List of Faculty Publications

Below is a list of Faculty publications imported from PubMed or manually added. By default, publications are sorted by year with titles displayed in ascending alphabetical order.
Shortcuts: Wühr, Martin | Wingreen, Ned | Wieschaus, Eric | Troyanskaya, Olga | Tilghman, Shirley | Storey, John | Singh, Mona | Shvartsman, Stanislav | Shaevitz, Joshua | Rabinowitz, Joshua | Murphy, Coleen | Levine, Michael {Levine, Michael S.} | Gregor, Thomas | Botstein, David | Bialek, William | Ayroles, Julien | Andolfatto, Peter | Akey, Joshua

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Escherichia coli Proteins
S. Wang, Furchtgott, L., Huang, K. Casey, and Shaevitz, J. W., “Helical insertion of peptidoglycan produces chiral ordering of the bacterial cell wall.”, Proc Natl Acad Sci U S A, vol. 109, no. 10, pp. E595-604, 2012.
J. W. Shaevitz, Abbondanzieri, E. A., Landick, R., and Block, S. M., “Backtracking by single RNA polymerase molecules observed at near-base-pair resolution.”, Nature, vol. 426, no. 6967, pp. 684-7, 2003.
N. Ouzounov, Nguyen, J. P., Bratton, B. P., Jacobowitz, D., Gitai, Z., and Shaevitz, J. W., “MreB Orientation Correlates with Cell Diameter in Escherichia coli.”, Biophys J, vol. 111, no. 5, pp. 1035-43, 2016.
R. M. Morgenstein, Bratton, B. P., Nguyen, J. P., Ouzounov, N., Shaevitz, J. W., and Gitai, Z., “RodZ links MreB to cell wall synthesis to mediate MreB rotation and robust morphogenesis.”, Proc Natl Acad Sci U S A, vol. 112, no. 40, pp. 12510-5, 2015.
G. S. Liu, Bratton, B. P., Gitai, Z., and Shaevitz, J. W., “The effect of antibiotics on protein diffusion in the Escherichia coli cytoplasmic membrane.”, PLoS One, vol. 12, no. 10, p. e0185810, 2017.
S. van Teeffelen, Wang, S., Furchtgott, L., Huang, K. Casey, Wingreen, N. S., Shaevitz, J. W., and Gitai, Z., “The bacterial actin MreB rotates, and rotation depends on cell-wall assembly.”, Proc Natl Acad Sci U S A, vol. 108, no. 38, pp. 15822-7, 2011.
J. W. Shaevitz and Gitai, Z., “The structure and function of bacterial actin homologs.”, Cold Spring Harb Perspect Biol, vol. 2, no. 9, p. a000364, 2010.
S. Wang, Arellano-Santoyo, H., Combs, P. A., and Shaevitz, J. W., “Actin-like cytoskeleton filaments contribute to cell mechanics in bacteria.”, Proc Natl Acad Sci U S A, vol. 107, no. 20, pp. 9182-5, 2010.
T. S. Ursell, Nguyen, J., Monds, R. D., Colavin, A., Billings, G., Ouzounov, N., Gitai, Z., Shaevitz, J. W., and Huang, K. Casey, “Rod-like bacterial shape is maintained by feedback between cell curvature and cytoskeletal localization.”, Proc Natl Acad Sci U S A, vol. 111, no. 11, pp. E1025-34, 2014.
Escherichia coli
N. Ouzounov, Nguyen, J. P., Bratton, B. P., Jacobowitz, D., Gitai, Z., and Shaevitz, J. W., “MreB Orientation Correlates with Cell Diameter in Escherichia coli.”, Biophys J, vol. 111, no. 5, pp. 1035-43, 2016.
R. M. Morgenstein, Bratton, B. P., Nguyen, J. P., Ouzounov, N., Shaevitz, J. W., and Gitai, Z., “RodZ links MreB to cell wall synthesis to mediate MreB rotation and robust morphogenesis.”, Proc Natl Acad Sci U S A, vol. 112, no. 40, pp. 12510-5, 2015.
G. S. Liu, Bratton, B. P., Gitai, Z., and Shaevitz, J. W., “The effect of antibiotics on protein diffusion in the Escherichia coli cytoplasmic membrane.”, PLoS One, vol. 12, no. 10, p. e0185810, 2017.
S. Wang, Arellano-Santoyo, H., Combs, P. A., and Shaevitz, J. W., “Measuring the bending stiffness of bacterial cells using an optical trap.”, J Vis Exp, no. 38, 2010.
T. Pilizota and Shaevitz, J. W., “Fast, multiphase volume adaptation to hyperosmotic shock by Escherichia coli.”, PLoS One, vol. 7, no. 4, p. e35205, 2012.
S. van Teeffelen, Wang, S., Furchtgott, L., Huang, K. Casey, Wingreen, N. S., Shaevitz, J. W., and Gitai, Z., “The bacterial actin MreB rotates, and rotation depends on cell-wall assembly.”, Proc Natl Acad Sci U S A, vol. 108, no. 38, pp. 15822-7, 2011.
E. A. Abbondanzieri, Greenleaf, W. J., Shaevitz, J. W., Landick, R., and Block, S. M., “Direct observation of base-pair stepping by RNA polymerase.”, Nature, vol. 438, no. 7067, pp. 460-5, 2005.
