Type 1 diabetes mellitus as a disease of the β-cell (do not blame the immune system?)

BO Roep, S Thomaidou, R van Tienhoven… - Nature Reviews …, 2021 - nature.com
Type 1 diabetes mellitus is believed to result from destruction of the insulin-producing β-cells
in pancreatic islets that is mediated by autoimmune mechanisms. The classic view is that …

Computational principles and challenges in single-cell data integration

R Argelaguet, ASE Cuomo, O Stegle… - Nature biotechnology, 2021 - nature.com
The development of single-cell multimodal assays provides a powerful tool for investigating
multiple dimensions of cellular heterogeneity, enabling new insights into development …

scGPT: toward building a foundation model for single-cell multi-omics using generative AI

H Cui, C Wang, H Maan, K Pang, F Luo, N Duan… - Nature …, 2024 - nature.com
Generative pretrained models have achieved remarkable success in various domains such
as language and computer vision. Specifically, the combination of large-scale diverse …

Single-nucleus and spatial transcriptome profiling of pancreatic cancer identifies multicellular dynamics associated with neoadjuvant treatment

WL Hwang, KA Jagadeesh, JA Guo, HI Hoffman… - Nature …, 2022 - nature.com
Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal and treatment-refractory
cancer. Molecular stratification in pancreatic cancer remains rudimentary and does not yet …

Map** single-cell data to reference atlases by transfer learning

M Lotfollahi, M Naghipourfar, MD Luecken… - Nature …, 2022 - nature.com
Large single-cell atlases are now routinely generated to serve as references for analysis of
smaller-scale studies. Yet learning from reference data is complicated by batch effects …

Transformer for one stop interpretable cell type annotation

J Chen, H Xu, W Tao, Z Chen, Y Zhao… - Nature …, 2023 - nature.com
Consistent annotation transfer from reference dataset to query dataset is fundamental to the
development and reproducibility of single-cell research. Compared with traditional …

scBERT as a large-scale pretrained deep language model for cell type annotation of single-cell RNA-seq data

F Yang, W Wang, F Wang, Y Fang, D Tang… - Nature Machine …, 2022 - nature.com
Annotating cell types on the basis of single-cell RNA-seq data is a prerequisite for research
on disease progress and tumour microenvironments. Here we show that existing annotation …

High-throughput total RNA sequencing in single cells using VASA-seq

F Salmen, J De Jonghe, TS Kaminski, A Alemany… - Nature …, 2022 - nature.com
Most methods for single-cell transcriptome sequencing amplify the termini of polyadenylated
transcripts, capturing only a small fraction of the total cellular transcriptome. This precludes …

Construction of a human cell landscape at single-cell level

X Han, Z Zhou, L Fei, H Sun, R Wang, Y Chen, H Chen… - Nature, 2020 - nature.com
Single-cell analysis is a valuable tool for dissecting cellular heterogeneity in complex
systems. However, a comprehensive single-cell atlas has not been achieved for humans …

Single-cell analysis defines a pancreatic fibroblast lineage that supports anti-tumor immunity

C Hutton, F Heider, A Blanco-Gomez, A Banyard… - Cancer cell, 2021 - cell.com
Fibroblasts display extensive transcriptional heterogeneity, yet functional annotation and
characterization of their heterocellular relationships remains incomplete. Using mass …