How to build the virtual cell with artificial intelligence: Priorities and opportunities

Charlotte Bunne; Yusuf Roohani; Yanay Rosen; Ankit Gupta; Xikun Zhang; Marcel Roed; Theo Alexandrov; Mohammed AlQuraishi; Patricia Brennan; Daniel B. Burkhardt; Andrea Califano; Jonah Cool; Abby F. Dernburg; Kirsty Ewing; Emily B. Fox; Matthias Haury; Amy E. Herr; Eric Horvitz; Patrick D. Hsu; Viren Jain; Gregory R. Johnson; Thomas Kalil; David R. Kelley; Shana O. Kelley; Anna Kreshuk; Tim Mitchison; Stephani Otte; Jay Shendure; Nicholas J. Sofroniew; Fabian Theis; Christina V. Theodoris; Srigokul Upadhyayula; Marc Valer; Bo Wang; Eric Xing; Serena Yeung-Levy; Marinka Zitnik; Theofanis Karaletsos; Aviv Regev; Emma Lundberg; Jure Leskovec; Stephen R. Quake

doi:10.1016/j.cell.2024.11.015

How to build the virtual cell with artificial intelligence: Priorities and opportunities

Charlotte Bunne
, Yusuf Roohani
, Yanay Rosen
, Ankit Gupta
, Xikun Zhang
, Marcel Roed
, Theo Alexandrov
, Mohammed AlQuraishi
, Patricia Brennan
, Daniel B. Burkhardt
, Andrea Califano
, Jonah Cool
, Abby F. Dernburg
, Kirsty Ewing
, Emily B. Fox
, Matthias Haury
, Amy E. Herr
, Eric Horvitz
, Patrick D. Hsu
, Viren Jain

Gregory R. Johnson, Thomas Kalil, David R. Kelley, Shana O. Kelley, Anna Kreshuk, Tim Mitchison, Stephani Otte, Jay Shendure, Nicholas J. Sofroniew, Fabian Theis, Christina V. Theodoris, Srigokul Upadhyayula, Marc Valer, Bo Wang, Eric Xing, Serena Yeung-Levy, Marinka Zitnik, Theofanis Karaletsos, Aviv Regev, Emma Lundberg, Jure Leskovec, Stephen R. Quake

Chair of Mathematical Modelling of Biological Systems

Stanford University
Genentech, Inc
Chan Zuckerberg Initiative
École Polytechnique Fédérale de Lausanne (EPFL)
Arc Institute
Center for Autonomous Systems
Department of Bioengineering
Department of Pharmacology
Department of Bioengineering
Cellarity, Inc.
Columbia University
Vagelos College of Physicians and Surgeons
Chan Zuckerberg Biohub New York
University of California at Berkeley
Chan Zuckerberg Biohub
Chan Zuckerberg Institute for Advanced Biological Imaging
Department of Bioengineering
Microsoft Research
Center for Computational Biology
Google Inc
NewLimit
Schmidt Futures
Calico Life Sciences LLC
Chan Zuckerberg Biohub Chicago
Northwestern University
European Molecular Biology Laboratory Heidelberg
Harvard Medical School
University of Washington School of Medicine
Brotman Baty Institute for Precision Medicine
Seattle Hub for Synthetic Biology
Howard Hughes Medical Institute
PBC
Helmholtz Zentrum München German Research Center for Environmental Health
Gladstone Institute of Cardiovascular Disease
University of California San Francisco
Lawrence Berkeley National Laboratory
University of Toronto
Vector Institute
Carnegie Mellon University
Mohamed Bin Zayed University of Artificial Intelligence
The Broad Institute of MIT and Harvard
Stanford University School of Medicine

Research output: Contribution to journal › Review article › peer-review

192 Scopus citations

Abstract

Cells are essential to understanding health and disease, yet traditional models fall short of modeling and simulating their function and behavior. Advances in AI and omics offer groundbreaking opportunities to create an AI virtual cell (AIVC), a multi-scale, multi-modal large-neural-network-based model that can represent and simulate the behavior of molecules, cells, and tissues across diverse states. This Perspective provides a vision on their design and how collaborative efforts to build AIVCs will transform biological research by allowing high-fidelity simulations, accelerating discoveries, and guiding experimental studies, offering new opportunities for understanding cellular functions and fostering interdisciplinary collaborations in open science.

