Transformers in single-cell omics: a review and new perspectives

A Szałata, K Hrovatin, S Becker, A Tejada-Lapuerta… - Nature …, 2024 - nature.com
Recent efforts to construct reference maps of cellular phenotypes have expanded the
volume and diversity of single-cell omics data, providing an unprecedented resource for …

Profiling cell identity and tissue architecture with single-cell and spatial transcriptomics

GS Gulati, JP D'Silva, Y Liu, L Wang… - … Reviews Molecular Cell …, 2024 - nature.com
Single-cell transcriptomics has broadened our understanding of cellular diversity and gene
expression dynamics in healthy and diseased tissues. Recently, spatial transcriptomics has …

Foundation models for bioinformatics

Z Chen, L Wei, G Gao - Quantitative Biology, 2024 - Wiley Online Library
Transformer‐based foundation models such as ChatGPTs have revolutionized our daily life
and affected many fields including bioinformatics. In this perspective, we first discuss about …

General-purpose pre-trained large cellular models for single-cell transcriptomics

H Bian, Y Chen, E Luo, X Wu, M Hao… - National Science …, 2024 - academic.oup.com
The great capability of AI large language models (LLMs) pre-trained on massive natural
language data has inspired scientists to develop a few …

scProAtlas: an atlas of multiplexed single-cell spatial proteomics imaging in human tissues

T Wang, X Chen, Y Han, J Yi, X Liu, P Kim… - Nucleic Acids …, 2024 - academic.oup.com
Spatial proteomics can visualize and quantify protein expression profiles within tissues at
single-cell resolution. Although spatial proteomics can only detect a limited number of …

Perspectives on benchmarking foundation models for network biology

CV Theodoris - Quantitative Biology, 2024 - Wiley Online Library
Transfer learning has revolutionized fields including natural language understanding and
computer vision by leveraging large‐scale general datasets to pretrain models with …

The development of AI foundation models for single-cell transcriptomics

H Bian, Y Chen, E Luo, X Wu, M Hao… - National Science …, 2024 - academic.oup.com
Recent development of large language models (LLMs) in AI has inspired scientists to
develop a few large-scale AI foundation models for single-cell transcriptomics or large …

Single Cell Advances in investigating and understanding Chronic Kidney Disease and Diabetic Kidney Disease

S Bhayana, PA Schytz, ETB Olesen, K Soh… - The American Journal of …, 2024 - Elsevier
Abstract Chronic Kidney Disease (CKD) and its subset Diabetic Kidney Disease (DKD) are
progressive conditions that affect more than 850 million people worldwide. Diabetes …

Integrated single-cell atlas of human atherosclerotic plaques

K Traeuble, M Munz, J Pauli, N Sachs, E Vafadarnejad… - bioRxiv, 2024 - biorxiv.org
Atherosclerosis, a major cause of cardiovascular diseases, is characterized by the buildup of
lipids and chronic inflammation in the arteries, leading to plaque formation and potential …