[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 …

Optimizing the Cell Painting assay for image-based profiling

BA Cimini, SN Chandrasekaran, M Kost-Alimova… - Nature protocols, 2023 - nature.com
In image-based profiling, software extracts thousands of morphological features of cells from
multi-channel fluorescence microscopy images, yielding single-cell profiles that can be used …

Masked autoencoders for microscopy are scalable learners of cellular biology

O Kraus, K Kenyon-Dean, S Saberian… - Proceedings of the …, 2024 - openaccess.thecvf.com
Featurizing microscopy images for use in biological research remains a significant
challenge especially for large-scale experiments spanning millions of images. This work …

[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 …

Learning representations for image-based profiling of perturbations

N Moshkov, M Bornholdt, S Benoit, M Smith… - Nature …, 2024 - nature.com
Measuring the phenotypic effect of treatments on cells through imaging assays is an efficient
and powerful way of studying cell biology, and requires computational methods for …

Evaluating batch correction methods for image-based cell profiling

J Arevalo, E Su, JD Ewald, R van Dijk… - Nature …, 2024 - nature.com
High-throughput image-based profiling platforms are powerful technologies capable of
collecting data from billions of cells exposed to thousands of perturbations in a time-and cost …

Deep learning in image-based phenotypic drug discovery

D Krentzel, SL Shorte, C Zimmer - Trends in cell biology, 2023 - cell.com
Modern drug discovery approaches often use high-content imaging to systematically study
the effect on cells of large libraries of chemical compounds. By automatically screening …

JUMP Cell Painting dataset: morphological impact of 136,000 chemical and genetic perturbations

SN Chandrasekaran, J Ackerman, E Alix, DM Ando… - BioRxiv, 2023 - biorxiv.org
Image-based profiling has emerged as a powerful technology for various steps in basic
biological and pharmaceutical discovery, but the community has lacked a large, public …

[HTML][HTML] CLOOME: contrastive learning unlocks bioimaging databases for queries with chemical structures

A Sanchez-Fernandez, E Rumetshofer… - Nature …, 2023 - nature.com
The field of bioimage analysis is currently impacted by a profound transformation, driven by
the advancements in imaging technologies and artificial intelligence. The emergence of …

Cell Painting: a decade of discovery and innovation in cellular imaging

S Seal, MA Trapotsi, O Spjuth, S Singh… - Nature …, 2024 - nature.com
Modern quantitative image analysis techniques have enabled high-throughput, high-content
imaging experiments. Image-based profiling leverages the rich information in images to …