Publications

2017

  • Optogenetic dissection of descending behavioral control in Drosophila

    Optogenetic dissection of descending behavioral control in Drosophila

    Jessica Cande, Gordon J Berman, Shigehiro Namiki, Jirui Qiu, Wyatt Korff, Gwyneth Card, Joshua W Shaevitz, David L Stern
    doi: https://doi.org/10.1101/230128

  • The effect of antibiotics on protein diffusion in the Escherichia coli cytoplasmic membrane

    The effect of antibiotics on protein diffusion in the Escherichia coli cytoplasmic membrane

    George Liu, Benjamin Bratton, Zemer Gitai, Joshua W. Shaevitz
    PLoS ONE 12(10): e0185810. 
    doi: 10.1371/journal.pone.0185810

  • A motility-induced phase transition drives Myxococcus xanthus aggregation

    A motility-induced phase transition drives Myxococcus xanthus aggregation

    Guannan Liu, Adam Patch, Fatmagul Bahar, David Yllanes, Roy D. Welch, M. Cristina Marchetti, Shashi Thutupalli, Joshua W. Shaevitz
    arXiv:1709.06012

  • A gated relaxation oscillator controls morphogenetic movements in bacteria

    A gated relaxation oscillator controls morphogenetic movements in bacteria

    Mathilde Guzzo, Seán M. Murray, Eugénie Martineau, Sébastien Lhospice, Grégory Baronian, Laetitia My, Yong Zhang, Leon Espinosa, Renaud Vincentelli, Benjamin P. Bratton, Joshua W. Shaevitz, Virginie Molle, Martin Howard, Tâm Mignot
    doi: 10.1101/137695, bioRxiv 137695

  • Force generation by groups of migrating bacteria

    Force generation by groups of migrating bacteria

    Benedikt Sabass, Matthias D. Koch, Guannan Liu, Howard A. Stone, and Joshua W. Shaevitz
    PNAS, July 11, 2017, vol. 114, no. 28 7266-7271
    doi: 10.1073/pnas.1621469114, arXiv:1701.00524

  • Automatically tracking neurons in a moving and deforming brain

    Automatically tracking neurons in a moving and deforming brain

    Nguyen JP, Linder AN, Plummer GS, Shaevitz JW, Leifer AM
    PLoS Comput Biol, May 18, 2017, 13(5): e1005517
    doi: 10.1371/journal.pcbi.1005517, arXiv:1610.04579

  • An unsupervised method for quantifying the behavior of paired animals

    An unsupervised method for quantifying the behavior of paired animals

    Ugne Klibaite, Gordon J Berman, Jessica Cande, David L Stern and Joshua W Shaevitz
    Physical Biology, February 16, 2017,  Volume 14, Number 1 
    doi: 10.1088/1478-3975.aa5c50, arXiv:1609.09345

  • A Periplasmic Polymer Curves Vibrio cholerae and Promotes Pathogenesis

    A Periplasmic Polymer Curves Vibrio cholerae and Promotes Pathogenesis

    Thomas M. Bartlett, Benjamin P. Bratton, Amit Duvshani, Amanda Miguel, Ying Sheng, Nicholas R. Martin, Jeffrey P. Nguyen, Alexandre Persat, Samantha M. Desmarais, Michael S. VanNieuwenhze, Kerwyn Casey Huang, Jun Zhu, Joshua W. Shaevitz, Zemer Gitai
    Cell , January 12, 2017, Volume 168 , Issue 1 , 172 - 185.e15
    doi: 10.1016/j.cell....

  • Introduction to Optical Tweezers

    Introduction to Optical Tweezers

    Matthias Koch, Joshua W. Shaevitz
    Chapter in "Optical Tweezers: Methods and Protocols"
    Methods in Molecular Biology
    Volume 1486 2017, Ed: Arne Gennerich
    ISBN: 978-1-4939-6419-2 

2016

  • Predictability and hierarchy in Drosophila behavior

    Predictability and hierarchy in Drosophila behavior

    Gordon J. Berman, William Bialek, and Joshua W. Shaevitz
    PNAS, October 18, 2016, vol. 113 no. 42 11943-11948
    doi: 10.1073/pnas.1607601113, arXiv:1605.03626

  • MreB Orientation Correlates with Cell Diameter in Escherichia coli

    MreB Orientation Correlates with Cell Diameter in Escherichia coli

    Nikolay Ouzounov, Jeffrey P. Nguyen, Benjamin P. Bratton, David Jacobowitz, Zemer Gitai, Joshua W. Shaevitz
    Biophysical Journal, September 6, 2016, Volume 111, Issue 5, 1035-1043
    doi: j.bpj.2016.07.017, arXiv:1503.0778

  • Biophysical Measurements of Bacterial Cell Shape

    Biophysical Measurements of Bacterial Cell Shape

    Jeffrey P. Nguyen, Benjamin P. Bratton, Joshua W. Shaevitz
    Chapter in "Bacterial Cell Wall Homeostasis"
    Methods in Molecular Biology
    Volume 1440 2016, Ed: HJ Hong
    ISBN: 978-1-4939-3674-8

