Wingreen Lab Publications

Recent Publications

Large-scale filament formation inhibits the activity of CTP synthetase.
Rachael Barry, Anne-Florence Bitbol, Alexander Lorestani, Emeric J. Charles, Chris H Habrian, Jesse m Hansen, Hsing-Jung LI, Enoch P Baldwin, Ned S Wingreen, Justin M Kollman, Zemer Gitai.
Elife. 2014; published ahead of print July 16, 2014 doi: 10.7554/eLife.03638
PubMed
 
Interpreting 16S metagenomic data without clustering to achieve sub-OTU resotution.
Mikhail Tikhonov, Robert W Leach and Ned S Wingreen
ISME J. 2014; published ahead of print July 11, 2014 doi:10.1038/ismej.2014.117
PubMed

Condensation and localization of the partitioning protein ParB on the bacterial chromosome.
Chase P. Broedersz, Xindan Wang, Yigal Meir, Joseph J. Loparo, David Z. Rudner, Ned S. Wingreen
PNAS 2014 ; published ahead of print June 3, 2014, PMCID: PMC4066521
 
Solutions to the public goods dilemma in bacterial biofilms.
Knut Drescher, Carey D. Nadell, Howard A. Stone, Ned S. Wingreen, Bonnie L. Bassler
Curr Biol. 2014 Jan 6;24(1): PMCID: PMC3935403 [Available on 2014/7/6]
 
Imprecision of adaptation in Escherichia coli chemotaxis.
Silke Neumann, Nikita Vladimirov, Anna K. Krembel, Ned S. Wingreen,Victor Sourjik
PLoS One. 2014 Jan 8;9(1):e84904, PMCID: PMC3885661
 
Predicting functionally informative mutations in Escherichia coli BamA using evolutionary covariance analysis.
Robert S. Dwyer, Dante P. Ricci, Lucy J. Colwell, Thomas J. Silhavy, Ned S. Wingreen.
Genetics. 2013 Aug 9. [Epub ahead of print] PMID:23934888
 
Chemical sensing by nonequilibrium cooperative receptors.
Monica Skoge, Sahin Naqvi, Yigal Meir, Ned S. Wingreen.
Physical Review Letters 110: 248102 (2013)
 
Non-local interaction via diffusible resource prevents coexistence of cooperators and cheaters in a lattice model.
David B. Borenstein, Yigal Meir, Joshua W. Shaevitz, Ned S. Wingreen.
PLoS One. May 17;8(5):e63304. (2013) PMCID:PMC3656920
 
Cell shape can mediate the spatial organization of the bacterial cytoskeleton.
Siyuan Wang, Ned S. Wingreen.
Biophysical Journal 104(3):541-52. (2013) PMCID:PMC3566457
 

Archive

 
Victor Sourjik, Ned S. Wingreen
Responding to chemical gradients: bacterial chemotaxis
Curr Opin Cell Biol. 2012 Apr;24(2):262-8. PMCID:PMC3320702
 
Robert M. Cooper, Ned S. Wingreen, Edward C. Cox
An excitable cortex and memory model successfully predicts new pseudopod dynamics
PLoS One. 2012;7(3):e33528. Epub 2012 Mar 22. PMCID:PMC3310873
 
Douglas Swanson, Ned S. Wingreen
Active biopolymers confer fast reorganization kinetics
Phys. Rev. Lett. 107, 218103 (2011). PMID: 22181930
 
Monica L. Skoge, Yigal Meir, Ned S. Wingreen
Dynamics of cooperativity in chemical sensing among cell-surface receptors
Phys Rev Lett. 2011 Oct 21;107(17):178101. PMID:22107586
 
Christopher D. Doucette, David J. Schwab, Ned S.Wingreen, Joshua D. Rabinowitz.
α-ketoglutarate coordinates carbon and nitrogen utilization via enzyme I inhibition
Nat Chem Biol. 2011 Oct 16. doi: 10.1038/nchembio.685. PMCID: PMC3218208
 
Edward J. Banigan, Michael A. Gelbart, Zemer Gitai, Ned S. Wingreen, Andrea J. Liu
Filament depolymerization can explain chromosome pulling during bacterial mitosis
PLoS Comput Biol. 2011 Sep; 7 (9):e1002145. PMCID: PMC3178632
 
Sven van Teeffelen, Siyuan Wang, Leon Furchtgott, Kerwyn Casey Huang, Ned S. Wingreen, Joshua W. Shaevitz, Zemer Gitai
The bacterial actin MreB rotates, and rotation depends on cell-wall assembly
Proc Natl Acad Sci U S A. 2011 Sep 20;108 (38):15822-7 PMCID: PMC3179079
 
R. Scott McIsaac, Kerwyn Casey Huang, Anirvan Sengupta, Ned S. Wingreen
Does the potential for chaos constrain the embryonic cell-cycle oscillator?
PLoS Comput Biol. 2011 Jul;7(7):e1002109. Epub 2011 Jul 14. PMCID: PMC3136431
 
