AIMC Topic: Gene Expression Profiling
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STHD: probabilistic cell typing of single spots in whole transcriptome spatial data with high definition.
Genome biology
Jul 18, 2025
Recent advances in spatial transcriptomics technologies have enabled gene expression profiling across the transcriptome in spots with subcellular resolution, but high sparsity and dimensionality present significant computational challenges. We presen...
Using machine learning to discover DNA metabolism biomarkers that direct prostate cancer treatment.
Scientific reports
Jul 18, 2025
DNA metabolism genes play pivotal roles in the regulation of cellular processes that contribute to cancer progression, immune modulation, and therapeutic response in prostate cancer (PC). Understanding the mechanisms by which these genes influence th...
Analyses of the mechanism and therapeutic targets of senescence related genes in ischemic stroke with multi-omics approach.
Scientific reports
Jul 18, 2025
Ischemic stroke (IS) affects 11 million people annually, posing substantial clinical and economic burdens. Current therapies remain limited by time sensitivity and variable efficacy, necessitating novel biomarkers. We developed a multi-omics framewor...
Bering: joint cell segmentation and annotation for spatial transcriptomics with transferred graph embeddings.
Nature communications
Jul 18, 2025
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 ...
Image-based inference of tumor cell trajectories enables large-scale cancer progression analysis.
Science advances
Jul 18, 2025
Current approaches to estimating cell trajectories, tumor progression dynamics, and cell population diversity of tumor microenvironment often depend on single-cell RNA sequencing, which is costly and resource intensive. To address this limitation, we...
Shared pathogenic mechanisms linking obesity and idiopathic pulmonary fibrosis revealed by bioinformatics and in vivo validation.
Scientific reports
Jul 17, 2025
Previous studies have suggested a potential correlation between obesity and idiopathic pulmonary fibrosis (IPF). This study aimed to elucidate pathogenic pathways connecting obesity and IPF and identify diagnostic biomarkers for obesity-related pulmo...
Identification of CTSK as a TLR-related critical biomarker in liver cirrhosis via integrative bioinformatics and pathological characterization.
Scientific reports
Jul 17, 2025
Liver cirrhosis (LC) is a common chronic disease worldwide with a poor prognosis, and its pathogenesis has not been fully elucidated. Toll-like receptors (TLRs) are crucial in LC progression. Here, we identified TLR-related genes, providing novel ins...
Potential diagnostic and therapeutic gene in chronic low back pain through pyroptosis modulation: A silico study based on the dataset analysis.
Scientific reports
Jul 16, 2025
Chronic low back pain (cLBP ) is a common condition that affects the quality of life, can be caused by disc degeneration, facet arthropathy, myofascial pain, sacroiliac joint pain, spondyloarthropathies, and nociplastic pain etc. Research suggests th...
Molecular mechanisms of efferocytosis imbalance in the idiopathic pulmonary fibrosis microenvironment: from gene screening to dynamic regulation analysis.
Biology direct
Jul 15, 2025
BACKGROUND: Idiopathic pulmonary fibrosis (IPF) is a chronic progressive pulmonary disease characterized by alveolar structural destruction and fibrosis. In recent years, efferocytosis has been recognized as playing a crucial role in the occurrence a...
Multi-transcriptomics predicts clinical outcome in systemically untreated breast cancer patients with extensive follow-up.
Breast cancer research : BCR
Jul 15, 2025
BACKGROUND: Prognostic tools for determining patients with indolent breast cancers (BCs) are far from optimal, leading to extensive overtreatment. Several studies have demonstrated mRNAs, lncRNAs and miRNAs to have prognostic potential in BC. Because...
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