  • The PSI–U1 snRNP interaction regulates male mating behavior in Drosophila

    The PSI–U1 snRNP interaction regulates male mating behavior in Drosophila

    Qingqing Wang, J. Matthew Taliaferro, Ugne Klibaite, Valérie Hilgers, Joshua W. Shaevitz, and Donald C. Rio
    PNAS, May 10, 2016, vol. 113 no. 19 5269-5274
    doi: 10.1073/pnas.1600936113

  • Whole-brain calcium imaging with cellular resolution in freely behaving Caenorhabditis elegans

    Whole-brain calcium imaging with cellular resolution in freely behaving Caenorhabditis elegans

    Jeffrey P. Nguyen, Frederick B. Shipley, Ashley N. Linder, George S. Plummer, Mochi Liu, Sagar U. Setru, Joshua W. Shaevitz, and Andrew M. Leifer
    PNAS, February 23, 2016, vol. 113 no. 8 E1074-E1081
    PNAS, doi:10.1073/pnas.1507110112; arXiv:1501.03463

2015

Earlier Publications

Origins of E. coli growth rate and cell shape changes at high external osmolality 
Pilizota, Shaevitz
Biophysical Journal, doi:10.1016/j.bpj.2014.08.025

Passive Mechanical Forces Control Cell Shape Change during Drosophila Ventral Furrow Formation
Polyakov, He, Swan, Shaevitz, Kaschube, Wieschaus
Biophysical Journal, doi:10.1016/j.bpj.2014.07.013

De novo morphogenesis in L-forms via geometric control of cell growth
Billings, Ouzounov, Ursell, Desmarais, Shaevitz, Gitai, Huang
Molecular Microbiology, doi: 10.1111/mmi.12703

Myxococcus xanthus Gliding Motors Are Elastically Coupled to the Substrate as Predicted by the Focal Adhesion Model of Gliding Motility
Balagam, Litwin, Czerwinski, Sun, Kaplan, Shaevitz, Igoshin
PLoS Computational Biology doi:10.1371/journal.pcbi.1003619; arXiv:1401.3220

Spatial Covariance Reconstructive (SCORE) Super-Resolution Fluorescence Microscopy
Deng, Sun, Lin, Ma, Shaevitz
PLoS One doi:10.1371/journal.pone.0094807

Rod-like bacterial shape is maintained by feedback between cell curvature and cytoskeletal localization
Ursell, Nguyen, Monds, Colavin, Billings, Ouzounov, Gitai, Shaevitz, Huang
Proceedings of the National Academy of Sciences doi:10.1073/pnas.1317174111

The biophysics of Myxococcus xanthus motility
Czerwinski, Shaevitz
In Zhaomin Yang and Penelope I Higgs (Eds.), Myxobacteria: Genomics, Cellular and Molecular Biology Caister Academic Press, 2014.

Mapping the stereotyped behaviour of freely-moving fruit flies
Berman, Choi, Bialek, Shaevitz
Royal Society Interface doi:10.1098/ rsif.2014.0672; arXiv:1310.4249

A versatile class of cell surface directional motors gives rise to gliding motility and sporulation in Myxococcus xanthus
Wartel, Ducret, Thutupalli, Czerwinski, Le Gall, Mauriello, Bergham, Brun, Shaevitz, Mignot
PLoS Biology doi:10.1371/journal.pbio.1001728

Combining Modeling and Experiment to Understand Bacterial Growth
Shaevitz
Biophysical Journal doi:10.1016/j.bpj.2013.05.007

Efficient Multiple Object Tracking Using Mutually Repulsive Active Membranes
Deng, Coen, Sun, Shaevitz
PLoS ONE doi:10.1371/journal.pone.0065769; arXiv:1212.6209

Plasmolysis and cell shape depend on solute outer-membrane permeability during hyperosmotic shock in E. coli
Pilizota, Shaevitz
Biophysical Journal doi:10.1016/j.bpj.2013.05.011

Non-local interaction via diffusible resource prevents coexistence of cooperators and cheaters in a lattice model
Borenstein, Meir, Shaevitz, Wingreen
PLoS ONE doi:10.1371/journal.pone.0063304

The mechanics of shape in prokaryotes
Wang, Shaevitz
Frontiers in Bioscience doi:10.2741/S390

The molecular origins of chiral growth in walled cells
Huang, Ehrhardt, Shaevitz
Current Opinions in Microbiology doi:10.1016/j.mib.2012.11.002

Fast, Multiphase Volume Adaptation to Hyperosmotic Shock by Escherichia coli
Pilizota, Shaevitz
PLoS ONE doi:10.1371/ journal.pone.0035205

Helical insertion of peptidoglycan produces elongation and chiral ordering of the bacterial cell wall
Wang, Furchtgott, Huang, Shaevitz
Proceedings of the National Academy of Sciences doi:10.1073/pnas.1117132109

Image analysis in fluorescence microscopy: bacterial dynamics as a case study
van Teeffelen, Shaevitz, Gitai
BioEssays doi:10.1002/bies.201100148

