Works by Wingreen, Ned S.

Results: 74

Nonequilibrium polysome dynamics promote chromosome segregation and its coupling to cell growth in Escherichia coli.

Published in:

eLife, 2025, p. 1, doi. 10.7554/eLife.104276

By:

Papagiannakis, Alexandros;
Qiwei Yu;
Govers, Sander K.;
Wei-Hsiang Lin;
Wingreen, Ned S.;
Jacobs-Wagner, Christine

Publication type:

Article

How Can Vaccines Against Influenza and Other Viral Diseases Be Made More Effective?

Published in:

2010

By:

Nara, Peter L.;
Tobin, Gregory J.;
Chaudhuri, A. Ray;
Trujillo, Jessie D.;
Lin, George;
Cho, Michael W.;
Levin, Simon A.;
Ndifon, Wilfred;
Wingreen, Ned S.

Publication type:

Essay

Self-Organization of the Escherichia coli Chemotaxis Network Imaged with Super-Resolution Light Microscopy.

Published in:

PLoS Biology, 2009, v. 7, n. 6, p. 1, doi. 10.1371/journal.pbio.1000137

By:

Greenfield, Derek;
McEvoy, Ann L.;
Shroff, Hari;
Crooks, Gavin E.;
Wingreen, Ned S.;
Betzig, Eric;
Liphardt, Jan

Publication type:

Article

Quantifying the Integration of Quorum-Sensing Signals with Single-Cell Resolution.

Published in:

PLoS Biology, 2009, v. 7, n. 3, p. e1000068, doi. 10.1371/journal.pbio.1000068

By:

Tao Long;
Kimberly C. Tu;
Yufang Wang;
Mehta, Pankaj;
N. P Ong;
Bassler, Bonnie L;
Wingreen, Ned S

Publication type:

Article

Evolution, Interactions, and Biological Networks.

Published in:

PLoS Biology, 2007, v. 5, n. 1, p. 10, doi. 10.1371/journal.pbio.0050011

By:

Weitz, Joshua S.;
Benfey, Philip N.;
Wingreen, Ned S.

Publication type:

Article

Cooperation among Microorganisms.

Published in:

2006

By:

Wingreen, Ned S.;
Levin, Simon A.

Publication type:

Essay

Global protein turnover quantification in Escherichia coli reveals cytoplasmic recycling under nitrogen limitation.

Published in:

Nature Communications, 2024, v. 15, n. 1, p. 1, doi. 10.1038/s41467-024-49920-8

By:

Gupta, Meera;
Johnson, Alex N. T.;
Cruz, Edward R.;
Costa, Eli J.;
Guest, Randi L.;
Li, Sophia Hsin-Jung;
Hart, Elizabeth M.;
Nguyen, Thao;
Stadlmeier, Michael;
Bratton, Benjamin P.;
Silhavy, Thomas J.;
Wingreen, Ned S.;
Gitai, Zemer;
Wühr, Martin

Publication type:

Article

Gibbs sampling and helix-cap motifs.

Published in:

Nucleic Acids Research, 2005, v. 33, n. 16, p. 5343, doi. 10.1093/nar/gki842

By:

Kruus, Erik;
Thumfort, Peter;
Tang, Chao;
Wingreen, Ned S.

Publication type:

Article

Fast accurate evaluation of protein solvent exposure.

Published in:

Proteins, 2004, v. 57, n. 3, p. 565, doi. 10.1002/prot.20191

By:

Zhang, Naigong;
Zeng, Chen;
Wingreen, Ned S.

Publication type:

Article

Toward an atomistic model for predicting transcription-factor binding sites.

Published in:

Proteins, 2004, v. 57, n. 2, p. 262, doi. 10.1002/prot.20199

By:

Endres, Robert G.;
Schulthess, Thomas C.;
Wingreen, Ned S.

Publication type:

Article

Flexibility of β-sheets: Principal component analysis of database protein structures.

Published in:

Proteins, 2004, v. 55, n. 1, p. 91, doi. 10.1002/prot.10618

By:

Eldon G. Emberly;
Ranjan Mukhopadhyay;
Chao Tang;
Ned S. Wingreen

Publication type:

Article

Designability of protein structures: A lattice-model study using the Miyazawa-Jernigan matrix.

Published in:

Proteins, 2002, v. 49, n. 3, p. 403, doi. 10.1002/prot.10239

By:

Li, Hao;
Tang, Chao;
Wingreen, Ned S.

Publication type:

Article

Emergence of highly designable protein-backbone conformations in an off-lattice model.

Published in:

Proteins, 2002, v. 47, n. 4, p. 506, doi. 10.1002/prot.10107

By:

Miller, Jonathan;
Zeng, Chen;
Wingreen, Ned S.;
Tang, Chao

Publication type:

Article

Identifying proteins of high designability via surface-exposure patterns.

