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Lab Publications

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  2. Publications
See all of our work on Google Scholar
  • Population Ecology-Quantitative Microbial Risk Assessment(QMRA) Model for Antibiotic-Resistant and Susceptible E. coli in Recreational Water

    • Ashley Heida, Mark T. Hamilton, Julia Gambino, Kaylee Sanderson, Mary E. Schoen, Michael A. Jahne, Jay Garland, Lucia Ramirez, Hunter Quon, Allison J. Lopatkin, and Kerry A. Hamilton
    • 2025
    • Environmental Science & Technology
  • The role of bacterial metabolism in antimicrobial resistance

    • Mehrose Ahmad, Sai Varun Aduru, Robert P. Smith, Zirui Zhao & Allison J. Lopatkin
    • 2025
    • Nature Reviews Microbiology
  • Quantifying conjugation rates in clinical and environmental matrices: a systematic review to inform risk assessment

    • Hunter Quon, Lucia Ramirez, Blakeley Bagwell, Jennifer Moralez, Richard J. Sheppard, Allison J. Lopatkin, Kerry A. Hamilton
    • 2025
    • Frontiers in Microbiomes
  • The metabolic burden associated with plasmid acquisition: An assessment of the unrecognized benefits to host cells

    • Heather D. Curtsinger, Sofía Martínez-Absalón, Yuchang Liu, Allison J. Lopatkin
    • 2024
    • BioEssays
  • Purine and pyrimidine synthesis differently affect the strength of the inoculum effect for aminoglycoside and β-lactam antibiotics

    • Daniella M. Hernandez, Melissa Marzouk, Madeline Cole, Marla C. Fortoul, Saipranavi Reddy Kethireddy, Rehan Contractor, Habibul Islam, Trent Moulder, Ariane R. Kalifa, Estefania Marin Meneses, Maximiliano Barbosa Mendoza, Ruth Thomas, Saad Masud, Sheena Pubien, Patricia Milanes, Gabriela Diaz-Tang, Allison J. Lopatkin, Robert P. Smith
    • 2024
    • Microbiology Spectrum
  • Selection and horizontal gene transfer underlie microdiversity-level heterogeneity in resistance gene fate during wastewater treatment

    • Connor L. Brown, Ayella Maile-Moskowitz, Allison J. Lopatkin, Kang Xia, Latania K Logan, Benjamin C. Davis, Liqing Zhang, Peter J. Vikesland & Amy Pruden
    • 2024
    • Nature Communications
  • Sub-inhibitory antibiotic treatment selects for enhanced metabolic efficiency

    • Sai Varun Aduru, Karolina Szenkiel, Anika Rahman, Mehrose Ahmad, Maya Fabozzi, Robert P. Smith, AJ Lopatkin
    • 2024
    • Microbiology Spectrum
  • Tradeoff between lag time and growth rate drives the plasmid acquisition cost.

    • Mehrose Ahmad, Hannah Prensky, Jacqueline Balestrieri, Shahd ElNaggar, Angela Gomez-Simmonds, Anne-Catrin Uhlemann, Beth Traxler, Abhyudai Singh & AJ Lopatkin
    • 2023
    • Nature Communications
  • Disturbing the Spatial Organization of Biofilm Communities Affects Expression of agr-Regulated Virulence Factors in Staphylococcus aureus

    • Ivana Barraza, Camryn Pajon, Gabriela Diaz-Tang, Estefania Marin Meneses,a Fatima Abu-Rumman, Laura García-Diéguez, Victor Castro, AJ Lopatkin, Robert P. Smith
    • 2023
    • Environmental Microbiology
  • Growth productivity as a determinant of the inoculum effect for bactericidal antibiotics.

    • Gabriela Diaz-Tang, Estefania Marin Menses, Kavish Patel, Sophia Mirkin, Laura Garcia-Dieguez, Camryn Pajon, Ivana Barrara, Vijay Patel, Helana Ghali, Angelica P. Tracey, Christopher A. Blanar, AJ Lopatkin, and Robert P. Smith
    • 2023
    • Science Advances
  • Metabolic genes on conjugative plasmids are highly prevalent in Escherichia coli and can protect against antibiotic treatment.