From individual cell motility to collective behaviors: insights from a prokaryote, Myxococcus xanthus
Zhang, Ducret, Shaevitz, Mignot
FEMS Microbiology Reviews doi:10.1111/j.1574-6976.2011.00307.x

Direct measurement of stress-stiffening and turgor pressure in live bacterial cells
Deng, Sun, Shaevitz
Physical Review Letters doi:10.1103/PhysRevLett.107.158101; arXiv:1104.1421

The bacterial actin MreB rotates, and rotation depends on cell-wall assembly
van Teeffelen, Wang, Furchtgott, Huang,  Wingreen, Shaevitz, Gitai
Proceedings of the National Academy of Sciences doi: 10.1073/pnas.1108999108

Motor-driven Intracellular Transport Powers Bacterial Gliding Motility
Sun, Wartel, Cascales, Shaevitz, Mignot
Proceedings of the National Academy of Sciences doi:10.1073/pnas.1101101108<\p>

Femtosecond diffractive imaging of biological cells
Seibert, Boutet, Svenda, Ekeberg, Maia, Bogan, Timneanu, Barty, Hau-Riege, Caleman, Frank, Benner, Lee, Marchesini, Shaevitz, Fletcher, Bajt, Andersson, Chapman, Hajdu
Journal of Physics B: Atomic, Molecular and Optical Physics doi:10.1088/0953-4075/43/19/194015

The structure and Function of Bacterial Actin Homologs
Shaevitz and Gitai
Cold Spring Harbor Perspectives in Biology  doi: 10.1101/cshperspect.a000364

An actin-like cytoskeleton contributes to cell mechanics in bacteria [SI]
Wang, Arellano-Santoyo, Combs, Shaevitz
Proceedings of the National Academy of Sciences doi: 10.1073/pnas.0911517107

Measuring the Bending Stiffness of Bacterial Cells Using an Optical Trap
Wang, Arellano-Santoyo, Combs, Shaevitz
Journal of Visual Experiments doi: 10.3791/2012

A Parallel Product-Convolution approach for representing the depth varying Point Spread Functions in 3D widefield microscopy based on principal component analysis
Arigovindan, Shaevitz, McGowan, Sedat, Agard
Optics Express doi:10.1364/OE.18.006461

The cytoskeleton: I-beams of the cell
Shaevitz and Nørrelykke
Physics Today 

The effect of aberrations on height calibration in three-dimensional microscopy and particle tracking
Deng and Shaevitz
Applied Optics doi:10.1364/AO.48.001886

Bayesian Estimation of the Axial Position in Astigmatism-Based Three-Dimensional Particle Tracking
Shaevitz
International Journal of Optics doi:10.1155/2009/896208

Active and Passive Mechanisms of Intracellular Transport and Localization in Bacteria
Mignot and Shaevitz
Current Opinions in Microbiology doi:10.1016/j.mib.2008.10.005

Slow stress propagation in adherent cells
Rosenbluth, Crow, Shaevitz, Fletcher
Biophysical Journal doi:10.1529/biophysj.108.139139

Massively parallel X-ray holography
Marchesini, Boutet, Sakdinawat, Bogan, Bajt, Barty, Chapman, Frank, Hau-Riege, Szoke, Cui, Shapiro, Howells, Spence, Shaevitz, Lee, Hajdu, Seibert
Nature Photonics doi:10.1038/nphoton.2008.154

Curvature and torsion in growing actin networks
Shaevitz and Fletcher
Physical Biology doi:10.1088/1478-3975/5/2/026006; arXiv:0709.0679

Super-resolution for a 3D world
Shaevitz
Nature Methods doi:10.1038/nmeth0608-471

Load fluctuations drive actin network growth
Shaevitz and Fletcher
PNAS doi: 10.1073/pnas.0702601104; arXiv:0708.1791 

Enhanced three-dimensional deconvolution microscopy using a measured depth-varying point spread function
Shaevitz and Fletcher
Journal of the Optical Society of America A doi:10.1364/JOSAA.24.002622

Evidence that Focal Adhesion Complexes Power Bacterial Gliding Motility
Mignot, Shaevitz, Hartzell, Zusman
Science doi:10.1126/science.1137223

Direct observation of base-pair stepping by RNA polymerase
Abbondanzieri, Greenleaf, Shaevitz, Landick, Block
Nature (2005)

Picocalorimetry of Transcription by RNA Polymerase
Abbondanzieri, Shaevitz, Block
Biophysical Journal (2005) 

Statistical Kinetics of Macromolecular Dynamics
Shaevitz, Schnitzer, Block
Biophysical Journal (2005)

Spiroplasma Swim by a Processive Change in Body Helicity
Shaevitz, Lee, Fletcher
Cell (2005)

Backtracking by single RNA polymerase molecules observed at near-base-pair resolution
Shaevitz, Abbondanzieri, Landick, Block
Nature (2003)

Probing the kinesin reaction cycle with a 2D optical force clamp
Block, Asbury, Shaevitz, Lang
Proceedings of the National Academy of Sciences (2003)

An Automated Two-Dimensional Optical Force Clamp for Single Molecule Studies
Lang, Asbury, Shaevitz, Block
Biophysical Journal (2002)