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Abbondanzieri, Elio A, Joshua W Shaevitz, and Steven M Block. (2005) 2005. “Picocalorimetry of Transcription by RNA Polymerase.”. Biophys J 89 (6).

Pilizota, Teuta, and Joshua W Shaevitz. 2012. “Fast, Multiphase Volume Adaptation to Hyperosmotic Shock by Escherichia Coli.”. PLoS One 7 (4): e35205.

Rabinowitz, Joshua D. (2007) 2007. “Cellular Metabolomics of Escherchia Coli.”. Expert Rev Proteomics 4 (2): 187-98.

Boldrick, Jennifer C, Ash A Alizadeh, Maximilian Diehn, Sandrine Dudoit, Chih Long Liu, Christopher E Belcher, David Botstein, Louis M Staudt, Patrick O Brown, and David A Relman. (2002) 2002. “Stereotyped and Specific Gene Expression Programs in Human Innate Immune Responses to Bacteria.”. Proc Natl Acad Sci U S A 99 (2): 972-7.

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.

Hansen, Clinton H, Victor Sourjik, and Ned S Wingreen. (2010) 2010. “A Dynamic-Signaling-Team Model for Chemotaxis Receptors in Escherichia Coli.”. Proc Natl Acad Sci U S A 107 (40): 17170-5.

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

Pritykin, Yuri, and Mona Singh. 2013. “Simple Topological Features Reflect Dynamics and Modularity in Protein Interaction Networks.”. PLoS Comput Biol 9 (10): e1003243.

Mora, Thierry, Howard Yu, and Ned S Wingreen. (2009) 2009. “Modeling Torque Versus Speed, Shot Noise, and Rotational Diffusion of the Bacterial Flagellar Motor.”. Phys Rev Lett 103 (24): 248102.

Huang, Kerwyn Casey, Yigal Meir, and Ned S 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.

DiMaggio, Peter A, Scott R McAllister, Christodoulos A Floudas, Xiao-Jiang Feng, Joshua D Rabinowitz, and Herschel A Rabitz. 2008. “Biclustering via Optimal Re-Ordering of Data Matrices in Systems Biology: Rigorous Methods and Comparative Studies.”. BMC Bioinformatics 9: 458.

Bajad, Sunil U, Wenyun Lu, Elizabeth H Kimball, Jie Yuan, Celeste Peterson, and Joshua D Rabinowitz. (2006) 2006. “Separation and Quantitation of Water Soluble Cellular Metabolites by Hydrophilic Interaction Chromatography-Tandem Mass Spectrometry.”. J Chromatogr A 1125 (1): 76-88.

Kidd, Philip B, and Ned S Wingreen. (2010) 2010. “Modeling the Role of Covalent Enzyme Modification in Escherichia Coli Nitrogen Metabolism.”. Phys Biol 7 (1): 016006.

Kwon, Yun Kyung, Wenyun Lu, Eugene Melamud, Nurussaba Khanam, Andrew Bognar, and Joshua D Rabinowitz. (2008) 2008. “A Domino Effect in Antifolate Drug Action in Escherichia Coli.”. Nat Chem Biol 4 (10): 602-8.

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.

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.

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

Rabinowitz, Joshua D, Jennifer J Hsiao, Kimberly R Gryncel, Evan R Kantrowitz, Xiao-Jiang Feng, Genyuan Li, and Herschel Rabitz. (2008) 2008. “Dissecting Enzyme Regulation by Multiple Allosteric Effectors: Nucleotide Regulation of Aspartate Transcarbamoylase.”. Biochemistry 47 (21): 5881-8.

Shaevitz, Joshua W, Elio A Abbondanzieri, Robert Landick, and Steven M Block. (2003) 2003. “Backtracking by Single RNA Polymerase Molecules Observed at Near-Base-Pair Resolution.”. Nature 426 (6967): 684-7.

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.

Furchtgott, Leon, Ned S Wingreen, and Kerwyn Casey Huang. (2011) 2011. “Mechanisms for Maintaining Cell Shape in Rod-Shaped Gram-Negative Bacteria.”. Mol Microbiol 81 (2): 340-53.

Abbondanzieri, Elio A, William J Greenleaf, Joshua W Shaevitz, Robert Landick, and Steven M Block. (2005) 2005. “Direct Observation of Base-Pair Stepping by RNA Polymerase.”. Nature 438 (7067): 460-5.

Kwon, Yun Kyung, Meytal B Higgins, and Joshua D Rabinowitz. (2010) 2010. “Antifolate-Induced Depletion of Intracellular Glycine and Purines Inhibits Thymineless Death in E. Coli.”. ACS Chem Biol 5 (8): 787-95.

Peterson, Celeste N, Igor Levchenko, Joshua D Rabinowitz, Tania A Baker, and Thomas J Silhavy. (2012) 2012. “RpoS Proteolysis Is Controlled Directly by ATP Levels in Escherichia Coli.”. Genes Dev 26 (6): 548-53.

Daly, Kristopher E, Kerwyn Casey Huang, Ned S Wingreen, and Ranjan Mukhopadhyay. (2011) 2011. “Mechanics of Membrane Bulging During Cell-Wall Disruption in Gram-Negative Bacteria.”. Phys Rev E Stat Nonlin Soft Matter Phys 83 (4 Pt 1): 041922.

