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)
Publications
2021
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Intensity uniformity optimization in spatial-light-modulator-based multifocal microscope
2020
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A hydrodynamic instability drives protein droplet formation on microtubules to nucleate branches.
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Competitive binding of independent extension and retraction motors explains the quantitative dynamics of type IV pili
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Distinct cytoskeletal proteins define zones of enhanced cell wall synthesis in Helicobacter pylori.
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Exploring a strongly non-Markovian animal behavior
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Localization precision in chromatic multifocal imaging
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SLEAP: Multi-animal pose tracking
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Topological defects promote layer formation in Myxococcus xanthus colonies
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Uniform intensity in multifocal microscopy using a spatial light modulator
2019
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Fast animal pose estimation using deep neural networks
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Molecular mechanism of microtubule nucleation from gamma-tubulin ring complex
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Paired fruit flies synchronize behavior: uncovering social interactions in Drosophila melanogaster
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Self-Driven Phase Transitions Drive Myxococcus xanthus Fruiting Body Formation
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Spatiotemporal organization of branched microtubule networks
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Substrate-rigidity dependent migration of an idealized twitching bacterium.
2018
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A gated relaxation oscillator controls morphogenetic movements in bacteria
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MreB polymers and curvature localization are enhanced by RodZ and predict E. coli's cylindrical uniformity.
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Optogenetic dissection of descending behavioral control in Drosophila
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Predicting natural behavior from whole-brain neural dynamics
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Temporal processing and context dependency in Caenorhabditis elegans response to mechanosensation.
2017
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The effect of antibiotics on protein diffusion in the Escherichia coli cytoplasmic membrane
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Force generation by groups of migrating bacteria
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Automatically tracking neurons in a moving and deforming brain
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An unsupervised method for quantifying the behavior of paired animals
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A Periplasmic Polymer Curves Vibrio cholerae and Promotes Pathogenesis
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Introduction to Optical Tweezers
2016
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Predictability and hierarchy in Drosophila behavior
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MreB Orientation Correlates with Cell Diameter in Escherichia coli
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Biophysical Measurements of Bacterial Cell Shape
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The PSI–U1 snRNP interaction regulates male mating behavior in Drosophila
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Whole-brain calcium imaging with cellular resolution in freely behaving Caenorhabditis elegans
2015
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RodZ links MreB to cell wall synthesis to mediate MreB rotation and robust morphogenesis
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Simple Experimental Methods for Determining the Apparent Focal Shift in a Microscope System
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Directional reversals enable Myxococcus xanthus cells to produce collective one-dimensional streams during fruiting-body formation
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)