Ned Wingreen

First name

Ned

Last name

Wingreen

Miller, Jonathan, Chen Zeng, Ned Wingreen, and Chao Tang. (2002) 2002. “Emergence of Highly Designable Protein-Backbone Conformations in an off-Lattice Model.”. Proteins 47 (4): 506-12. doi:10.1002/prot.10107.

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Emberly, Eldon, Jonathan Miller, Chen Zeng, Ned Wingreen, and Chao Tang. (2002) 2002. “Identifying Proteins of High Designability via Surface-Exposure Patterns.”. Proteins 47 (3): 295-304.

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Huang, Kerwyn Casey, Yigal Meir, and Ned Wingreen. (2003) 2003. “Dynamic Structures in Escherichia Coli: Spontaneous Formation of MinE Rings and MinD Polar Zones.”. Proc Natl Acad Sci U S A 100 (22): 12724-8. doi:10.1073/pnas.2135445100.

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Wingreen, Ned, Jonathan Miller, and Edward Cox. (2003) 2003. “Scaling of Mutational Effects in Models for Pleiotropy.”. Genetics 164 (3): 1221-8.

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Emberly, Eldon, Ranjan Mukhopadhyay, Ned Wingreen, and Chao Tang. (2003) 2003. “Flexibility of Alpha-Helices: Results of a Statistical Analysis of Database Protein Structures.”. J Mol Biol 327 (1): 229-37.

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Mok, Kenny, Ned Wingreen, and Bonnie Bassler. (2003) 2003. “Vibrio Harveyi Quorum Sensing: A Coincidence Detector for Two Autoinducers Controls Gene Expression.”. EMBO J 22 (4): 870-81. doi:10.1093/emboj/cdg085.

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Hirose, Kenji, Yigal Meir, and Ned Wingreen. (2003) 2003. “Local Moment Formation in Quantum Point Contacts.”. Phys Rev Lett 90 (2): 026804. doi:10.1103/PhysRevLett.90.026804.

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Meir, Yigal, Kenji Hirose, and Ned Wingreen. (2002) 2002. “Kondo Model for the ‘0.7 Anomaly’ in Transport through a Quantum Point Contact.”. Phys Rev Lett 89 (19): 196802. doi:10.1103/PhysRevLett.89.196802.

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Li, Hao, Chao Tang, and Ned Wingreen. (2002) 2002. “Designability of Protein Structures: A Lattice-Model Study Using the Miyazawa-Jernigan Matrix.”. Proteins 49 (3): 403-12. doi:10.1002/prot.10239.

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Emberly, Eldon, Ned Wingreen, and Chao Tang. (2002) 2002. “Designability of Alpha-Helical Proteins.”. Proc Natl Acad Sci U S A 99 (17): 11163-8. doi:10.1073/pnas.162105999.

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Emberly, Eldon, Ranjan Mukhopadhyay, Chao Tang, and Ned Wingreen. (2004) 2004. “Flexibility of Beta-Sheets: Principal Component Analysis of Database Protein Structures.”. Proteins 55 (1): 91-8. doi:10.1002/prot.10618.

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Mukhopadhyay, Ranjan, Eldon Emberly, Chao Tang, and Ned Wingreen. (2003) 2003. “Statistical Mechanics of RNA Folding: Importance of Alphabet Size.”. Phys Rev E Stat Nonlin Soft Matter Phys 68 (4 Pt 1): 041904. doi:10.1103/PhysRevE.68.041904.

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Emberly, Eldon, and Ned Wingreen. (2006) 2006. “Hourglass Model for a Protein-Based Circadian Oscillator.”. Phys Rev Lett 96 (3): 038303. doi:10.1103/PhysRevLett.96.038303.

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Keymer, Juan, Robert Endres, Monica Skoge, Yigal Meir, and Ned Wingreen. (2006) 2006. “Chemosensing in Escherichia Coli: Two Regimes of Two-State Receptors.”. Proc Natl Acad Sci U S A 103 (6): 1786-91. doi:10.1073/pnas.0507438103.

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Huang, Kerwyn Casey, and Ned Wingreen. (2004) 2004. “Min-Protein Oscillations in Round Bacteria.”. Phys Biol 1 (3-4): 229-35. doi:10.1088/1478-3967/1/4/005.

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Kruus, Erik, Peter Thumfort, Chao Tang, and Ned Wingreen. 2005. “Gibbs Sampling and Helix-Cap Motifs.”. Nucleic Acids Res 33 (16): 5343-53. doi:10.1093/nar/gki842.

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Kulkarni, Rahul, Kerwyn Casey Huang, Morten Kloster, and Ned Wingreen. (2004) 2004. “Pattern Formation Within Escherichia Coli: Diffusion, Membrane Attachment, and Self-Interaction of MinD Molecules.”. Phys Rev Lett 93 (22): 228103. doi:10.1103/PhysRevLett.93.228103.