Original language	English
Pages (from-to)	7045-7063
Number of pages	19
Journal	Cell
Volume	187
Issue number	25
DOIs	https://doi.org/10.1016/j.cell.2024.11.015
State	Published - 12 Dec 2024

Keywords

AI
ML
cell biology
virtual cell

Access to Document

10.1016/j.cell.2024.11.015

Cite this

Bunne, C., Roohani, Y., Rosen, Y., Gupta, A., Zhang, X., Roed, M., Alexandrov, T., AlQuraishi, M., Brennan, P., Burkhardt, D. B., Califano, A., Cool, J., Dernburg, A. F., Ewing, K., Fox, E. B., Haury, M., Herr, A. E., Horvitz, E., Hsu, P. D., ... Quake, S. R. (2024). How to build the virtual cell with artificial intelligence: Priorities and opportunities. Cell, 187(25), 7045-7063. https://doi.org/10.1016/j.cell.2024.11.015

@article{cb6a5c3bf7e54b4588dd1b12ffe41463,

title = "How to build the virtual cell with artificial intelligence: Priorities and opportunities",

abstract = "Cells are essential to understanding health and disease, yet traditional models fall short of modeling and simulating their function and behavior. Advances in AI and omics offer groundbreaking opportunities to create an AI virtual cell (AIVC), a multi-scale, multi-modal large-neural-network-based model that can represent and simulate the behavior of molecules, cells, and tissues across diverse states. This Perspective provides a vision on their design and how collaborative efforts to build AIVCs will transform biological research by allowing high-fidelity simulations, accelerating discoveries, and guiding experimental studies, offering new opportunities for understanding cellular functions and fostering interdisciplinary collaborations in open science.",

keywords = "AI, ML, cell biology, virtual cell",

author = "Charlotte Bunne and Yusuf Roohani and Yanay Rosen and Ankit Gupta and Xikun Zhang and Marcel Roed and Theo Alexandrov and Mohammed AlQuraishi and Patricia Brennan and Burkhardt, \{Daniel B.\} and Andrea Califano and Jonah Cool and Dernburg, \{Abby F.\} and Kirsty Ewing and Fox, \{Emily B.\} and Matthias Haury and Herr, \{Amy E.\} and Eric Horvitz and Hsu, \{Patrick D.\} and Viren Jain and Johnson, \{Gregory R.\} and Thomas Kalil and Kelley, \{David R.\} and Kelley, \{Shana O.\} and Anna Kreshuk and Tim Mitchison and Stephani Otte and Jay Shendure and Sofroniew, \{Nicholas J.\} and Fabian Theis and Theodoris, \{Christina V.\} and Srigokul Upadhyayula and Marc Valer and Bo Wang and Eric Xing and Serena Yeung-Levy and Marinka Zitnik and Theofanis Karaletsos and Aviv Regev and Emma Lundberg and Jure Leskovec and Quake, \{Stephen R.\}",

