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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4-Butyrolactone
L. R. Swem, Swem, D. L., Wingreen, N. S., and Bassler, B. L., “Deducing receptor signaling parameters from in vivo analysis: LuxN/AI-1 quorum sensing in Vibrio harveyi.”, Cell, vol. 134, no. 3, pp. 461-73, 2008.
K. C. Mok, Wingreen, N. S., and Bassler, B. L., “Vibrio harveyi quorum sensing: a coincidence detector for two autoinducers controls gene expression.”, EMBO J, vol. 22, no. 4, pp. 870-81, 2003.
T. Long, Tu, K. C., Wang, Y., Mehta, P., Ong, N. P., Bassler, B. L., and Wingreen, N. S., “Quantifying the integration of quorum-sensing signals with single-cell resolution.”, PLoS Biol, vol. 7, no. 3, p. e68, 2009.
Actins
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.
Acyl-Butyrolactones
L. R. Swem, Swem, D. L., Wingreen, N. S., and Bassler, B. L., “Deducing receptor signaling parameters from in vivo analysis: LuxN/AI-1 quorum sensing in Vibrio harveyi.”, Cell, vol. 134, no. 3, pp. 461-73, 2008.
Adaptation, Physiological
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.
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.
O. Oleksiuk, Jakovljevic, V., Vladimirov, N., Carvalho, R., Paster, E., Ryu, W. S., Meir, Y., Wingreen, N. S., Kollmann, M., and Sourjik, V., “Thermal robustness of signaling in bacterial chemotaxis.”, Cell, vol. 145, no. 2, pp. 312-21, 2011.
S. Neumann, Vladimirov, N., Krembel, A. K., Wingreen, N. S., and Sourjik, V., “Imprecision of adaptation in Escherichia coli chemotaxis.”, PLoS One, vol. 9, no. 1, p. e84904, 2014.
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.
Adenosine Triphosphatases
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.
K. Casey Huang, Meir, Y., and Wingreen, N. S., “Dynamic structures in Escherichia coli: spontaneous formation of MinE rings and MinD polar zones.”, Proc Natl Acad Sci U S A, vol. 100, no. 22, pp. 12724-8, 2003.
Adenosine Triphosphate
K. Casey Huang, Meir, Y., and Wingreen, N. S., “Dynamic structures in Escherichia coli: spontaneous formation of MinE rings and MinD polar zones.”, Proc Natl Acad Sci U S A, vol. 100, no. 22, pp. 12724-8, 2003.
Algorithms
R. G. Endres and Wingreen, N. S., “Maximum likelihood and the single receptor.”, Phys Rev Lett, vol. 103, no. 15, p. 158101, 2009.
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.
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.
J. M. Guberman, Fay, A., Dworkin, J., Wingreen, N. S., and Gitai, Z., “PSICIC: noise and asymmetry in bacterial division revealed by computational image analysis at sub-pixel resolution.”, PLoS Comput Biol, vol. 4, no. 11, p. e1000233, 2008.
C. P. Broedersz, Wang, X., Meir, Y., Loparo, J. J., Rudner, D. Z., and Wingreen, N. S., “Condensation and localization of the partitioning protein ParB on the bacterial chromosome.”, Proc Natl Acad Sci U S A, vol. 111, no. 24, pp. 8809-14, 2014.
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.
R. G. Endres and Wingreen, N. S., “Weight matrices for protein-DNA binding sites from a single co-crystal structure.”, Phys Rev E Stat Nonlin Soft Matter Phys, vol. 73, no. 6 Pt 1, p. 061921, 2006.
S. Goyal and Wingreen, N. S., “Growth-induced instability in metabolic networks.”, Phys Rev Lett, vol. 98, no. 13, p. 138105, 2007.
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.
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.
M. Wyart, Botstein, D., and Wingreen, N. S., “Evaluating gene expression dynamics using pairwise RNA FISH data.”, PLoS Comput Biol, vol. 6, no. 11, p. e1000979, 2010.
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.
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.
Amdinocillin
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.
Amino Acid Motifs
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.
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.
Amino Acid Sequence
L. R. Swem, Swem, D. L., Wingreen, N. S., and Bassler, B. L., “Deducing receptor signaling parameters from in vivo analysis: LuxN/AI-1 quorum sensing in Vibrio harveyi.”, Cell, vol. 134, no. 3, pp. 461-73, 2008.
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.
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.
Amino Acid Substitution
R. S. Dwyer, Ricci, D. P., Colwell, L. J., Silhavy, T. J., and Wingreen, N. S., “Predicting functionally informative mutations in Escherichia coli BamA using evolutionary covariance analysis.”, Genetics, vol. 195, no. 2, pp. 443-55, 2013.
