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Spatial Transcriptomics Inc multi omics spatial molecular data
a SEPAR is a framework based on graph-regularized NMF designed to identify spatially aware metagene patterns using both spatial location and gene expression as input. Spatial location data is leveraged to construct weighted graph regularization capturing the spatial relationships of the spots or cells. Sparsity regularization and dissimilarity regularization are applied to ensure distinct spatial metagene patterns. b SEPAR supports efficient and robust downstream analyses of SRT data, including metagene expression pattern recognition, pattern-specific gene analysis, SVG identification, spatial domain delineation, gene expression denoising and <t>spatial</t> <t>multi-omics</t> data analysis.
Multi Omics Spatial Molecular Data, supplied by Spatial Transcriptomics Inc, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/spatial+multi-omics/cell+single/pmc12820152-293-39-6
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multi omics spatial molecular data - by Bioz Stars, 2026-09
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Article Title: SEPAR enables spatial metagene discovery and associated molecular pattern characterization in spatial transcriptomics and multi-omics datasets

Journal: Communications Biology

doi: 10.1038/s42003-025-09340-w

a SEPAR is a framework based on graph-regularized NMF designed to identify spatially aware metagene patterns using both spatial location and gene expression as input. Spatial location data is leveraged to construct weighted graph regularization capturing the spatial relationships of the spots or cells. Sparsity regularization and dissimilarity regularization are applied to ensure distinct spatial metagene patterns. b SEPAR supports efficient and robust downstream analyses of SRT data, including metagene expression pattern recognition, pattern-specific gene analysis, SVG identification, spatial domain delineation, gene expression denoising and spatial multi-omics data analysis.
Figure Legend Snippet: a SEPAR is a framework based on graph-regularized NMF designed to identify spatially aware metagene patterns using both spatial location and gene expression as input. Spatial location data is leveraged to construct weighted graph regularization capturing the spatial relationships of the spots or cells. Sparsity regularization and dissimilarity regularization are applied to ensure distinct spatial metagene patterns. b SEPAR supports efficient and robust downstream analyses of SRT data, including metagene expression pattern recognition, pattern-specific gene analysis, SVG identification, spatial domain delineation, gene expression denoising and spatial multi-omics data analysis.

Techniques Used: Gene Expression, Construct, Expressing, Biomarker Discovery

Related Articles

other:

Article Title: A spatial and projection-based transcriptomic atlas of paraventricular hypothalamic cell types.
Article Snippet: We leveraged single-cell and spatial transcriptomics technologies to develop a high-resolution, spatially resolved atlas of the mouse PVH region.

Article Title: Immunological mechanisms underlying fibrotic diseases via single-cell technologies
Article Snippet: In a study that analyzed both the fibrotic progression and resolution phases of the bleomycin model using single-cell and spatial transcriptomics , CSMD1 + fibroblasts with ECM-secreting properties were induced during the progression phase, whereas CD248 + fibroblasts with tissue repair-promoting properties were induced during the resolution phase ( ).

Article Title: Advancing Cardiovascular Research With Single-Cell and Spatial Transcriptomics
Article Snippet: Single-cell and spatial transcriptomics technologies have transformed the landscape of cardiovascular research, leading to novel insights into cellular heterogeneity and tissue architecture in health and disease.. These technologies enable researchers to deconvolute complex tissues and map gene expression patterns within their spatial contexts, providing critical information on the interplay between cell types and pathways affecting tissue regeneration or progression to fibrosis.. This review presents an overview of the recently developed applications of single-cell and spatial transcriptomics methods and their impact on cardiovascular research.

Construct:

Article Title: Neuro‐Immune Crosstalk: Molecular Mechanisms, Biological Functions, Diseases, and Therapeutic Targets
Article Snippet: .. To overcome these challenges, researchers have developed cutting‐edge tools, including: (1) high‐resolution spatial multiomics platforms (e.g., integrated spatial transcriptomics‐proteomics) for spatiotemporal mapping of neuro‐immune interactions to construct comprehensive “neuro‐immune connectomes”; (2) optimized organoid coculture systems, particularly brain–immune cell interaction models; and (3) advanced in vivo imaging techniques (e.g., two‐photon microscopy coupled with specific reporter systems) for real‐time observation of neuro‐immune processes. ..

