Publications

Google Scholar Page: https://scholar.google.com/citations?user=Gl-C1osAAAAJ&hl=en

2026

Bhattarai N., Moore J.P., Payne S., and Harshey R.M. (2026). “Aer is a bidirectional redox sensor mediating negative chemotaxis to antibiotic-induced ROS in Escherichia coli.” mBio. https://journals.asm.org/doi/10.1128/mbio.00381-26

Ho K., and Harshey R.M. (2026). “Phage Mu enlists the β-sliding clamp for late gene transcription.” Proceedings of the National Academy of Sciences. https://www.pnas.org/doi/10.1073/pnas.2519494123

2025

Bhattarai N., Guo W., Partridge J.D., and Harshey R.M. (2025). “Texas 2-step: a new model for YcgR::c-di-GMP action at the flagellar motor.” Journal of Bacteriology. https://doi.org/10.1128/jb.00353-25

Hwang Y., Perez M., Holzel R., and Harshey R.M. (2025). “c-di-GMP is required for swarming in E. coli, producing colanic acid that acts as surfactant.” mBio. https://doi.org/10.1128/mbio.00916-25

Ho K., and Harshey R.M. (2025) “Membrane-associated σ factors disrupt rRNA operon clustering in Escherichia coli.” PLOS Biology. https://doi.org/10.1371/journal.pbio.3003113

2024

Bhattacharyya S., Lopez S., and Singh A., and Harshey, R. (2024). “Flagellar motility is mutagenic.” Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.2412541121

Partridge J., and Harshey R. (2024). “Flagellar protein FliL: A many‐splendored thing.” Molecular Microbiology. https://doi.org/10.1111/mmi.15301

2023

Bhattacharyya S., Bhattarai N., Pfannenstiel D., Wilkins B., Singh A., and Harshey, R. (2023). “A heritable iron memory enables decision-making in Escherichia coli.” Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.2309082120

Partridge J., Dufour Y., Hwang Y., and Harshey, R. (2023). “Flagellar motor remodeling during swarming requires FliL.” Molecular Microbiology. https://onlinelibrary.wiley.com/doi/10.1111/mmi.15148

Hwang Y., and Harshey R. (2023). “A Second Role for the Second Messenger Cyclic-di-GMP in E. coli: Arresting Cell Growth by Altering Metabolic Flow.” mBio. https://pmc.ncbi.nlm.nih.gov/articles/PMC10942728/

2022

Bhattacharyya S., Bhattacharyya M., Pfannenstiel D.M., Nandi A.K., Hwang Y., Ho K., Harshey R.M. (2022). “Efflux-linked accelerated evolution of antibiotic resistance at a population edge.” Molecular Cell. https://pmc.ncbi.nlm.nih.gov/articles/PMC9699456/

2021

Ho K., and Harshey R. M. (2021). “Goodbye PAM: Phage λ’s Red recombination system cripples PAMs and helps dodge CRISPR attacks.” Cell Host & Microbe. https://pmc.ncbi.nlm.nih.gov/articles/PMC9990376/

2020

Bhattacharyya S., Walker, D.M., and Harshey R.M. (2020). “Dead cells release a ‘necrosignal’ that activates antibiotic survival pathways in bacterial swarming.” Nature Communications. https://www.nature.com/articles/s41467-020-17709-0

Walker D.M., and Harshey R.M. (2020). “Deep sequencing reveals new roles for MuB in transposition immunity and target-capture, and redefines the insular Ter region of E. coli.” Mobile DNA. https://pmc.ncbi.nlm.nih.gov/articles/PMC7350765/

Partridge J.D., Nhu N.T.Q., Dufour Y., and Harshey R.M. (2020). “Tumble Suppression is a Conserved Feature of Swarming Motility.” mBio. https://pmc.ncbi.nlm.nih.gov/articles/PMC7298715/

Partridge J.D., and Harshey R.M. (2020). “Investigating Flagella-Driven Motility in Escherichia coli by Applying Three Established Techniques in a series.” Journal of Visualized Experiments. https://pmc.ncbi.nlm.nih.gov/articles/PMC8453667/

Walker D.M., Freddolino P.L., and Harshey R.M. (2020). “A Well-Mixed E. coli Genome: Widespread Contacts Revealed by Tracking Mu Transposition.” Cell. https://pmc.ncbi.nlm.nih.gov/articles/PMC7369145/

2019

Nieto V., Partridge J.D., Severin G.B., Lai R.Z., Waters C.M., Parkinson J.S., and Harshey R.M. (2019). “Under Elevated c-di-GMP in Escherichia coli, YcgR Alters Flagellar Motor Bias and Speed Sequentially, with Additional Negative Control of the Flagellar Regulon via the Adaptor Protein RssB.” Journal of Bacteriology. https://pmc.ncbi.nlm.nih.gov/articles/PMC6932234/

Partridge J.D., Nhu N.T.Q., Dufour Y.S., and Harshey R.M. (2019). “Escherichia coli remodels the chemotaxis pathway for swarming.” mBio. https://doi.org/10.1128/mbio.00316-19

2018

Bhattacharyya S., Soniat M.M., Walker D., Jang S., Finkelstein I.J., and Harshey R.M. (2018). “Phage Mu Gam protein promotes NHEJ in concert with Escherichia coli ligase.” Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1816606115

Partridge J.D., Ariel G., Schvartz O., Harshey R.M., and Be’er A. (2018). “The 2D architecture of a bacterial swarm has implications for antibiotic tolerance.” Scientific Reports. https://www.nature.com/articles/s41598-018-34192-2