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.
Amino Acids
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.
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.
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.
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.
Ammonia
J. Yuan, Doucette, C. D., Fowler, W. U., Feng, X. - J., Piazza, M., Rabitz, H. A., Wingreen, N. S., and Rabinowitz, J. D., “Metabolomics-driven quantitative analysis of ammonia assimilation in E. coli.”, Mol Syst Biol, vol. 5, p. 302, 2009.
Anabaena
N. S. Wingreen and Levin, S. A., “Cooperation among microorganisms.”, PLoS Biol, vol. 4, no. 9, p. e299, 2006.
Animals
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.
V. Sourjik and Wingreen, N. S., “Turning to the cold.”, Nat Cell Biol, vol. 9, no. 9, pp. 1029-31, 2007.
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.
N. S. Wingreen and Levin, S. A., “Cooperation among microorganisms.”, PLoS Biol, vol. 4, no. 9, p. e299, 2006.
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.
Anti-Bacterial Agents
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.
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.
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.
Antibodies, Viral
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.
Antigens, Viral
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.
Arginine
B. M. Zee, Levin, R. S., Xu, B., LeRoy, G., Wingreen, N. S., and Garcia, B. A., “In vivo residue-specific histone methylation dynamics.”, J Biol Chem, vol. 285, no. 5, pp. 3341-50, 2010.
Aspartic Acid
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.
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.
Bacillus subtilis
J. M. Guberman, Fay, A., Dworkin, J., Wingreen, N. S., and Gitai, Z., “PSICIC: noise and asymmetry in bacterial division revealed by computational image analysis at sub-pixel resolution.”, PLoS Comput Biol, vol. 4, no. 11, p. e1000233, 2008.
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.
P. Mehta, Mukhopadhyay, R., and Wingreen, N. S., “Exponential sensitivity of noise-driven switching in genetic networks.”, Phys Biol, vol. 5, no. 2, p. 026005, 2008.
Bacteria
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.
J. M. Guberman, Fay, A., Dworkin, J., Wingreen, N. S., and Gitai, Z., “PSICIC: noise and asymmetry in bacterial division revealed by computational image analysis at sub-pixel resolution.”, PLoS Comput Biol, vol. 4, no. 11, p. e1000233, 2008.
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.
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.
Bacterial Outer Membrane Proteins
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. S. Dwyer, Ricci, D. P., Colwell, L. J., Silhavy, T. J., and Wingreen, N. S., “Predicting functionally informative mutations in Escherichia coli BamA using evolutionary covariance analysis.”, Genetics, vol. 195, no. 2, pp. 443-55, 2013.
Bacterial Physiological Phenomena
C. P. Broedersz, Wang, X., Meir, Y., Loparo, J. J., Rudner, D. Z., and Wingreen, N. S., “Condensation and localization of the partitioning protein ParB on the bacterial chromosome.”, Proc Natl Acad Sci U S A, vol. 111, no. 24, pp. 8809-14, 2014.
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.
Bacterial Proteins
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.
K. C. Tu, Long, T., Svenningsen, S. L., Wingreen, N. S., and Bassler, B. L., “Negative feedback loops involving small regulatory RNAs precisely control the Vibrio harveyi quorum-sensing response.”, Mol Cell, vol. 37, no. 4, pp. 567-79, 2010.
L. R. Swem, Swem, D. L., Wingreen, N. S., and Bassler, B. L., “Deducing receptor signaling parameters from in vivo analysis: LuxN/AI-1 quorum sensing in Vibrio harveyi.”, Cell, vol. 134, no. 3, pp. 461-73, 2008.
E. J. Banigan, Gelbart, M. A., Gitai, Z., Wingreen, N. S., and Liu, A. J., “Filament depolymerization can explain chromosome pulling during bacterial mitosis.”, PLoS Comput Biol, vol. 7, no. 9, p. e1002145, 2011.
C. P. Broedersz, Wang, X., Meir, Y., Loparo, J. J., Rudner, D. Z., and Wingreen, N. S., “Condensation and localization of the partitioning protein ParB on the bacterial chromosome.”, Proc Natl Acad Sci U S A, vol. 111, no. 24, pp. 8809-14, 2014.
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.
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.
Y. Wang, Tu, K. C., Ong, N. P., Bassler, B. L., and Wingreen, N. S., “Protein-level fluctuation correlation at the microcolony level and its application to the Vibrio harveyi quorum-sensing circuit.”, Biophys J, vol. 100, no. 12, pp. 3045-53, 2011.
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.