Yufang Wang, Kimberly C. Tu, Nai Phuan Ong, Bonnie L. Bassler, Ned S. Wingreen
Protein-Level Fluctuation Correlation at the Microcolony Level and Its Application to the Vibrio harveyi Quorum-Sensing Circuit
Biophysics Journal 2011; 100(12):3045-53. PubMed PMCID: PMC3123921
 
Shu-Wen Teng, Jessica N Schaffer, Kimberley C. Tu, Pankaj Mehta, Wenyun Lu, Nai Phuan Ong, Bonnie L. Bassler, Ned S. Wingreen
Active regulation of receptor ratios controls integration of quorum-sensing signals in Vibrio harveyi
Molecular Systems Biology 2011;7:491. PubMed PMCID: PMC3130561
 
Kristopher E. Daly, Kerwyn C. Huang, Ned S. Wingreen, Ranjan Mukhopadhyay
Mechanics of membrane bulging during cell-wall disruption in Gram-negative bacteria
Physical Revue E Stat Nonlin Soft Matter Phys. 2011;83(4-1):041922. PubMed: PMCID:PMC3134142
 
Leon Furchtgott, Ned S. Wingreen, Kerwyn C. Huang
Mechanisms for maintaining cell shape in rod-shaped Gram-negative bacteria
Molecular Microbiology. 2011.1365-2958.2011.07616.x. PubMed  PMCID: PMC3134142
 
Olga Oleksiuk, Vladimir Jakovljevic, Nikita Vladimirov, Ricardo Carvalho, Eli Paster, William S. Ryu, Yigal Meir, Ned S. Wingreen, Markus Kollmann and Victor Sourjik
Thermal robustness of signaling in bacterial chemotaxis
Cell. 2011;145(2):312-21. PMCID: PMC3098529
 
Thierry Mora, Fan Bai, Yong-Suk Che, Tohru Minamino, Keiichi Namba and Ned S Wingreen
Non-genetic individuality in Escherichia coli motor switching
Physical Bioogy. 2011 Apr;8(2):024001. PubMed: PMCID: PMC3140400 
 
Peter L. Nara, Gregory J. Tobin, A. Ray Chaudhuri, Jessie D. Trujillo, George Lin, Michael W. Cho, Simon A. Levin, Wilfred Ndifon, and Ned S. Wingreen
How can vaccines against influenza and other viral diseases be made more effective?
PLoS Biology. 2010 ;8(12):e1000571. PMCID: PMC3006352.
 
Matthieu Wyart, David Botstein, and Ned S. Wingreen
Evaluating gene expression dynamics using pairwise RNA FISH data
PLoS Compututational Biology. 2010 ;6(11):e1000979. PMCID: PMC2973809
 
Yigal Meir, Vladimir Jakovljevic, Olga Oleksiuk, Victor Sourjik, Ned S. Wingreen
Precision and kinetics of adaptation in bacterial chemotaxis
Biophysical Journal 99(9):2766-74 (2010). PMCID: PMC2965943
 
Thierry Mora, Ned S. Wingreen
Limits of sensing temporal concentration changes by single cells
Physical Review Letters 104(24):248101 (2010)
 
Clinton H. Hansen, Victor Sourjik, Ned S. Wingreen
A dynamic-signaling-team model for chemotaxis receptors in Escherichia coli
Proceedings of the National Academy of Science 107(40):17170-5 (2010). PMCID: PMC2951395
 
Silke Neumann, Clinton H. Hansen, Ned S. Wingreen, Victor Sourjik
Differences in signalling by directly and indirectly binding ligands in bacterial chemotaxis
EMBO Journal 29(20):3484-95 (2010). PMCID: PMC296417
 
Sidhartha Goyal, Jie Yuan, Thomas Chen, Joshua D. Rabinowitz, Ned S. Wingreen
Achieving Optimal Growth through Product Feedback Inhibition in Metabolism
PLoS Computational Biology 2010 Jun 3;6(6):e1000802. PMCID: PMC2880561
 
Barry M. Zee, Rebecca S. Levin, Bo Xu, Gary LeRoy, Ned S. Wingreen, Benjamin A. Garcia
In vivo residue-specific histone methylation dynamics
Journal of Biological Chemistry 2010; 285(5):3341-50. PMCID: 2823435
 
Kimberly C. Tu , Tao Long , Sine L. Svenningsen, Ned S. Wingreen, Bonnie L. Bassler
Negative feedback loops involving small regulatory RNAs precisely control the Vibrio harveyi quorum-sensing response
Molecular Cell 2010; 37(4):567-79. PMCID: 2844700
 
Shu-Wen Teng, Yufang Wang, Kimberly C. Tu, Tao Long, Pankaj Mehta, Ned S. Wingreen, Bonnie L. Bassler, N.P. Ong
Measurement of the Copy Number of the Master Quorum-Sensing Regulator of a Bacterial Cell
Biophysical Journal 2010 May 19; 98(9):2024-31. PMCID: 2862190
 