note = "Publisher Copyright: {\textcopyright} 2024 The Authors",

year = "2024",

month = dec,

day = "12",

doi = "10.1016/j.cell.2024.11.015",

language = "English",

volume = "187",

pages = "7045--7063",

journal = "Cell",

issn = "0092-8674",

publisher = "Elsevier B.V.",

number = "25",

}

Bunne, C, Roohani, Y, Rosen, Y, Gupta, A, Zhang, X, Roed, M, Alexandrov, T, AlQuraishi, M, Brennan, P, Burkhardt, DB, Califano, A, Cool, J, Dernburg, AF, Ewing, K, Fox, EB, Haury, M, Herr, AE, Horvitz, E, Hsu, PD, Jain, V, Johnson, GR, Kalil, T, Kelley, DR, Kelley, SO, Kreshuk, A, Mitchison, T, Otte, S, Shendure, J, Sofroniew, NJ, Theis, F, Theodoris, CV, Upadhyayula, S, Valer, M, Wang, B, Xing, E, Yeung-Levy, S, Zitnik, M, Karaletsos, T, Regev, A, Lundberg, E, Leskovec, J & Quake, SR 2024, 'How to build the virtual cell with artificial intelligence: Priorities and opportunities', Cell, vol. 187, no. 25, pp. 7045-7063. https://doi.org/10.1016/j.cell.2024.11.015

TY - JOUR

T1 - How to build the virtual cell with artificial intelligence

T2 - Priorities and opportunities

AU - Bunne, Charlotte

AU - Roohani, Yusuf

AU - Rosen, Yanay

AU - Gupta, Ankit

AU - Zhang, Xikun

AU - Roed, Marcel

AU - Alexandrov, Theo

AU - AlQuraishi, Mohammed

AU - Brennan, Patricia

AU - Burkhardt, Daniel B.

AU - Califano, Andrea

AU - Cool, Jonah

AU - Dernburg, Abby F.

AU - Ewing, Kirsty

AU - Fox, Emily B.

AU - Haury, Matthias

AU - Herr, Amy E.

AU - Horvitz, Eric

AU - Hsu, Patrick D.

AU - Jain, Viren

AU - Johnson, Gregory R.

AU - Kalil, Thomas

AU - Kelley, David R.

AU - Kelley, Shana O.

AU - Kreshuk, Anna

AU - Mitchison, Tim

AU - Otte, Stephani

AU - Shendure, Jay

AU - Sofroniew, Nicholas J.

AU - Theis, Fabian

AU - Theodoris, Christina V.

AU - Upadhyayula, Srigokul

AU - Valer, Marc

AU - Wang, Bo

AU - Xing, Eric

AU - Yeung-Levy, Serena

AU - Zitnik, Marinka

AU - Karaletsos, Theofanis

AU - Regev, Aviv

AU - Lundberg, Emma

AU - Leskovec, Jure

AU - Quake, Stephen R.

PY - 2024/12/12

Y1 - 2024/12/12

N2 - Cells are essential to understanding health and disease, yet traditional models fall short of modeling and simulating their function and behavior. Advances in AI and omics offer groundbreaking opportunities to create an AI virtual cell (AIVC), a multi-scale, multi-modal large-neural-network-based model that can represent and simulate the behavior of molecules, cells, and tissues across diverse states. This Perspective provides a vision on their design and how collaborative efforts to build AIVCs will transform biological research by allowing high-fidelity simulations, accelerating discoveries, and guiding experimental studies, offering new opportunities for understanding cellular functions and fostering interdisciplinary collaborations in open science.

AB - Cells are essential to understanding health and disease, yet traditional models fall short of modeling and simulating their function and behavior. Advances in AI and omics offer groundbreaking opportunities to create an AI virtual cell (AIVC), a multi-scale, multi-modal large-neural-network-based model that can represent and simulate the behavior of molecules, cells, and tissues across diverse states. This Perspective provides a vision on their design and how collaborative efforts to build AIVCs will transform biological research by allowing high-fidelity simulations, accelerating discoveries, and guiding experimental studies, offering new opportunities for understanding cellular functions and fostering interdisciplinary collaborations in open science.

KW - AI

KW - ML

KW - cell biology

KW - virtual cell

UR - https://www.scopus.com/pages/publications/85211477743

U2 - 10.1016/j.cell.2024.11.015

DO - 10.1016/j.cell.2024.11.015

M3 - Review article

AN - SCOPUS:85211477743

SN - 0092-8674

VL - 187

SP - 7045

EP - 7063

JO - Cell

JF - Cell

IS - 25

ER -

How to build the virtual cell with artificial intelligence: Priorities and opportunities

Abstract

Keywords

Access to Document

Other files and links

Fingerprint

Cite this