Author

J. W. Shepherd

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Biophysics· 6

Signature Assays, Organisms & Methods

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Assay:fluorescence / live-cell microscopy· 4 Research Focus:cell signaling & trafficking· 2 Research Focus:cell type annotation· 2 Research Focus:clustering· 2 Approach:deep learning· 2 Organism:E. coli· 2 Approach:microscopy & imaging analysis· 2 Approach:statistical model· 2

Frequent Co-Authors

M. C. Leake· 5 shared A. L. Payne-Dwyer· 2 shared A. Syeda· 2 shared A. C. Noy· 1 shared A. J. Wollman· 1 shared A. Noy· 1 shared C. MacDonald· 1 shared E. Higgins· 1 shared

Activity by Year

2019-2022 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 13 mutual co-author links

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5 shared papersBiophysics

M. C. Leake

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6 papers

Recent·Most cited

Correlating viscosity and molecular crowding with fluorescent nanobeads and molecular probes: in vitro and in vivo

S. Lecinski, J. W. Shepherd, K. Bunting, L. Dresser, S. D. Quinn, C. MacDonald, M. C. Leake

The paper investigates intracellular viscosity and molecular crowding using fluorescent nanobeads and molecular probes in vitro and in live yeast cells.

bioRxiv · Jun 27, 2022Biophysics

RecA and RecB: probing complexes of DNA repair proteins with mitomycin C in live Escherichia coli with single-molecule sensitivity

A. L. Payne-Dwyer, A. Syeda, J. W. Shepherd, L. Frame, M. C. Leake

This study uses super-resolved fluorescence microscopy to analyze RecA and RecB dynamics in live E. coli under DNA damage, revealing their spatial organization and stoichiometry changes.

bioRxiv · Oct 4, 2021Biophysics

PySTACHIO: Python Single-molecule TrAcking stoiCHiometry Intensity and simulatiOn, a flexible, extensible, beginner-friendly and optimized program for analysis of single-molecule microscopy

J. W. Shepherd, E. Higgins, A. J. Wollman, M. C. Leake

The paper introduces PySTACHIO, a Python program for single-molecule microscopy analysis that offers improved performance, flexibility, and accessibility compared to existing tools.

bioRxiv · Mar 18, 2021Biophysics

Combining single-molecule super-resolved localization microscopy with fluorescence polarization imaging to study cellular processes

J. W. Shepherd, A. L. Payne-Dwyer, J.-E. Lee, A. Syeda, M. C. Leake

This paper combines single-molecule super-resolved localization microscopy with fluorescence polarization imaging to simultaneously measure spatial location, molecular stoichiometry, and diffusion coefficients of tracked molecular complexes.

bioRxiv · Jan 6, 2021Biophysics

SerraNA: a program to determine nucleic acids elasticity from simulation data

V. Velasco-Berrelleza, M. Burman, J. W. Shepherd, M. C. Leake, R. Golestanian, A. Noy

SerraNA calculates elastic parameters of nucleic acids from simulation data, revealing sequence-dependent elasticity and global bendability from local bending angles.

Physical Chemistry Chemical Physics · Jan 1, 2020Peer-reviewedBiophysics

The emergence of sequence-dependent structural motifs in stretched, torsionally constrained DNA

J. W. Shepherd, R. J. Greenall, M. I. J. Probert, A. C. Noy, M. Leake

This study shows that DNA sequence affects structural motifs under mechanical stress, with GC-rich sequences being more stable than AT-rich ones.

bioRxiv · Apr 4, 2019Biophysics