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«Ned S. Wingreen Howard A. Prior Professor of the Life Sciences Department of Molecular Biology & Lewis-Sigler Institute for Integrative Genomics ...»

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Ned S. Wingreen

Howard A. Prior Professor of the Life Sciences

Department of Molecular Biology & Lewis-Sigler Institute for Integrative Genomics

PRINCETON UNIVERSITY

Princeton, NJ 08544-1014

PHONE: 609-258-8476 FAX: 609-258-7599 EMAIL: wingreen@princeton.edu

EDUCATION

California Institute of Technology Physics B.S. 1984

Cornell University Physics M.S. 1988 Cornell University Physics Ph.D. 1989 Dissertation: Resonant Tunneling with Electron-Phonon Interaction.

Thesis adviser: Professor John W. Wilkins.

PROFESSIONAL EMPLOYMENT

9/84 – 5/89 Fannie and John Hertz Foundation Fellow, Lab of Atomic and Solid State Physics, Cornell University 5/89 – 9/89 Visiting Scientist, Weizmann Institute of Science, Israel 9/89 – 9/91 Postdoctoral Associate, Physics Department, MIT, Supervisor: Patrick A. Lee 9/91 – 3/99 Research Scientist, Physical Sciences Division, NEC Research Institute 4/99 – 10/02 Senior Research Scientist, Physical Sciences Division, NEC Research Institute 8/99 – 5/00 Sabbatical Visitor, University of California, Berkeley 11/02 – 1/04 Senior Research Staff Member, NEC Laboratories America, Inc.

2/04 – Present Professor, Department of Molecular Biology, Princeton University 10/06 – Present Associated Faculty, Department of Physics, Princeton University 5/08 – Present Member, Lewis-Sigler Institute, Princeton University 7/11 – Present Associate Director, Lewis-Sigler Institute, Princeton University 1/13 – Present Acting Director, Lewis-Sigler Institute, Princeton University

HONORS

Academic:

California Institute of Technology (1980-1984) Presidential Scholar (1980) Carnation Merit Scholarship (1982-1983) Caltech Merit Scholarship (1983-1984) Jack E. Froehlich Memorial Award (1983) McKinney Prize in Literature (1984) Cornell University (1984-1989) Fannie and John Hertz Foundation Fellowship (1984-1989)

Professional:

Fellow of the American Physical Society Fellow of the American Association for the Advancement of Science (AAAS)

PATENTS

U.S. Patent No. 5,963,571, October 5, 1999, “Quantum-Dot Cascade Laser, Ned S. Wingreen U.S. Patent No. 5,699,215, December 16, 1997, “Non-Magnetic Magnetoresistive Reading Head Using Corbino Structure,” Stuart A. Solin, Ned S. Wingreen Wingreen CV-page 1 U.S. Patent No. 5,692,003, November 25, 1997, “Quantum-Dot Cascade Laser,” Ned S.

Wingreen, Charles A. Stafford U.S. Patent No. 7,405,050, July 29, 2008, “Small RNAs and Bacterial Strains Involved in Quorum Sensing,” Derrick H. Lenz, Kenny C. Mok, Ned S. Wingreen, Bonnie L. Bassler

PUBLICATIONS

Michele Castellana, Maxwell Z Wilson, Yifan Xu, Preeti Joshi, Ileana M Cristea, Joshua • D Rabinowitz, Zemer Gitai, Ned S Wingreen Enzyme clustering accelerates processing of intermediates through metabolic channeling.

Nature Biotechnology. 2014 Sep 28. doi: 10.1038/nbt.3018. [Epub ahead of print] PMID:

25262299 [PubMed - as supplied by publisher] Rachael M. Barry, Anne-Florence Bitbol, Alexander Lorestani, Emeric J. Charles, Chris • H. Habrian, Jesse M. Hansen, Hsin-Jung Li, Enoch P. Baldwin, Ned S. Wingreen, Justin M. Kollman, Zemer Gitai.

Large-scale filament formation inhibits the activity of CTP synthetase Elife. 2014 Jul 16;3:e03638. PMCID: PMC4126345 Mikhail Tikhonov, Robert W Leach, Ned S Wingreen • Interpreting 16S metagenomic data without clustering to achieve sub-OTU resolution ISME Journal. 2014 Jul 11. doi: 10.1038/ismej.2014.117. [Epub ahead of print] PMID: 25012900 [PubMed - as supplied by publisher] Chase P. Broedersz, Xindan Wang, Yigal Meir, Joseph J. Loparo, David Z. Rudner, Ned • S. Wingreen.

Condensation and localization of the partitioning protein ParB on the bacterial chromosome.

Proceedings of the National Academy of Science. 2014 ; published ahead of print June 3, 2014, doi:10.1073/pnas.1402529111 Knut Drescher, Carey D. Nadell, Howard A. Stone, Ned S. Wingreen, Bonnie L. Bassler.

• Solutions to the public goods dilemma in bacterial biofilms.

