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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Machine Learning
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.
Macromolecular Substances
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.
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.
Male
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.
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.
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.
Mechanical Processes
J. W. Shaevitz, “Combining modeling and experiment to understand bacterial growth.”, Biophys J, vol. 104, no. 12, p. 2573, 2013.
Methylcellulose
J. W. Shaevitz, Lee, J. Y., and Fletcher, D. A., “Spiroplasma swim by a processive change in body helicity.”, Cell, vol. 122, no. 6, pp. 941-5, 2005.
Mice
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.
Microbial Interactions
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.
Microbial Viability
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.
Microchemistry
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.
Microscopy
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.
Microscopy, Atomic Force
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.
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.
Microscopy, Electron
J. W. Shaevitz, “Super-resolution for a 3D world.”, Nat Methods, vol. 5, no. 6, pp. 471-2, 2008.
Microscopy, Fluorescence
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.
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.
B. P. Bratton and Shaevitz, J. W., “Simple Experimental Methods for Determining the Apparent Focal Shift in a Microscope System.”, PLoS One, vol. 10, no. 8, p. e0134616, 2015.
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, 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.
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.
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.
Microscopy, Phase-Contrast
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.
Microscopy, Video
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.
Microspheres
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.
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.
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.
Models, Biological
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. 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.
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.
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.
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.
S. Thutupalli, Sun, M., Bunyak, F., Palaniappan, K., and Shaevitz, J. W., “Directional reversals enable Myxococcus xanthus cells to produce collective one-dimensional streams during fruiting-body formation.”, J R Soc Interface, vol. 12, no. 109, p. 20150049, 2015.
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.
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.
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.
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.
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.
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.
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.
Models, Chemical
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.
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.
Models, Statistical
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.
Models, Theoretical
B. P. Bratton and Shaevitz, J. W., “Simple Experimental Methods for Determining the Apparent Focal Shift in a Microscope System.”, PLoS One, vol. 10, no. 8, p. e0134616, 2015.
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.
Molecular Conformation
J. W. Shaevitz and Fletcher, D. A., “Curvature and torsion in growing actin networks.”, Phys Biol, vol. 5, no. 2, p. 026006, 2008.
Molecular Imaging
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.
Molecular Motor Proteins
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.
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.
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.
Mollusca
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.
Monte Carlo Method
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.
Morphogenesis
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.
Motion
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.
Movement
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.
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. 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.
J. W. Shaevitz, Lee, J. Y., and Fletcher, D. A., “Spiroplasma swim by a processive change in body helicity.”, Cell, vol. 122, no. 6, pp. 941-5, 2005.
Mutagenesis
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.
Mutation
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.
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.
Myxococcus xanthus
S. Thutupalli, Sun, M., Bunyak, F., Palaniappan, K., and Shaevitz, J. W., “Directional reversals enable Myxococcus xanthus cells to produce collective one-dimensional streams during fruiting-body formation.”, J R Soc Interface, vol. 12, no. 109, p. 20150049, 2015.
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.
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.
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.