[HTML][HTML] Empowering biomedical discovery with AI agents

S Gao, A Fang, Y Huang, V Giunchiglia, A Noori… - Cell, 2024 - cell.com
We envision" AI scientists" as systems capable of skeptical learning and reasoning that
empower biomedical research through collaborative agents that integrate AI models and …

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

C Bunne, Y Roohani, Y Rosen, A Gupta, X Zhang… - Cell, 2024 - cell.com
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 …

Establishing a conceptual framework for holistic cell states and state transitions

SM Rafelski, JA Theriot - Cell, 2024 - cell.com
Cell states were traditionally defined by how they looked, where they were located, and what
functions they performed. In this post-genomic era, the field is largely focused on a …

Opportunities and challenges for deep learning in cell dynamics research

B Chai, C Efstathiou, H Yue, VM Draviam - Trends in Cell Biology, 2024 - cell.com
The growth of artificial intelligence (AI) has led to an increase in the adoption of computer
vision and deep learning (DL) techniques for the evaluation of microscopy images and …

Spatial modeling algorithms for reactions and transport in biological cells

EA Francis, JG Laughlin, JS Dokken… - Nature Computational …, 2024 - nature.com
Biological cells rely on precise spatiotemporal coordination of biochemical reactions to
control their functions. Such cell signaling networks have been a common focus for …

Toward generalizable phenotype prediction from single-cell morphology representations

J Tomkinson, R Kern, C Mattson, GP Way - BMC Methods, 2024 - Springer
Functional cell processes (eg, molecular signaling, response to stimuli, mitosis, etc.) impact
cell phenotypes, which scientists can measure with cell morphology. However, linking these …

Spatial modeling algorithms for reactions and transport (SMART) in biological cells

EA Francis, JG Laughlin, JS Dokken… - arxiv preprint arxiv …, 2024 - arxiv.org
Biological cells rely on precise spatiotemporal coordination of biochemical reactions to
control their many functions. Such cell signaling networks have been a common focus for …

AI: A transformative opportunity in cell biology

A Carr, J Cool, T Karaletsos, D Li, AR Lowe… - Molecular Biology of …, 2024 - molbiolcell.org
The success of artificial intelligence (AI) algorithms in predicting protein structure and more
recently, protein interactions, demonstrates the power and potential of machine learning and …

A platform for multimodal in vivo pooled genetic screens reveals regulators of liver function

RA Saunders, WE Allen, X Pan, J Sandhu, J Lu, TK Lau… - bioRxiv, 2024 - biorxiv.org
Organ function requires coordinated activities of thousands of genes in distinct, spatially
organized cell types. Understanding the basis of emergent tissue function requires …

CellFlow: Simulating Cellular Morphology Changes via Flow Matching

Y Zhang, Y Su, C Wang, T Li, Z Wefers, J Nirschl… - arxiv preprint arxiv …, 2025 - arxiv.org
Building a virtual cell capable of accurately simulating cellular behaviors in silico has long
been a dream in computational biology. We introduce CellFlow, an image-generative model …