Endres, Robert G, Thomas C Schulthess, and Ned S Wingreen. (2004) 2004. “Toward an Atomistic Model for Predicting Transcription-Factor Binding Sites.”. Proteins 57 (2): 262-8.

Ng, Wai-Leung, Yunzhou Wei, Lark J Perez, Jianping Cong, Tao Long, Matthew Koch, Martin F Semmelhack, Ned S Wingreen, and Bonnie L Bassler. (2010) 2010. “Probing Bacterial Transmembrane Histidine Kinase Receptor-Ligand Interactions With Natural and Synthetic Molecules.”. Proc Natl Acad Sci U S A 107 (12): 5575-80.

Endres, Robert G, and Ned S Wingreen. (2009) 2009. “Maximum Likelihood and the Single Receptor.”. Phys Rev Lett 103 (15): 158101.

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

Ndifon, Wilfred, Ned S Wingreen, and Simon A 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.

van Teeffelen, Sven, Siyuan Wang, Leon Furchtgott, Kerwyn Casey Huang, Ned S Wingreen, Joshua W Shaevitz, and Zemer Gitai. (2011) 2011. “The Bacterial Actin MreB Rotates, and Rotation Depends on Cell-Wall Assembly.”. Proc Natl Acad Sci U S A 108 (38): 15822-7.

Oleksiuk, Olga, Vladimir Jakovljevic, Nikita Vladimirov, Ricardo Carvalho, Eli Paster, William S Ryu, Yigal Meir, Ned S Wingreen, Markus Kollmann, and Victor Sourjik. (2011) 2011. “Thermal Robustness of Signaling in Bacterial Chemotaxis.”. Cell 145 (2): 312-21.

Dwyer, Robert S, Dante P Ricci, Lucy J Colwell, Thomas J Silhavy, and Ned S Wingreen. (2013) 2013. “Predicting Functionally Informative Mutations in Escherichia Coli BamA Using Evolutionary Covariance Analysis.”. Genetics 195 (2): 443-55.

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

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

Neumann, Silke, Clinton H Hansen, Ned S Wingreen, and Victor Sourjik. (2010) 2010. “Differences in Signalling by Directly and Indirectly Binding Ligands in Bacterial Chemotaxis.”. EMBO J 29 (20): 3484-95.

Teng, Shu-Wen, Jessica N Schaffer, Kimberly C Tu, Pankaj Mehta, Wenyun Lu, N P Ong, Bonnie L Bassler, and Ned S Wingreen. (2011) 2011. “Active Regulation of Receptor Ratios Controls Integration of Quorum-Sensing Signals in Vibrio Harveyi.”. Mol Syst Biol 7: 491.

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

Meir, Yigal, Vladimir Jakovljevic, Olga Oleksiuk, Victor Sourjik, and Ned S Wingreen. (2010) 2010. “Precision and Kinetics of Adaptation in Bacterial Chemotaxis.”. Biophys J 99 (9): 2766-74.

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

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

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

Swanson, Douglas, and Ned S Wingreen. (2011) 2011. “Active Biopolymers Confer Fast Reorganization Kinetics.”. Phys Rev Lett 107 (21): 218103.

Mukhopadhyay, Ranjan, Eldon Emberly, Chao Tang, and Ned S 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.

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

Mora, Thierry, and Ned S Wingreen. (2010) 2010. “Limits of Sensing Temporal Concentration Changes by Single Cells.”. Phys Rev Lett 104 (24): 248101.

Emberly, Eldon G, Ranjan Mukhopadhyay, Ned S 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.

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

Goyal, Sidhartha, Jie Yuan, Thomas Chen, Joshua D Rabinowitz, and Ned S Wingreen. (2010) 2010. “Achieving Optimal Growth through Product Feedback Inhibition in Metabolism.”. PLoS Comput Biol 6 (6): e1000802.

Drescher, Knut, Carey D Nadell, Howard A Stone, Ned S Wingreen, and Bonnie L Bassler. (2014) 2014. “Solutions to the Public Goods Dilemma in Bacterial Biofilms.”. Curr Biol 24 (1): 50-5.

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

Barry, Rachael M, Anne-Florence Bitbol, Alexander Lorestani, Emeric J Charles, Chris H Habrian, Jesse M Hansen, Hsin-Jung Li, et al. 2014. “Large-Scale Filament Formation Inhibits the Activity of CTP Synthetase.”. Elife 3: e03638.

Banigan, Edward J, Michael A Gelbart, Zemer Gitai, Ned S Wingreen, and Andrea J Liu. (2011) 2011. “Filament Depolymerization Can Explain Chromosome Pulling During Bacterial Mitosis.”. PLoS Comput Biol 7 (9): e1002145.

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

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

Lenz, Derrick H, Kenny C Mok, Brendan N Lilley, Rahul Kulkarni V, Ned S Wingreen, and Bonnie L 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.

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

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

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

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

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

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

Borenstein, David Bruce, Yigal Meir, Joshua W Shaevitz, and Ned S Wingreen. 2013. “Non-Local Interaction via Diffusible Resource Prevents Coexistence of Cooperators and Cheaters in a Lattice Model.”. PLoS One 8 (5): e63304.

Ureta, Alejandro R, Robert G Endres, Ned S Wingreen, and Thomas J 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.

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

Mukhopadhyay, Ranjan, and Ned S Wingreen. (2009) 2009. “Curvature and Shape Determination of Growing Bacteria.”. Phys Rev E Stat Nonlin Soft Matter Phys 80 (6 Pt 1): 062901.

Li, Sophia Hsin-Jung, Zhiyuan Li, Junyoung O Park, Christopher G King, Joshua D Rabinowitz, Ned S Wingreen, and Zemer Gitai. (2018) 2018. “Escherichia Coli Translation Strategies Differ across Carbon, Nitrogen and Phosphorus Limitation Conditions.”. Nat Microbiol 3 (8): 939-47. doi:10.1038/s41564-018-0199-2.

Greenfield, Derek, Ann L McEvoy, Hari Shroff, Gavin E Crooks, Ned S 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.

Mora, Thierry, Fan Bai, Yong-Suk Che, Tohru Minamino, Keiichi Namba, and Ned S Wingreen. (2011) 2011. “Non-Genetic Individuality in Escherichia Coli Motor Switching.”. Phys Biol 8 (2): 024001.

Tikhonov, Mikhail, Robert W Leach, and Ned S Wingreen. (2015) 2015. “Interpreting 16S Metagenomic Data Without Clustering to Achieve Sub-OTU Resolution.”. ISME J 9 (1): 68-80.

Cooper, Robert M, Ned S Wingreen, and Edward C Cox. 2012. “An Excitable Cortex and Memory Model Successfully Predicts New Pseudopod Dynamics.”. PLoS One 7 (3): e33528.

Wingreen, Ned S, and Simon A Levin. (2006) 2006. “Cooperation Among Microorganisms.”. PLoS Biol 4 (9): e299.

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

Tu, Kimberly C, Tao Long, Sine L Svenningsen, Ned S Wingreen, and Bonnie L Bassler. (2010) 2010. “Negative Feedback Loops Involving Small Regulatory RNAs Precisely Control the Vibrio Harveyi Quorum-Sensing Response.”. Mol Cell 37 (4): 567-79.

Mehta, Pankaj, Sidhartha Goyal, Tao Long, Bonnie L Bassler, and Ned S Wingreen. 2009. “Information Processing and Signal Integration in Bacterial Quorum Sensing.”. Mol Syst Biol 5: 325.