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.
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.
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.
T. Mora, Bai, F., Che, Y. - S., Minamino, T., Namba, K., and Wingreen, N. S., “Non-genetic individuality in Escherichia coli motor switching.”, Phys Biol, vol. 8, no. 2, p. 024001, 2011.
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.
K. Casey Huang and Wingreen, N. S., “Min-protein oscillations in round bacteria.”, Phys Biol, vol. 1, no. 3-4, pp. 229-35, 2004.
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.
A. J. Pompeani, Irgon, J. J., Berger, M. F., Bulyk, M. L., Wingreen, N. S., and Bassler, B. L., “The Vibrio harveyi master quorum-sensing regulator, LuxR, a TetR-type protein is both an activator and a repressor: DNA recognition and binding specificity at target promoters.”, Mol Microbiol, vol. 70, no. 1, pp. 76-88, 2008.
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. Long, Tu, K. C., Wang, Y., Mehta, P., Ong, N. P., Bassler, B. L., and Wingreen, N. S., “Quantifying the integration of quorum-sensing signals with single-cell resolution.”, PLoS Biol, vol. 7, no. 3, p. e68, 2009.
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.
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.
Bacteriophages
J. S. Weitz, Benfey, P. N., and Wingreen, N. S., “Evolution, interactions, and biological networks.”, PLoS Biol, vol. 5, no. 1, p. e11, 2007.
Base Composition
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.
Base Sequence
K. C. Tu, Long, T., Svenningsen, S. L., Wingreen, N. S., and Bassler, B. L., “Negative feedback loops involving small regulatory RNAs precisely control the Vibrio harveyi quorum-sensing response.”, Mol Cell, vol. 37, no. 4, pp. 567-79, 2010.
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.
beta-Galactosidase
K. C. Mok, Wingreen, N. S., and Bassler, B. L., “Vibrio harveyi quorum sensing: a coincidence detector for two autoinducers controls gene expression.”, EMBO J, vol. 22, no. 4, pp. 870-81, 2003.
Binding Sites
C. P. Broedersz, Wang, X., Meir, Y., Loparo, J. J., Rudner, D. Z., and Wingreen, N. S., “Condensation and localization of the partitioning protein ParB on the bacterial chromosome.”, Proc Natl Acad Sci U S A, vol. 111, no. 24, pp. 8809-14, 2014.
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. 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. G. Endres and Wingreen, N. S., “Weight matrices for protein-DNA binding sites from a single co-crystal structure.”, Phys Rev E Stat Nonlin Soft Matter Phys, vol. 73, no. 6 Pt 1, p. 061921, 2006.
A. J. Pompeani, Irgon, J. J., Berger, M. F., Bulyk, M. L., Wingreen, N. S., and Bassler, B. L., “The Vibrio harveyi master quorum-sensing regulator, LuxR, a TetR-type protein is both an activator and a repressor: DNA recognition and binding specificity at target promoters.”, Mol Microbiol, vol. 70, no. 1, pp. 76-88, 2008.
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.
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.
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.
Biochemistry
B. M. Zee, Levin, R. S., Xu, B., LeRoy, G., Wingreen, N. S., and Garcia, B. A., “In vivo residue-specific histone methylation dynamics.”, J Biol Chem, vol. 285, no. 5, pp. 3341-50, 2010.
Biofilms
K. Drescher, Nadell, C. D., Stone, H. A., Wingreen, N. S., and Bassler, B. L., “Solutions to the public goods dilemma in bacterial biofilms.”, Curr Biol, vol. 24, no. 1, pp. 50-5, 2014.
Biological Clocks
E. Emberly and Wingreen, N. S., “Hourglass model for a protein-based circadian oscillator.”, Phys Rev Lett, vol. 96, no. 3, p. 038303, 2006.
Biological Evolution
S. Goyal and Wingreen, N. S., “Growth-induced instability in metabolic networks.”, Phys Rev Lett, vol. 98, no. 13, p. 138105, 2007.
Biological Factors
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.
Biological Transport
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.
Biomass
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.
C. D. Doucette, Schwab, D. J., Wingreen, N. S., and Rabinowitz, J. D., “α-Ketoglutarate coordinates carbon and nitrogen utilization via enzyme I inhibition.”, Nat Chem Biol, vol. 7, no. 12, pp. 894-901, 2011.
Biophysical Phenomena
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.
Biophysics
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.
Biopolymers
D. Swanson and Wingreen, N. S., “Active biopolymers confer fast reorganization kinetics.”, Phys Rev Lett, vol. 107, no. 21, p. 218103, 2011.
Brain
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.
Calcium
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.