    • Alana Palomino, Danya Gewurz, Lela DeVine, Ujana Zajmi, Jenifer Moralez, Fatima Abu-Rumman, Robert P. Smith & AJ Lopatkin
    • 2022
    • ISME
  • Horizontal gene transfer enables programmable gene stability in synthetic microbiota.

    • T Wang, A Weiss, A aqeel, F Wu, AJ Lopatkin, LA David, L You
    • 2022
    • Nature Chemical Biology
  • Population structure of blaKPC-harbouring IncN plasmids at a New York City medical centre and evidence for multi-species horizontal transmission.

    • A Gomez-Simmonds, MK Annavajhala, N Tang, FD Rozenberg, M Ahmad, H Park, AJ Lopatkin, and AC Uhlemann
    • 2022
    • Antimicrobial Chemotherapy
  • Phylogenetic analysis of two antibiotic susceptible non-clinical Acinetobacter baumannii strains belonging to global clone 1 reveals close relationship with multiply-antibiotic resistant clinical strains.

    • J Koong, C Johnson, R Rafei, M Hamze, GSA Myers, AJ Lopatkin, and M Hamidian
    • 2021
    • Microbial Genomics
  • Quantitative Microbial Risk Assessment of Antimicrobial Resistant and Susceptible Staphylococcus aureus in Reclaimed Wastewaters

    • M. E. Schoen, M. A. Jahne, J. Garland, L. Ramirez, A. J. Lopatkin, and K. A. Hamilton
    • 2021
    • Environmental science & technology
  • Thermal stress induces tissue damage and a broad shift in regenerative signaling pathways in the honey bee digestive tract.

    • DM Bach, MA Holzman, F Wague, JJ Miranda, AJ Lopatkin, JH Mansfield, and JW Snow
    • 2021
    • Journal of Experimental Biology
  • Honey bee sHSP are responsive to diverse proteostatic stresses and potentially promising biomarkers of honey bee stress.

    • SR Shih, D Bach, N Rondeau, J Sam, NL Lovinger, AJ Lopatkin, and JW Snow
    • 2021
    • Scientific Reports
  • Quantitative analysis of horizontal gene transfer in complex systems.

    • J Moralez, K Szenkiel, K Hamilton, A Pruden, AJ Lopatkin
    • 2021
    • Current Opinion in Microbiology
  • Investigation of the prevalence and catalytic activity of rubredoxin-fused alkane monooxygenases (AlkBs).

    • SC Williams, AP Forsberg, J Lee, C Vizcarra, AJ Lopatkin, RN Austin
    • 2021
    • Journal of Inorganic Biochemistry
  • Conjugation dynamics depend on both the plasmid acquisition cost and the fitness cost.

    • H Prensky, A Gomez-Simmons, AC Uhlemann, AJ Lopatkin
    • 2021
    • Molecular Systems Biology
  • Clinically relevant mutations in core metabolic genes confer antibiotic resistance.

    • AJ Lopatkin, SC Bening, AL Manson, JM Stokes, MA Kohanski, AH Badran, AM Earl, NJ Cheney, JH Yang, JJ Collins
    • 2021
    • Science
  • Nucleotide metabolism and antibiotic treatment failure.

    • AJ Lopatkin, JH Yang
    • 2021
    • Frontiers in Digital Health
  • Predictive biology: modelling, understanding and harnessing microbial complexity.

    • AJ Lopatkin and J Collins
    • 2020
    • Nature Microbiology Reviews
  • Environmental and genetic determinants of plasmid mobility in pathogenic Escherichia coli.

    • JH Bethke, A Davidovich, L Cheng, AJ Lopatkin, W. Song, JT Thaden, VG Fowler Jr, M Xiao, L You
    • 2020
    • Science Advances
  • Growth‐Stage‐Dependent Regulation of Conjugation.

    • TA Sysoeva, YL Kim, J Rodriguez, AJ Lopatkin, L You
    • 2019
    • AlChE
  • Bacterial metabolic state more accurately predicts antibiotic lethality than growth rate.