Wai-Leung Ng, Yunzhou Wei, Lark J. Perez, Jianping Cong, Tao Long, Matthew Koch, Martin F. Semmelhack, Ned S. Wingreen, Bonnie L. Bassler
Probing bacterial transmembrane histidine kinase receptor-ligand interactions with natural and synthetic molecules
Proceedings of the National Academy of Science 2010;107(12):5575-80. PMCID: 2851778
 
Phillip B. Kidd, Ned S.Wingreen
Modeling the role of covalent enzyme modification in Escherichia coli nitrogen metabolism
Physical Biology 2010 Jan 7;7:16006
 
Ranjan Mukhopadhyay, Ned S. Wingreen
Curvature and shape determination of growing bacteria
Physical Review E 2009 Dec;80(6 Pt 1):062901. PMCID: PMC287
 
Thierry Mora, Howard Yu, Ned S. Wingreen
Modeling Torque Versus Speed, Shot Noise, and Rotational Diffusion of the Bacterial Flagellar Motor
Physical Review Letters 103, 248102-1-4, December 2009
 
Pankaj Mehta, Sidhartha Goyal, Bonnie L. Bassler, Ned S. Wingreen
Information processing and signal interation in bacteria quorum sensing
Molecular System Biology 2009:5:325
 
Thierry Mora Howard Yu, Yoshiyuki Sowa, Ned S. Wingreen
Steps in bacterial flagellar motor
PLoS Computational Biology 2009 Oct;5(10):e1000540. Epub 2009 Oct 23
 
Jie Yuan, Christopher D Doucette, William U Fowler, Xiao-Jiang Feng, Matthew Piazza, Herschel A Rabitz, Ned S Wingreen, Joshua D Rabinowitz
Metabolomics-driven quantitative analysis of ammonia assimilation in E. coli
Molecular System Biology 2009;5:302
 
Robert G. Endres, Ned S. Wingreen
Maximum Likelihood and the Single Receptor
Physical Review Letters 2009. 103, 158101
 
Derek Greenfield, Ann L. McEvoy, Hari Shroff, Gavin E. Crooks, Ned S. Wingreen, Eric Betzig, Jan Liphardt
Self-organization of the Escherichia coli chemotaxis network imaged with super-resolution light microscopy
PLoS Biology 2009 Jun 16;7(6):e1000137
 
Robert G. Endres, Ned S. Wingreen
Accuracy of direct gradient sensing by cell-surface receptors
Progress in Biophysics and Molecular Biology 2009, 100:33-39
 
Wilfred Ndifon, Ned S. Wingreen, Simon A. Levin
Differential neutralization efficiency of hemagglutinin epitopes, antibody interference, and the design of influenza vaccines
Proceedings of the National Academy of Science 2009
 
Tao Long, Kimberly C. Tu, Yufang Wang, Pankaj Mehta, Nai Phuan Ong, Bonnie L. Bassler,   Ned S. Wingreen
Quantifying the Integration of Quorum-Sensing Signals with Single-Cell Resolution
PLoS Biology 2009 Mar 24;7(3):e68. pp. 0640-0649 (2009)
 
Kerwyn C. Huang, Ranjan Mukhopadhyay, Bingni Wen, Zemer Gitai, Ned S. Wingreen
Cell shape and cell-wall organization in Gram-negative bacteria
Proceedings of the National Academy of Science Dec 2 105(49):19282-7. (2008)
 
Jonathan M. Guberman, Allison Fay, Jonathan Dworkin, Ned S. Wingreen, Zemer Gitai
PSICIC: Noise and Asymmetry in Bacterial Division Revealed by Computational Image Analysis at Sub-Pixel Resolution
PLoS Computational Biology 4: e1000233. Epub 2008 Nov 28
 
Hui Wang, Ned S. Wingreen, Ranjan Mukhopadhyay
Self-Organized Periodicity of Protein Clusters in Growing Bacteria
Physical Review Letters 101: 21 Epub 2008 Nov 20.
 
Pankaj Mehta, Sidhartha Goyal, Ned S. Wingreen
A quantitative comparison of sRNA-based and protein-based gene regulation
Molecular System Biology. 4: pp.221. Epub 2008 Oct 14
 
Robert G. Endres, Ned S. Wingreen
Accuracy of direct gradient sensing by single cells
Proceedings of the National Academy of Science 105 (41): pp.15749-54. (2008)
 
Lee R. Swem, Danielle L. Swem, Ned S. Wingreen, Bonnie L. Bassler
Deducing receptor signaling parameters from in vivo analysis: LuxN/AI-1 quorum sensing in Vibrio harveyi
Cell 134 (3): pp. 461-73. (2008)
 
Robert G. Endres, Olga Oleksiuk, Clinton H. Hansen, Yigal Meir, Victor Sourjik, Ned S Wingreen
Variable sizes of Escherichia coli chemoreceptor signaling teams
Molecular System Biology 4: pp. 211. (2008)
 
Audra J. Pompeani, Joseph J. Irgon, Michael F. Berger, Martha L. Bulyk, Ned S. Wingreen Bonnie L. Bassler
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
Molecular Microbiology 70 (1): pp. 76-88. (2008)
 
