AIMC Topic: Single-Cell Analysis

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Exploring the comorbidity mechanisms of ITGB2 in rheumatoid arthritis and membranous nephropathy through integrated bioinformatics analysis.

Renal failure
BACKGROUND: Patients with rheumatoid arthritis (RA) are more likely to comorbid renal diseases, with membranous nephropathy (MN) being the most common. This study aimed to explore the common pathogenesis between RA and MN using integrated bioinformat...

Integrating transcriptomics, network analysis, and single-cell RNA sequencing to identify and validate key target genes of gynostemma in the treatment of non-alcoholic fatty liver disease.

European journal of pharmaceutical sciences : official journal of the European Federation for Pharmaceutical Sciences
This study explores the therapeutic targets and mechanisms of Gynostemma pentaphyllum in non-alcoholic fatty liver disease (NAFLD). Using network analysis and bioinformatics, we identified target genes of Gynostemma's active metabolites in NAFLD thro...

Identification of podocyte molecular markers in diabetic kidney disease via single-cell RNA sequencing and machine learning.

PloS one
Diabetic kidney disease (DKD) is a major cause of end-stage renal disease globally, with podocytes being implicated in its pathogenesis. However, the underlying mechanisms of podocyte involvement remain unclear. The aim of the present study was to id...

Bering: joint cell segmentation and annotation for spatial transcriptomics with transferred graph embeddings.

Nature communications
Single-cell spatial transcriptomics can provide subcellular resolution for a deep understanding of molecular mechanisms. However, accurate segmentation and annotation remain a major challenge that limits downstream analysis. Current machine learning ...

Integrating bulk and single cell sequencing data to identify prognostic biomarkers and drug candidates in HBV associated hepatocellular carcinoma.

Scientific reports
Hepatitis B virus (HBV) infection is a major driver of hepatocellular carcinoma (HCC), yet the mechanisms by which HBV triggers HCC and how it interacts with the immune system remain largely undefined. In this study, 53 immune-related key genes invol...

Sceptic: pseudotime analysis for time-series single-cell sequencing and imaging data.

Genome biology
Several computational methods have been developed to construct single-cell pseudotime embeddings for extracting the temporal order of transcriptional cell states from time-series scRNA-seq datasets. However, existing methods suffer from low predictiv...

Integrative scATAC-seq and mtDNA mutation analysis reveals disease-driven regulatory aberrations in AML.

Science bulletin
Disturbances in transcriptional regulation during hematopoiesis can lead to aberrant hematopoietic differentiation and potential leukemogenesis. Given the high relapse risk of acute myeloid leukemia (AML), understanding its progression mechanisms and...

Quantitative phase imaging with temporal kinetics predicts hematopoietic stem cell diversity.

Nature communications
Innovative identification technologies for hematopoietic stem cells (HSCs) have expanded the scope of stem cell biology. Clinically, the functional quality of HSCs critically influences the safety and therapeutic efficacy of stem cell therapies. Howe...

Single-cell spatial transcriptomics reveals immunotherapy-driven bone marrow niche remodeling in AML.

Science advances
Given the graft-versus-leukemia effect observed with allogeneic hematopoietic stem cell transplantation in refractory or relapsed acute myeloid leukemia (AML), immunotherapies have been explored in nontransplant settings. We applied a multiomic appro...