Published in:

Proteins, 2002, v. 47, n. 3, p. 295, doi. 10.1002/prot.10067

By:

Emberly, Eldon G.;
Miller, Jonathan;
Zeng, Chen;
Wingreen, Ned S.;
Tang, Chao

Publication type:

Article

Analysis of gene expression within individual cells reveals spatiotemporal patterns underlying Vibrio cholerae biofilm development.

Published in:

PLoS Biology, 2025, v. 23, n. 5, p. 1, doi. 10.1371/journal.pbio.3003187

By:

Johnson, Grace E.;
Fei, Chenyi;
Wingreen, Ned S.;
Bassler, Bonnie L.

Publication type:

Article

Global and gene-specific translational regulation in Escherichia coli across different conditions.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 10, p. 1, doi. 10.1371/journal.pcbi.1010641

By:

Zhang, Di;
Li, Sophia Hsin-Jung;
King, Christopher G.;
Wingreen, Ned S.;
Gitai, Zemer;
Li, Zhiyuan

Publication type:

Article

Decoding the physical principles of two- component biomolecular phase separation.

Published in:

eLife, 2021, p. 1, doi. 10.7554/eLife.62403

By:

Yaojun Zhang;
Bin Xu;
Weiner, Benjamin G.;
Meir, Yigal;
Wingreen, Ned S.

Publication type:

Article

Subcellular localization of type IV pili regulates bacterial multicellular development.

Published in:

Nature Communications, 2022, v. 13, n. 1, p. 1, doi. 10.1038/s41467-022-33564-7

By:

Ellison, Courtney K.;
Fei, Chenyi;
Dalia, Triana N.;
Wingreen, Ned S.;
Dalia, Ankur B.;
Shaevitz, Joshua W.;
Gitai, Zemer

Publication type:

Article

Chemotaxis Receptor Complexes: From Signaling to Assembly.

Published in:

PLoS Computational Biology, 2007, v. 3, n. 7, p. e150, doi. 10.1371/journal.pcbi.0030150

By:

Endres, Robert G.;
Falke, Joseph J.;
Wingreen, Ned S.

Publication type:

Article

A Curvature-Mediated Mechanism for Localization of Lipids to Bacterial Poles.

Published in:

PLoS Computational Biology, 2006, v. 2, n. 11, p. 1357, doi. 10.1371/journal.pcbi.0020151

By:

Huang, Kerwyn Casey;
Ranjan Mukhopadhyay;
Wingreen, Ned S.

Publication type:

Article

The exchange dynamics of biomolecular condensates.

Published in:

eLife, 2024, p. 1, doi. 10.7554/eLife.91680

By:

Yaojun Zhang;
Pyo, Andrew G. T.;
Kliegman, Ross;
Yoyo Jiang;
Brangwynne, Clifford P.;
Stone, Howard A.;
Wingreen, Ned S.

Publication type:

Article

Lytic and temperate phage naturally coexist in a dynamic population model.

Published in:

ISME Journal: Multidisciplinary Journal of Microbial Ecology, 2024, v. 18, n. 1, p. 1, doi. 10.1093/ismejo/wrae093

By:

Kimchi, Ofer;
Meir, Yigal;
Wingreen, Ned S

Publication type:

Article

Publisher Correction: Modeling the ecology of parasitic plasmids.

Published in:

2021

By:

Lopez, Jaime G.;
Donia, Mohamed S.;
Wingreen, Ned S.

Publication type:

Correction Notice

Modeling the ecology of parasitic plasmids.

Published in:

ISME Journal: Multidisciplinary Journal of Microbial Ecology, 2021, v. 15, n. 10, p. 2843, doi. 10.1038/s41396-021-00954-6

By:

Lopez, Jaime G.;
Donia, Mohamed S.;
Wingreen, Ned S.

Publication type:

Article

Extracellular matrix structure governs invasion resistance in bacterial biofilms.

Published in:

ISME Journal: Multidisciplinary Journal of Microbial Ecology, 2015, v. 9, n. 8, p. 1700, doi. 10.1038/ismej.2014.246

By:

Nadell, Carey D;
Drescher, Knut;
Wingreen, Ned S;
Bassler, Bonnie L

Publication type:

Article

Interpreting 16S metagenomic data without clustering to achieve sub-OTU resolution.

Published in:

ISME Journal: Multidisciplinary Journal of Microbial Ecology, 2015, v. 9, n. 1, p. 68, doi. 10.1038/ismej.2014.117

By:

Tikhonov, Mikhail;
Leach, Robert W;
Wingreen, Ned S

Publication type:

Article

An improved pairwise decomposable finite-difference Poisson–Boltzmann method for computational protein design.