Pankaj Mehta, Ranjan Mukhopadhyay, Ned S. Wingreen
Exponential sensitivity of noise-driven switching in genetic networks
Physical Biology 5 (2): pp. 26005 (2008)
 
Ranjan Mukhopadhyay, Kerwyn C. Huang, Ned S. Wingreen
Lipid localization in bacterial cells through curvature-mediated microphase separation
Biophysical Journal 95 (3): pp.1034-49. (2008)
 
Clinton H. Hansen, Robert G. Endres, Ned S. Wingreen
Chemotaxis in Escherichia coli: a Molecular Model for Robust Precise Adaptation
PLoS Computational Biology 4: pp. 14-27 (2008)
 
Christina L. Vizcarra,   Naigong Zhang, Shannon A. Marshall, Ned S. Wingreen, Chen Zeng, Stephen L. Mayo
An Improved Pairwise Decomposable Finite-difference Poisson-Boltzmann Method for Computational Protein Design
Journal of Computational Chemistry 29: pp. 1153-62 (2008)
 
Victor Sourjik, Ned S. Wingreen
Turning to the Cold
Nature Cell Biology 9: pp. 1029-31 (2007)
 
Robert G. Endres, Joseph J. Falke, Ned S. Wingreen
Chemotaxis Receptor Complexes: From Signaling to Assembly
PLoS Computational Biology 3: pp. 1385-93 (2007)
 
Sidhartha Goyal, Ned S. Wingreen
Growth-Induced Instability in Metabolic Networks
Physical Review Letters 98: 138105(pp. 1-4) (2007)
 
Je-Luen Li, Roberto Car, Chao Tang, Ned S. Wingreen
Hydrophobic Interaction and Hydrogen-bond Network for a Methane Pair in Liquid Water
Proceedings of the National Academy of Science 104: pp. 2626-30 (2007)
 
Joshua S.Weitz, Philip N. Benfey, Ned S. Wingreen
Evolution, Interactions, and Biological Networks
PLoS Biology 5: pp. 10-12 (2007)
 
Alejandro R. Ureta, Robert G. Endres, Ned S. Wingreen, Thomas J. Silhavy
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
Journal of Bacteriology 189: pp. 446-54 (2007)
 
Ned S. Wingreen, Simon A. Levin
Cooperation among Microorganisms
PLoS Biology 4: pp. 1486-88 (2006). PMCID: PMC1569662
 
Kerwyn C. Huang, Ranjan Mukhopadhyay, Ned S. Wingreen
A Curvature-Mediated Mechanism for Localization of Lipids to Bacterial Poles
PLoS Computational Biology 2: pp. 1357-64 (2006). PMCID: PMC1635540
 
Robert G. Endres, Ned S. Wingreen
Weight Matrices for Protein-DNA Binding Sites from a Single Co-crystal Structure
Physical Review E 73: 061921(pp. 1-5) (2006). PMID: 16906878
 
Ned S. Wingreen, David Botstein
Back to the Future: Education for Systems-level Biologists
Nature Reviews Molecular Cell Biology 7: pp. 829-32 (2006)
 
Robert G. Endres, Ned S. Wingreen
Precise Adaptation in Chemotaxis through “Assistance Neighborhoods”
Proceedings of the National Academy of Science 103: pp. 13040-4 (2006). PMCID: PMC1559749
 
Monica L. Skoge, Robert G. Endres, Ned S. Wingreen
Receptor-Receptor Coupling in Bacterial Chemotaxis: Evidence for Strongly Coupled Clusters
Biophysical Journal 90: pp. 4317-26 (2006). PMCID: PMC1471836
 
Juan E. Keymer, Robert G. Endres, Monica Skoge, Ned S. Wingreen
Chemosensing in Escherichia coli: Two Regimes of Two-state Receptors
Proceedings of the National Academy of Science 103: pp. 1786-91 (2006). PMCID: PMC1413630
 
Eldon Emberly, Ned S. Wingreen
Hourglass Model for a Protein-based Circadian Oscillator
Physical Review Letters 96: 038303(pp. 1-4) (2006). PMCID: PMC1995810
 
Je-Luen Li , Jaehun Chun, Ned S. Wingreen, Roberto Car, Ilhan A. Aksay, Dudley A. Saville
Use of Dielectric Functions in the Theory of Dispersion Forces
Physical Review B 71: 235412(pp. 1-6) (2005)
 
Erik Kruus, Peter Thumfort, Chao Tang, Ned S. Wingreen
Gibbs Sampling and Helix-Cap Motifs
Nucleic Acids Research. 33: pp. 5343-53 (2005). PMCID: PMC1234247
 
Morten Kloster, Chao Tang, Ned S. Wingreen
Finding Regulatory Modules through Large-Scale Gene-Expression Data Analysis
Bioinformatics 21: pp. 1172-9 (2005). PMID: 15513996
 
Kerwyn C. Huang, Ned S. Wingreen
Min-protein Oscillations in Round Bacteria
Physical Biology 1: pp. 229-235 (2004). PMID: 16204843
 
