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 …

[HTML][HTML] 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 …

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 …

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 …

[HTML][HTML] Mapping 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 …

[HTML][HTML] Benchmarking atlas-level data integration in single-cell genomics

MD Luecken, M Büttner, K Chaichoompu, A Danese… - Nature …, 2022 - nature.com
Single-cell atlases often include samples that span locations, laboratories and conditions,
leading to complex, nested batch effects in data. Thus, joint analysis of atlas datasets …

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 …

[PDF][PDF] 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 …

ACE2 expression in pancreas may cause pancreatic damage after SARS-CoV-2 infection

F Liu, X Long, B Zhang, W Zhang, X Chen… - Clinical …, 2020 - cghjournal.org
Methods A public database was used to explore the expression and distribution of ACE2 in
normal pancreases. We also retrospectively analyzed patients diagnosed with COVID-19 …

[HTML][HTML] A benchmark of batch-effect correction methods for single-cell RNA sequencing data

HTN Tran, KS Ang, M Chevrier, X Zhang, NYS Lee… - Genome biology, 2020 - Springer
Background Large-scale single-cell transcriptomic datasets generated using different
technologies contain batch-specific systematic variations that present a challenge to batch …