Allison Lopatkin

Assistant Professor of Biological Sciences




1014 Altschul Hall
Office Hours: Mondays 12 - 2 pm


Research in the Lopatkin lab focuses on understanding how bacterial metabolism contributes to the spread of antibiotic resistance. We do this using a combination of systems and synthetic biology: predictive mathematical modeling with experimental validation. The ultimate goal is to elucidate key underlying principles that govern the spread of resistance in microbial populations so that we can leverage these dynamics to develop effective therapeutic strategies.

  • University of Rochester, B.S.
  • Duke University, Ph.D
  • MIT; Broad Institute of MIT & Harvard, Postdoctoral Scholar

  • Microbiology
  • Systems and synthetic biology
  • Mathematical modeling
  • Evolution of antibiotic resistance

  • BIOL BC2500 MATLAB for Scientists 
  • BIOL BC3590 Senior Seminar in Biology: Bacteria by Design

  1. A. J. Lopatkin and J. J. Collins. “Predictive biology: modeling, understanding, and harnessing microbial complexity,” Nature Microbiology Reviews (2020). doi:
  2. J. Bethke, A. Davidovich, L. Cheng, A.J. Lopatkin, J. T. Thaden, V. G. Fowler Jr., M Xiao, and L. You. “Environmental and genetic determinants of plasmid mobility in pathogenic Escherichia Coli,” Science Advances (2020). doi: 10.1126/sciadv.aax3173
  3. T. Sysoeva, Y. L. Kim, J. Rodriguez, A. J. Lopatkin, and L. You. “Growth-stage dependent regulation of conjugation,” AlChE Journal (2019). doi: 10.1002/aic.16848.
  4. A. J. Lopatkin, J. Stokes, E. Zheng, J. H. Yang, M. Takahashi, L. You, and J. Collins. “Bacterial metabolic state more accurately predicts antibiotic lethality than growth rate,” Nature Microbiology (2019). doi: 10.1038/s41564-019-0536-0
  5. J. M. Stokes, A. J. Lopatkin, M. A. Lobritz, J. J. Collins. “Bacterial Metabolism and Antibiotic Efficacy,” Cell Metabolism (2019). doi:
  6. J. H. Yang, S. N. Wright*, M. Hamblin*, D. McCloskey, M. A. Alcantar, L. Schrubbers, A. J. Lopatkin, S. Satish, A. Nili, J. J. Collins. “A white-box machine learning approach for revealing antibiotic mechanisms of action,” Cell (2019). doi:
  7. J. Stokes*, A. Gutierrez*, A. J. Lopatkin, I. Andersson, and J. Collins. “A high-throughput killing assay for screening antibiotic lethality,” Nature Methods (2019). 10.1038/s41592-019-0333-y
  8. F. Wu, A. J. Lopatkin, D. Needs, C. Lee, S. Mukherjee, and L. You. “A unifying framework for interpreting and predicting mutualistic systems,” Nature Communications (2019). doi: 10.1038/s41467-018-08188-5
  9. H. R. Meredith, V. Andreani, A. J. Lee, A. J. Lopatkin, G. Batt, and L. You. “Differentiating resilience and resistance informs how to manipulate bacterial antibiotic response.” Science Advances (2018). doi: 10.1126/sciadv.aau1873.
  10. J. K. Srimani, S. Huang, A. J. Lopatkin, and L. You. “Drug detoxification dynamics explain the postantibiotic effect.” Molecular System Biology, vol. 13, p. 948 (2017). doi: 10.15252/msb.20177723.
  11. A. J. Lopatkin, H. R. Meredith, J. K. Srimani, C. Pfeiffer, R. Durrett, and L. You, “Promotion and reversal of plasmid-mediated antibiotic resistance.” Nature Communications, vol. 8, p. 1689 (2017). doi: 10.1038/s41467-017-01532-1.
  12. C. E. Wilson, A. J. Lopatkin, T. J. A. Craddock, W. Driscoll, Omar T. Eldakar, Jose V. Lopez and R. P. Smith. “Cooperation and competition shape ecological resistance during periodic spatial disturbance of engineered bacteria.” Scientific Reports, vol. 7, p. 440 (2017). doi:10.1038/s41598-017-00588-9.
  13. Y. Cao*, A. J. Lopatkin* and L. You. “Elements of biological oscillations in time and space,” Nature Structural & Molecular Biology, vol. 23, p. 1030-1034 (2016). doi:10.1038/nsmb.3320.
  14. A. J. Lopatkin, T. A. Sysoeva, L. You, “Dissecting the effects of antibiotics on horizontal gene transfer: Analysis suggests a critical role of selection dynamics,” Bioessays, vol. 38, p. 1283-1292 (2016). doi: 10.1002/bies.201600133.
  15. A. J. Lopatkin, S. Huang, R. P. Smith, J. K. Srimani, T. A. Sysoeva, S. Bewick, D. K. Karig, and L. You, “Antibiotics as a selective driver for conjugation dynamics,” Nature Microbiology, p. 16044 (2016). doi: 10.1038/nmicrobiol.2016.44.
  16. S. Huang, J. K. Srimani, A. J. Lee, Y. Zhang, A. J. Lopatkin, K. W. Leong, and L. You, “Dynamic control and quantification of bacterial population dynamics in droplets,” Biomaterials, vol. 61, pp. 239–45 (2015). doi: 10.1016/j.biomaterials.2015.05.038.
  17. T. J. Lee, J. Wong, S. Bae, A. J. Lee, A. Lopatkin, F. Yuan, and L. You, “A power-law dependence of bacterial invasion on Mammalian host receptors,” PLoS Comput. Biol., vol. 11, no. 4, p. e1004203 (2015). doi: 10.1016/j.micinf.2008.07.004.
  18. H. R. Meredith, A. J. Lopatkin, D. J. Anderson, and L. You, “Bacterial Temporal Dynamics Enable Optimal Design of Antibiotic Treatment,” PLoS Comput Biol, vol. 11, no. 4, p. e1004201 (2015). doi: 10.1371/journal.pcbi.1004201.
  19. H. R. Meredith, J. K. Srimani, A. J. Lee, A. J. Lopatkin, and L. You, “Collective antibiotic tolerance: mechanisms, dynamics and intervention,” Nat Chem Biol, vol. 11, no. 3, pp. 182–188 (2015). doi: 10.1038/nchembio.1754.
  20. A. J. Lopatkin and L. You, “Synthetic biology looks good on paper,” Cell, vol. 159, no. 4, pp. 718–720 (2014). doi:

In The News

This year, U.S. Antibiotic Awareness Week takes place Nov 18–24. Dr. Allison Lopatkin, who investigates the mechanisms underlying the evolution of antibiotic resistance and joined the Department of Biological Sciences at the start of this year, joins us today to discuss her work, computational biology more broadly, and mentoring in the lab.

November 18, 2020