Calcium Signaling
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.
Carbon
C. D. Doucette, Schwab, D. J., Wingreen, N. S., and Rabinowitz, J. D., “α-Ketoglutarate coordinates carbon and nitrogen utilization via enzyme I inhibition.”, Nat Chem Biol, vol. 7, no. 12, pp. 894-901, 2011.
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.
S. Hsin- Jung Li, Li, Z., Park, J. O., King, C. G., Rabinowitz, J. D., Wingreen, N. S., and Gitai, Z., “Escherichia coli translation strategies differ across carbon, nitrogen and phosphorus limitation conditions.”, Nat Microbiol, vol. 3, no. 8, pp. 939-947, 2018.
Cardiolipins
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.
Carrier Proteins
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.
Catalytic Domain
J. Yuan, Doucette, C. D., Fowler, W. U., Feng, X. - J., Piazza, M., Rabitz, H. A., Wingreen, N. S., and Rabinowitz, J. D., “Metabolomics-driven quantitative analysis of ammonia assimilation in E. coli.”, Mol Syst Biol, vol. 5, p. 302, 2009.
Caulobacter crescentus
E. J. Banigan, Gelbart, M. A., Gitai, Z., Wingreen, N. S., and Liu, A. J., “Filament depolymerization can explain chromosome pulling during bacterial mitosis.”, PLoS Comput Biol, vol. 7, no. 9, p. e1002145, 2011.
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.
Cell Communication
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.
Cell Cycle
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.
Cell Cycle Proteins
K. Casey Huang, Meir, Y., and Wingreen, N. S., “Dynamic structures in Escherichia coli: spontaneous formation of MinE rings and MinD polar zones.”, Proc Natl Acad Sci U S A, vol. 100, no. 22, pp. 12724-8, 2003.
Cell Division
J. M. Guberman, Fay, A., Dworkin, J., Wingreen, N. S., and Gitai, Z., “PSICIC: noise and asymmetry in bacterial division revealed by computational image analysis at sub-pixel resolution.”, PLoS Comput Biol, vol. 4, no. 11, p. e1000233, 2008.
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.
Cell Enlargement
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.
Cell Growth Processes
S. Goyal and Wingreen, N. S., “Growth-induced instability in metabolic networks.”, Phys Rev Lett, vol. 98, no. 13, p. 138105, 2007.
Cell Membrane
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. 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.
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.
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.
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.
Cell Movement
V. Sourjik and Wingreen, N. S., “Turning to the cold.”, Nat Cell Biol, vol. 9, no. 9, pp. 1029-31, 2007.
Cell Polarity
K. Casey Huang, Meir, Y., and Wingreen, N. S., “Dynamic structures in Escherichia coli: spontaneous formation of MinE rings and MinD polar zones.”, Proc Natl Acad Sci U S A, vol. 100, no. 22, pp. 12724-8, 2003.
Cell Proliferation
S. Neumann, Vladimirov, N., Krembel, A. K., Wingreen, N. S., and Sourjik, V., “Imprecision of adaptation in Escherichia coli chemotaxis.”, PLoS One, vol. 9, no. 1, p. e84904, 2014.
Cell Size
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.
Cell Wall
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.
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.
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.
Cells
R. G. Endres and Wingreen, N. S., “Maximum likelihood and the single receptor.”, Phys Rev Lett, vol. 103, no. 15, p. 158101, 2009.
S. Goyal and Wingreen, N. S., “Growth-induced instability in metabolic networks.”, Phys Rev Lett, vol. 98, no. 13, p. 138105, 2007.
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.
Chemoreceptor Cells
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.
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.
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.
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.
Chemotactic Factors
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.
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.
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.
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.
Chemotaxis
V. Sourjik and Wingreen, N. S., “Responding to chemical gradients: bacterial chemotaxis.”, Curr Opin Cell Biol, vol. 24, no. 2, pp. 262-8, 2012.
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.
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.
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.
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.
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.
O. Oleksiuk, Jakovljevic, V., Vladimirov, N., Carvalho, R., Paster, E., Ryu, W. S., Meir, Y., Wingreen, N. S., Kollmann, M., and Sourjik, V., “Thermal robustness of signaling in bacterial chemotaxis.”, Cell, vol. 145, no. 2, pp. 312-21, 2011.
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.
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.
S. Neumann, Vladimirov, N., Krembel, A. K., Wingreen, N. S., and Sourjik, V., “Imprecision of adaptation in Escherichia coli chemotaxis.”, PLoS One, vol. 9, no. 1, p. e84904, 2014.