In Vivo Imaging:

Article Title: Neuro‐Immune Crosstalk: Molecular Mechanisms, Biological Functions, Diseases, and Therapeutic Targets
Article Snippet: .. To overcome these challenges, researchers have developed cutting‐edge tools, including: (1) high‐resolution spatial multiomics platforms (e.g., integrated spatial transcriptomics‐proteomics) for spatiotemporal mapping of neuro‐immune interactions to construct comprehensive “neuro‐immune connectomes”; (2) optimized organoid coculture systems, particularly brain–immune cell interaction models; and (3) advanced in vivo imaging techniques (e.g., two‐photon microscopy coupled with specific reporter systems) for real‐time observation of neuro‐immune processes. ..

Microscopy:

Article Title: Neuro‐Immune Crosstalk: Molecular Mechanisms, Biological Functions, Diseases, and Therapeutic Targets
Article Snippet: .. To overcome these challenges, researchers have developed cutting‐edge tools, including: (1) high‐resolution spatial multiomics platforms (e.g., integrated spatial transcriptomics‐proteomics) for spatiotemporal mapping of neuro‐immune interactions to construct comprehensive “neuro‐immune connectomes”; (2) optimized organoid coculture systems, particularly brain–immune cell interaction models; and (3) advanced in vivo imaging techniques (e.g., two‐photon microscopy coupled with specific reporter systems) for real‐time observation of neuro‐immune processes. ..

Single Cell:

Article Title: Co-localization analysis of spatial transcriptomics in ligand-receptor pairs from tumor microenvironment.
Article Snippet: Ligand-receptor pair analysis, a key aspect of cell-to-cell interactions, is vital for understanding physiological and pathological processes in organisms.. However, most analytical tools fail to incorporate spatial in situ information, resulting in false positive predictions.. Spatial transcriptomics, which integrates gene expression data with cellular localization, has emerged as a powerful method for inferring cell-cell interactions.

Article Title: Immunometabolic reprogramming of macrophages: Emerging roles in skeletal muscle regeneration and therapeutic perspectives.
Article Snippet: .. Recent advances in single-cell and spatial transcriptomics technologies have revealed the remarkable heterogeneity of macrophage subpopulations within skeletal muscle. ..

Transcriptomics:

Article Title: Co-localization analysis of spatial transcriptomics in ligand-receptor pairs from tumor microenvironment.
Article Snippet: Ligand-receptor pair analysis, a key aspect of cell-to-cell interactions, is vital for understanding physiological and pathological processes in organisms.. However, most analytical tools fail to incorporate spatial in situ information, resulting in false positive predictions.. Spatial transcriptomics, which integrates gene expression data with cellular localization, has emerged as a powerful method for inferring cell-cell interactions.

Cell Characterization:

Article Title: Ontogeny of the spinal cord dorsal horn.
Article Snippet: INTRODUCTION: In every part of our bodies, cell types and anatomy are organized to carry out specialized functions, and the dorsal horn of the mammalian spinal cord serves as a prime example.. It is characterized by a vast array of cell types arranged in a layered microcircuit architecture, with each layer receiving a specific set of sensory and descending neural inputs and contributing in a distinctive manner to animal behavior.. In this way, the dorsal horn represents a common motif of neural organization found throughout the animal kingdom, from the vertebrate midbrain to the fly’s optic lobe.

Article Title: Ontogeny of the spinal cord dorsal horn
Article Snippet: .. For EdU cell count coordinates (and later also for spatial transcriptomics cell coordinates), cell coordinates were normalized so that statistics and graphics could be produced systematically on cell coordinates across sections and experimental groups. ..

Spatial Transcriptomics:

Article Title: Ontogeny of the spinal cord dorsal horn.
Article Snippet: INTRODUCTION: In every part of our bodies, cell types and anatomy are organized to carry out specialized functions, and the dorsal horn of the mammalian spinal cord serves as a prime example.. It is characterized by a vast array of cell types arranged in a layered microcircuit architecture, with each layer receiving a specific set of sensory and descending neural inputs and contributing in a distinctive manner to animal behavior.. In this way, the dorsal horn represents a common motif of neural organization found throughout the animal kingdom, from the vertebrate midbrain to the fly’s optic lobe.