T. Pilizota and Shaevitz, J. W., “Plasmolysis and cell shape depend on solute outer-membrane permeability during hyperosmotic shock in E. coli.”, Biophys J, vol. 104, no. 12, pp. 2733-42, 2013.
S. Wang, Arellano-Santoyo, H., Combs, P. A., and Shaevitz, J. W., “Actin-like cytoskeleton filaments contribute to cell mechanics in bacteria.”, Proc Natl Acad Sci U S A, vol. 107, no. 20, pp. 9182-5, 2010.
E. A. Abbondanzieri, Shaevitz, J. W., and Block, S. M., “Picocalorimetry of transcription by RNA polymerase.”, Biophys J, vol. 89, no. 6, pp. L61-3, 2005.
T. S. Ursell, Nguyen, J., Monds, R. D., Colavin, A., Billings, G., Ouzounov, N., Gitai, Z., Shaevitz, J. W., and Huang, K. Casey, “Rod-like bacterial shape is maintained by feedback between cell curvature and cytoskeletal localization.”, Proc Natl Acad Sci U S A, vol. 111, no. 11, pp. E1025-34, 2014.
Y. Deng, Sun, M., and Shaevitz, J. W., “Direct measurement of cell wall stress stiffening and turgor pressure in live bacterial cells.”, Phys Rev Lett, vol. 107, no. 15, p. 158101, 2011.
J. W. Shaevitz, Abbondanzieri, E. A., Landick, R., and Block, S. M., “Backtracking by single RNA polymerase molecules observed at near-base-pair resolution.”, Nature, vol. 426, no. 6967, pp. 684-7, 2003.
S. Wang, Furchtgott, L., Huang, K. Casey, and Shaevitz, J. W., “Helical insertion of peptidoglycan produces chiral ordering of the bacterial cell wall.”, Proc Natl Acad Sci U S A, vol. 109, no. 10, pp. E595-604, 2012.
Equipment Design
M. J. Lang, Asbury, C. L., Shaevitz, J. W., and Block, S. M., “An automated two-dimensional optical force clamp for single molecule studies.”, Biophys J, vol. 83, no. 1, pp. 491-501, 2002.
Enzyme Activation
E. A. Abbondanzieri, Shaevitz, J. W., and Block, S. M., “Picocalorimetry of transcription by RNA polymerase.”, Biophys J, vol. 89, no. 6, pp. L61-3, 2005.
Endothelial Cells
M. J. Rosenbluth, Crow, A., Shaevitz, J. W., and Fletcher, D. A., “Slow stress propagation in adherent cells.”, Biophys J, vol. 95, no. 12, pp. 6052-9, 2008.
Electroporation
M. Sun, Wartel, M., Cascales, E., Shaevitz, J. W., and Mignot, T., “Motor-driven intracellular transport powers bacterial gliding motility.”, Proc Natl Acad Sci U S A, vol. 108, no. 18, pp. 7559-64, 2011.
Drosophila Proteins
Q. Wang, J Taliaferro, M., Klibaite, U., Hilgers, V., Shaevitz, J. W., and Rio, D. C., “The PSI-U1 snRNP interaction regulates male mating behavior in Drosophila.”, Proc Natl Acad Sci U S A, vol. 113, no. 19, pp. 5269-74, 2016.
Drosophila melanogaster
Y. Deng, Coen, P., Sun, M., and Shaevitz, J. W., “Efficient multiple object tracking using mutually repulsive active membranes.”, PLoS One, vol. 8, no. 6, p. e65769, 2013.
U. Klibaite, Berman, G. J., Cande, J., Stern, D. L., and Shaevitz, J. W., “An unsupervised method for quantifying the behavior of paired animals.”, Phys Biol, vol. 14, no. 1, p. 015006, 2017.
Drosophila
Q. Wang, J Taliaferro, M., Klibaite, U., Hilgers, V., Shaevitz, J. W., and Rio, D. C., “The PSI-U1 snRNP interaction regulates male mating behavior in Drosophila.”, Proc Natl Acad Sci U S A, vol. 113, no. 19, pp. 5269-74, 2016.
Dose-Response Relationship, Drug
S. van Teeffelen, Wang, S., Furchtgott, L., Huang, K. Casey, Wingreen, N. S., Shaevitz, J. W., and Gitai, Z., “The bacterial actin MreB rotates, and rotation depends on cell-wall assembly.”, Proc Natl Acad Sci U S A, vol. 108, no. 38, pp. 15822-7, 2011.
DNA-Directed RNA Polymerases
J. W. Shaevitz, Abbondanzieri, E. A., Landick, R., and Block, S. M., “Backtracking by single RNA polymerase molecules observed at near-base-pair resolution.”, Nature, vol. 426, no. 6967, pp. 684-7, 2003.
E. A. Abbondanzieri, Greenleaf, W. J., Shaevitz, J. W., Landick, R., and Block, S. M., “Direct observation of base-pair stepping by RNA polymerase.”, Nature, vol. 438, no. 7067, pp. 460-5, 2005.
E. A. Abbondanzieri, Shaevitz, J. W., and Block, S. M., “Picocalorimetry of transcription by RNA polymerase.”, Biophys J, vol. 89, no. 6, pp. L61-3, 2005.