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., “Accuracy of direct gradient sensing by cell-surface receptors.”, Prog Biophys Mol Biol, vol. 100, no. 1-3, pp. 33-9, 2009.
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.
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.
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.
Chitin
K. Drescher, Nadell, C. D., Stone, H. A., Wingreen, N. S., and Bassler, B. L., “Solutions to the public goods dilemma in bacterial biofilms.”, Curr Biol, vol. 24, no. 1, pp. 50-5, 2014.
Chitinase
K. Drescher, Nadell, C. D., Stone, H. A., Wingreen, N. S., and Bassler, B. L., “Solutions to the public goods dilemma in bacterial biofilms.”, Curr Biol, vol. 24, no. 1, pp. 50-5, 2014.
Chromatography, High Pressure Liquid
J. Yuan, Doucette, C. D., Fowler, W. U., Feng, X. - J., Piazza, M., Rabitz, H. A., Wingreen, N. S., and Rabinowitz, J. D., “Metabolomics-driven quantitative analysis of ammonia assimilation in E. coli.”, Mol Syst Biol, vol. 5, p. 302, 2009.
Chromatography, Liquid
B. M. Zee, Levin, R. S., Xu, B., LeRoy, G., Wingreen, N. S., and Garcia, B. A., “In vivo residue-specific histone methylation dynamics.”, J Biol Chem, vol. 285, no. 5, pp. 3341-50, 2010.
Chromosome Segregation
E. J. Banigan, Gelbart, M. A., Gitai, Z., Wingreen, N. S., and Liu, A. J., “Filament depolymerization can explain chromosome pulling during bacterial mitosis.”, PLoS Comput Biol, vol. 7, no. 9, p. e1002145, 2011.
Chromosomes, Bacterial
E. J. Banigan, Gelbart, M. A., Gitai, Z., Wingreen, N. S., and Liu, A. J., “Filament depolymerization can explain chromosome pulling during bacterial mitosis.”, PLoS Comput Biol, vol. 7, no. 9, p. e1002145, 2011.
C. P. Broedersz, Wang, X., Meir, Y., Loparo, J. J., Rudner, D. Z., and Wingreen, N. S., “Condensation and localization of the partitioning protein ParB on the bacterial chromosome.”, Proc Natl Acad Sci U S A, vol. 111, no. 24, pp. 8809-14, 2014.
Circadian Rhythm
E. Emberly and Wingreen, N. S., “Hourglass model for a protein-based circadian oscillator.”, Phys Rev Lett, vol. 96, no. 3, p. 038303, 2006.
Circadian Rhythm Signaling Peptides and Proteins
E. Emberly and Wingreen, N. S., “Hourglass model for a protein-based circadian oscillator.”, Phys Rev Lett, vol. 96, no. 3, p. 038303, 2006.
Cluster Analysis
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.
M. Wyart, Botstein, D., and Wingreen, N. S., “Evaluating gene expression dynamics using pairwise RNA FISH data.”, PLoS Comput Biol, vol. 6, no. 11, p. e1000979, 2010.
Colony Count, Microbial
Y. Wang, Tu, K. C., Ong, N. P., Bassler, B. L., and Wingreen, N. S., “Protein-level fluctuation correlation at the microcolony level and its application to the Vibrio harveyi quorum-sensing circuit.”, Biophys J, vol. 100, no. 12, pp. 3045-53, 2011.
Computational Biology
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.
R. S. Dwyer, Ricci, D. P., Colwell, L. J., Silhavy, T. J., and Wingreen, N. S., “Predicting functionally informative mutations in Escherichia coli BamA using evolutionary covariance analysis.”, Genetics, vol. 195, no. 2, pp. 443-55, 2013.
N. Zhang, Zeng, C., and Wingreen, N. S., “Fast accurate evaluation of protein solvent exposure.”, Proteins, vol. 57, no. 3, pp. 565-76, 2004.
M. Wyart, Botstein, D., and Wingreen, N. S., “Evaluating gene expression dynamics using pairwise RNA FISH data.”, PLoS Comput Biol, vol. 6, no. 11, p. e1000979, 2010.
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.
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.
Computer Simulation
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.
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.
R. G. Endres and Wingreen, N. S., “Maximum likelihood and the single receptor.”, Phys Rev Lett, vol. 103, no. 15, p. 158101, 2009.
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. 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.
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. J. Banigan, Gelbart, M. A., Gitai, Z., Wingreen, N. S., and Liu, A. J., “Filament depolymerization can explain chromosome pulling during bacterial mitosis.”, PLoS Comput Biol, vol. 7, no. 9, p. e1002145, 2011.
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.
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.
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.
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.
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.

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