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 …

METTL3 inhibition induced by M2 macrophage-derived extracellular vesicles drives anti-PD-1 therapy resistance via M6A-CD70-mediated immune suppression in …

J Ning, X Hou, J Hao, W Zhang, Y Shi… - Cell Death & …, 2023 - nature.com
The treatment options for advanced papillary thyroid cancer (PTC) and anaplastic thyroid
cancer (ATC) refractory to standard therapies are limited. Although anti-PD-1 therapy has a …

Development of a deep learning model for cancer diagnosis by inspecting cell-free DNA end-motifs

H Shen, M Yang, J Liu, K Chen, X Li - NPJ Precision Oncology, 2024 - nature.com
Accurate discrimination between patients with and without cancer from cfDNA is crucial for
early cancer diagnosis. Herein, we develop and validate a deep-learning-based model …

Generative pretraining from large-scale transcriptomes for single-cell deciphering

H Shen, J Liu, J Hu, X Shen, C Zhang, D Wu, M Feng… - Iscience, 2023 - cell.com
Exponential accumulation of single-cell transcriptomes poses great challenge for efficient
assimilation. Here, we present an approach entitled generative pretraining from …

scGAA: a general gated axial-attention model for accurate cell-type annotation of single-cell RNA-seq data

T Kong, T Yu, J Zhao, Z Hu, N Xiong, J Wan, X Dong… - Scientific Reports, 2024 - nature.com
Single-cell RNA sequencing (scRNA-seq) is a key technology for investigating cell
development and analysing cell diversity across various diseases. However, the high …

[HTML][HTML] Deep-learning methods for unveiling large-scale single-cell transcriptomes

X Shen, X Li - Cancer Biology & Medicine, 2023 - ncbi.nlm.nih.gov
The rapidly evolving realm of single-cell transcriptomics offers vital new perspectives into the
understanding of intra-and inter-cellular molecular dynamics governing development …