2022
Talmo D. Pereira, Nathaniel Tabris, Junyu Li, Shruthi Ravindranath, Eleni S. Papadoyannis, Z. Yan Wang, David M. Turner, Grace McKenzie-Smith, Sarah D. Kocher, Annegret L. Falkner, Joshua W. Shaevitz, Mala Murthy
Nature Methods, 19, pages 486–495 (2022), bioRxiv 2020.08.31.276246
Katherine E Overman, Daniel M Choi, Kawai Leung, Joshua W Shaevitz, Gordon J Berman
PLOS Computational Biology 18(2): e1009867 (2022), arXiv:2106.07610.
Ugne Klibaite, Mikhail Kislin, Jessica L Verpeut, Xiaoting Sun, Joshua W Shaevitz, Samuel S-H Wang.
Molecular Autism 13, 12 (2022), bioRxiv 2021.02.16.431500.
ME Black, JW Shaevitz.
arXiv:2111.12623
Z Yan Wang, Grace C McKenzie-Smith, Weijie Liu, Hyo Jin Cho, Talmo D Pereira, Zahra Dhanerawala, Joshua W Shaevitz, Sarah D Kocher.
Current Biology, 32 (12), P2754-2764.E5 2022, bioRxiv 2021.12.16.472962
2021
Sagar U. Setru, Bernardo Gouveia, Raymundo Alfaro-Aco, Joshua W. Shaevitz, Howard A. Stone, Sabine Petry.
Nature Physics 17, 493–498 (2021). arXiv:2001.06389
Courtney K Ellison, Triana N Dalia, Catherine A Klancher, Joshua W Shaevitz, Zemer Gitai, Ankur B Dalia.
Nature Communications 12, 3744 (2021).
Matthias D. Koch, Chenyi Fei, Ned S. Wingreen, Joshua W. Shaevitz, Zemer Gitai
PNAS February 23, 2021 118 (8) e2014926118, bioRxiv 2020.02.12.946426
Kelsey M Hallinen, Ross Dempsey, Monika Scholz, Xinwei Yu, Ashley Linder, Francesco Randi, Anuj Sharma, Joshua W Shaevitz, Andrew M Leifer.
eLife, 2021;10:e66135, 2021.
M. Junaid Amin, Sabine Petry, Haw Yang, Joshua W. Shaevitz. Proceedings Volume 11649, Three-Dimensional and Multidimensional Microscopy: Image Acquisition and Processing XXVIII; 116490P (2021)
M. Junaid Amin, Sabine Petry, Joshua W. Shaevitz, Haw Yang.
J. Opt. Soc. Am. B 38, 2792-2798 (2021), arXiv:2008.10488
Endao Han, Lailai Zhu, Joshua W Shaevitz, Howard A Stone.
PNAS July 20, 2021 118 (29) e2022000118. arXiv:2105.04096
Matthias D Koch, Matthew E Black, Endao Han, Joshua W Shaevitz, Zemer Gitai
PNAS, 119(20) e2119434119, 2022, bioRxiv 2021.08.26.457786
Katherine Copenhagen, Ricard Alert, Ned S. Wingreen, Joshua W. Shaevitz.
Nature Physics 17, 211–215 (2021). arXiv:2001.03804
2020
Taylor JA, Bratton BP, Sichel SR, Blair KM, Jacobs HM, DeMeester KE, Kuru E, Gray J, Biboy J, VanNieuwenhze MS, Vollmer W, Grimes CL, Joshua W. Shaevitz, Salama NR. eLife doi:10.7554/eLife.52482, bioRxiv:545517
Vasyl Alba, Gordon J. Berman, William Bialek, Joshua W. Shaevitz
arXiv:2012.15681 (2020)
Talmo D Pereira, Joshua W Shaevitz, Mala Murthy
Nat Neurosci 23, 1537–1549 (2020).
M. Junaid Amin, Sabine Petry, Haw Yang, Joshua W. Shaevitz
PLOS ONE 15(3): e0230217.
2019
Talmo Pereira, Diego Aldarondo, Lindsay Willmore, Mikhail Kislin, Samuel S. Wang, Mala Murthy, Joshua W. Shaevitz
Nature Methods, doi: 10.1038/s41592-018-0234-5
Akanksha Thawani, Howard A Stone, Joshua W Shaevitz, Sabine Petry
bioRxiv 853010
Ugne Klibaite, Joshua W. Shaevitz
PLoS Comput Biol 16(10): e1008230. bioRxiv 545483
Guannan Liu, Adam Patch, Fatmagul Bahar, David Yllanes, Roy D. Welch, M. Cristina Marchetti, Shashi Thutupalli, Joshua W. Shaevitz
Phys. Rev. Lett. 122, 248102; arXiv:1709.06012
Akanksha Thawani, Howard A Stone , Joshua W Shaevitz, Sabine Petry
eLife, doi: 10.7554/eLife.43890
Simsek AN, Braeutigam A, Koch MD, Joshua W. Shaevitz, Huang Y, Gompper G, Sabass B. Soft Matter doi:10.1039/C9SM00541B; bioRxiv:581348.
2018
Nat Microbiol. 2018 Aug;3(8):948-959. doi: 10.1038/s41564-018-0203-x
doi: 10.1101/137695, bioRxiv 137695
Nature Commun. 2018 Jul 18;9(1):2797. doi: 10.1038/s41467-018-05186-5.
Elife. 2018 Jun 26;7. pii: e34275. doi: 10.7554/eLife.34275.
doi: https://doi.org/10.1101/230128
Monika Scholz, Ashley N Linder, Francesco Randi, Anuj K Sharma, Xinwei Yu, Joshua W Shaevitz, Andrew M Leifer
bioRxiv 445643
Elife. 2018 Jun 26;7. pii: e36419. doi: 10.7554/eLife.36419
2017
George Liu, Benjamin Bratton, Zemer Gitai, Joshua W. Shaevitz
PLoS ONE 12(10): e0185810.
doi: 10.1371/journal.pone.0185810
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
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
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
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.2016.12.019
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
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
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
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
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
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
Randy M. Morgenstein, Benjamin P. Bratton, Jeffrey P. Nguyen, Nikolay Ouzounov, Joshua W. Shaevitz, and Zemer Gitai
PNAS, October 6, 2015, vol. 112 no. 40 12510-12515
doi:10.1073/pnas.1509610112
Benjamin P. Bratton, Joshua W. Shaevitz
PLoS ONE, August 13, 2015, 10(8): e0134616
doi:10.1371/journal.pone.0134616
Shashi Thutupalli, Mingzhai Sun, Filiz Bunyak, Kannappan Palaniappan, Joshua W. Shaevitz
Journal of the Royal Society Interface, August 5, 2015, vol. 12, issue 109
doi: 10.1098/rsif.2015.0049, arXiv:1410.7230
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)