Published in:

Journal of Computational Chemistry, 2008, v. 29, n. 7, p. 1153, doi. 10.1002/jcc.20878

By:

Vizcarra, Christina L.;
Naigong Zhang;
Marshall, Shannon A.;
Wingreen, Ned S.;
Chen Zeng;
Mayo, Stephen L.

Publication type:

Article

Motif-pattern dependence of biomolecular phase separation driven by specific interactions.

Published in:

PLoS Computational Biology, 2021, v. 17, n. 12, p. 1, doi. 10.1371/journal.pcbi.1009748

By:

Weiner, Benjamin G.;
Pyo, Andrew G. T.;
Meir, Yigal;
Wingreen, Ned S.

Publication type:

Article

Quantitative input–output dynamics of a c-di-GMP signal transduction cascade in Vibrio cholerae.

Published in:

PLoS Biology, 2022, v. 20, n. 3, p. 1, doi. 10.1371/journal.pbio.3001585

By:

Bridges, Andrew A.;
Prentice, Jojo A.;
Fei, Chenyi;
Wingreen, Ned S.;
Bassler, Bonnie L.

Publication type:

Article

FisB relies on homo-oligomerization and lipid binding to catalyze membrane fission in bacteria.

Published in:

PLoS Biology, 2021, p. 1, doi. 10.1371/journal.pbio.3001314

By:

Landajuela, Ane;
Braun, Martha;
Rodrigues, Christopher D. A.;
Martínez-Calvo, Alejandro;
Doan, Thierry;
Horenkamp, Florian;
Andronicos, Anna;
Shteyn, Vladimir;
Williams, Nathan D.;
Lin, Chenxiang;
Wingreen, Ned S.;
Rudner, David Z.;
Karatekin, Erdem

Publication type:

Article

Bacterial Biofilm Material Properties Enable Removal and Transfer by Capillary Peeling.

Published in:

Advanced Materials, 2019, v. 31, n. 4, p. N.PAG, doi. 10.1002/adma.201807586

By:

Yan, Jing;
Moreau, Alexis;
Khodaparast, Sepideh;
Perazzo, Antonio;
Feng, Jie;
Fei, Chenyi;
Mao, Sheng;
Mukherjee, Sampriti;
Košmrlj, Andrej;
Wingreen, Ned S.;
Bassler, Bonnie L.;
Stone, Howard A.

Publication type:

Article

Bacterial Biofilm Material Properties Enable Removal and Transfer by Capillary Peeling.

Published in:

Advanced Materials, 2018, v. 30, n. 46, p. N.PAG, doi. 10.1002/adma.201804153

By:

Yan, Jing;
Moreau, Alexis;
Khodaparast, Sepideh;
Perazzo, Antonio;
Feng, Jie;
Fei, Chenyi;
Mao, Sheng;
Mukherjee, Sampriti;
Košmrlj, Andrej;
Wingreen, Ned S.;
Bassler, Bonnie L.;
Stone, Howard A.

Publication type:

Article

Mechanisms for maintaining cell shape in rod-shaped Gram-negative bacteria.

Published in:

Molecular Microbiology, 2011, v. 81, n. 2, p. 340, doi. 10.1111/j.1365-2958.2011.07616.x

By:

Furchtgott, Leon;
Wingreen, Ned S.;
Huang, Kerwyn Casey

Publication type:

Article

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.

Published in:

Molecular Microbiology, 2008, v. 70, n. 1, p. 76, doi. 10.1111/j.1365-2958.2008.06389.x

By:

Pompeani, Audra J.;
Irgon, Joseph J.;
Berger, Michael F.;
Bulyk, Martha L.;
Wingreen, Ned S.;
Bassler, Bonnie L.

Publication type:

Article

Extracellular-matrix-mediated osmotic pressure drives Vibrio cholerae biofilm expansion and cheater exclusion.

Published in:

Nature Communications, 2017, v. 8, n. 1, p. 1, doi. 10.1038/s41467-017-00401-1

By:

Jing Yan;
Nadell, Carey D.;
Stone, Howard A.;
Wingreen, Ned S.;
Bassler, Bonnie L.

Publication type:

Article

Physical limits to biomechanical sensing in disordered fibre networks.

Published in:

Nature Communications, 2017, v. 8, n. 7, p. 16096, doi. 10.1038/ncomms16096

By:

Beroz, Farzan;
Jawerth, Louise M.;
Münster, Stefan;
Weitz, David A.;
Broedersz, Chase P.;
Wingreen, Ned S.

Publication type:

Article

Established Microbial Colonies Can Survive Type VI Secretion Assault.

Published in:

PLoS Computational Biology, 2015, v. 11, n. 10, p. 1, doi. 10.1371/journal.pcbi.1004520

By:

Borenstein, David Bruce;
Ringel, Peter;
Basler, Marek;
Wingreen, Ned S.