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Wingreen, Ned. (2004) 2004. “Ammonia Transport.”. EcoSal Plus 1 (1). doi:10.1128/ecosalplus.3.3.2.1.

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Zhang, Naigong, Chen Zeng, and Ned Wingreen. (2004) 2004. “Fast Accurate Evaluation of Protein Solvent Exposure.”. Proteins 57 (3): 565-76. doi:10.1002/prot.20191.

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Endres, Robert, Thomas Schulthess, and Ned Wingreen. (2004) 2004. “Toward an Atomistic Model for Predicting Transcription-Factor Binding Sites.”. Proteins 57 (2): 262-8. doi:10.1002/prot.20199.

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Lenz, Derrick, Kenny Mok, Brendan Lilley, Rahul Kulkarni, Ned Wingreen, and Bonnie Bassler. (2004) 2004. “The Small RNA Chaperone Hfq and Multiple Small RNAs Control Quorum Sensing in Vibrio Harveyi and Vibrio Cholerae.”. Cell 118 (1): 69-82. doi:10.1016/j.cell.2004.06.009.

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Wingreen, Ned. (2004) 2004. “Physics. Quantum Many-Body Effects in a Single-Electron Transistor.”. Science 304 (5675): 1258-9. doi:10.1126/science.1098302.

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Wingreen, Ned, and Simon Levin. (2006) 2006. “Cooperation Among Microorganisms.”. PLoS Biol 4 (9): e299. doi:10.1371/journal.pbio.0040299.

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Endres, Robert, and Ned Wingreen. (2006) 2006. “Precise Adaptation in Bacterial Chemotaxis through ‘assistance neighborhoods’.”. Proc Natl Acad Sci U S A 103 (35): 13040-4. doi:10.1073/pnas.0603101103.

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Endres, Robert, and Ned Wingreen. (2006) 2006. “Weight Matrices for Protein-DNA Binding Sites from a Single Co-Crystal Structure.”. Phys Rev E Stat Nonlin Soft Matter Phys 73 (6 Pt 1): 061921. doi:10.1103/PhysRevE.73.061921.

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Skoge, Monica, Robert Endres, and Ned Wingreen. (2006) 2006. “Receptor-Receptor Coupling in Bacterial Chemotaxis: Evidence for Strongly Coupled Clusters.”. Biophys J 90 (12): 4317-26. doi:10.1529/biophysj.105.079905.

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Goyal, Sidhartha, and Ned Wingreen. (2007) 2007. “Growth-Induced Instability in Metabolic Networks.”. Phys Rev Lett 98 (13): 138105. doi:10.1103/PhysRevLett.98.138105.

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Li, Je-Luen, Roberto Car, Chao Tang, and Ned Wingreen. (2007) 2007. “Hydrophobic Interaction and Hydrogen-Bond Network for a Methane Pair in Liquid Water.”. Proc Natl Acad Sci U S A 104 (8): 2626-30. doi:10.1073/pnas.0610945104.

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Weitz, Joshua, Philip Benfey, and Ned Wingreen. (2007) 2007. “Evolution, Interactions, and Biological Networks.”. PLoS Biol 5 (1): e11. doi:10.1371/journal.pbio.0050011.

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Huang, Kerwyn Casey, Ranjan Mukhopadhyay, and Ned Wingreen. (2006) 2006. “A Curvature-Mediated Mechanism for Localization of Lipids to Bacterial Poles.”. PLoS Comput Biol 2 (11): e151. doi:10.1371/journal.pcbi.0020151.

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Ureta, Alejandro, Robert Endres, Ned Wingreen, and Thomas Silhavy. (2007) 2007. “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 189 (2): 446-54. doi:10.1128/JB.01103-06.

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Endres, Robert, and Ned Wingreen. (2008) 2008. “Accuracy of Direct Gradient Sensing by Single Cells.”. Proc Natl Acad Sci U S A 105 (41): 15749-54. doi:10.1073/pnas.0804688105.

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Swem, Lee, Danielle Swem, Ned Wingreen, and Bonnie Bassler. (2008) 2008. “Deducing Receptor Signaling Parameters from in Vivo Analysis: LuxN AI-1 Quorum Sensing in Vibrio Harveyi.”. Cell 134 (3): 461-73. doi:10.1016/j.cell.2008.06.023.

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Endres, Robert, Olga Oleksiuk, Clinton Hansen, Yigal Meir, Victor Sourjik, and Ned Wingreen. 2008. “Variable Sizes of Escherichia Coli Chemoreceptor Signaling Teams.”. Mol Syst Biol 4: 211. doi:10.1038/msb.2008.49.