DNA
J. W. Shaevitz, Abbondanzieri, E. A., Landick, R., and Block, S. M., “Backtracking by single RNA polymerase molecules observed at near-base-pair resolution.”, Nature, vol. 426, no. 6967, pp. 684-7, 2003.
E. A. Abbondanzieri, Greenleaf, W. J., Shaevitz, J. W., Landick, R., and Block, S. M., “Direct observation of base-pair stepping by RNA polymerase.”, Nature, vol. 438, no. 7067, pp. 460-5, 2005.
Diffusion
S. van Teeffelen, Shaevitz, J. W., and Gitai, Z., “Image analysis in fluorescence microscopy: bacterial dynamics as a case study.”, Bioessays, vol. 34, no. 5, pp. 427-36, 2012.
Depsipeptides
S. van Teeffelen, Wang, S., Furchtgott, L., Huang, K. Casey, Wingreen, N. S., Shaevitz, J. W., and Gitai, Z., “The bacterial actin MreB rotates, and rotation depends on cell-wall assembly.”, Proc Natl Acad Sci U S A, vol. 108, no. 38, pp. 15822-7, 2011.
Cytoskeleton
T. S. Ursell, Nguyen, J., Monds, R. D., Colavin, A., Billings, G., Ouzounov, N., Gitai, Z., Shaevitz, J. W., and Huang, K. Casey, “Rod-like bacterial shape is maintained by feedback between cell curvature and cytoskeletal localization.”, Proc Natl Acad Sci U S A, vol. 111, no. 11, pp. E1025-34, 2014.
S. Wang, Furchtgott, L., Huang, K. Casey, and Shaevitz, J. W., “Helical insertion of peptidoglycan produces chiral ordering of the bacterial cell wall.”, Proc Natl Acad Sci U S A, vol. 109, no. 10, pp. E595-604, 2012.
S. Wang and Shaevitz, J. W., “The mechanics of shape in prokaryotes.”, Front Biosci (Schol Ed), vol. 5, pp. 564-74, 2013.
M. J. Rosenbluth, Crow, A., Shaevitz, J. W., and Fletcher, D. A., “Slow stress propagation in adherent cells.”, Biophys J, vol. 95, no. 12, pp. 6052-9, 2008.
J. W. Shaevitz and Gitai, Z., “The structure and function of bacterial actin homologs.”, Cold Spring Harb Perspect Biol, vol. 2, no. 9, p. a000364, 2010.
S. Wang, Arellano-Santoyo, H., Combs, P. A., and Shaevitz, J. W., “Actin-like cytoskeleton filaments contribute to cell mechanics in bacteria.”, Proc Natl Acad Sci U S A, vol. 107, no. 20, pp. 9182-5, 2010.
Cytoskeletal Proteins
R. M. Morgenstein, Bratton, B. P., Nguyen, J. P., Ouzounov, N., Shaevitz, J. W., and Gitai, Z., “RodZ links MreB to cell wall synthesis to mediate MreB rotation and robust morphogenesis.”, Proc Natl Acad Sci U S A, vol. 112, no. 40, pp. 12510-5, 2015.
S. Wang, Arellano-Santoyo, H., Combs, P. A., and Shaevitz, J. W., “Actin-like cytoskeleton filaments contribute to cell mechanics in bacteria.”, Proc Natl Acad Sci U S A, vol. 107, no. 20, pp. 9182-5, 2010.
Cytoplasm
G. S. Liu, Bratton, B. P., Gitai, Z., and Shaevitz, J. W., “The effect of antibiotics on protein diffusion in the Escherichia coli cytoplasmic membrane.”, PLoS One, vol. 12, no. 10, p. e0185810, 2017.
Courtship
Q. Wang, J Taliaferro, M., Klibaite, U., Hilgers, V., Shaevitz, J. W., and Rio, D. C., “The PSI-U1 snRNP interaction regulates male mating behavior in Drosophila.”, Proc Natl Acad Sci U S A, vol. 113, no. 19, pp. 5269-74, 2016.
Computer Simulation
J. W. Shaevitz, Block, S. M., and Schnitzer, M. J., “Statistical kinetics of macromolecular dynamics.”, Biophys J, vol. 89, no. 4, pp. 2277-85, 2005.
D. Bruce Borenstein, Meir, Y., Shaevitz, J. W., and Wingreen, N. S., “Non-local interaction via diffusible resource prevents coexistence of cooperators and cheaters in a lattice model.”, PLoS One, vol. 8, no. 5, p. e63304, 2013.
S. van Teeffelen, Wang, S., Furchtgott, L., Huang, K. Casey, Wingreen, N. S., Shaevitz, J. W., and Gitai, Z., “The bacterial actin MreB rotates, and rotation depends on cell-wall assembly.”, Proc Natl Acad Sci U S A, vol. 108, no. 38, pp. 15822-7, 2011.
Y. Deng, Sun, M., and Shaevitz, J. W., “Direct measurement of cell wall stress stiffening and turgor pressure in live bacterial cells.”, Phys Rev Lett, vol. 107, no. 15, p. 158101, 2011.
T. S. Ursell, Nguyen, J., Monds, R. D., Colavin, A., Billings, G., Ouzounov, N., Gitai, Z., Shaevitz, J. W., and Huang, K. Casey, “Rod-like bacterial shape is maintained by feedback between cell curvature and cytoskeletal localization.”, Proc Natl Acad Sci U S A, vol. 111, no. 11, pp. E1025-34, 2014.
