32 papers.

Deep learning–enabled discovery of antibiotics effective against Neisseria gonorrhoeae

M. N. Anahtar, J. A. Valeri, S. M. Modaresi, A. Krishnan, N. M. Donghia, S. G. Palace, E. J. Zheng, A. Gulati, A. Jorgenson, A. Junaid, P. Bandyopadhyay, A. Luttens, K. Suresh, P. Edwards, F. Wong, Y. Zhang, D. Ritz, M. Gaborieau, E. Loh, M. Gaetani, M.-S. Aschtgen, A. A. Saei, Y. H. Grad, D. E. Ingber, and J. J. Collins

Science Translational Medicine 18, eads4699 (2026)

FATE-MAP predicts teratogenicity and human gastrulation failure modes by integrating deep learning and mechanistic modeling

J. Rufo, C. Qiu, D. Han, N. Baxter, G. Daley, J. Dhillon, F. Wong, J. J. Collins, and M. Z. Wilson

Nature Communications 17, 3327 (2026)

MONET — Virtual cell painting of brightfield images and time lapses using reference consistent diffusion

A. Peysakhovich, W. Berman, J. Rufo, F. Wong, and M. Z. Wilson

arXiv 2512.11928 (2025)

A generative deep learning approach to de novo antibiotic design

A. Krishnan*, M. N. Anahtar*, J. A. Valeri*, W. Jin, N. M. Donghia, L. Sieben, A. Luttens, Y. Zhang, M. Modaresi, A. Hennes, J. Fromer, P. Bandyopadhyay, J. C. Chen, D. Rehman, R. Desai, P. Edwards, R. S. Lach, M.-S. Aschtgen, M. Gaborieau, M. Gaetani, S. G. Palace, S. Omori, L. Khonde, Y. S. Moroz, B. Blough, C. Jin, E. Loh, Y. H. Grad, A. A. Saei, C. W. Coley, F. Wong, and J. J. Collins

Cell 188, 5962-5979.e22 (2025)

Optogenetics-enabled discovery of integrated stress response modulators

F. Wong*, A. Li*, S. Omori*, R. S. Lach*, J. Nunez, Y. Ren, S. P. Brown, V. Singhal, B. R. Lyda, T. Batjargal, E. Dickson, J. R. R. Reyes, J. M. U. Vargas, S. Wahane, H. Kim, J. J. Collins, and M. Z. Wilson

Cell 188, 4950-4967.e22 (2025)

An explainable deep learning platform for molecular discovery

F. Wong, S. Omori, A. Li, A. Krishnan, R. S. Lach, J. Ruffo, M. Z. Wilson, and J. J. Collins

Nature Protocols 20, 1020–1056 (2025)

Eating a way out of antibiotics

F. Wong

Nature Chemical Biology 21, 164–165 (2025)

Accurate RNA 3D structure prediction using a language model-based deep learning approach

T. Shen*, Z. Hu*, S. Sun*, D. Liu*, F. Wong, J. Wang, J. Chen, Y. Wang, L. Hong, J. Xiao, L. Zheng, T. Krishnamoorthi, I. King, S. Wang, P. Yin, J. J. Collins, and Y. Li

Nature Methods 21, 2287-2298 (2024)

Deep generative design of RNA aptamers using structural predictions

F. Wong*, D. He*, A. Krishnan, L. Hong, A. Z. Wang, J. Wang, Z. Hu, S. Omori, A. Li, J. Rao, Q. Yu, W. Jin, T. Zhang, K. Ilia, J. X. Chen, S. Zheng, I. King, Y. Li, and J. J. Collins

Nature Computational Science 4, 829-839 (2024)

Synthetic control of actin polymerization and symmetry breaking in active protocells

S. Razavi, F. Wong, B. Abubaker-Sharif, H. T. Matsubayashi, H. Nakamura, N. T. H. Nguyen, D. N. Robinson, B. Chen, P. A. Iglesias, and T. Inoue

Science Advances 10, adk9731 (2024)

Machine learning for antimicrobial peptide identification and design

F. Wan*, F. Wong*, J. J. Collins, and C. de la Fuente-Nunez

Nature Reviews Bioengineering 2, 392-407 (2024)

Discovery of a structural class of antibiotics with explainable deep learning

F. Wong*, E. J. Zheng*, J. A. Valeri, N. M. Donghia, M. N. Anahtar, S. Omori, A. Li, A. Cubillos-Ruiz, A. Krishnan, W. Jin, A. L. Manson, J. Friedrichs, R. Helbig, B. Hajian, D. K. Fiejtek, F. F. Wagner, H. H. Soutter, A. M. Earl, J. M. Stokes, L. D. Renner, and J. J. Collins

Nature 626, 177-185 (2024)

