AIMC Topic: Single-Cell Analysis
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Imputing single-cell protein abundance in multiplex tissue imaging.
Nature communications
May 22, 2025
Multiplex tissue imaging enables single-cell spatial proteomics and transcriptomics but remains limited by incomplete molecular profiling, tissue loss, and probe failure. Here, we apply machine learning to impute single-cell protein abundance using m...
Single-cell and bulk transcriptome analyses reveal elevated amino acid metabolism promoting tumor-directed immune evasion in colorectal cancer.
Frontiers in immunology
May 22, 2025
INTRODUCTION: Colorectal cancer (CRC), the third most common cancer worldwide, often shows limited responsiveness to immunotherapy due to its predominantly immune-excluded phenotype. Despite increasing insights into the complex tumor microenvironment...
Cell Line, Tumor
Single-Cell Analysis
Gene Expression Regulation, Neoplastic
Lymphocytes, Tumor-Infiltrating
Male
Gene Expression Profiling
Transcriptome
Tumor Escape
CD8-Positive T-Lymphocytes
Amino Acids
Programmed Cell Death 1 Receptor
Humans
Colorectal Neoplasms
Tumor Microenvironment
Prognosis
Female
Extensible Immunofluorescence (ExIF) accessibly generates high-plexity datasets by integrating standard 4-plex imaging data.
Nature communications
May 17, 2025
Standard immunofluorescence imaging captures just ~4 molecular markers (4-plex) per cell, limiting dissection of complex biology. Inspired by multimodal omics-based data integration approaches, we propose an Extensible Immunofluorescence (ExIF) frame...
Advanced droplet microfluidic platform for high-throughput screening of industrial fungi.
Biosensors & bioelectronics
May 16, 2025
Industrial fungi are pivotal candidates for the production of a diverse array of bioproducts. To enhance their productivity, these strains are frequently subjected to genetic modifications. Following transformation, the selection of optimal productio...
Machine learning approach to single cell transcriptomic analysis of Sjogren's disease reveals altered activation states of B and T lymphocytes.
Journal of autoimmunity
May 2, 2025
Sjogren's Disease (SjD) is an autoimmune disorder characterized by salivary and lacrimal gland dysfunction and immune cell infiltration leading to gland inflammation and destruction. Although SjD is a common disease, its pathogenesis is not fully und...
GRACE: Unveiling Gene Regulatory Networks With Causal Mechanistic Graph Neural Networks in Single-Cell RNA-Sequencing Data.
IEEE transactions on neural networks and learning systems
May 2, 2025
Reconstructing gene regulatory networks (GRNs) using single-cell RNA sequencing (scRNA-seq) data holds great promise for unraveling cellular fate development and heterogeneity. While numerous machine-learning methods have been proposed to infer GRNs ...
TransAnno-Net: A Deep Learning Framework for Accurate Cell Type Annotation of Mouse Lung Tissue Using Self-supervised Pretraining.
Computer methods and programs in biomedicine
Apr 24, 2025
BACKGROUND: Single-cell RNA sequencing (scRNA-seq) has become a significant tool for addressing complex issuess in the field of biology. In the context of scRNA-seq analysis, it is imperative to accurately determine the type of each cell. However, co...
Exploring hypoxia driven subtypes of pulmonary arterial hypertension through transcriptomics single cell sequencing and machine learning.
Scientific reports
Apr 24, 2025
Pulmonary arterial hypertension (PAH) is a progressive cardiovascular disease characterized by elevated pulmonary arterial pressure, leading to right heart failure and death. Despite advancements in diagnosis and treatment, it remains incurable, and ...
Leveraging TME features and multi-omics data with an advanced deep learning framework for improved Cancer survival prediction.
Scientific reports
Apr 24, 2025
Glioma, a malignant intracranial tumor with high invasiveness and heterogeneity, significantly impacts patient survival. This study integrates multi-omics data to improve prognostic prediction and identify therapeutic targets. Using single-cell data ...
Advancing personalized, predictive, and preventive medicine in bladder cancer: a multi-omics and machine learning approach for novel prognostic modeling, immune profiling, and therapeutic target discovery.
Frontiers in immunology
Apr 22, 2025
OBJECTIVE: This study aimed to identify and analyze immunogenic cell death (ICD)-related multi-omics features in bladder cancer (BLCA) using single-cell RNA sequencing (scRNA-seq) and bulk RNA-seq data. By integrating these datasets, we sought to con...
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