Kim H. K., and Harshey R.M. (2018). “A diguanylate cyclase acts as a cell division inhibitor in a two-step response to reductive and envelope stresses.” mBio. https://doi.org/10.1128/mbio.00822-16

2015

Ariel G., Rabani A., Benisty S., Partridge J., Harshey R.M., and Be’er A. (2015). “Swarming Bacteria Migrate by Levy Walk.” Nature Communications. https://www.nature.com/articles/ncomms9396

Harshey R.M., and Partridge J.D. (2015). “Shelter in a Swarm.” Journal of Molecular Biology. https://doi.org/10.1016/j.jmb.2015.07.025

Jang S., and Harshey R.M. (2015). “Repair of transposable phage Mu DNA insertions begins only when the E. coli replisome collides with the transpososome.” Molecular Microbiology. https://pmc.ncbi.nlm.nih.gov/articles/PMC4536152/

Partridge J. D., Nieto V., and Harshey R.M. (2015). “A new player at the flagellar motor: FliL controls both motor output and bias.” mBio. https://doi.org/10.1128/mbio.02367-14

Lee J., Monzingo A.F., Keatinge-Clay A.T., and Harshey R.M. (2015). “Structure of Salmonella FlhE, conserved member of a flagellar type III secretion operon.” Journal of Molecular Biology. https://pmc.ncbi.nlm.nih.gov/articles/PMC4355100/

2014

Harshey R.M. “Transposable Phage Mu.” (2014). Microbiology Spectrum. https://doi.org/10.1128/microbiolspec.mdna3-0007-2014

Choi W., Jang S., and Harshey R.M. (2014) “Mu transpososome and RecBCD nuclease collaborate in the repair of simple Mu insertions.” Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1407562111

Choi W., Saha R.P., Jang S., and Harshey R.M. (2014). “Controlling DNA degradation from a distance: a new role for the Mu transposition enhancer.” Molecular Microbiology. https://pmc.ncbi.nlm.nih.gov/articles/PMC4213243/

2013

Saha R.P., Lou Z., Meng L., and Harshey R.M. (2013). “Transposable prophage Mu is organized as a stable chromosomal domain of E. coli.” PLOS Genetics. https://doi.org/10.1371/journal.pgen.1003902

Partridge, J.D. and Harshey, R.M. (2013). “Swarming: flexible roaming plans.” Journal of Bacteriology. https://journals.asm.org/doi/10.1128/jb.02063-12

Partridge J.D., and Harshey R.M. (2013). “More than motility: Salmonella flagella contribue to overriding friction and facilitating colony hydration during swarming.” Journal of Bacteriology. https://journals.asm.org/doi/full/10.1128/jb.02064-12

2012

Lazova M.D., Butler M.T., Shimizu T.S., and Harshey R.M. (2012). “Salmonella chemoreceptors McpB and McpC mediate a repellent response to L-cystine: a potential mechanism to avoid oxidative conditions.” Molecular Microbiology. https://pmc.ncbi.nlm.nih.gov/articles/PMC4285363/

Harshey R.M. (2012). “The Mu story: how a maverick phage moved the field forward.” Mobile DNA. https://pmc.ncbi.nlm.nih.gov/articles/PMC3562280/

Jang S., Sandler S.J., and Harshey R.M. (2012). “Mu insertions are repaired by the double strand break repair pathway of E. coli.” PLOS Genetics. https://pmc.ncbi.nlm.nih.gov/articles/PMC3325207/

Lee J., and Harshey R.M. (2012). “Loss of FlhE in the flagellar type III secretion system allows proton inflx into Salmonella and E. coli.” Molecular Microbiology. https://pmc.ncbi.nlm.nih.gov/articles/PMC3331934/

2011

Be’er A., and Harshey, R.M. (2011). “Collective motion of surfactant-producing bacteria imparts superdiffusivity to their upper surface.” Biophysical Journal. https://pmc.ncbi.nlm.nih.gov/articles/PMC3164129/

Ge J., Lou Z., Cui H., Shang L., and Harshey R.M. (2011). “Analysis of phage Mu DNA transposition by whole-genome E. coli tiling arrays reveals a complex relationship to distribution of large selection protein B, transcription and chromosome architectural elements.” Journal of Biosciences. https://pmc.ncbi.nlm.nih.gov/articles/PMC3712764/

2010

Paul K., Nieto V., Carliquist W.C., Blair D.F., and Harshey R.M. (2010). “The c-di-GMP binding protein YcgR controls flagellar motor direction and speed to affect chemotaxis by a ‘backstop break’ mechanism.” Molecular Cell. https://pmc.ncbi.nlm.nih.gov/articles/PMC2929022/

Choi W., and Harshey, R.M. (2010). “DNA repair by the cryptic endonuclease activity of Mu transposase.” Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.0912615107

Butler M., Wang Q., and Harshey R.M. (2010). “Cell density and mobility protect swarming bacteria against antibiotic.” Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.0910934107

Alexander R.P., Lowenthal A.C., Harshey R. M., and Ottemann K.M. (2010). “CheV: CheW-like coupling proteins at the core of the chemotaxis signaling network.” Trends Microbial. https://pmc.ncbi.nlm.nih.gov/articles/PMC2975053/

Ge J., Lou Z., and Harshey R.M. (2010). “Immunity of replicating Mu to self-integration: a novel mechanism employing MuB protein.” Mobile DNA. https://pmc.ncbi.nlm.nih.gov/articles/PMC2837660/