Current Biology. 2014 Jan 6;24(1): PMCID: PMC3935403 Silke Neumann, Nikita Vladimirov, Anna K. Krembel, Ned S. Wingreen,Victor Sourjik.

• Imprecision of adaptation in Escherichia coli chemotaxis.

PLOS ONE. 2014 Jan 8;9(1):e84904, PMCID: PMC3885661 Robert S. Dwyer, Dante P. Ricci, Lucy J. Colwell, Thomas J. Silhavy, Ned S. Wingreen.

• Predicting functionally informative mutations in Escherichia coli BamA using evolutionary covariance analysis.

Genetics 195: 443-55 (2013). PMID:23934888 Monica Skoge, Sahin Naqvi, Yigal Meir, Ned S. Wingreen.

• Chemical sensing by nonequilibrium cooperative receptors.

Physical Review Letters 110: 248102 (2013).

David B. Borenstein, Yigal Meir, Joshua W. Shaevitz, Ned S. Wingreen. •

Wingreen CV-page 2 Non-local interaction via diffusible resource prevents coexistence of cooperators and cheaters in a lattice model.

PLoS One 8(5):e63304. (2013) PMCID:PMC3656920 Siyuan Wang, Ned S. Wingreen.

• Cell shape can mediate the spatial organization of the bacterial cytoskeleton.





Biophysical Journal 104(3):541-52. (2013) PMCID:PMC3566457 Victor Sourjik, Ned S. Wingreen.

• Responding to chemical gradients: bacterial chemotaxis.

Current Opinion in Cell Biology 2012 Apr;24(2):262-8. Epub 2011 Dec 9.

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.

Physical Review Letters 107, 218103 (2011). PMID: 22181930 Monica L. Skoge, Yigal Meir, Ned S. Wingreen.

• Dynamics of cooperativity in chemical sensing among cell-surface receptors.

Physical Review Letters 2011 Oct 21;107(17):178101. Epub 2011 Oct 18 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.

Nature Chemical Biology. 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 Computational Biology. 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.

Proceedings of the National Academy of Science. 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 Computational Biology. 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.

Wingreen CV-page 3 Biophysics Journal 2011; 100(12):3045-53. 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. 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 Review E 2011;83(4-1):041922. Epub 2011 Apr 25. 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. PMCID: PMC3134142 Olga Oleksiuk, Vladimir Jakovljevic, Nikita Vladimirov, Ricardo Carvalho, Eli Paster, • William S. Ryu, Yigal Meir, Ned S. Wingreen, Markus Kollmann, 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, Ned S • Wingreen.

Non-genetic individuality in Escherichia coli motor switching.

Physical Biology. 2011 Apr;8(2):024001. 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, Ned S. Wingreen.

• Evaluating gene expression dynamics using pairwise RNA FISH data.

PLoS Computational 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: PMC2964171 Wingreen CV-page 4 Sidhartha Goyal, Jie Yuan, Thomas Chen, Joshua D. Rabinowitz, Ned S. Wingreen, • Achieving Optimal Growth through Product Feedback Inhibition in Metabolism, PLoS Computational Biology 6(6):e1000802 (2010). 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 285(5):3341-5 (2010). PMCID: PMC2823435 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 37(4):567-79 (2010). PMCID: PMC2844700 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 98(9):2024-31 (2010). PMCID: PMC2862190 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 107(12):5575-80 (2010). PMCID:

PMC2851778 Phillip B. Kidd, Ned S.Wingreen, • Modeling the role of covalent enzyme modification in Escherichia coli nitrogen metabolism, Physical Biology 7:16006 (2010). PubMed - as supplied by publisher Ranjan Mukhopadhyay, Ned S. Wingreen, • Curvature and shape determination of growing bacteria, Physical Review E 80:06290 (2009). PMCID: PMC2873841 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 (2009). PMCID: PMC2874687 Pankaj Mehta, Sidhartha Goyal, Bonnie L. Bassler, Ned S. Wingreen • Information processing and signal integration in bacteria quorum sensing, Molecular System Biology 5:325 (2009). PMCID: PMC2795473 Thierry Mora Howard Yu, Yoshiyuki Sowa, Ned S. Wingreen, • Steps in bacterial flagellar motor, PLoS Computational Biology 5(10):e1000540 (2009). PMCID: PMC2759076 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 5:302 (2009). PMCID: PMC2736657 Wingreen CV-page 5 Robert G. Endres, Ned S. Wingreen, • Maximum Likelihood and the Single Receptor, Physical Review Letters 103, 158101 (2009). PubMed - indexed for MEDLINE 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 superresolution light microscopy, PLoS Biology 7(6):e1000137 (2009). PMCID: PMC2691949 Robert G. Endres, Ned S. Wingreen, • Accuracy of direct gradient sensing by cell-surface receptors, Progress in Biophysics and Molecular Biology 100:33-39 (2009). PubMed - indexed for MEDLINE 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 106(21):8701-6 (2009). PMCID:

PMC2688967 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 7(3):e68, 0640-0649 (2009). PMCID: PMC2661960 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 105(49):19282-7 (2008). PMCID:



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