spatial-transcriptomics

Documents about spatial-transcriptomics

• A Targeted Spatial Transcriptomics Framework for a High-Resolution Human Skin Cell Atlas#4834Europe PMC
• The applications of single-cell and spatial transcriptomics in neuroscience and brain disorders.#218915NCBI PubMed Central
• Exploration of RNA outside segmented cells in spatial transcriptomics reveals extrasomatic RNA organization#367257Europe PMC
• OmniCell: Unified Foundation Modeling of Single-Cell and Spatial Transcriptomics for Cellular and Molecular Insights#390846bioRxiv / medRxiv
• AddaGCN: Spatial transcriptomics deconvolution using graph convolutional networks with adversarial discriminative domain adaptation.#449987NCBI PubMed Central
• Benchmarking sketching methods on spatial transcriptomics data#485395Europe PMC
• Integrative single-cell and spatial transcriptomic approaches to decipher the tumor microenvironment and therapeutic resistance in pancreatic cancer#642689Europe PMC
• A systematic benchmark of bioinformatics methods for single-cell and spatial RNA-seq Nanopore long-read data#669996HAL (France)
• ​​Integrating machine learning and spatial transcriptomics uncovers shared immunomodulatory deubiquitinases in MAFLD and HCC.#3915NCBI PubMed Central
• Reconstructing 3D transcriptional organization from spatial transcriptomics reveals consistent oncogenic translocations and developmental dynamics.#148335NCBI PubMed Central
• SMIntegration: A web tool for comprehensive spatial metabolomics and transcriptomics integrated analysis and visualization.#174627NCBI PubMed Central
• Interpretable, flexible and spatially aware integration of multiple spatial transcriptomics datasets from diverse sources.#193594NCBI PubMed Central
• Label-free selection of marker genes in single-cell and spatial transcriptomics with geneCover.#247700NCBI PubMed Central
• 4D single-cell spatial transcriptomics reveals dynamic morphogenetic gradients and regenerative domains in planarians.#288815NCBI PubMed Central
• Spatial transcriptomics uncovers vasculature-centered cellular interactions driving Japanese encephalitis progression in a mouse model.#159905NCBI PubMed Central
• Reconstructing cell-cell interaction network in single-cell spatial transcriptomics via directed heterogeneous graph autoencoder.#219005NCBI PubMed Central
• Spatial transcriptomics uncovers the hybrid molecular identity, ciliated phenotype, and immune signature of adenomyosis lesions.#312520NCBI PubMed Central
• Lipedema as a disorder of adipose tissue heterogeneity: insights from single-cell and spatial transcriptomics.#334868NCBI PubMed Central
• Mapping safety in space: the emerging role of spatial transcriptomics in safe drug development.#368091NCBI PubMed Central
• SCAPeSCLC v1.3.5: Reproducible R Workflows#417074Zenodo (CERN)
• Single cell spatial transcriptomics track the evolutionary hierarchy and microenvironment remodeling during breast carcinoma invasion.#449871NCBI PubMed Central
• A significant enrichment that is not: spatial nulls, co-expression, and the imaging transcriptomics of EEG alpha-power genetics#480150bioRxiv / medRxiv
• Ten quick tips for spatial transcriptomics analysis#928022PLOS
• STP-BENCH: A Unified Systematic Benchmark for Virtual Spatial Transcriptomics from Histopathology Images#973571arXiv (All)
• Harmonised benchmarking of foundation models for single-cell and spatial transcriptomics reveals context-dependent generalisation#1013626arXiv (All)
• Spatial transcriptomics identifies fibroblast-T cell crosstalk as a driver of Th2 polarization in allergic rhinitis.#152268NCBI PubMed Central
• Single-cell spatial transcriptomics and snRNA-seq decoding the organizational principles of functional modules in the mouse amygdala#339557bioRxiv / medRxiv
• GxP-Ready Single-Cell RNA-seq and Spatial Transcriptomics End-to-End Pipeline for Clinical Research.#371402NCBI PubMed Central
• Variational sparse Gaussian-process method for detecting spatially variable genes and cellular interactions in spatial transcriptomics.#371687NCBI PubMed Central
• Single-cell and spatial transcriptomics analysis of osteoarthritis: pathway regulation, cell interaction networks, and therapeutic translation.#472404NCBI PubMed Central
• SpCAST enables scalable and interpretable integration of single-cell RNA sequencing and single-cell-resolved spatial transcriptomics#999243arXiv (All)
• How Do We Visualize Space in Molecular Biology? A Study of Spatial Transcriptomics Visualization Practices#1034089arXiv (All)
• Spatial transcriptomics unveils immune cellular ecosystems associated with patient survival in diffuse large B-cell lymphoma.#125387NCBI PubMed Central
• Integrated single-cell and spatial transcriptomics reveal divergent immunological and stromal programs in peritoneal versus ovarian endometriosis.#251103NCBI PubMed Central
• Decoding early lung adenocarcinoma progression by single-cell and spatial transcriptomics reveals a CMA-related prognostic signature.#399645NCBI PubMed Central
• Accurate trajectory inference in time-series spatial transcriptomics with structurally-constrained optimal transport#485115Europe PMC
• Optimal gene panel selection for targeted spatial transcriptomics experiments#485192Europe PMC
• Spatial transcriptomics unveils immune cellular ecosystems associated with patient survival in diffuse large B-cell lymphoma#130413Unpaywall
• Single-cell spatial transcriptomics reveals tumor microenvironment heterogeneity in primary and lymph node-metastatic small cell lung cancer.#148375NCBI PubMed Central
• Integrating spatial and single-cell transcriptomics via machine learning to characterize efferocytosis in hepatocellular carcinoma prognosis and immunotherapy.#227790NCBI PubMed Central
• Integrating optogenetic fMRI and spatial transcriptomics to reveal circuit-specific gene signatures in fronto- and hippo-thalamic networks.#295299NCBI PubMed Central
• Path2ST: Hierarchical Cell-Tissue Grounded Cross-Modal Translation for Spatial Transcriptomics#609143arXiv (OAI Expanded)
• Correlation-Guided Flow Matching with Annealed Masking for Spatial Transcriptomics Generation#1036870arXiv (All)
• scGPD: single-cell informed gene panel design for targeted spatial transcriptomics#1052979Europe PMC
• Metabolic Dysfunction-Associated Steatohepatitis (MASH) GeoMx and COMET Dataset#211387KU Leuven RDR Dataverse OAI Archive
• PIASO tutorial and processed single-cell omics datasets#124827DataCite
• PIASO tutorial and processed single-cell omics datasets#124828DataCite
• Spatial and single-cell transcriptomics reveal a HIF-1α/NF-κB-driven hypoxia-induced senescence axis in BPH epithelium.#298876NCBI PubMed Central
• Impact of data quality on deep learning prediction of spatial transcriptomics from histology images#484950Europe PMC
• Identification of Ferro-Aging-Related Biomarkers for Ulcerative Colitis Through Integrated Machine Learning, Single-Cell Analysis, and Spatial Transcriptomics.#621049NCBI PubMed Central