Computational Biology
S. Wang, Furchtgott, L., Huang, K. Casey, and Shaevitz, J. W., “Helical insertion of peptidoglycan produces chiral ordering of the bacterial cell wall.”, Proc Natl Acad Sci U S A, vol. 109, no. 10, pp. E595-604, 2012.
Cluster Analysis
J. P. Nguyen, Linder, A. N., Plummer, G. S., Shaevitz, J. W., and Leifer, A. M., “Automatically tracking neurons in a moving and deforming brain.”, PLoS Comput Biol, vol. 13, no. 5, p. e1005517, 2017.
Cephalexin
S. Wang, Arellano-Santoyo, H., Combs, P. A., and Shaevitz, J. W., “Measuring the bending stiffness of bacterial cells using an optical trap.”, J Vis Exp, no. 38, 2010.
T. Mignot, Shaevitz, J. W., Hartzell, P. L., and Zusman, D. R., “Evidence that focal adhesion complexes power bacterial gliding motility.”, Science, vol. 315, no. 5813, pp. 853-6, 2007.
Cell Wall
Y. Deng, Sun, M., and Shaevitz, J. W., “Direct measurement of cell wall stress stiffening and turgor pressure in live bacterial cells.”, Phys Rev Lett, vol. 107, no. 15, p. 158101, 2011.
T. S. Ursell, Nguyen, J., Monds, R. D., Colavin, A., Billings, G., Ouzounov, N., Gitai, Z., Shaevitz, J. W., and Huang, K. Casey, “Rod-like bacterial shape is maintained by feedback between cell curvature and cytoskeletal localization.”, Proc Natl Acad Sci U S A, vol. 111, no. 11, pp. E1025-34, 2014.
S. Wang, Furchtgott, L., Huang, K. Casey, and Shaevitz, J. W., “Helical insertion of peptidoglycan produces chiral ordering of the bacterial cell wall.”, Proc Natl Acad Sci U S A, vol. 109, no. 10, pp. E595-604, 2012.
S. Wang and Shaevitz, J. W., “The mechanics of shape in prokaryotes.”, Front Biosci (Schol Ed), vol. 5, pp. 564-74, 2013.
J. W. Shaevitz, “Combining modeling and experiment to understand bacterial growth.”, Biophys J, vol. 104, no. 12, p. 2573, 2013.
R. M. Morgenstein, Bratton, B. P., Nguyen, J. P., Ouzounov, N., Shaevitz, J. W., and Gitai, Z., “RodZ links MreB to cell wall synthesis to mediate MreB rotation and robust morphogenesis.”, Proc Natl Acad Sci U S A, vol. 112, no. 40, pp. 12510-5, 2015.
S. van Teeffelen, Wang, S., Furchtgott, L., Huang, K. Casey, Wingreen, N. S., Shaevitz, J. W., and Gitai, Z., “The bacterial actin MreB rotates, and rotation depends on cell-wall assembly.”, Proc Natl Acad Sci U S A, vol. 108, no. 38, pp. 15822-7, 2011.
S. Wang, Arellano-Santoyo, H., Combs, P. A., and Shaevitz, J. W., “Actin-like cytoskeleton filaments contribute to cell mechanics in bacteria.”, Proc Natl Acad Sci U S A, vol. 107, no. 20, pp. 9182-5, 2010.
K. Casey Huang, Ehrhardt, D. W., and Shaevitz, J. W., “The molecular origins of chiral growth in walled cells.”, Curr Opin Microbiol, vol. 15, no. 6, pp. 707-14, 2012.
Cell Tracking
S. van Teeffelen, Shaevitz, J. W., and Gitai, Z., “Image analysis in fluorescence microscopy: bacterial dynamics as a case study.”, Bioessays, vol. 34, no. 5, pp. 427-36, 2012.
Cell Shape
S. Wang and Shaevitz, J. W., “The mechanics of shape in prokaryotes.”, Front Biosci (Schol Ed), vol. 5, pp. 564-74, 2013.
K. Casey Huang, Ehrhardt, D. W., and Shaevitz, J. W., “The molecular origins of chiral growth in walled cells.”, Curr Opin Microbiol, vol. 15, no. 6, pp. 707-14, 2012.
Cell Movement
J. W. Shaevitz and Fletcher, D. A., “Load fluctuations drive actin network growth.”, Proc Natl Acad Sci U S A, vol. 104, no. 40, pp. 15688-92, 2007.
S. van Teeffelen, Shaevitz, J. W., and Gitai, Z., “Image analysis in fluorescence microscopy: bacterial dynamics as a case study.”, Bioessays, vol. 34, no. 5, pp. 427-36, 2012.
Cell Membrane Permeability
T. Pilizota and Shaevitz, J. W., “Plasmolysis and cell shape depend on solute outer-membrane permeability during hyperosmotic shock in E. coli.”, Biophys J, vol. 104, no. 12, pp. 2733-42, 2013.
Cell Membrane
T. Pilizota and Shaevitz, J. W., “Plasmolysis and cell shape depend on solute outer-membrane permeability during hyperosmotic shock in E. coli.”, Biophys J, vol. 104, no. 12, pp. 2733-42, 2013.
