Catacutan DB*, Alexander J*, Arnold A, Stokes JM. Machine learning in preclinical drug discovery. Nature Chemical Biology (2024). PDF

Swanson K*, Liu G*, Catacutan DB, Arnold A, Zou J**, Stokes JM**. Generative AI for designing and validating easily synthesizable and structurally novel antibiotics. Nature Machine Intelligence (2024). PDF

Wong F*, Zheng EJ*, Valeri JA, Donghia NM, Anahtar MN, Omori S, Li A, Cubillos-Ruiz A, Krishnan A, Jin W, Manson AL, Friedrichs J, Helbig R, Hajian B, Fietjek DK, Wagner FF, Soutter HH, Earl AM, Stokes JM, Renner LD, Collins JJ. Discovery of a structural class of antibiotics with explainable deep learning. Nature (2023). PDF

Sarkar N, Stokes JM. Practical applications of machine learning for anti-infective drug discovery ACS Medicinal Chemistry Reviews 345-375 (2023). PDF

Zheng EJ*, Valeri, JA*, Andrews IW*, Krishnan A, Bandyopadhyay P, Anahtar MN, Herneisen A, Schulte F, Linnehan B, Wong F, Stokes JM, Renner LD, Lourido S, Collins JJ. Discovery of antibiotics that selectively kill metabolically dormant bacteria. Cell Chemical Biology S2451-9456(23)00387-2 (2023). PDF

Arnold A*, Alexander J*, Liu G, Stokes JM. Applications of machine learning in microbial natural product drug discovery. Expert Opinion on Drug Discovery 11, 1259-1272 (2023). PDF

Liu G*, Catacutan B*, Rathod K*, Swanson K, Jin W, Mohammed JC, Chiappino-Pepe A, Syed SA, Fragis M, Rachwalski K, Magolan J, Surette MG, Coombes BK, Jaakkola T, Barzilay R, Collins JJ, Stokes JM. Deep learning-guided discovery of a narrow-spectrum antibiotic against Acinetobacter baumannii. Nature Chemical Biology 11, 1342-1350 (2023). PDF

Lluka T, Stokes JM. Antibiotic discovery in the artificial intelligence era. Annals of the New York Academy of Sciences 1519, 74-93 (2023). PDF

Wong F, Stokes JM, Bening SC, Vidoudez C, Trader SA, Collins JJ. Reactive metabolic byproducts contribute to antibiotic lethality under anaerobic conditions. Molecular Cell 82, 3499-3512 (2022). PDF

Liu G, Stokes JM. A brief guide to machine learning for antibiotic discovery. Current Opinion in Microbiology 69, 102190 (2022). PDF

Jin W, Stokes JM, Eastman ET, Itkin ZZ, Zakharov AV, Collins JJ, Jaakkola TS, Barzilay R. Deep learning identifies synergistic drug combinations for treating COVID-19. PNAS 118, e2105070118 (2021). PDF

Wong F, Stokes JM, Cervantes B, Friedrichs J, Renner LD, Collins JJ. Cytoplasmic condensation induced by membrane damage is associated with antibiotic lethality. Nature Communications 12, 2321 (2021). PDF

Lopatkin AJ, Bening SC, Manson AL, Stokes JM, Kohanski MA, Badran AH, Earl AM, Cheney NJ, Yang JH, Collins JJ. Clinically relevant mutations in core metabolic genes confer antibiotic resistance. Science 371, eaba0862 (2021). PDF

Zheng EJ, Stokes JM*, Collins JJ*. Eradicating bacterial persisters with combinations of strongly and weakly metabolism-dependent antibiotics. Cell Chemical Biology 27, 1544-1552.e3 (2020). PDF

Stokes JM, Yang K*, Swanson K*, Jin W, Cubillos-Ruiz A, Donghia NM, MacNair CR, French S, Carfrae LA, Bloom-Ackermann Z, Tran VM, Chiappino-Pepe A, Badran AH, Andrews IW, Chory EJ, Church GM, Brown ED, Jaakkola TS, Barzilay R, Collins JJ. A deep learning approach to antibiotic discovery. Cell 180, 688-702 (2020). Cover article. PDF

Lopatkin AJ, Stokes JM, Zheng EJ, Yang J, Takahashi MK, You L, Collins JJ. Antibiotic lethality is better correlated with metabolic state than growth rate. Nature Microbiology 4, 2109-2117 (2019). PDF

Stokes JM, Lopatkin AJ, Lobritz MA, Collins JJ. Bacterial metabolism and antibiotic efficacy. Cell Metabolism 30, 251-259 (2019). PDF

Stokes JM*, Gutierrez A*, Lopatkin AJ, Andrews IW, French S, Matic I, Brown ED, Collins JJ. A multiplexable assay for screening antibiotic lethality against drug-tolerant bacteria. Nature Methods 16, 303-306 (2019). PDF

Gutierrez A*, Stokes JM*, Matic I. Our evolving understanding of the mechanism of quinolones. Antibiotics 7, 32 (2018). PDF

MacNair CR, Stokes JM, Carfrae LA, Mulvey MR, Brown ED. Overcoming mcr-1 mediated colistin resistance with colistin in combination with other antibiotics. Nature Communications 9, 458 (2018). PDF

Farha MA, French S, Stokes JM, Brown ED. Bicarbonate alters bacterial susceptibility to antibiotics by targeting the proton motive force. ACS Infectious Diseases 7b00194 (2018). PDF

Stokes JM, MacNair CR, Ilyas B, French S, Cote JP, Bouwman C, Farha MA, Sieron AO, Whitfield C, Coombes BK, Brown ED. Pentamidine sensitizes Gram-negative pathogens to antibiotics and overcomes acquired colistin resistance. Nature Microbiology 2:17028 (2017). PDF

French S*, Cote JP*, Stokes JM, Truant R, Brown ED. Bacteria getting into shape: genetic determinants of E. coli morphology. mBio 8, e01977-16 (2017). PDF

MacNair CR, Stokes JM, French S, Myers C, Iyer KR, Brown ED. A cell-based approach to characterize antimicrobial compounds through kinetic dose-response. Bioorganic and Medicinal Chemistry 24, 6315-6319 (2016). PDF

Stokes JM, French S, Ovchinnikova OG, Bouwman C, Whitfield C, Brown ED. Cold stress makes Escherichia coli susceptible to glycopeptide antibiotics by altering outer membrane integrity. Cell Chemical Biology 23, 267-277 (2016). PDF

Stokes JM, Brown ED. Chemical modulators of ribosome biogenesis as biological probes. Nature Chemical Biology 11, 924-932 (2015). PDF

Stokes JM, Selin C, Cardona ST, Brown ED. Chemical inhibition of bacterial ribosome biogenesis shows efficacy in a worm infection model. Antimicrobial Agents and Chemotherapy 59, 2918-2920 (2015). PDF

Stokes JM, Davis JH, Mangat CS, Williamson JR, Brown ED. Discovery of a small molecule that inhibits bacterial ribosome biogenesis. eLife 3, e03574 (2014). Cover article. PDF