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Pompeani, Audra, Joseph Irgon, Michael Berger, Martha Bulyk, Ned Wingreen, and Bonnie Bassler. (2008) 2008. “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 70 (1): 76-88. doi:10.1111/j.1365-2958.2008.06389.x.

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Mehta, Pankaj, Ranjan Mukhopadhyay, and Ned Wingreen. (2008) 2008. “Exponential Sensitivity of Noise-Driven Switching in Genetic Networks.”. Phys Biol 5 (2): 026005. doi:10.1088/1478-3975/5/2/026005.

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Mukhopadhyay, Ranjan, Kerwyn Casey Huang, and Ned Wingreen. (2008) 2008. “Lipid Localization in Bacterial Cells through Curvature-Mediated Microphase Separation.”. Biophys J 95 (3): 1034-49. doi:10.1529/biophysj.107.126920.

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Hansen, Clinton, Robert Endres, and Ned Wingreen. (2008) 2008. “Chemotaxis in Escherichia Coli: A Molecular Model for Robust Precise Adaptation.”. PLoS Comput Biol 4 (1): e1. doi:10.1371/journal.pcbi.0040001.

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Vizcarra, Christina, Naigong Zhang, Shannon Marshall, Ned Wingreen, Chen Zeng, and Stephen Mayo. (2008) 2008. “An Improved Pairwise Decomposable Finite-Difference Poisson-Boltzmann Method for Computational Protein Design.”. J Comput Chem 29 (7): 1153-62. doi:10.1002/jcc.20878.

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Sourjik, Victor, and Ned Wingreen. (2007) 2007. “Turning to the Cold.”. Nat Cell Biol 9 (9): 1029-31. doi:10.1038/ncb0907-1029.

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Endres, Robert, Joseph Falke, and Ned Wingreen. (2007) 2007. “Chemotaxis Receptor Complexes: From Signaling to Assembly.”. PLoS Comput Biol 3 (7): e150. doi:10.1371/journal.pcbi.0030150.

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Mehta, Pankaj, Sidhartha Goyal, and Ned Wingreen. 2008. “A Quantitative Comparison of SRNA-Based and Protein-Based Gene Regulation.”. Mol Syst Biol 4: 221. doi:10.1038/msb.2008.58.

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Mora, Thierry, Howard Yu, Yoshiyuki Sowa, and Ned Wingreen. (2009) 2009. “Steps in the Bacterial Flagellar Motor.”. PLoS Comput Biol 5 (10): e1000540. doi:10.1371/journal.pcbi.1000540.

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Yuan, Jie, Christopher Doucette, William Fowler, Xiao-Jiang Feng, Matthew Piazza, Herschel Rabitz, Ned Wingreen, and Joshua Rabinowitz. 2009. “Metabolomics-Driven Quantitative Analysis of Ammonia Assimilation in E. Coli.”. Mol Syst Biol 5: 302. doi:10.1038/msb.2009.60.

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Greenfield, Derek, Ann McEvoy, Hari Shroff, Gavin Crooks, Ned Wingreen, Eric Betzig, and Jan Liphardt. (2009) 2009. “Self-Organization of the Escherichia Coli Chemotaxis Network Imaged With Super-Resolution Light Microscopy.”. PLoS Biol 7 (6): e1000137. doi:10.1371/journal.pbio.1000137.

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Endres, Robert, and Ned Wingreen. (2009) 2009. “Accuracy of Direct Gradient Sensing by Cell-Surface Receptors.”. Prog Biophys Mol Biol 100 (1-3): 33-9. doi:10.1016/j.pbiomolbio.2009.06.002.

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Ndifon, Wilfred, Ned Wingreen, and Simon Levin. (2009) 2009. “Differential Neutralization Efficiency of Hemagglutinin Epitopes, Antibody Interference, and the Design of Influenza Vaccines.”. Proc Natl Acad Sci U S A 106 (21): 8701-6. doi:10.1073/pnas.0903427106.

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Long, Tao, Kimberly Tu, Yufang Wang, Pankaj Mehta, Ong, Bonnie Bassler, and Ned Wingreen. (2009) 2009. “Quantifying the Integration of Quorum-Sensing Signals With Single-Cell Resolution.”. PLoS Biol 7 (3): e68. doi:10.1371/journal.pbio.1000068.

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Wang, Hui, Ned Wingreen, and Ranjan Mukhopadhyay. (2008) 2008. “Self-Organized Periodicity of Protein Clusters in Growing Bacteria.”. Phys Rev Lett 101 (21): 218101. doi:10.1103/PhysRevLett.101.218101.

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Huang, Kerwyn Casey, Ranjan Mukhopadhyay, Bingni Wen, Zemer Gitai, and Ned Wingreen. (2008) 2008. “Cell Shape and Cell-Wall Organization in Gram-Negative Bacteria.”. Proc Natl Acad Sci U S A 105 (49): 19282-7. doi:10.1073/pnas.0805309105.

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