Cell Division
K. Casey Huang, Ehrhardt, D. W., and Shaevitz, J. W., “The molecular origins of chiral growth in walled cells.”, Curr Opin Microbiol, vol. 15, no. 6, pp. 707-14, 2012.
Cell Communication
D. Bruce Borenstein, Meir, Y., Shaevitz, J. W., and Wingreen, N. S., “Non-local interaction via diffusible resource prevents coexistence of cooperators and cheaters in a lattice model.”, PLoS One, vol. 8, no. 5, p. e63304, 2013.
Cell Adhesion
M. J. Rosenbluth, Crow, A., Shaevitz, J. W., and Fletcher, D. A., “Slow stress propagation in adherent cells.”, Biophys J, vol. 95, no. 12, pp. 6052-9, 2008.
Cattle
S. M. Block, Asbury, C. L., Shaevitz, J. W., and Lang, M. J., “Probing the kinesin reaction cycle with a 2D optical force clamp.”, Proc Natl Acad Sci U S A, vol. 100, no. 5, pp. 2351-6, 2003.
M. J. Rosenbluth, Crow, A., Shaevitz, J. W., and Fletcher, D. A., “Slow stress propagation in adherent cells.”, Biophys J, vol. 95, no. 12, pp. 6052-9, 2008.
Calorimetry
E. A. Abbondanzieri, Shaevitz, J. W., and Block, S. M., “Picocalorimetry of transcription by RNA polymerase.”, Biophys J, vol. 89, no. 6, pp. L61-3, 2005.
Calibration
S. M. Block, Asbury, C. L., Shaevitz, J. W., and Lang, M. J., “Probing the kinesin reaction cycle with a 2D optical force clamp.”, Proc Natl Acad Sci U S A, vol. 100, no. 5, pp. 2351-6, 2003.
Y. Deng and Shaevitz, J. W., “Effect of aberration on height calibration in three-dimensional localization-based microscopy and particle tracking.”, Appl Opt, vol. 48, no. 10, pp. 1886-90, 2009.
M. J. Lang, Asbury, C. L., Shaevitz, J. W., and Block, S. M., “An automated two-dimensional optical force clamp for single molecule studies.”, Biophys J, vol. 83, no. 1, pp. 491-501, 2002.
Calcium
J. P. Nguyen, Shipley, F. B., Linder, A. N., Plummer, G. S., Liu, M., Setru, S. U., Shaevitz, J. W., and Leifer, A. M., “Whole-brain calcium imaging with cellular resolution in freely behaving Caenorhabditis elegans.”, Proc Natl Acad Sci U S A, vol. 113, no. 8, pp. E1074-81, 2016.
Caenorhabditis elegans
J. P. Nguyen, Shipley, F. B., Linder, A. N., Plummer, G. S., Liu, M., Setru, S. U., Shaevitz, J. W., and Leifer, A. M., “Whole-brain calcium imaging with cellular resolution in freely behaving Caenorhabditis elegans.”, Proc Natl Acad Sci U S A, vol. 113, no. 8, pp. E1074-81, 2016.
J. P. Nguyen, Linder, A. N., Plummer, G. S., Shaevitz, J. W., and Leifer, A. M., “Automatically tracking neurons in a moving and deforming brain.”, PLoS Comput Biol, vol. 13, no. 5, p. e1005517, 2017.
Brain
J. P. Nguyen, Linder, A. N., Plummer, G. S., Shaevitz, J. W., and Leifer, A. M., “Automatically tracking neurons in a moving and deforming brain.”, PLoS Comput Biol, vol. 13, no. 5, p. e1005517, 2017.
S. M. Block, Asbury, C. L., Shaevitz, J. W., and Lang, M. J., “Probing the kinesin reaction cycle with a 2D optical force clamp.”, Proc Natl Acad Sci U S A, vol. 100, no. 5, pp. 2351-6, 2003.
Blotting, Western
M. Sun, Wartel, M., Cascales, E., Shaevitz, J. W., and Mignot, T., “Motor-driven intracellular transport powers bacterial gliding motility.”, Proc Natl Acad Sci U S A, vol. 108, no. 18, pp. 7559-64, 2011.
Biopolymers
J. W. Shaevitz, Block, S. M., and Schnitzer, M. J., “Statistical kinetics of macromolecular dynamics.”, Biophys J, vol. 89, no. 4, pp. 2277-85, 2005.
Biophysics
S. Wang, Furchtgott, L., Huang, K. Casey, and Shaevitz, J. W., “Helical insertion of peptidoglycan produces chiral ordering of the bacterial cell wall.”, Proc Natl Acad Sci U S A, vol. 109, no. 10, pp. E595-604, 2012.
S. M. Block, Asbury, C. L., Shaevitz, J. W., and Lang, M. J., “Probing the kinesin reaction cycle with a 2D optical force clamp.”, Proc Natl Acad Sci U S A, vol. 100, no. 5, pp. 2351-6, 2003.
M. J. Lang, Asbury, C. L., Shaevitz, J. W., and Block, S. M., “An automated two-dimensional optical force clamp for single molecule studies.”, Biophys J, vol. 83, no. 1, pp. 491-501, 2002.