Publication type:

Article

Optimal Census by Quorum Sensing.

Published in:

PLoS Computational Biology, 2015, v. 11, n. 5, p. 1, doi. 10.1371/journal.pcbi.1004238

By:

Taillefumier, Thibaud;
Wingreen, Ned S.

Publication type:

Article

The Role of Membrane-Mediated Interactions in the Assembly and Architecture of Chemoreceptor Lattices.

Published in:

PLoS Computational Biology, 2014, v. 10, n. 12, p. 1, doi. 10.1371/journal.pcbi.1003932

By:

Haselwandter, Christoph A.;
Wingreen, Ned S.

Publication type:

Article

Filament Depolymerization Can Explain Chromosome Pulling during Bacterial Mitosis.

Published in:

PLoS Computational Biology, 2011, v. 7, n. 9, p. 1, doi. 10.1371/journal.pcbi.1002145

By:

Banigan, Edward J.;
Gelbart, Michael A.;
Gitai, Zemer;
Wingreen, Ned S.;
Liu, Andrea J.

Publication type:

Article

Does the Potential for Chaos Constrain the Embryonic Cell-Cycle Oscillator?

Published in:

PLoS Computational Biology, 2011, v. 7, n. 7, p. 1, doi. 10.1371/journal.pcbi.1002109

By:

McIsaac, R. Scott;
Huang, Kerwyn Casey;
Sengupta, Anirvan;
Wingreen, Ned S.

Publication type:

Article

Evaluating Gene Expression Dynamics Using Pairwise RNA FISH Data.

Published in:

PLoS Computational Biology, 2010, v. 6, n. 11, p. 1, doi. 10.1371/journal.pcbi.1000979

By:

Wyart, Matthieu;
Botstein, David;
Wingreen, Ned S.

Publication type:

Article

Achieving Optimal Growth through Product Feedback Inhibition in Metabolism.

Published in:

PLoS Computational Biology, 2010, v. 6, n. 6, p. 1, doi. 10.1371/journal.pcbi.1000802

By:

Goyal, Sidhartha;
Jie Yuan;
Chen, Thomas;
Rabinowitz, Joshua D.;
Wingreen, Ned S.

Publication type:

Article

Steps in the Bacterial Flagellar Motor.

Published in:

PLoS Computational Biology, 2009, v. 5, n. 10, p. 1, doi. 10.1371/journal.pcbi.1000540

By:

Mora, Thierry;
Yu, Howard;
Sowa, Yoshiyuki;
Wingreen, Ned S.

Publication type:

Article

Steps in the Bacterial Flagellar Motor.

Published in:

PLoS Computational Biology, 2009, v. 5, n. 9, p. 1, doi. 10.1371/journal.pcbi.1000540

By:

Mora, Thierry;
Yu, Howard;
Sowa, Yoshiyuki;
Wingreen, Ned S.

Publication type:

Article

PSICIC: Noise and Asymmetry in Bacterial Division Revealed by Computational Image Analysis at Sub-Pixel Resolution.

Published in:

PLoS Computational Biology, 2008, v. 4, n. 11, p. 1, doi. 10.1371/journal.pcbi.1000233

By:

Guberman, Jonathan M.;
Fay, Allison;
Dworkin, Jonathan;
Wingreen, Ned S.;
Gitai, Zemer

Publication type:

Article

Chemotaxis in Escherichia coli: A Molecular Model for Robust Precise Adaptation.

Published in:

PLoS Computational Biology, 2008, v. 4, n. 1, p. e1, doi. 10.1371/journal.pcbi.0040001

By:

Hansen, Clinton H;
Endres, Robert G;
Wingreen, Ned S

Publication type:

Article

piRNAs of Caenorhabditis elegans broadly silence nonself sequences through functionally random targeting.

Published in:

Nucleic Acids Research, 2022, v. 50, n. 3, p. 1416, doi. 10.1093/nar/gkab1290

By:

McEnany, John;
Meir, Yigal;
Wingreen, Ned S

Publication type:

Article

Differences in signalling by directly and indirectly binding ligands in bacterial chemotaxis.

Published in:

EMBO Journal, 2010, v. 29, n. 20, p. 3484, doi. 10.1038/emboj.2010.224

By:

Neumann, Silke;
Hansen, Clinton H.;
Wingreen, Ned S.;
Sourjik, Victor

Publication type:

Article

Vibrio harveyi quorum sensing: a coincidence detector for two autoinducers controls gene expression.

Published in:

EMBO Journal, 2003, v. 22, n. 4, p. 870, doi. 10.1093/emboj/cdg085

By:

Mok, Kenny C.;
Wingreen, Ned S.;
Bassler, Bonnie L.

Publication type:

Article