Deng, Yi, Mingzhai Sun, and Joshua W Shaevitz. (2011) 2011. “Direct Measurement of Cell Wall Stress Stiffening and Turgor Pressure in Live Bacterial Cells.”. Phys Rev Lett 107 (15): 158101.

Wang, Siyuan, Hugo Arellano-Santoyo, Peter A Combs, and Joshua W Shaevitz. (2010) 2010. “Actin-Like Cytoskeleton Filaments Contribute to Cell Mechanics in Bacteria.”. Proc Natl Acad Sci U S A 107 (20): 9182-5.

Ursell, Tristan S, Jeffrey Nguyen, Russell D Monds, Alexandre Colavin, Gabriel Billings, Nikolay Ouzounov, Zemer Gitai, Joshua W Shaevitz, and Kerwyn Casey Huang. (2014) 2014. “Rod-Like Bacterial Shape Is Maintained by Feedback Between Cell Curvature and Cytoskeletal Localization.”. Proc Natl Acad Sci U S A 111 (11).

Wang, Siyuan, Hugo Arellano-Santoyo, Peter A Combs, and Joshua W Shaevitz. 2010. “Measuring the Bending Stiffness of Bacterial Cells Using an Optical Trap.”. J Vis Exp, no. 38.

Yuan, Jie, and Joshua D Rabinowitz. (2007) 2007. “Differentiating Metabolites Formed from De Novo Synthesis Versus Macromolecule Decomposition.”. J Am Chem Soc 129 (30): 9294-5.

Rabinowitz, Joshua D, and Elizabeth Kimball. (2007) 2007. “Acidic Acetonitrile for Cellular Metabolome Extraction from Escherichia Coli.”. Anal Chem 79 (16): 6167-73.

Sourjik, Victor, and Ned S Wingreen. (2012) 2012. “Responding to Chemical Gradients: Bacterial Chemotaxis.”. Curr Opin Cell Biol 24 (2): 262-8.

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.

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.

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.

Goodarzi, Hani, Bryson D Bennett, Sasan Amini, Marshall L Reaves, Alison K Hottes, Joshua D Rabinowitz, and Saeed Tavazoie. (2010) 2010. “Regulatory and Metabolic Rewiring During Laboratory Evolution of Ethanol Tolerance in E. Coli.”. Mol Syst Biol 6: 378.

Yuan, Jie, William U Fowler, Elizabeth Kimball, Wenyun Lu, and Joshua D Rabinowitz. (2006) 2006. “Kinetic Flux Profiling of Nitrogen Assimilation in Escherichia Coli.”. Nat Chem Biol 2 (10): 529-30.

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.

Khan, Zia, Sasan Amini, Joshua S Bloom, Cristian Ruse, Amy A Caudy, Leonid Kruglyak, Mona Singh, David H Perlman, and Saeed Tavazoie. 2011. “Accurate Proteome-Wide Protein Quantification from High-Resolution 15N Mass Spectra.”. Genome Biol 12 (12): R122.

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

Yuan, Jie, Bryson D Bennett, and Joshua D Rabinowitz. 2008. “Kinetic Flux Profiling for Quantitation of Cellular Metabolic Fluxes.”. Nat Protoc 3 (8): 1328-40.

Jim, Kam, Kush Parmar, Mona Singh, and Saeed Tavazoie. (2004) 2004. “A Cross-Genomic Approach for Systematic Mapping of Phenotypic Traits to Genes.”. Genome Res 14 (1): 109-15.

Bennett, Bryson D, Jie Yuan, Elizabeth H Kimball, and Joshua D Rabinowitz. 2008. “Absolute Quantitation of Intracellular Metabolite Concentrations by an Isotope Ratio-Based Approach.”. Nat Protoc 3 (8): 1299-311.

Reaves, Marshall Louis, Brian D Young, Aaron M Hosios, Yi-Fan Xu, and Joshua D Rabinowitz. (2013) 2013. “Pyrimidine Homeostasis Is Accomplished by Directed Overflow Metabolism.”. Nature 500 (7461): 237-41.

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.

Hunter, Christine, Patricia Sung, Eyal D Schejter, and Eric Wieschaus. (2002) 2002. “Conserved Domains of the Nullo Protein Required for Cell-Surface Localization and Formation of Adherens Junctions.”. Mol Biol Cell 13 (1): 146-57.

Bennett, Bryson D, Elizabeth H Kimball, Melissa Gao, Robin Osterhout, Stephen J Van Dien, and Joshua D Rabinowitz. (2009) 2009. “Absolute Metabolite Concentrations and Implied Enzyme Active Site Occupancy in Escherichia Coli.”. Nat Chem Biol 5 (8): 593-9.

Guberman, Jonathan M, Allison Fay, Jonathan Dworkin, Ned S Wingreen, and Zemer Gitai. (2008) 2008. “PSICIC: Noise and Asymmetry in Bacterial Division Revealed by Computational Image Analysis at Sub-Pixel Resolution.”. PLoS Comput Biol 4 (11): e1000233.

Lu, Wenyun, Yun Kyung Kwon, and Joshua D Rabinowitz. (2007) 2007. “Isotope Ratio-Based Profiling of Microbial Folates.”. J Am Soc Mass Spectrom 18 (5): 898-909.