J. W. Shaevitz, “Super-resolution for a 3D world.”, Nat Methods, vol. 5, no. 6, pp. 471-2, 2008.
T. S. Ursell, Nguyen, J., Monds, R. D., Colavin, A., Billings, G., Ouzounov, N., Gitai, Z., Shaevitz, J. W., and Huang, K. Casey, “Rod-like bacterial shape is maintained by feedback between cell curvature and cytoskeletal localization.”, Proc Natl Acad Sci U S A, vol. 111, no. 11, pp. E1025-34, 2014.
Biomechanical Phenomena
S. Wang, Arellano-Santoyo, H., Combs, P. A., and Shaevitz, J. W., “Actin-like cytoskeleton filaments contribute to cell mechanics in bacteria.”, Proc Natl Acad Sci U S A, vol. 107, no. 20, pp. 9182-5, 2010.
Biological Factors
D. Bruce Borenstein, Meir, Y., Shaevitz, J. W., and Wingreen, N. S., “Non-local interaction via diffusible resource prevents coexistence of cooperators and cheaters in a lattice model.”, PLoS One, vol. 8, no. 5, p. e63304, 2013.
Binding Sites
J. W. Shaevitz, Abbondanzieri, E. A., Landick, R., and Block, S. M., “Backtracking by single RNA polymerase molecules observed at near-base-pair resolution.”, Nature, vol. 426, no. 6967, pp. 684-7, 2003.
Behavior, Animal
Y. Deng, Coen, P., Sun, M., and Shaevitz, J. W., “Efficient multiple object tracking using mutually repulsive active membranes.”, PLoS One, vol. 8, no. 6, p. e65769, 2013.
J. P. Nguyen, Shipley, F. B., Linder, A. N., Plummer, G. S., Liu, M., Setru, S. U., Shaevitz, J. W., and Leifer, A. M., “Whole-brain calcium imaging with cellular resolution in freely behaving Caenorhabditis elegans.”, Proc Natl Acad Sci U S A, vol. 113, no. 8, pp. E1074-81, 2016.
U. Klibaite, Berman, G. J., Cande, J., Stern, D. L., and Shaevitz, J. W., “An unsupervised method for quantifying the behavior of paired animals.”, Phys Biol, vol. 14, no. 1, p. 015006, 2017.
Bayes Theorem
Y. Deng, Coen, P., Sun, M., and Shaevitz, J. W., “Efficient multiple object tracking using mutually repulsive active membranes.”, PLoS One, vol. 8, no. 6, p. e65769, 2013.
Base Pairing
J. W. Shaevitz, Abbondanzieri, E. A., Landick, R., and Block, S. M., “Backtracking by single RNA polymerase molecules observed at near-base-pair resolution.”, Nature, vol. 426, no. 6967, pp. 684-7, 2003.
E. A. Abbondanzieri, Greenleaf, W. J., Shaevitz, J. W., Landick, R., and Block, S. M., “Direct observation of base-pair stepping by RNA polymerase.”, Nature, vol. 438, no. 7067, pp. 460-5, 2005.
Bacteriological Techniques
S. Wang, Arellano-Santoyo, H., Combs, P. A., and Shaevitz, J. W., “Measuring the bending stiffness of bacterial cells using an optical trap.”, J Vis Exp, no. 38, 2010.
Bacterial Proteins
T. M. Bartlett, Bratton, B. P., Duvshani, A., Miguel, A., Sheng, Y., Martin, N. R., Nguyen, J. P., Persat, A., Desmarais, S. M., VanNieuwenhze, M. S., Huang, K. Casey, Zhu, J., Shaevitz, J. W., and Gitai, Z., “A Periplasmic Polymer Curves Vibrio cholerae and Promotes Pathogenesis.”, Cell, vol. 168, no. 1-2, pp. 172-185.e15, 2017.
T. Mignot, Shaevitz, J. W., Hartzell, P. L., and Zusman, D. R., “Evidence that focal adhesion complexes power bacterial gliding motility.”, Science, vol. 315, no. 5813, pp. 853-6, 2007.
T. Mignot and Shaevitz, J. W., “Active and passive mechanisms of intracellular transport and localization in bacteria.”, Curr Opin Microbiol, vol. 11, no. 6, pp. 580-5, 2008.
S. van Teeffelen, Shaevitz, J. W., and Gitai, Z., “Image analysis in fluorescence microscopy: bacterial dynamics as a case study.”, Bioessays, vol. 34, no. 5, pp. 427-36, 2012.
S. Wang, Furchtgott, L., Huang, K. Casey, and Shaevitz, J. W., “Helical insertion of peptidoglycan produces chiral ordering of the bacterial cell wall.”, Proc Natl Acad Sci U S A, vol. 109, no. 10, pp. E595-604, 2012.
Bacterial Physiological Phenomena
J. W. Shaevitz and Gitai, Z., “The structure and function of bacterial actin homologs.”, Cold Spring Harb Perspect Biol, vol. 2, no. 9, p. a000364, 2010.
K. Casey Huang, Ehrhardt, D. W., and Shaevitz, J. W., “The molecular origins of chiral growth in walled cells.”, Curr Opin Microbiol, vol. 15, no. 6, pp. 707-14, 2012.
Bacterial Adhesion
T. Mignot, Shaevitz, J. W., Hartzell, P. L., and Zusman, D. R., “Evidence that focal adhesion complexes power bacterial gliding motility.”, Science, vol. 315, no. 5813, pp. 853-6, 2007.
