS Comput Biol, vol. 4, no. 1, p. e1, 2008.
E. Emberly and Wingreen, N. S., Hourglass model for a protein-based circadian oscillator., Phys Rev Lett, vol. 96, no. 3, p. 038303, 2006.
H. Wang, Wingreen, N. S., and Mukhopadhyay, R., Self-organized periodicity of protein clusters in growing bacteria., Phys Rev Lett, vol. 101, no. 21, p. 218101, 2008.
J. E. Keymer, Endres, R. G., Skoge, M., Meir, Y., and Wingreen, N. S., Chemosensing in Escherichia coli: two regimes of two-state receptors., Proc Natl Acad Sci U S A, vol. 103, no. 6, pp. 1786-91, 2006.
D. Greenfield, McEvoy, A. L., Shroff, H., Crooks, G. E., Wingreen, N. S., Betzig, E., and Liphardt, J., Self-organization of the Escherichia coli chemotaxis network imaged with super-resolution light microscopy., PLoS Biol, vol. 7, no. 6, p. e1000137, 2009.
K. Casey Huang, Mukhopadhyay, R., Wen, B., Gitai, Z., and Wingreen, N. S., Cell shape and cell-wall organization in Gram-negative bacteria., Proc Natl Acad Sci U S A, vol. 105, no. 49, pp. 19282-7, 2008.
T. Mora, Yu, H., and Wingreen, N. S., Modeling torque versus speed, shot noise, and rotational diffusion of the bacterial flagellar motor., Phys Rev Lett, vol. 103, no. 24, p. 248102, 2009.
S. van Teeffelen, Wang, S., Furchtgott, L., Huang, K. Casey, Wingreen, N. S., Shaevitz, J. W., and Gitai, Z., The bacterial actin MreB rotates, and rotation depends on cell-wall assembly., Proc Natl Acad Sci U S A, vol. 108, no. 38, pp. 15822-7, 2011.
P. B. Kidd and Wingreen, N. S., Modeling the role of covalent enzyme modification in Escherichia coli nitrogen metabolism., Phys Biol, vol. 7, no. 1, p. 016006, 2010.
Models, Anatomic
R. Mukhopadhyay and Wingreen, N. S., Curvature and shape determination of growing bacteria., Phys Rev E Stat Nonlin Soft Matter Phys, vol. 80, no. 6 Pt 1, p. 062901, 2009.
Microtubules
D. Swanson and Wingreen, N. S., Active biopolymers confer fast reorganization kinetics., Phys Rev Lett, vol. 107, no. 21, p. 218103, 2011.