Faculty

Selected Honors and Awards

NSF CAREER Award (2025)
Pew Biomedical Scholars (2024)
Edward Mallinckrodt Jr. Foundation Award (2023)
NIH R35 Maximizing Investigators’’ Research Award (MIRA) (2023)
NIH R15 Research Enhancement Award (REA) (2021)
NSF Research in Undergraduate Institutions Award (2021)
Keewaunee Student Achievement Award, Duke University (2017)
ACS Synthetic biology second place poster prize, Winter qBio (2015)
Howard G. Clark Graduate Research Grant, Duke University (2014 – 2015)

Courses

CHE 116: Numerical Methods and Stats

CHE 436: Introduction to Systems and Synthetic Biology

Recent Publications

Ahmad, M.; Prensky, H.; Balestrieri, J.; ElNaggar, S.; Gomez-Simmonds, A.; Uhlemann, A.C.; Traxler, B.; Singh, A.; Lopatkin, A.J., "Tradeoff between lag time and growth rate drives the plasmid acquisition cost," Nature Communications, 2023, doi.org/10.1038/s41467-023-38022-6

Palomino, A.; Gewurz, D.; DeVine, L.; Zajmi, U.; Moralez, J.; Abu-Rumman, F.; Smith, R.P.; Lopatkin, A.J.,"Metabolic genes on conjugative plasmids are highly prevalent inEscherichia coliand can protect against antibiotic treatment," Nature ISME Journal, 2022. doi.org/10.1038/s41396-022-01329-1

Gomez-Simmonds, A.; Annavajhala, M.K.; Tang, N.; Rozenberg, F.D.; Ahmad, M.; Park, H.; Lopatkin, A.J.; Uhlemann, A.C., “Population structure of blaKPC-harbouring incN plasmids at a New York City medical center and evidence for multi-species horizontal transmission,” Journal of Antimicrobial Chemotherapy, 2022. doi: 10.1093/jac/dkac114

Persons, J.; Abhilash, L.; Lopatkin, A.J.; Roelofs, A.; Bell, E.V.; Fernandez, M.P.; Shafer III, O.T., “PHASE: A MATLAB based program for the analysis of Drosophila phase, activity, and sleep under entrainment,” bioRxiv, 2021. doi: 10.1101/2021.12.14.472617

Koong, J.; Johnson, C.; Rafei, R.; Hamze, M.; Myers, G.S.A.; Lopatkin, A.J.; Hamidian, M., “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,” Microbial Genomics, 2021. doi: 10.1099/mgen.0.000705

Shoen, M.E.; Jahne, M.A.; Garland, J.; Ramirez, L.; Lopatkin, A.J.; Hamilton, K., “Quantitative microbial risk assessment of antibacterial resistant and susceptible Staphylococcus aureus in reclaimed wastewater,” Environmental Science & Technology,2021. doi: 10.1021/acs.est.1c04038

Moralez, J.; Szenkiel, K.; Hamilton, K.; Pruden, A.; Lopatkin, A.J., “Quantitative analysis of horizontal gene transfer in complex systems,” Current Opinions in Microbiology, 2021. doi: 10.1016/j.mib.2021.05.001

Williams, S.C.; Forsberg, A.P.; Lee, J.; Vizcarra, C.; Lopatkin, A.J.; Austin, R.N., “Investigation of the prevalence and catalytic activity of fused-rubredoxin alkane monooxygenases (AlkBs),” Journal of Inorganic Biochemistry, 2021.doi: 10.1016/j.jinorgbio.2021.111409

Prensky, H.; Gomez-Simmonds, A.; Uhlemann, A.C.; Lopatkin, A.J., “Conjugation dynamics depend on both the plasmid acquisition cost and the fitness cost,” Molecular Systems Biology, 2021. doi: 10.1525/msb.20209913

Lopatkin, A.J.; Bening, S.C.; Manson, A.L.; Stokes, J.M.; Kohanski, M.A.; Badram, A. H.; Earl, A.M.; Cheney, N.J.; Yang, J.H.; Collins, J.J., "Clinically relevant mutations in core metabolic genes confer antibiotic resistance,” Science, 2021. doi: 10.1126/science.aba0862

Lopatkin, A.J.; Yang, J.H., “Nucleotide metabolism and antibiotic treatment failure,” Frontiers in Microbiology, 2021. doi: 10.3389/fdgth.2021.583468

Lopatkin, A.J.; Collins, J.J., “Predictive biology: modeling, understanding, and harnessing microbial complexity,” Nature Microbiology Reviews, 2020. doi: 10.1038/s41579-020-0372-5