Bacteria
S. Wang and Shaevitz, J. W., “The mechanics of shape in prokaryotes.”, Front Biosci (Schol Ed), vol. 5, pp. 564-74, 2013.
T. Mignot and Shaevitz, J. W., “Active and passive mechanisms of intracellular transport and localization in bacteria.”, Curr Opin Microbiol, vol. 11, no. 6, pp. 580-5, 2008.
J. W. Shaevitz and Gitai, Z., “The structure and function of bacterial actin homologs.”, Cold Spring Harb Perspect Biol, vol. 2, no. 9, p. a000364, 2010.
S. van Teeffelen, Shaevitz, J. W., and Gitai, Z., “Image analysis in fluorescence microscopy: bacterial dynamics as a case study.”, Bioessays, vol. 34, no. 5, pp. 427-36, 2012.
K. Casey Huang, Ehrhardt, D. W., and Shaevitz, J. W., “The molecular origins of chiral growth in walled cells.”, Curr Opin Microbiol, vol. 15, no. 6, pp. 707-14, 2012.
Bacillus subtilis
S. Wang, Furchtgott, L., Huang, K. Casey, and Shaevitz, J. W., “Helical insertion of peptidoglycan produces chiral ordering of the bacterial cell wall.”, Proc Natl Acad Sci U S A, vol. 109, no. 10, pp. E595-604, 2012.
J. W. Shaevitz, “Combining modeling and experiment to understand bacterial growth.”, Biophys J, vol. 104, no. 12, p. 2573, 2013.
Automation
M. J. Lang, Asbury, C. L., Shaevitz, J. W., and Block, S. M., “An automated two-dimensional optical force clamp for single molecule studies.”, Biophys J, vol. 83, no. 1, pp. 491-501, 2002.
Artifacts
Y. Deng and Shaevitz, J. W., “Effect of aberration on height calibration in three-dimensional localization-based microscopy and particle tracking.”, Appl Opt, vol. 48, no. 10, pp. 1886-90, 2009.
J. W. Shaevitz and Fletcher, D. A., “Enhanced three-dimensional deconvolution microscopy using a measured depth-varying point-spread function.”, J Opt Soc Am A Opt Image Sci Vis, vol. 24, no. 9, pp. 2622-7, 2007.
Anti-Bacterial Agents
G. S. Liu, Bratton, B. P., Gitai, Z., and Shaevitz, J. W., “The effect of antibiotics on protein diffusion in the Escherichia coli cytoplasmic membrane.”, PLoS One, vol. 12, no. 10, p. e0185810, 2017.
T. Mignot, Shaevitz, J. W., Hartzell, P. L., and Zusman, D. R., “Evidence that focal adhesion complexes power bacterial gliding motility.”, Science, vol. 315, no. 5813, pp. 853-6, 2007.
S. van Teeffelen, Wang, S., Furchtgott, L., Huang, K. Casey, Wingreen, N. S., Shaevitz, J. W., and Gitai, Z., “The bacterial actin MreB rotates, and rotation depends on cell-wall assembly.”, Proc Natl Acad Sci U S A, vol. 108, no. 38, pp. 15822-7, 2011.
Animals
S. M. Block, Asbury, C. L., Shaevitz, J. W., and Lang, M. J., “Probing the kinesin reaction cycle with a 2D optical force clamp.”, Proc Natl Acad Sci U S A, vol. 100, no. 5, pp. 2351-6, 2003.
T. M. Bartlett, Bratton, B. P., Duvshani, A., Miguel, A., Sheng, Y., Martin, N. R., Nguyen, J. P., Persat, A., Desmarais, S. M., VanNieuwenhze, M. S., Huang, K. Casey, Zhu, J., Shaevitz, J. W., and Gitai, Z., “A Periplasmic Polymer Curves Vibrio cholerae and Promotes Pathogenesis.”, Cell, vol. 168, no. 1-2, pp. 172-185.e15, 2017.
J. W. Shaevitz, “Super-resolution for a 3D world.”, Nat Methods, vol. 5, no. 6, pp. 471-2, 2008.
M. J. Rosenbluth, Crow, A., Shaevitz, J. W., and Fletcher, D. A., “Slow stress propagation in adherent cells.”, Biophys J, vol. 95, no. 12, pp. 6052-9, 2008.
J. P. Nguyen, Shipley, F. B., Linder, A. N., Plummer, G. S., Liu, M., Setru, S. U., Shaevitz, J. W., and Leifer, A. M., “Whole-brain calcium imaging with cellular resolution in freely behaving Caenorhabditis elegans.”, Proc Natl Acad Sci U S A, vol. 113, no. 8, pp. E1074-81, 2016.
U. Klibaite, Berman, G. J., Cande, J., Stern, D. L., and Shaevitz, J. W., “An unsupervised method for quantifying the behavior of paired animals.”, Phys Biol, vol. 14, no. 1, p. 015006, 2017.
Q. Wang, J Taliaferro, M., Klibaite, U., Hilgers, V., Shaevitz, J. W., and Rio, D. C., “The PSI-U1 snRNP interaction regulates male mating behavior in Drosophila.”, Proc Natl Acad Sci U S A, vol. 113, no. 19, pp. 5269-74, 2016.