    • AJ Lopatkin, JM Stokes, EJ Zheng, JH Yang, MK Takahashi, L You, JJ Collins
    • 2019
    • Nature Microbiology
  • Bacterial Metabolism and Antibiotic Efficacy.

    • JM Stokes, AJ Lopatkin, MA Lobritz, JJ Collins
    • 2019
    • Cell Metabolism
  • A white-box machine learning approach for revealing antibiotic mechanisms of action.

    • JH Yang, SN Wright, M Hamblin, D McCloskey, MA Alcantar, L Schrubbers, AJ Lopatkin, S Sateesh, A Nili, BO Palsson, GC Walker, JJ Collins
    • 2019
    • Cell
  • A multiplexable assay for screening antibiotic lethality against drug-tolerant bacteria.

    • JM Stokes, A Gutierrez, AJ Lopatkin, IW Andrews, S French, I Matic, ED Brown, JJ Collins
    • 2019
    • Nature Methods
  • A unifying framework for interpreting and predicting mutualistic systems.

    • F Wu, AJ Lopatkin, DA Needs, CT Lee, S Mukherjee, L You
    • 2019
    • Nature Communications
  • Applying ecological resistance and resilience to dissect bacterial antibiotic responses.

    • HR Meredith, V Andreani, HR Ma, AJ Lopatkin, AJ Lee, DJ Anderson, AJ Lee, DJ Anderson, G Batt, L You
    • 2018
    • Scientific Advances
  • Persistence and reversal of plasmid-mediated antibiotic resistance.

    • AJ Lopatkin, HR Meredith, JK Srimani, C Pfeiffer, R Durrett, L You
    • 2017
    • Nature Communications
  • Drug detoxification dynamics explain the postantibiotic effect.

    • JK Srimani, S Huang, AJ Lopatkin, L You
    • 2017
    • Molecular Systems Biology
  • Cooperation and competition shape ecological resistance during periodic spatial disturbance of engineered bacteria.

    • CE Wilson, AJ Lopatkin, TJA Craddock, WW Driscoll, OT Eldakar, JV Lopez, RP Smith
    • 2017
    • Scientific Reports
  • Antibiotics as a selective driver for conjugation dynamics.

    • AJ Lopatkin, S Huang, RP Smith, JK Srimani, TA Sysoeva, S Bewick, DK Karig, L You
    • 2016
    • Nature Microbiology
  • Elements of biological oscillations in time and space.

    • Y Cao, AJ Lopatkin, L You
    • 2016
    • Nature Structural & Molecular Biology
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  • Dissecting the effects of antibiotics on horizontal gene transfer: Analysis suggests a critical role of selection dynamics.

    • AJ Lopatkin, TA Sysoeva, L You
    • 2016
    • Bioessays
  • Collective antibiotic tolerance: mechanisms, dynamics and intervention.

    • HR Meredith, JK Srimani, AJ Lee, AJ Lopatkin, L You
    • 2015
    • Nature Chemical Biology
  • Dynamic control and quantification of bacterial population dynamics in droplets.

    • S Huang, JK Srimani, AJ Lee, Y Zhang, AJ Lopatkin, KW Leong, L You
    • 2015
    • Biomaterials
  • Dynamic control and quantification of bacterial population dynamics in droplets.

    • HR Meredith, AJ Lopatkin, DJ Anderson, L You
    • 2015
    • PLoS Computational Biology
  • A power-law dependence of bacterial invasion on mammalian host receptors.

    • TJ Lee, J Wong, S Bae, AJ Lee, AJ Lopatkin, F Yuan, L You
    • 2015
    • PLoS Computational Biology
  • Synthetic biology looks good on paper.

    • AJ Lopatkin, L You
    • 2014
    • Cell

Affiliations

  • Dept. of Chemical Engineering
  • URMC,
    Microbiology & Immunology

Contact Us

313 Gavett Hall
Univeristy of Rochester
Rochester, NY 14627

Email: lopatkinlab@gmail.com

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