A review of single-cell RNA-Seq annotation, integration, and cell–cell communication

C Cheng, W Chen, H Jin, X Chen - Cells, 2023 - mdpi.com
Single-cell RNA sequencing (scRNA-seq) has emerged as a powerful tool for investigating
cellular biology at an unprecedented resolution, enabling the characterization of cellular …

Spatiotemporal immune landscape of colorectal cancer liver metastasis at single-cell level

Y Wu, S Yang, J Ma, Z Chen, G Song, D Rao, Y Cheng… - Cancer discovery, 2022 - AACR
Liver metastasis, the leading cause of colorectal cancer mortality, exhibits a highly
heterogeneous and suppressive immune microenvironment. Here, we sequenced 97 …

Single-cell RNA sequencing reveals profibrotic roles of distinct epithelial and mesenchymal lineages in pulmonary fibrosis

AC Habermann, AJ Gutierrez, LT Bui, SL Yahn… - Science …, 2020 - science.org
Pulmonary fibrosis (PF) is a form of chronic lung disease characterized by pathologic
epithelial remodeling and accumulation of extracellular matrix (ECM). To comprehensively …

A fast, scalable and versatile tool for analysis of single-cell omics data

K Zhang, NR Zemke, EJ Armand, B Ren - Nature methods, 2024 - nature.com
Single-cell omics technologies have revolutionized the study of gene regulation in complex
tissues. A major computational challenge in analyzing these datasets is to project the large …

Secretory cells dominate airway CFTR expression and function in human airway superficial epithelia

K Okuda, H Dang, Y Kobayashi, G Carraro… - American journal of …, 2021 - atsjournals.org
Rationale: Identification of the specific cell types expressing CFTR (cystic fibrosis [CF]
transmembrane conductance regulator) is required for precision medicine therapies for CF …

Single-cell multi-omics analysis of human pancreatic islets reveals novel cellular states in type 1 diabetes

M Fasolino, GW Schwartz, AR Patil, A Mongia… - Nature …, 2022 - nature.com
Abstract Type 1 diabetes (T1D) is an autoimmune disease in which immune cells destroy
insulin-producing beta cells. The aetiology of this complex disease is dependent on the …

Prioritization of cell types responsive to biological perturbations in single-cell data with Augur

JW Squair, MA Skinnider, M Gautier, LJ Foster… - Nature …, 2021 - nature.com
Advances in single-cell genomics now enable large-scale comparisons of cell states across
two or more experimental conditions. Numerous statistical tools are available to identify …

Inherited PD-1 deficiency underlies tuberculosis and autoimmunity in a child

M Ogishi, R Yang, C Aytekin, D Langlais, M Bourgey… - Nature medicine, 2021 - nature.com
The pathophysiology of adverse events following programmed cell death protein 1 (PD-1)
blockade, including tuberculosis (TB) and autoimmunity, remains poorly characterized. We …

Single-cell profiling reveals distinct adaptive immune hallmarks in MDA5+ dermatomyositis with therapeutic implications

Y Ye, Z Chen, S Jiang, F Jia, T Li, X Lu, J Xue… - Nature …, 2022 - nature.com
Anti-melanoma differentiation-associated gene 5-positive dermatomyositis (MDA5+ DM) is
an autoimmune condition associated with rapidly progressive interstitial lung disease and …

Neutrophil profiling illuminates anti-tumor antigen-presenting potency

Y Wu, J Ma, X Yang, F Nan, T Zhang, S Ji, D Rao… - Cell, 2024 - cell.com
Neutrophils, the most abundant and efficient defenders against pathogens, exert opposing
functions across cancer types. However, given their short half-life, it remains challenging to …