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2701 results

Full text 2026

Uncovering the mechanism of arecoline's effect on oral submucous fibrosis: integrating transcriptomics and <i>in vitro</i> and <i>in vivo</i> experiments

Liu Z, Yi J, Zeng F, et al.

<h4>Objective</h4>This study aimed to elucidate the potential targets and molecular mechanisms underlying arecoline-induced oral submucous fibrosis through integrated transcriptomic profiling and experimental validation.<h4>Methods</h4>Transcriptomic sequencing was first employed to identify key pathways and targets influenced by …

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Transcriptomics

Full text 2026

Estimating tumour immune infiltration: methodological convergence across histology and spatial technologies

Bian B, Cao Y, Yang JYH.

Estimating tumour immune infiltration is critical for understanding cancer biology and predicting patient response to surgery and immunotherapy. A wide array of experimental platforms supports various computational approaches for quantifying tumour-infiltrating lymphocytes and immune infiltration …

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Transcriptomics

Full text 2026

Integrated multi-omics identifies distinct macrophage alterations during progression of metabolic dysfunction-associated steatohepatitis

Boesch M, Anak S, El Abyad D, et al.

Metabolic dysfunction-associated steatotic liver disease (MASLD) is a chronic condition impacting over 30% population, yet the dynamic changes in macrophage composition from steatosis to steatohepatitis (metabolic dysfunction-associated steatohepatitis, MASH) remain unclear. Here, by integrating single-nucleus …

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Transcriptomics

Full text 2026

Deep learning-based prediction of gene expression from histopathology identifies NR5A1 as a candidate biomarker and druggable target in high-grade serous ovarian carcinoma

Lingasamy P, Ostrowska-Leśko M, Tsakalis P, et al.

<h4>Background</h4>High-grade serous ovarian cancer (HGSOC) is the most lethal ovarian cancer subtype, responsible for ~ 70% of ovarian cancer-related deaths and marked by late-stage diagnosis and frequent platinum resistance. Although transcriptomic profiling enables molecular stratification …

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Transcriptomics

Full text 2026

An Unbiased Molecular Characterization of Peripartum Cardiomyopathy Hearts Identifies Mast Cell Chymase as a New Diagnostic Candidate

Mulvey JF, Sailer C, Achter JS, et al.

Peripartum cardiomyopathy (PPCM) is a rare form of acute heart failure that develops in women toward the end of pregnancy or early postpartum. No effective, specific treatment for PPCM is available and heart transplantation or …

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Single-Cell Transcriptomics

Full text 2026

Sea buckthorn seed oil triggers mitochondrial dysfunction and apoptosis in <i>Aspergillus niger</i> by activating the AGE-RAGE-like signaling pathway

Xin Y, Qin A, Yang J, et al.

<h4>Background</h4>Fungal infections, in particular those caused by <i>Aspergillus niger</i> (<i>A. niger</i>), pose a severe threat to human health, and the situation has been getting worse because of increasing resistance against the frontline triazole antifungals. Sea …

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Transcriptomics

Full text 2026

Spatial transcriptomic profiling uncovers the molecular effects of the neurotoxicant polychlorinated biphenyls (PCBs) in the brains of adult mice

Basu B, Breese NM, Lombardi S, et al.

Polychlorinated biphenyls (PCBs) are highly stable synthetic organic compounds that are present in air, water, and soil. PCBs have been identified in post-mortem human brains, indicating a possible link between environmental factors and disease risk. …

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Transcriptomics

Full text 2026

Decoding clone evolution in HER2 amplified breast cancer through single-cell and spatial transcriptomics analysis of copy number variations

Yang J, Li Y, Luo S, et al.

HER2-positive breast cancer exhibits marked genomic instability and heterogeneity, yet the clonal architecture and copy number variation (CNV) dynamics between ductal carcinoma in situ (DCIS) and invasive ductal carcinoma (IDC), remain poorly understood. We analyzed …

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Structural Variants Transcriptomics

Full text 2026

A cross-scale multimodal framework identifies clinically actionable immunotherapy biomarkers in melanoma through bulk to single-cell and spatial transcriptomics integration

Huoshen W, Yuan K, Xiong J, et al.

BACKGROUND: Melanoma, a type of skin cancer that can spread to other parts of the body, currently lacks highly precise individualized treatment options. METHODS: We performed multi-omics integration on The Cancer Genome Atlas Skin Cutaneous …

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Single-Cell Transcriptomics

Full text 2026

Multiscale Cortical Remodeling Following Abrupt Visual Deafferentation in Rhegmatogenous Retinal Detachment: Imaging Transcriptomics and Neurotransmitter Mapping

Ji Y, Huang X, Wang YY, et al.