Rahul V. Kulkarni, Kerwyn C. Huang, Morten Kloster, Ned S. Wingreen
Pattern Formation within Escherichia coli: Diffusion, Membrane Attachment, and Self-interaction of MinD Molecules
Physical Review Letters 93: 228103(pp. 1-4) (2004). PMID: 15601121
 
Naigong Zhang, Chen Zeng, Ned S. Wingreen
Fast Accurate Evaluation of Protein Solvent Exposure
Proteins 57: pp. 565-76 (2004). PMID: 15382246
 
Robert G. Endres, Thomas C. Schulthess, Ned S. Wingreen
Toward an Atomistic Model for Predicting Transcription-Factor Binding Sites
Proteins 57: pp. 262-8 (2004). PMID: 15340913
 
Ned S. Wingreen
Quantum Many-Body Effects in a Single-Electron Transistor
Science 304: pp. 1258-9 (2004). PMID: 15166353
 
Kenji Hirose, Yigal Meir, Ned S. Wingreen
Time-Dependent Density Functional Theory of Excitation Energies of Closed-Shell Quantum Dots
Physica E 22: pp. 486-489 (2004).
 
Derrick H. Lenz, Kenny C. Mok, Brendan N. Lilley, Rahul V. Kulkarni, Ned S. Wingreen,  Bonnie L. Bassler
The Small RNA Chaperone Hfq and Multiple Small RNAs Control Quorum Sensing in Vibrio harveyi and Vibrio cholerae
Cell 118: pp. 69-82 (2004). PMID: 15242645
 
Eldon G. Emberly, Ranjan Mukhopadhyay, Chao Tang, Ned S. Wingreen
Flexibility of Beta-Sheets: Principal Component Analysis of Database Protein Structures
Proteins: Structure, Function, and Genetics 55: pp. 91-98 (2004). PMID:14997543
 
Kerwyn Casey Huang, Yigal Meir, Ned S. Wingreen
Dynamic Structures in Escherichia coli: Spontaneous Formation of MinE Rings and MinD Polar Zones
Proceedings of the National Academy of Science 100: (22), pp. 12724-12728 (2003). PMCID: PMC240685
 
Ned S. Wingreen, Hao Li, Chao Tang
Designability and Thermal Stability of Protein Structures
Polymer 45: (2), pp. 699-705 (2004)
 
Ranjan Mukhopadhyay, Eldon Emberly, Chao Tang, and Ned S. Wingreen
Statistical Mechanics of RNA Folding: Importance of Alphabet Size
Physical Review E 68: 041904(pp. 1-4) (2003). PMID: 14682970
 
Ned S. Wingreen, Jonathan Miller, Edward C. Cox
Scaling of Mutational Effects in Models for Pleiotropy
Genetics 164: pp. 1221-28 (2003). PMCID: PMC1462609
 
Kenji Hirose, Ned S. Wingreen
Stabilization of Ground-State of Minimal Spin in Disordered Quantum Dots
Physica E 18:(1-3), pp. 79-80 (2003)
 
Eldon Emberly, Ranjan Mukhopadhyay, Ned S. Wingreen, Chao Tang
Flexibility of Alpha-Helices: Results of a Statistical Analysis of Database Protein Structures
Journal of Molecular Biology 327: pp. 229-37 (2003). PMID: 12614621
 
Kenny C. Mok, Ned S. Wingreen, Bonnie L. Bassler
Vibrio harveyi Quorum Sensing: A Coincidence Detector for Two Autoinducers Controls Gene Expression
EMBO Journal 22: pp. 870-881 (2003). PMCID: PMC145445
 
Kenji Hirose, Yigal Meir, Ned S. Wingreen
Local Moment Formation in Quantum Point Contacts
Physical Review Letters 90: (2), 026804(pp. 1-4) (2003). PMID:12570569
 
Eldon Emberly, Ned S. Wingreen, Chao Tang
Designability of Alpha-Helical Proteins
Proceedings of the National Academy of Science 99: pp. 11163-8 (2002). PMCID: PMC123227
 
Hao Li, Chao Tang, Ned S. Wingreen
Designability of Protein Structures: A Lattice-Model Study using the Miyazawa-Jernigan Matrix
Proteins : Structure, Function, and Genetics 49: pp. 403-412 (2002). PMID:12360530
 
Jonathan Miller, Chen Zeng, Ned S. Wingreen, Chao Tang
Emergence of Highly Designable Protein-Backbone Conformations in an Off-Lattice Model
Proteins : Structure, Function, and Genetics 47: pp. 506-512 (2002). PMID:12001229
 
Eldon Emberly, Jonathan Miller, Chen Zeng, Ned S. Wingreen, Chao Tang
Identifying Proteins of High Designability Via Surface Exposure Patterns
Proteins : Structure, Function, and Genetics 47: (3), pp. 295-304 (2002). PMID: 11948783
 
Yigal Meir, Kenji Hirose, Ned S. Wingreen
Kondo Model for the 0.7 Anomaly in Transport through a Quantum Point Contact
Physical Review Letters 89: (19), pp. 196802(1-4) (2002). PMID: 12443139
 