Article Title: Immunometabolic reprogramming of macrophages: Emerging roles in skeletal muscle regeneration and therapeutic perspectives.
Article Snippet: .. Recent advances in single-cell and spatial transcriptomics technologies have revealed the remarkable heterogeneity of macrophage subpopulations within skeletal muscle. ..

Article Title: Ontogeny of the spinal cord dorsal horn
Article Snippet: .. For EdU cell count coordinates (and later also for spatial transcriptomics cell coordinates), cell coordinates were normalized so that statistics and graphics could be produced systematically on cell coordinates across sections and experimental groups. ..

Produced:

Article Title: Ontogeny of the spinal cord dorsal horn.
Article Snippet: INTRODUCTION: In every part of our bodies, cell types and anatomy are organized to carry out specialized functions, and the dorsal horn of the mammalian spinal cord serves as a prime example.. It is characterized by a vast array of cell types arranged in a layered microcircuit architecture, with each layer receiving a specific set of sensory and descending neural inputs and contributing in a distinctive manner to animal behavior.. In this way, the dorsal horn represents a common motif of neural organization found throughout the animal kingdom, from the vertebrate midbrain to the fly’s optic lobe.

Article Title: Ontogeny of the spinal cord dorsal horn
Article Snippet: .. For EdU cell count coordinates (and later also for spatial transcriptomics cell coordinates), cell coordinates were normalized so that statistics and graphics could be produced systematically on cell coordinates across sections and experimental groups. ..



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Image Search Results


a SEPAR is a framework based on graph-regularized NMF designed to identify spatially aware metagene patterns using both spatial location and gene expression as input. Spatial location data is leveraged to construct weighted graph regularization capturing the spatial relationships of the spots or cells. Sparsity regularization and dissimilarity regularization are applied to ensure distinct spatial metagene patterns. b SEPAR supports efficient and robust downstream analyses of SRT data, including metagene expression pattern recognition, pattern-specific gene analysis, SVG identification, spatial domain delineation, gene expression denoising and spatial multi-omics data analysis.

Journal: Communications Biology

Article Title: SEPAR enables spatial metagene discovery and associated molecular pattern characterization in spatial transcriptomics and multi-omics datasets

doi: 10.1038/s42003-025-09340-w

Figure Lengend Snippet: a SEPAR is a framework based on graph-regularized NMF designed to identify spatially aware metagene patterns using both spatial location and gene expression as input. Spatial location data is leveraged to construct weighted graph regularization capturing the spatial relationships of the spots or cells. Sparsity regularization and dissimilarity regularization are applied to ensure distinct spatial metagene patterns. b SEPAR supports efficient and robust downstream analyses of SRT data, including metagene expression pattern recognition, pattern-specific gene analysis, SVG identification, spatial domain delineation, gene expression denoising and spatial multi-omics data analysis.

Article Snippet: Beyond demonstrating robust performance in diverse spatial transcriptomics technologies (10 × Visium, Stereo-seq, osmFISH and MERFISH), where SEPAR consistently identified biologically meaningful spatial patterns and revealed tissue-specific expression programs across different resolution scales and measurement principles, SEPAR effectively handles multi-omics spatial molecular data.

Techniques: Gene Expression, Construct, Expressing, Biomarker Discovery

Technologies for assaying intratumoral heterogeneity.

Journal: Cancers

Article Title: Heterogeneity in Cancer

doi: 10.3390/cancers17030441

Figure Lengend Snippet: Technologies for assaying intratumoral heterogeneity.

Article Snippet: Spatial multi-omics (e.g., GeoMX) , Combines IF with spatial transcriptomics through UV cleavage of ROIs , High-throughput spatial profiling of both transcriptome and protein panel in a tissue sample , [ ] .

Techniques: Gene Expression, Fluorescence, Expressing, Protein-Protein interactions, Activity Assay, In Situ, Biomarker Discovery