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: Author is Wingreen, Ned S  [Clear All Filters]
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Computer Simulation
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.
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.
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, Falke, J. J., and Wingreen, N. S., Chemotaxis receptor complexes: from signaling to assembly., PLoS Comput Biol, vol. 3, no. 7, p. e150, 2007.
Cooperative Behavior
N. S. Wingreen and Levin, S. A., Cooperation among microorganisms., PLoS Biol, vol. 4, no. 9, p. e299, 2006.
Cross-Linking Reagents
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.
Cyclic AMP
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.
Drug Design
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.
N. Zhang, Zeng, C., and Wingreen, N. S., Fast accurate evaluation of protein solvent exposure., Proteins, vol. 57, no. 3, pp. 565-76, 2004.
Escherichia coli
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.
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.
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, 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. 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. 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.
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.
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.
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. 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.
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. 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.
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.
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.
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.
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.
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.
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.
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. 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.
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.
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. 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.
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.
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, 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.
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.
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.
V. Sourjik and Wingreen, N. S., Turning to the cold., Nat Cell Biol, vol. 9, no. 9, pp. 1029-31, 2007.
Escherichia coli 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.
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.
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, 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.
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.
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.
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.
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.
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.
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.
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. 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.
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.
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.
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.
Feedback
S. Goyal and Wingreen, N. S., Growth-induced instability in metabolic networks., Phys Rev Lett, vol. 98, no. 13, p. 138105, 2007.
Gene Expression Profiling
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.
Gene Expression Regulation, Bacterial
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.
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.
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.
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.
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.
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. 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.
Gene Expression Regulation, Enzymologic
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.
Gene Expression Regulation, Fungal
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.
Gene Regulatory Networks
J. S. Weitz, Benfey, P. N., and Wingreen, N. S., Evolution, interactions, and biological networks., PLoS Biol, vol. 5, no. 1, p. e11, 2007.
Genetics, Population
N. S. Wingreen, Miller, J., and Cox, E. C., Scaling of mutational effects in models for pleiotropy., Genetics, vol. 164, no. 3, pp. 1221-8, 2003.
Gram-Negative Bacteria
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.
Host-Parasite Interactions
J. S. Weitz, Benfey, P. N., and Wingreen, N. S., Evolution, interactions, and biological networks., PLoS Biol, vol. 5, no. 1, p. e11, 2007.
In Situ Hybridization, Fluorescence
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.
Kinetics
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.
D. Swanson and Wingreen, N. S., Active biopolymers confer fast reorganization kinetics., Phys Rev Lett, vol. 107, no. 21, p. 218103, 2011.
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.
S. Goyal and Wingreen, N. S., Growth-induced instability in metabolic networks., Phys Rev Lett, vol. 98, no. 13, p. 138105, 2007.
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.
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.
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.
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.
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.
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.
Likelihood Functions
R. G. Endres and Wingreen, N. S., Maximum likelihood and the single receptor., Phys Rev Lett, vol. 103, no. 15, p. 158101, 2009.

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