S. M. Cronenwett, H. J. Lynch, D. Goldhaber-Gordon, L. P. Kouwenhoven, C. M. Marcus, Kenji Hirose, Ned S. Wingreen, V. Umansky
Low-Temperature Fate of the 0.7 Structure in a Point Contact: a Kondo-Like Correlated State in an Open System
Physical Review Letters 88: (22), 226805(pp. 1-4) (2002). PMID: 12059445
 
Kenji Hirose, Ned S. Wingreen
Ground-State Energy and Spin in Disordered Quantum Dots
Physical Review B 65: (19), 193305(pp. 1-4) (2002)
 
Henry Cejtin, Jan Elder, Allan Gottlieb, Robert Helling, Hao Li, James Philbin, Chao Tang, Ned Wingreen
Fast Tree Search For Enumeration of a Lattice Model of Protein Folding
Journal of Chemical Physics 116: (1), pp. 352-359, (2002)
 
Robert Helling, Hao Li, Regis Melin, Jonathan Miller, Ned S. Wingreen, Chen Zeng, Chao Tang,
The Designability of Protein Structures
Journal of Molecular Graphics and Modelling 19:(1), pp. 157-167 (2001)
 
Hao Li, Chao Tang, Ned S. Wingreen
Designing Protein Structures
Phase Transition and Self-Organization in Electronic and Molecular Networks, Phillips, J.C. (ed.) Klewer pp. 441-445 (2001)
 
Kenji Hirose, Shu-Shen Li, Ned S. Wingreen
Mechanisms for Extra Conductance Plateaus in Quantum Wires
Physical Review B 63:(3), 033315(pp. 1-4) (2001)
 
Kenji Hirose, Fei Zhou, Ned S. Wingreen
Density-Functional Theory of Spin-Polarized Disordered Quantum Dots
Physical Review B 63:(7), 075301(pp. 1-5) (2001)
 
Kenji Hirose, Fei Zhou, Ned S. Wingreen
Spin-Density-Functional Theory of Clean and Disordered Quantum Dots
Proceedings of the 25th International Conference on the Physics of Semiconductors-ICPS, Miura, N.(ed.), Springer, pp. 1349-1350 (2001)
 
Kenji Hirose, Ned S. Wingreen
Temperature-Dependent Suppression of Conductance in Quantum Wires: Anomalous Activation Energy from Pinning of the Band Edge
Physical Review B 64:(7), 073305(pp. 1-4) (2001)
 
Ned S. Wingreen
The Kondo Effect in Novel Systems
Materials Science and Engineering B 84:, pp. 22-25 (2001)
 
V. Madhavan, W. Chen, T. Jamneala, M.F. Crommie, Ned S. Wingreen
Local Spectroscopy of a Kondo Impurity: Co on Au(111)
Physical Review B 64:(16), 165412(pp. 1-11) (2001)
 
D.E. Grupp, T. Zhang, G.J. Dolan, Ned S. Wingreen
Dynamical Offset Charges in Single-Electron Transistors
Physical Review Letters 87:(18), 186805(pp. 1-4) (2001)
 
Tairan Wang, Jonathan Miller, Chao Tang, Ned S. Wingreen, Ken A. Dill
Symmetry and Designability for Lattice Protein Models
Journal of Chemical Physics 113:(18), pp. 8329-8336 (2000)
 
Peter Nordlander, Ned S. Wingreen, Yigal Meir, David C. Langreth
Kondo Physics in the Single Electron Transistor with ac Driving
Physical Review B 61:(3), pp. 2146-2150 (2000)
 
Regis Melin, Hao Li, Ned S. Wingreen, Chao Tang
Designability, Thermodynamic Stability, and Dynamics in Protein Folding: A Lattice Model Study
Journal of Chemical Physics 1110: pp. 1252-1262 (1999)
 
Kenji Hirose, Ned S. Wingreen
Spin-Density-Functional Theory of Circular and Elliptical Quantum Dots
Physical Review B 59:(7), pp. 4604-4607 (1999)
 
Peter Nordlander, Michael Pustilnik, Yigal Meir, Ned S. Wingreen, David C. Langreth
How Long Does it Take for the Kondo Effect to Develop?
Physical Review Letters 83:(4), pp. 808-811 (1999)
 
Igor E. Smolyarenko, Ned S. Wingreen
Kondo Effect in Systems With Spin Disorder
Physical Review B 60:(13), pp. 9675-9689 (1999)
 
K. Hirose, N. S. Wingreen
Electronic Structure Calculations of Quantum Dots
NEC Research and Development 40:(4), pp. 419-423 (1999)
 
C. Heide, R. J. Elliott, Ned S. Wingreen
Spin-Polarized Tunnel Current in Magnetic-Layer Systems and its Relation to the Interlayer Exchange Interaction
Physical Review B 59:(6), pp. 4287-4304 (1999)
 
