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 …

Eleven grand challenges in single-cell data science

D Lähnemann, J Köster, E Szczurek, DJ McCarthy… - Genome biology, 2020 - Springer
The recent boom in microfluidics and combinatorial indexing strategies, combined with low
sequencing costs, has empowered single-cell sequencing technology. Thousands—or even …

Locoregional delivery of IL-13Rα2-targeting CAR-T cells in recurrent high-grade glioma: a phase 1 trial

CE Brown, JC Hibbard, D Alizadeh, MS Blanchard… - Nature medicine, 2024 - nature.com
Chimeric antigen receptor T cell (CAR-T) therapy is an emerging strategy to improve
treatment outcomes for recurrent high-grade glioma, a cancer that responds poorly to current …

Single-cell RNA-seq reveals cell type–specific molecular and genetic associations to lupus

RK Perez, MG Gordon, M Subramaniam, MC Kim… - Science, 2022 - science.org
Systemic lupus erythematosus (SLE) is a heterogeneous autoimmune disease. Knowledge
of circulating immune cell types and states associated with SLE remains incomplete. We …

Single-cell eQTL map** identifies cell type–specific genetic control of autoimmune disease

S Yazar, J Alquicira-Hernandez, K Wing, A Senabouth… - Science, 2022 - science.org
The human immune system displays substantial variation between individuals, leading to
differences in susceptibility to autoimmune disease. We present single-cell RNA sequencing …

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 …

Doublet identification in single-cell sequencing data using scDblFinder

PL Germain, A Lun, CG Meixide, W Macnair… - …, 2022 - pmc.ncbi.nlm.nih.gov
Doublets are prevalent in single-cell sequencing data and can lead to artifactual findings. A
number of strategies have therefore been proposed to detect them. Building on the strengths …

Regorafenib plus nivolumab in unresectable hepatocellular carcinoma: the phase 2 RENOBATE trial

HD Kim, S Jung, HY Lim, BY Ryoo, MH Ryu, S Chuah… - Nature Medicine, 2024 - nature.com
Regorafenib has anti-tumor activity in patients with unresectable hepatocellular carcinoma
(uHCC) with potential immunomodulatory effects, suggesting that its combination with …

A clinically applicable integrative molecular classification of meningiomas

F Nassiri, J Liu, V Patil, Y Mamatjan, JZ Wang… - Nature, 2021 - nature.com
Meningiomas are the most common primary intracranial tumour in adults. Patients with
symptoms are generally treated with surgery as there are no effective medical therapies. The …