Discovery of antibiotics that selectively kill metabolically dormant bacteria

E. J. Zheng, J. A. Valeri, I. W. Andrews, A. Krishnan, P. Bandyopadhyay, M. N. Anahtar, A. Herneisen, F. Schulte, B. Linnehan, F. Wong, J. M. Stokes, L. D. Renner, S. Lourido, and J. J. Collins

Cell Chemical Biology 31, 712-728 (2024)

Leveraging artificial intelligence in the fight against infectious diseases

F. Wong, C. de la Fuente-Nunez, and J. J. Collins

Science 381, 164-170 (2023)

BioAutoMATED: An end-to-end automated machine learning tool for explanation and design of biological sequences

J. A. Valeri, L. R. Soenksen, K. M. Collins, P. Ramesh, G. Cai, R. Powers, N. M. Angenent-Mari, D. M. Camacho, F. Wong, T. K. Lu, and J. J. Collins

Cell Systems 14, 525-542 (2023)

Discovering small-molecule senolytics with deep neural networks

F. Wong*, S. Omori*, N. M. Donghia, E. J. Zheng, and J. J. Collins

Nature Aging 3, 734-750 (2023)

Benchmarking AlphaFold-enabled molecular docking predictions for antibiotic discovery

F. Wong*, A. Krishnan*, E. J. Zheng, H. Stärk, A. L. Manson, A. M. Earl, T. Jaakkola, and J. J. Collins

Molecular Systems Biology 18, e11081 (2022)

Reactive metabolic byproducts contribute to antibiotic lethality under anaerobic conditions

F. Wong, J. M. Stokes, S. C. Bening, C. Vidoudez, S. A. Trauger, and J. J. Collins

Molecular Cell 82, 3499-3512 (2022)

Increased energy demand from anabolic-catabolic processes drives β-lactam antibiotic lethality

M. A. Lobritz*, I. W. Andrews*, D. Braff, C. B. M. Porter, A. Gutierrez, Y. Furuta, L. B. G. Cortes, T. Ferrante, S. C. Bening, F. Wong, C. Gruber, C. Bakerlee, G. Lambert, G. C. Walker, D. J. Dwyer, and J. J. Collins

Cell Chemical Biology 29, 276-286 (2022)

Understanding beta-lactam-induced lysis at the single-cell level

F. Wong*, S. Wilson*, R. Helbig, S. Hegde, O. Aftenieva, H. Zheng, C. Liu, T. Pilizota, E. C. Garner, A. Amir, and L. D. Renner

Frontiers in Microbiology 12, 712007 (2021)

Cytoplasmic condensation induced by membrane damage is associated with antibiotic lethality

F. Wong, J. M. Stokes, B. Cervantes, S. Penkov, J. Friedrichs, L. D. Renner, and J. J. Collins

Nature Communications 12, 2321 (2021)

Allosteric conformational ensembles have unlimited capacity for integrating information

J. Biddle,* R. Martinez-Corral,* F. Wong, and J. Gunawardena

eLife 10, e65498 (2021)

Evidence that coronavirus superspreading is fat-tailed

F. Wong and J. J. Collins

Proceedings of the National Academy of Sciences USA 117, 29416-29418 (2020)

Gene regulation in and out of equilibrium

F. Wong and J. Gunawardena

Annual Reviews of Biophysics 49, 199-226 (2020). Full Text

Mechanics and dynamics of bacterial cell lysis

F. Wong and A. Amir

Biophysical Journal 116, 2378-2389 (2019)

Mechanics and dynamics of translocating MreB filaments on curved membranes

F. Wong, E. C. Garner, and A. Amir

eLife 8, e40472 (2019)

Structural conditions on complex networks for the Michaelis-Menten input-output response

F. Wong, A. Dutta, D. Chowdhury, and J. Gunawardena

Proceedings of the National Academy of Sciences USA 115, 9738-9743 (2018)

Energy-speed-accuracy relation in complex networks for biological discrimination

F. Wong, A. Amir, and J. Gunawardena

Physical Review E 98, 012420 (2018)

MreB filaments align along greatest principal membrane curvature to orient cell wall synthesis

S. Hussain*, C. N. Wivagg*, P. Szwedziak, F. Wong, K. Schaefer, T. Izoré, L. D. Renner, M. J. Holmes, Y. Sun, A. W. Bisson-Filho, S. Walker, A. Amir, J. Löwe, and E. C. Garner

eLife 7, e32471 (2018)

Mechanical strain sensing implicated in cell shape recovery in Escherichia coli

F. Wong*, L. D. Renner*, G. Özbaykal, J. Paulose, D. B. Weibel, S. van Teeffelen, and A. Amir

Nature Microbiology 2, 17115 (2017)

Information integration and energy expenditure in gene regulation

J. Estrada, F. Wong, A. DePace, and J. Gunawardena

Cell 166, 234-244 (2016)

A framework for modelling gene regulation which accommodates non-equilibrium mechanisms

T. Ahsendorf*, F. Wong*, R. Eils, and J. Gunawardena

BMC Biology 12, 102 (2014)

*Equal contributors