P. Jauho, Ned S. Wingreen
Theory of Phase-Sensitive Measurement of Photon-Assisted Tunneling Through a Quantum Dot
Physical Review B 58:(15), pp. 9619-9622 (1998)
 
N. S. Wingreen, B. L. Altshuler, Y. Meir
Erratum: Comment on "2-Channel Kondo Scaling in Conductance Signals from 2-Level Tunneling Systems"
Physical Review Letters 81:(19), pp. 4280 (1998)
 
Naama Barkai, Mark D. Rose, Ned S. Wingreen
Protease Helps Yeast Find Mating Partners
Nature 396:(6710), pp. 422-423 (1998)
 
V. Madhavan, W. Chen, T. Jamneala, M.F. Crommie, Ned S. Wingreen
Tunneling into a Single Magnetic Atom: Spectroscopic Evidence of the Kondo Resonance
Science 280: pp. 567-569 (1998)
 
Hao Li, Chao Tang, Ned S. Wingreen
Are Protein Folds Atypical?
Proceedings of the National Academy of Science 95: pp. 4987-4990 (1998). PMCID: PMC20200
 
L. P. Kouwenhoven, C. M. Marcus, P. L. McEuen, S. Tarucha, R. M. Westervelt, N. S. Wingreen
Electron Transport in Quantum Dots
Proceedings of the NATO Advanced Study Institute on Mesoscopic Electron Transport edited by L.L. Sohn, L.P. Kouwenhoven, and G. Schon (Kluwer Series E345) pp. 105-204 (1997)
 
L. Aleiner, Ned S. Wingreen, Yigal Meir
Dephasing and the Orthogonality Catastrophe in Tunneling Through a Quantum Dot: The ``Which Path?" Interferometer
Physical Review Letters 79: pp. 3740-3743 (1997)
 
Hao Li, Chao Tang, Ned S. Wingreen
Nature of Driving Force for Protein Folding: A Result from Analyzing the Statistical Potential
Physical Review Letters 79: pp. 765-768 (1997)
 
Ned S. Wingreen, Charles A. Stafford
Quantum-Dot Cascade Laser: Proposal for an Ultralow-Threshold Semiconductor Laser
IEEE Journal of Quantum Electronics 33: pp. 1170-1173 (1997)
 
Oded Agam, Ned S. Wingreen, Boris Altshuler, D. C. Ralph, M. Tinkham,
Chaos, Interactions, and Nonequilibrium Effects in the Tunneling Resonance Spectra of Ultrasmall Metallic Particles
Physical Review Letters 78: pp. 1956-1959 (1997)
 
Yacoby, H.L. Stormer, Ned S. Wingreen, L. N. Pfeiffer, K. W. Baldwin, K. W. West,
Nonuniversal Conductance Quantization in Quantum Wires
Physical Review Letters 77: pp. 4612-4615 (1996)
 
N.F. Schwabe, R.J. Elliott, Ned S. Wingreen
The Ruderman-Kittel-Kasuya-Yosida (RKKY) Interaction Across a Tunneling Junction Out of Equilibrium
Physical Review B 54: pp. 12953-12968 (1996)
 
Noam Sivan, Ned S. Wingreen
The Single Impurity Anderson Model Out of Equilibrium
Physical Review B 54: pp. 11622-11629 (1996)
 
Hao Li, Robert Helling, Chao Tang, Ned S. Wingreen
Emergence of Preferred Structures in a Simple Model of Protein Folding
Science 273: pp. 666-669 (1996)
 
A. Stafford, Ned S. Wingreen
Resonant Photon-assisted Tunneling Through a Double Quantum Dot: An Electron Pump from Spatial Rabi Oscillations
Physical Review Letters 76: pp. 1916-1919 (1996)
 
Ned S. Wingreen, Eugen Schenfeld
Size-speed Trade-off in Optical Switching Elements
Applied Optics 34: pp. 5907-5912 (1995)
 
Ned S. Wingreen, Boris Altshuler, Yigal Meir
Comment on "2-Channel Kondo Scaling in Conductance Signals from 2-Level Tunneling Systems,"
Physical Review Letters 75: pp. 769 (1995)
 
Yigal Meir, Ned S. Wingreen
Spin-orbit Scattering and the Kondo Effect
Physical Review B (Rapid Communications) 50: pp. 4947-4950 (1994)
 
Antti-Pekka Jauho, Ned S. Wingreen, Yigal Meir
Time-dependent Transport in Interacting and Noninteracting Resonant-tunneling Systems
Physical Review B 50: pp. 5528-5544 (1994)
 
Antti-Pekka Jauho, Ned S. Wingreen, Yigal Meir
Time-dependent Transport in Mesoscopic Systems: General Formalism and Applications
Semiconductor Science and Technology 9: pp. 926-929 (1994)
 
Ned S. Wingreen, Yigal Meir
Anderson Model out of Equilibrium: Noncrossing-approximation Approach to Transport Through a Quantum Dot
Physical Review B 49: pp. 11040-11052 (1994)
 
