| A deep learning approach to antibiotic discovery JM Stokes, K Yang, K Swanson, W Jin, A Cubillos-Ruiz, NM Donghia, ... Cell 180 (4), 688-702. e13, 2020 | 1782 | 2020 |
| Bacterial metabolism and antibiotic efficacy JM Stokes, AJ Lopatkin, MA Lobritz, JJ Collins Cell metabolism 30 (2), 251-259, 2019 | 411 | 2019 |
| Pentamidine sensitizes Gram-negative pathogens to antibiotics and overcomes acquired colistin resistance JM Stokes, CR MacNair, B Ilyas, S French, JP Côté, C Bouwman, ... Nature microbiology 2 (5), 1-8, 2017 | 309 | 2017 |
| Overcoming mcr-1 mediated colistin resistance with colistin in combination with other antibiotics CR MacNair, JM Stokes, LA Carfrae, AA Fiebig-Comyn, BK Coombes, ... Nature communications 9 (1), 458, 2018 | 267 | 2018 |
| Clinically relevant mutations in core metabolic genes confer antibiotic resistance AJ Lopatkin, SC Bening, AL Manson, JM Stokes, MA Kohanski, ... Science 371 (6531), eaba0862, 2021 | 233 | 2021 |
| Bacterial metabolic state more accurately predicts antibiotic lethality than growth rate AJ Lopatkin, JM Stokes, EJ Zheng, JH Yang, MK Takahashi, L You, ... Nature microbiology 4 (12), 2109-2117, 2019 | 192 | 2019 |
| Deep learning-guided discovery of an antibiotic targeting Acinetobacter baumannii G Liu, DB Catacutan, K Rathod, K Swanson, W Jin, JC Mohammed, ... Nature Chemical Biology 19 (11), 1342-1350, 2023 | 125 | 2023 |
| Deep learning identifies synergistic drug combinations for treating COVID-19 W Jin, JM Stokes, RT Eastman, Z Itkin, AV Zakharov, JJ Collins, ... Proceedings of the National Academy of Sciences 118 (39), e2105070118, 2021 | 120 | 2021 |
| Bicarbonate alters bacterial susceptibility to antibiotics by targeting the proton motive force MA Farha, S French, JM Stokes, ED Brown ACS infectious diseases 4 (3), 382-390, 2017 | 115 | 2017 |
| Cold stress makes Escherichia coli susceptible to glycopeptide antibiotics by altering outer membrane integrity JM Stokes, S French, OG Ovchinnikova, C Bouwman, C Whitfield, ... Cell chemical biology 23 (2), 267-277, 2016 | 90 | 2016 |
| Discovery of a small molecule that inhibits bacterial ribosome biogenesis JM Stokes, JH Davis, CS Mangat, JR Williamson, ED Brown Elife 3, e03574, 2014 | 87 | 2014 |
| Eradicating bacterial persisters with combinations of strongly and weakly metabolism-dependent antibiotics EJ Zheng, JM Stokes, JJ Collins Cell chemical biology 27 (12), 1544-1552. e3, 2020 | 64 | 2020 |
| Cytoplasmic condensation induced by membrane damage is associated with antibiotic lethality F Wong, JM Stokes, B Cervantes, S Penkov, J Friedrichs, LD Renner, ... Nature communications 12 (1), 2321, 2021 | 60 | 2021 |
| Discovery of a structural class of antibiotics with explainable deep learning F Wong, EJ Zheng, JA Valeri, NM Donghia, MN Anahtar, S Omori, A Li, ... Nature 626 (7997), 177-185, 2024 | 43 | 2024 |
| A multiplexable assay for screening antibiotic lethality against drug-tolerant bacteria JM Stokes, A Gutierrez, AJ Lopatkin, IW Andrews, S French, I Matic, ... Nature Methods 16 (4), 303-306, 2019 | 35 | 2019 |
| Our evolving understanding of the mechanism of quinolones A Gutierrez, JM Stokes, I Matic Antibiotics 7 (2), 32, 2018 | 35 | 2018 |
| Bacteria Getting into Shape: Genetic Determinants of E. coli Morphology S French, JP Côté, JM Stokes, R Truant, ED Brown MBio 8 (2), 10.1128/mbio. 01977-16, 2017 | 26 | 2017 |
| Antibiotic discovery in the artificial intelligence era T Lluka, JM Stokes Annals of the New York Academy of Sciences 1519 (1), 74-93, 2023 | 22 | 2023 |
| Bicarbonate alters bacterial susceptibility to antibiotics by targeting the proton motive force. ACS Infect Dis 4: 382–390 MA Farha, S French, JM Stokes, ED Brown | 21 | 2018 |
| Pentamidine sensitizes Gram-negative pathogens to antibiotics and overcomes acquired colistin resistance. Nat Microbiol 2: 17028 JM Stokes, CR MacNair, B Ilyas, S French, JP Côté, C Bouwman, ... | 21 | 2017 |
