publications


  1. 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. Journal of Antimicrobial Chemotherapy (2022)

  2. 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. Microbial Genomics (2021)

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

  4. 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. Scientific Reports (2021)

  5. Quantitative microbial risk assessment of antibacterial resistant and susceptible Staphylococcus aureus in reclaimed wastewaters.
    ME Shoen, MA Jahne, J Garland, L Ramirez, AJ Lopatkin, and K Hamilton. Environmental Science & Technology (2021)

  6. Quantitative analysis of horizontal gene transfer in complex systems.
    J Moralez, K Szenkiel, K Hamilton, A Pruden, AJ Lopatkin. Current Opinion in Microbiology (2021)

  7. 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. Journal of Inorganic Biochemistry (2021)

  8. Conjugation dynamics depend on both the plasmid acquisition cost and the fitness cost.
    H Prensky, A Gomez-Simmons, AC Uhlemann, AJ Lopatkin. Molecular Systems Biology (2021)

  9. 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. Science (2021)

  10. Nucleotide metabolism and antibiotic treatment failure.
    AJ Lopatkin, JH Yang. Frontiers in Digital Health (2021)

  11. Predictive biology: modelling, understanding and harnessing microbial complexity.
    AJ Lopatkin and J Collins. Nature Microbiology Reviews (2020)

  12. 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. Science Advances (2020)

  13. Growth‐Stage‐Dependent Regulation of Conjugation.
    TA Sysoeva, YL Kim, J Rodriguez, AJ Lopatkin, L You. AlChE (2019)

  14. 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. Nature Microbiology (2019)

  15. Bacterial Metabolism and Antibiotic Efficacy.
    JM Stokes, AJ Lopatkin, MA Lobritz, JJ Collins. Cell Metabolism (2019)

  16. 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. Cell 177 (1-13) (2019)

  17. 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. Nature methods (2019)

  18. A unifying framework for interpreting and predicting mutualistic systems.
    F Wu, AJ Lopatkin, DA Needs, CT Lee, S Mukherjee, L You. Nature communications 1 (6), 16044 (2019)

  19. 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. Scientific advances 4 (12), eaau1873 (2018)

  20. Persistence and reversal of plasmid-mediated antibiotic resistance.
    AJ Lopatkin, HR Meredith, JK Srimani, C Pfeiffer, R Durrett, L You. Nature communications 8 (1), 1689 (2017)

  21. Drug detoxification dynamics explain the postantibiotic effect.
    JK Srimani, S Huang, AJ Lopatkin, L You. Molecular systems biology 13 (10), 948 (2017)

  22. 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. Scientific reports 7 (1), 440 (2017)

  23. Antibiotics as a selective driver for conjugation dynamics.
    AJ Lopatkin, S Huang, RP Smith, JK Srimani, TA Sysoeva, S Bewick, DK Karig, L You. Nature microbiology 1 (6), 16044 (2016)

  24. Elements of biological oscillations in time and space.
    Y Cao, AJ Lopatkin, L You. Nature structural & molecular biology 23 (12), 1030 (2016)

  25. Dissecting the effects of antibiotics on horizontal gene transfer: Analysis suggests a critical role of selection dynamics.
    AJ Lopatkin, TA Sysoeva, L You. Bioessays 38 (12), 1283-1292 (2016)

  26. Collective antibiotic tolerance: mechanisms, dynamics and intervention.
    HR Meredith, JK Srimani, AJ Lee, AJ Lopatkin, L You. Nature chemical biology 11 (3), 182 (2015)

  27. Dynamic control and quantification of bacterial population dynamics in droplets.
    S Huang, JK Srimani, AJ Lee, Y Zhang, AJ Lopatkin, KW Leong, L You. Biomaterials 61, 239-245 (2015)

  28. Bacterial temporal dynamics enable optimal design of antibiotic treatment.
    HR Meredith, AJ Lopatkin, DJ Anderson, L You. PLoS computational biology 11 (4), e1004201 (2015)

  29. 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. PLoS computational biology 11 (4), e1004203 3 (2015)

  30. Synthetic biology looks good on paper.
    AJ Lopatkin, L You. Cell 159 (4), 718-720 (2014)