[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 …

Harnessing the deep learning power of foundation models in single-cell omics

Q Ma, Y Jiang, H Cheng, D Xu - Nature Reviews Molecular Cell Biology, 2024 - nature.com
Foundation models hold great promise for analyzing single-cell omics data, yet various
challenges remain that require further advancements. In this Comment, we discuss the …

Universal cell embeddings: A foundation model for cell biology

Y Rosen, Y Roohani, A Agarwal, L Samotorčan… - bioRxiv, 2023 - biorxiv.org
Developing a universal representation of cells which encompasses the tremendous
molecular diversity of cell types within the human body and more generally, across species …

A cell atlas foundation model for scalable search of similar human cells

G Heimberg, T Kuo, DJ DePianto, O Salem, T Heigl… - Nature, 2024 - nature.com
Single-cell RNA-seq (scRNA-seq) has profiled hundreds of millions of human cells across
organs, diseases, development, and perturbations to date. Mining these growing atlases …

Scalable querying of human cell atlases via a foundational model reveals commonalities across fibrosis-associated macrophages

G Heimberg, T Kuo, D DePianto, T Heigl, N Diamant… - BioRxiv, 2023 - biorxiv.org
Single-cell RNA-seq (scRNA-seq) studies have profiled over 100 million human cells across
diseases, developmental stages, and perturbations to date. A singular view of this vast and …

MuSe-GNN: learning unified gene representation from multimodal biological graph data

T Liu, Y Wang, R Ying, H Zhao - Advances in neural …, 2024 - proceedings.neurips.cc
Discovering genes with similar functions across diverse biomedical contexts poses a
significant challenge in gene representation learning due to data heterogeneity. In this …

AI-driven multi-omics integration for multi-scale predictive modeling of causal genotype-environment-phenotype relationships

Y Wu, L Xie - arXiv preprint arXiv:2407.06405, 2024 - arxiv.org
Despite the wealth of single-cell multi-omics data, it remains challenging to predict the
consequences of novel genetic and chemical perturbations in the human body. It requires …

Deeper evaluation of a single-cell foundation model

R Boiarsky, NM Singh, A Buendia, AP Amini… - Nature Machine …, 2024 - nature.com
Large-scale foundation models, which are pre-trained on massive, unlabelled datasets and
subsequently fine-tuned on specific tasks, have recently achieved unparalleled success on …

Differentiating visceral sensory ganglion organoids from induced pluripotent stem cells

K Ahn, HS Park, S Choi, H Lee, H Choi, SB Hong… - Nature …, 2024 - nature.com
The ability to generate visceral sensory neurons (VSN) from induced pluripotent stem (iPS)
cells may help to gain insights into how the gut–nerve–brain axis is involved in neurological …

[HTML][HTML] Artificial intelligence and machine learning applications for cultured meat

ME Todhunter, S Jubair, R Verma, R Saqe… - Frontiers in Artificial …, 2024 - frontiersin.org
Cultured meat has the potential to provide a complementary meat industry with reduced
environmental, ethical, and health impacts. However, major technological challenges …