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TUSCAN: Tumor segmentation and classification analysis in spatial transcriptomics
No abstract available.
Read PDFSpatial and Functional Immune Profiling Identifies Impaired Vascular Repair in Human Myocardial Infarction
<b>Background:</b> In an earlier murine model of myocardial infarction (MI), we showed that CD8 cells and myeloid dendritic cells (mDCs) infiltrate the infarcted myocardium within the first week. However, in humans, the spatial interplay between …
Read PDFSpatial transcriptomic-metabolic features of tumor foci and tumor capsule in microvascular invasion with hepatocellular carcinoma: A spatial multi-omics study
<h4>Background</h4>Microvascular invasion (MVI) is closely related to the recurrence and metastasis of hepatocellular carcinoma (HCC), but the underlying cellular mechanism remains largely elusive. This study aims to elucidate the regional cellular discrepancy between MVI-positive (MVI+) …
Read PDFMulti-Scale Transcriptomics Redefining the Tumor Immune Microenvironment
The tumor immune microenvironment (TIME) is closely involved in tumor initiation, malignant progression, immune escape, and response to immunotherapy. With the continued development of high-throughput sequencing technologies, transcriptomic approaches have become essential for examining the …
Read PDFSingle-cell transcriptomics of granulocytes in asthma and atopic diseases
Since their early association with atopic disease, granulocytes, particularly eosinophils, have been widely used as biomarkers, yet the mechanisms underlying their role in airway and atopic inflammatory diseases remain incompletely understood. Single-cell transcriptomic approaches have …
Read PDFStroke-induced gut microbiome dysbiosis accelerates Alzheimer's disease progression
Stroke survivors face an elevated risk of developing Alzheimer's disease (AD), yet the biological mechanisms linking these conditions remain poorly defined. Here, we show that a stroke-induced gut microbiome is a key driver of AD-related …
Read PDFEnhancing Synthesis Efficiency in Microbial 1,5-Pentanediol Production Through Transcriptomics-Informed Metabolic Engineering of <i>Escherichia coli</i>
The microbial production of 1,5-pentanediol (1,5-PDO), a versatile platform chemical with extensive industrial applications, remains limited by suboptimal fermentation titers and incomplete understanding of metabolic bottlenecks. To address these challenges, this study employed comparative transcriptomics …
Read PDFAugGCL: Multimodal graph learning for spatial transcriptomics analysis with enhanced gene and morphological data
Spatial transcriptomics enables the measurement of gene expression in intact tissues. Despite this, reconstructing anatomically accurate spatial domains remains challenging, primarily due to expression sparsity, complex tissue architecture that is characterized by sharp boundaries and …
Read PDFIntegrating optogenetic fMRI and spatial transcriptomics to reveal circuit-specific gene signatures in fronto- and hippo-thalamic networks
Elucidating how microscale molecular architecture shapes macroscale brain network organization requires integrative frameworks that link transcriptional profiles, structural connectivity, and functional dynamics across scales. However, existing evidence largely relies on cross-modal data acquired from different …
Read PDFSTGNET: extending panel coverage in imaging-based spatial transcriptomics using deep generative adversarial networks
Imaging-based spatial transcriptomics (ST) technologies offer unparalleled resolution for mapping gene expression within intact tissues but are fundamentally constrained by the limited size of their gene panels. This restriction hinders comprehensive biological discovery by omitting …
Read PDFDecoding neurodegeneration one cell at a time
Neurodegenerative diseases are characterized by protein misfolding and the selective vulnerability of specific neuronal subtypes. This selective vulnerability presents a paradox; most neurodegenerative disease genes are expressed broadly throughout the brain, and some ubiquitously, but …
Read PDFModern genomic and omics-based technologies for millet breeding and genetic improvement
Millets are a diverse group of small seeded grasses that have long served as vital staple foods and forage crops across a wide range of agro-ecological regions. Known for their exceptional adaptability to marginal and …
Read PDFFrom Variant to Biomarker in NSCLC Immunotherapy Resistance: Multiomics Evidence Chains and Accountable AI Integration
Immune checkpoint inhibitors have become integral to the management of non-small cell lung cancer (NSCLC), yet both primary and acquired resistance remain frequent and are only partially captured by routine biomarkers such as programmed death-ligand …
Read PDFSpatial transcriptomics: challenges and future directions in musculoskeletal diseases
<h4>Purpose of review</h4>This review examines recent advancements in spatial transcriptomics and its current and potential use to advance musculoskeletal (MSK) research. These insights will be vital to address the complexity of MSK diseases and will …
Read PDFSpatially resolved ex vivo drug response profiling in SMARCB1-deficient sinonasal carcinoma
SMARCB1-deficient sinonasal carcinoma (SDSC) is a rare, highly aggressive malignancy with limited therapeutic options and no established preclinical models. Here, single-nucleus RNA sequencing (snRNAseq), spatial transcriptomics, and ex vivo patient-derived tissue slice culture (TSC) were …
Read PDFSpatial and multi-omic profiling reveals pericyte-derived CCL19 as a key prognostic factor in CNS lymphoma
Biological mechanisms underlying clinical heterogeneity in central nervous system lymphoma (CNSL) are largely unknown. While previous studies suggest the chemokine CLL19 as a crucial factor for the formation of CNSL in murine models, its role …
Read PDFIntegrated network pharmacology, transcriptomics and experimental validation to explore mechanisms of Wenyang Jiedu Granule on IAV-induced pneumonia
<h4>Objective</h4>Wenyang Jiedu Granule (WYJD) is an effective traditional Chinese medicine (TCM) preparation that has been generally applied for treating respiratory infectious diseases. Clinical observations involving thousands of cases have demonstrated that WYJD could alleviate disease …
Read PDFUsing an integrated omics approach to uncover the mechanisms underlying chemotherapy-induced peripheral neuropathy (CIPN)
Chemotherapy-induced peripheral neuropathy (CIPN) is a debilitating side effect with limited treatment options. The primary challenge in developing therapies is the lack of identified neurotoxic mechanisms. To address this, an integrated omics approach, combining transcriptomics, …
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