Mark Lee, Ned S. Wingreen, S. A. Solin, P. A. Wolff,
Giant Growth Axis Longitudinal Magnetoresistance from In-plane Conduction in Semiconductor Superlattices
Solid State Communications 89: pp. 687-691 (1994)
 
Alan Middleton, Ned S. Wingreen
Collective Transport in Arrays of Quantum Dots
Physical Review Letters 71: pp. 3198-3201(1993)
 
Jari M. Kinaret, Ned S. Wingreen
Coulomb Blockade and Partially Transparent Tunneling Barriers in the Quantum Hall Regime
Physical Review B 48: pp. 11113-11119 (1993)
 
Ned S. Wingreen, Antti-Pekka Jauho, Yigal Meir
Time-dependent Transport Through a Mesoscopic Structure
Physical Review B (Rapid Communications) 48: pp. 8487-8490 (1993)
 
P. L. McEuen, Ned S. Wingreen, E. B. Foxman, Jari Kinaret, U. Meirav, M. A. Kastner, Yigal Meir
Coulomb Interactions and Energy-level Spectrum of a Small Electron Gas
Physica B 189: pp. 70-79 (1993)
 
E. B. Foxman, P. L. McEuen, U. Meirav, Ned S. Wingreen, Yigal Meir, Paul A. Belk, N. R. Belk, M. A. Kastner, S. J. Wind
Effects of Quantum Levels on Transport Through a Coulomb Island
Physical Review B (Rapid Communications) 47: pp. 10020-10023 (1993)
 
Yigal Meir, Ned S. Wingreen, Patrick A. Lee
Low-temperature Transport Through a Quantum Dot: The Anderson Model out of Equilibrium
Physical Review Letters 70: pp. 2601-2604 (1993)
 
Jari M. Kinaret, Yigal Meir, Ned S. Wingreen, Patrick Lee, Xiao-Gang Wen
Conductance Through a Quantum Dot in the Fractional Quantum Hall Regime
Physical Review B (Rapid Communications) 45: pp. 9489-9492 (1992)
 
Jari M. Kinaret, Yigal Meir, Ned S. Wingreen, Patrick Lee, Xiao-Gang Wen
Many-body Coherence Effects in Conduction Through a Quantum Dot in the Fractional Quantum Hall Regime
Physical Review B 46: pp. 4681-4689 (1992)
 
Yigal Meir, Ned S. Wingreen
Landauer Formula for for the Current Through an Interacting Electron Region
Physical Review Letters 68: pp. 2512-2515 (1992)
 
Jari M. Kinaret, Yigal Meir, Ned S. Wingreen, Patrick Lee, Xiao-Gang Wen
Conductance Through a Quantum Dot in the Fractional Quantum Hall Regime
Physical Review B (Rapid Communications) 45: pp. 9489-9492 (1992)
 
P. L. McEuen, E. B. Foxman, Jari Kinaret, U. Meirav, M. A. Kastner, Ned S. Wingreen, S. J. Wind
Self-consistent Addition Spectrum of a Coulomb Island in the Quantum Hall Regime
Physical Review B (Rapid Communications) 45: pp. 11419-11422 (1992)
 
P. L. McEuen, E.B. Foxman, U. Meirav, M.A. Kastner, Yigal Meir, Ned S. Wingreen
Transport Spectroscopy of a Coulomb Island in the Quantum Hall Regime
Physical Review Letters 66: pp. 1926-1929 (1991)
 
Yigal Meir, Ned S. Wingreen, Ora Entin-Wohlman, Boris L. Altshuler
Spin-Orbit Scattering for Localized Electrons: Absence of Negative Magnetoconductance
Physical Review Letters 66: pp. 1517-1520 (1991)
 
Yigal Meir, Ned S. Wingreen, Patrick A. Lee
Transport Through a Strongly Interacting Electron System: Theory of Periodic Conductance Oscillations
Physical Review Letters 66: pp. 3048-3051 (1991)
 
Ned S. Wingreen
Rectification by Resonant Tunneling Diodes
Applied Physics Letters 56: pp. 253-255 (1990)
 
Ned S. Wingreen, Karsten W. Jacobsen, John W. Wilkins
Inelastic Scattering in Resonant Tunneling
Physical Review B 40: pp. 11834-11850 (1989)
 
Ned S. Wingreen, Monique Combescot
Electron-electron Scattering: Collision Integral and Relaxation Rate
Physical Review B 40: pp. 3191-3196 (1989)
 
Ned S. Wingreen, Monique Combescot
Ohm's Law for Hot Carriers: the Role of Carrier-carrier Scattering at High Fields
Solid State Communications 70: pp. 185-189 (1989)
 
Ned S. Wingreen, Karsten W. Jacobsen, John W. Wilkins
Resonant Tunneling with Electron-Phonon Interaction: An Exactly Solvable Model
Physical Review Letters 61: pp. 1396-1399 (1988)
 
Ned S. Wingreen, Chris J. Stanton, John W. Wilkins
Electron-electron Scattering in Nondegenerate Semiconductors: Driving the Anisotropic Distribution Toward a Displaced Maxwellian
Physical Review Letters 57: pp. 1084-1087 (1986)