<h4>Background</h4>Neuroimaging evidence indicates brain alterations in rhegmatogenous retinal detachment (RRD), but the molecular and neurochemical correlates of these macroscale patterns remain unclear.<h4>Methods</h4>We examined gray matter volume (GMV), intrinsic neural timescale (INT) and structural covariance network …

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Transcriptomics

Full text 2025

Artificial Intelligence-driven spatial transcriptomics in OSCC: Mapping the tumor microenvironment and personalizing therapy

Manogaran S, Ramadoss R, Selvam SP, et al.

Spatial transcriptomics (ST) represents a transformative approach in cancer research, offering high-resolution insights into the spatial organization of gene expression within tissues, particularly relevant for the complex tumor microenvironment (TME) of oral squamous cell carcinoma …

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Transcriptomics

Full text 2026

Multi-Omics Landscape of Circadian Clock Dysregulation Across the Chronic Liver Disease Spectrum

Tong S, Chen W, Chen J, et al.

The liver circadian clock coordinates hepatic lipid metabolism, bile acid synthesis, and glucose homeostasis through interlocking transcription-translation feedback loops. Disruption of this temporal organization is increasingly recognized as a shared pathological feature across the chronic …

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Bioinformatics Epigenetics Single-Cell

Full text 2025

Application of transcriptomics techniques in skin cancer

Ma Y, Wang F, Xu S.

Skin cancer is one of the most common malignant tumors worldwide, with its mortality rate showing a significant upward trend, thereby increasing the disease burden on patients and society. With the rapid development of next-generation …

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Single-Cell Transcriptomics

Full text 2026

Adding highly variable genes to spatially variable genes can improve cell type clustering performance in spatial transcriptomics data

Li Y, Stanojevic S, He B, et al.

<h4>Motivation</h4>Spatial transcriptomics has allowed researchers to analyze transcriptome data in its tissue sample's spatial context. Various methods have been developed for detecting spatially variable genes (SV genes), whose gene expression over the tissue space shows …

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Transcriptomics

Full text 2026

Spatial multi-omics identifies a NOTCH3-mediated capillary-mCAF crosstalk driving immune exclusion in hepatocellular carcinoma

Ji F, Li H, Wang Q, et al.

Fibrosis induced immune exclusion is a hepatocellular carcinoma (HCC) hallmark, underscoring the key role of cancer-associated fibroblasts (CAFs) in immune regulation. Through HCC spatial multi-omics data and integrating pan-cancer scRNA-seq profiles of CAFs under immune …

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Single-Cell Transcriptomics

Full text 2026

Integrating Single-Cell and Spatial Multi-Omics to Decode Plant–Microbe Interactions at Cellular Resolution

Li Y, Vigil J, Pradhan R, et al.

No abstract available.

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Transcriptomics

Full text 2026

A POSTN<sup>+</sup> CAF/APOE<sup>+</sup> TAM Axis is Associated with Tumor Progression and Potential Immunotherapy Resistance in Laryngeal Squamous Cell Carcinoma

Ma K, Tian J, Wu H, et al.

<h4>Background</h4>Laryngeal squamous cell carcinoma (LSCC) is a prevalent malignancy of the head and neck, characterized by a complex tumor microenvironment (TME) that hinders the effectiveness of immunotherapy.<h4>Objective</h4>This study aimed to comprehensively characterize the features, interactions, …

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Transcriptomics

Full text 2026

Spatially resolved molecular signatures of Lewy body dementia

Jin Y, Chen K, Wixom AQ, et al.

Lewy body dementia (LBD), encompassing dementia with Lewy bodies and Parkinson's disease dementia, is neuropathologically defined by neuronal accumulation of α-synuclein encoded by the SNCA gene. Genetic risk factors strongly influence LBD susceptibility, including SNCA …

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Transcriptomics

Full text 2026

RESCUE: recovery of unattributed expression patterns in spatial transcriptomics

Lee YJ, Yeo S, Schrader AW, et al.

Spatial transcriptomics (ST) enables gene expression profiling while preserving the spatial architecture of intact tissue. Analyzing ST data often proceeds by first extracting cell-level information, typically through cell segmentation or cell-type deconvolution. However, a critical …

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Transcriptomics

Full text 2026

Multiomics Reveals IL-17 Drives Epithelial Keratinization and Proliferation via EHF in Odontogenic Keratocysts

Yi JR, Zhong NN, Liu XH, et al.

This study aims to investigate epithelial cell (EpC) heterogeneity in odontogenic keratocysts (OKCs) and the molecular mechanisms driving their characteristic keratinization and rapid proliferation. We integrated single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics to profile …

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Transcriptomics