Allison Lopatkin
Assistant Professor of Biological Sciences
Department
Biology
Office
1014 Altschul Hall
Office Hours: Mondays 12 - 2 pm
Contact
alopatkin@barnard.edu
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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
Data Science Institute, Columbia University, Affiliated Faculty
Evolutionary Genomics group, Columbia University, Member
American Society for Microbiology, Member
A. J. Lopatkin and J. J. Collins. “Predictive biology: modeling, understanding, and harnessing microbial complexity,” Nature Microbiology Reviews (2020). doi: https://doi.org/10.1038/s41579-020-0372-5
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
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.
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
J. M. Stokes, A. J. Lopatkin, M. A. Lobritz, J. J. Collins. “Bacterial Metabolism and Antibiotic Efficacy,” Cell Metabolism (2019). doi: https://doi.org/10.1016/j.cmet.2019.06.009
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: https://doi.org/10.1016/j.cell.2019.04.016
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
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
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
A. J. Lopatkin and L. You, “Synthetic biology looks good on paper,” Cell, vol. 159, no. 4, pp. 718–720 (2014). doi: http://dx.doi.org/10.1016/j.cell.2014.10.003.
In The News
Professors María de la Paz Fernández and Allison Lopatkin Publish Journal Article about a Research Tool they Developed to Solve a Problem Central to Circadian Biology
July 7, 2022
Professor Allison Lopatkin Receives Research Grant from the National Institutes of Health (NIH) for Collaborative Project with Nova Southeastern University
March 11, 2022
Professor Jonathan Snow, Alongside Several Barnard Affiliates, Publishes New Research on Biomarkers of Stress in Honey Bees
November 18, 2021
Professor Allison Lopatkin Publishes New Research on Infection Risks and Disease Burdens from Exposures in Wastewaters
November 4, 2021
Meet the New Faces on the 10th Floor!
Today, we sat down to chat with the two new faces on the 10th floor of Altschul: Mehrose Ahmad (BC '21) and Corey Marshalleck. As lab technicians for Professors Allison Lopatkin and Jon Snow respectively, Mehrose and Corey discuss research, mentorship, and life outside of Altschul.?
September 27, 2021
Professors Jonathan Snow, JJ Miranda, Allison Lopatkin, and Jennifer Mansfield Publish New Research on How Thermal Stress Affects Honey Bee Digestion
September 10, 2021
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