J. P. Nguyen, Linder, A. N., Plummer, G. S., Shaevitz, J. W., and Leifer, A. M., “Automatically tracking neurons in a moving and deforming brain.”, PLoS Comput Biol, vol. 13, no. 5, p. e1005517, 2017.
Y. Deng, Coen, P., Sun, M., and Shaevitz, J. W., “Efficient multiple object tracking using mutually repulsive active membranes.”, PLoS One, vol. 8, no. 6, p. e65769, 2013.
Animal Distribution
Y. Deng, Coen, P., Sun, M., and Shaevitz, J. W., “Efficient multiple object tracking using mutually repulsive active membranes.”, PLoS One, vol. 8, no. 6, p. e65769, 2013.
Amino Acid Sequence
T. M. Bartlett, Bratton, B. P., Duvshani, A., Miguel, A., Sheng, Y., Martin, N. R., Nguyen, J. P., Persat, A., Desmarais, S. M., VanNieuwenhze, M. S., Huang, K. Casey, Zhu, J., Shaevitz, J. W., and Gitai, Z., “A Periplasmic Polymer Curves Vibrio cholerae and Promotes Pathogenesis.”, Cell, vol. 168, no. 1-2, pp. 172-185.e15, 2017.
Amdinocillin
S. van Teeffelen, Wang, S., Furchtgott, L., Huang, K. Casey, Wingreen, N. S., Shaevitz, J. W., and Gitai, Z., “The bacterial actin MreB rotates, and rotation depends on cell-wall assembly.”, Proc Natl Acad Sci U S A, vol. 108, no. 38, pp. 15822-7, 2011.
Alternative Splicing
Q. Wang, J Taliaferro, M., Klibaite, U., Hilgers, V., Shaevitz, J. W., and Rio, D. C., “The PSI-U1 snRNP interaction regulates male mating behavior in Drosophila.”, Proc Natl Acad Sci U S A, vol. 113, no. 19, pp. 5269-74, 2016.
Algorithms
Y. Deng, Coen, P., Sun, M., and Shaevitz, J. W., “Efficient multiple object tracking using mutually repulsive active membranes.”, PLoS One, vol. 8, no. 6, p. e65769, 2013.
Y. Deng and Shaevitz, J. W., “Effect of aberration on height calibration in three-dimensional localization-based microscopy and particle tracking.”, Appl Opt, vol. 48, no. 10, pp. 1886-90, 2009.
J. W. Shaevitz, “Super-resolution for a 3D world.”, Nat Methods, vol. 5, no. 6, pp. 471-2, 2008.
J. W. Shaevitz and Fletcher, D. A., “Enhanced three-dimensional deconvolution microscopy using a measured depth-varying point-spread function.”, J Opt Soc Am A Opt Image Sci Vis, vol. 24, no. 9, pp. 2622-7, 2007.
J. P. Nguyen, Linder, A. N., Plummer, G. S., Shaevitz, J. W., and Leifer, A. M., “Automatically tracking neurons in a moving and deforming brain.”, PLoS Comput Biol, vol. 13, no. 5, p. e1005517, 2017.
J. W. Shaevitz, Block, S. M., and Schnitzer, M. J., “Statistical kinetics of macromolecular dynamics.”, Biophys J, vol. 89, no. 4, pp. 2277-85, 2005.
Adenosine Triphosphate
S. M. Block, Asbury, C. L., Shaevitz, J. W., and Lang, M. J., “Probing the kinesin reaction cycle with a 2D optical force clamp.”, Proc Natl Acad Sci U S A, vol. 100, no. 5, pp. 2351-6, 2003.
M. Sun, Wartel, M., Cascales, E., Shaevitz, J. W., and Mignot, T., “Motor-driven intracellular transport powers bacterial gliding motility.”, Proc Natl Acad Sci U S A, vol. 108, no. 18, pp. 7559-64, 2011.
Adaptation, Physiological
T. Pilizota and Shaevitz, J. W., “Fast, multiphase volume adaptation to hyperosmotic shock by Escherichia coli.”, PLoS One, vol. 7, no. 4, p. e35205, 2012.
Actins
J. W. Shaevitz and Fletcher, D. A., “Curvature and torsion in growing actin networks.”, Phys Biol, vol. 5, no. 2, p. 026006, 2008.
J. W. Shaevitz and Fletcher, D. A., “Load fluctuations drive actin network growth.”, Proc Natl Acad Sci U S A, vol. 104, no. 40, pp. 15688-92, 2007.
S. van Teeffelen, Wang, S., Furchtgott, L., Huang, K. Casey, Wingreen, N. S., Shaevitz, J. W., and Gitai, Z., “The bacterial actin MreB rotates, and rotation depends on cell-wall assembly.”, Proc Natl Acad Sci U S A, vol. 108, no. 38, pp. 15822-7, 2011.
M. J. Rosenbluth, Crow, A., Shaevitz, J. W., and Fletcher, D. A., “Slow stress propagation in adherent cells.”, Biophys J, vol. 95, no. 12, pp. 6052-9, 2008.
J. W. Shaevitz and Gitai, Z., “The structure and function of bacterial actin homologs.”, Cold Spring Harb Perspect Biol, vol. 2, no. 9, p. a000364, 2010.

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