Felix Wong, MIT

Publications

  1. 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). PDF
  2. Eating a way out of antibiotics
    F. Wong
    Nature Chemical Biology 21, 164–165 (2025). PDF
  3. 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). PDF
  4. 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). PDF
  5. 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). PDF
  6. 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). PDF
  7. 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). PDF
    Press Release | Nature Research Briefing (PDF) | MIT News | Broad Institute News | Wyss Institute News | IPFDD News | New York Times - Hard Fork Interview | Scientific American | The New Yorker | Nature Reviews Drug Discovery | Nature Computational Science | The Lancet Infectious Diseases | Ground Truths | GEN | New Scientist | Interesting Engineering | Medscape | Fierce Biotech | BioWorld | BioSpace | Bio-IT World | The Microbiologist | C&EN | American Council on Science and Health | Yale Scientific Magazine | Le Monde | Euronews | Corriere della Sera | Público | La Opinión | Mirror | Yohap News | The Korea Times | The Hindu | DeepLearning.AI | BioWorld 生物世界 | Yicai 第一财经 | AI Era 新智元 | Chinese Academy of Sciences 中国科学报 | 甲子光年
  8. 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). PDF
  9. 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). PDF
    Science Special Issue Press Release
  10. 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). PDF
    MIT News | Wyss Institute News | GEN
  11. 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). PDF
    Press Release | Nature Aging Research Briefing (PDF) | MIT Technology Review China (科技评论) Interview | Translating Aging Podcast Interview | Medscape | BioWorld | The Boston Globe | BioSpace | BioCentury | GEN | Freethink | Biocompare | Lifespan.io | Longevity.Technology | Fight Aging! | Bioengineer.org | Bionity.com | Earth.com | The Economic Times | Esquire | Bangalore Mirror | La Opinión | Forskning.no | eBiotrade (生物通) | synbio深波 | 生辉 (SciPhi) | Sing Tao Daily (星島日報) | WuXi AppTec (药明康德​) | 南方都市报 | Asharq Al-Awsat (الشرق الأوسط) | National Geographic Indonesia
  12. 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). PDF
    MIT News | NIH Director's Blog | Science: In the Pipeline | Biocompare | The Medicine Maker | The Register | The Conversation | AI Magazine | Cosmos Magazine | Medical News | BioTechniques | AI Tech Talk (AI科技评论) | SciTouTiao (学术头条)
  13. 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). PDF
  14. 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). PDF
  15. 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). PDF
  16. 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). PDF
    Nature Microbiology Community: Behind the Paper | Editors' Highlight
  17. Allosteric conformational ensembles have unlimited capacity for integrating information
    J. Biddle,* R. Martinez-Corral,* F. Wong, and J. Gunawardena
    eLife 10, e65498 (2021). PDF
  18. 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). PDF
    PNAS "Most Read" Article, November 2020
    MIT News | WBUR CommonHealth Interview | Radio-Canada Interview | WCVB Boston Interview | The Washington Post | AFP News | France 24 | World Economic Forum | NPR | MIT Technology Review | Slate.fr | WIRED Italy | Business Insider Germany | Business Insider Spain | Medical News Today | Medical Xpress | Washington City Paper | STAT News | Exame | RTL | n-tv | Deutsches Ärzteblatt | MDR Wissen Germany | Münchner Merkur | Wiener Zeitung | La Provence | Radio Sarajevo | TimesLIVE | La Nación | El Universo | El País Uruguay | Diario Panorama | La Prensa Gráfica | Los Tiempos | SAPO | Večernji List | The Times of India | Hindustan Times | The Tribune India | ScienceAlert | RFI | Barron's | Gulf News | News.com.au | Donga Science (과학동아) | Japan Today | The Japan Times
  19. Gene regulation in and out of equilibrium
    F. Wong and J. Gunawardena
    Annual Reviews of Biophysics 49, 199-226 (2020). Full Text
  20. Mechanics and dynamics of bacterial cell lysis
    F. Wong and A. Amir
    Biophysical Journal 116, 2378-2389 (2019). PDF
    BPS Blog: Modeling Lysis | BPS Blog: My Favorite Biophysical Journal Papers of 2019
  21. Mechanics and dynamics of translocating MreB filaments on curved membranes
    F. Wong, E. C. Garner, and A. Amir
    eLife 8, e40472 (2019). PDF
  22. 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). PDF
  23. Energy-speed-accuracy relation in complex networks for biological discrimination
    F. Wong, A. Amir, and J. Gunawardena
    Physical Review E 98, 012420 (2018). PDF
  24. 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). PDF
  25. 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). PDF
    Harvard SEAS News | Nature Microbiology Community: Behind the Paper | Biophysical Journal Poster Prize | GEN
  26. Information integration and energy expenditure in gene regulation
    J. Estrada, F. Wong, A. DePace, and J. Gunawardena
    Cell 166, 234-244 (2016). PDF
  27. 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). PDF
    BMC Biology Commentary
    *Equal contributors