Search Results - "Spatial Transcriptomics"

Integrated spatial morpho-transcriptomics predicts functional traits in pancreatic cancer.

Authors: Gong D Liu R Cui Y et al.

Source: Science advances [Sci Adv] 2025 Oct 17; Vol. 11 (42), pp. eadx0632. Date of Electronic Publication: 2025 Oct 17.

Publication Type: Journal Article

Journal Info: Publisher: American Association for the Advancement of Science Country of Publication: United States NLM ID: 101653440 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 2375-2548 (Electronic) Linking ISSN: 23752548 NLM ISO Abbreviation: Sci Adv Subsets: MEDLINE

MeSH Terms: Pancreatic Neoplasms*/drug therapy , Pancreatic Neoplasms*/genetics , Pancreatic Neoplasms*/pathology , Carcinoma, Pancreatic Ductal*/drug therapy , Carcinoma, Pancreatic Ductal*/genetics , Carcinoma, Pancreatic Ductal*/pathology , Proto-Oncogene Proteins p21(ras)*/antagonists & inhibitors , Proto-Oncogene Proteins p21(ras)*/genetics , Proto-Oncogene Proteins p21(ras)*/metabolism , Spatial Transcriptomics*/economics , Spatial Transcriptomics*/methods, Gene Expression Regulation, Neoplastic/drug effects ; Drug Resistance, Neoplasm/drug effects ; Drug Resistance, Neoplasm/genetics ; Antineoplastic Agents/pharmacology ; Antineoplastic Agents/therapeutic use ; Precision Medicine/economics ; Precision Medicine/methods ; Single-Cell Analysis/economics ; Single-Cell Analysis/methods ; Biomarkers, Tumor/analysis ; Biomarkers, Tumor/genetics ; Biomarkers, Tumor/metabolism ; Cell Line, Tumor ; Transcriptome ; Humans ; Cost-Effectiveness Analysis ; Heterocyclic Compounds, 2-Ring ; Naphthalenes ; Piperazines

Spatial transcriptomics and immunophenotyping uncover chronic inflammation-induced immune adaptations favoring dysplasia development in patients at risk of colitis-associated cancer.

Authors: Frigerio S Khan HN Amini M et al.

Source: Journal of Crohn's & colitis [J Crohns Colitis] 2025 Nov 08; Vol. 19 (10).

Publication Type: Clinical Study; Journal Article

Journal Info: Publisher: Oxford University Press Country of Publication: England NLM ID: 101318676 Publication Model: Print Cited Medium: Internet ISSN: 1876-4479 (Electronic) Linking ISSN: 18739946 NLM ISO Abbreviation: J Crohns Colitis Subsets: MEDLINE

MeSH Terms: Spatial Transcriptomics*/methods , Immunophenotyping*/methods , Colorectal Neoplasms*/etiology , Colorectal Neoplasms*/genetics , Colorectal Neoplasms*/immunology , Colorectal Neoplasms*/pathology , Colitis*/complications , Colitis*/genetics , Colitis*/immunology , Colitis*/pathology , Inflammatory Bowel Diseases*/complications , Inflammatory Bowel Diseases*/genetics , Inflammatory Bowel Diseases*/immunology , Inflammatory Bowel Diseases*/pathology, Stress, Physiological/genetics ; Stress, Physiological/immunology ; Colon/immunology ; Colon/metabolism ; Colon/pathology ; Intestinal Mucosa/immunology ; Intestinal Mucosa/metabolism ; Intestinal Mucosa/pathology ; Interleukin-10/metabolism ; CD8-Positive T-Lymphocytes/immunology ; Humans ; Inflammation ; Risk Factors ; Risk Assessment ; Male ; Female ; Adult ; Middle Aged ; Aged

Spatial hallmarks of cancer: blueprinting precision oncology in MIBC and beyond

Authors: Sibai, Mustafa

Thesis Advisors: Porta Pardo, Eduard, Lorenzo Rivera, Julia

Source: TDX (Tesis Doctorals en Xarxa)

Subject Terms: Transcriptòmica espacial, Spatial transcriptomics, Transcriptómica espacial, Característiques distintives d, Cancer hallmarks, Características distintivas de, Oncologia de precisió, Precision oncology, Oncología de precisión, Ciències de la Salut

File Description: application/pdf

Access URL: http://hdl.handle.net/10803/695955

Spatial gene expression profiling reveals the distinct microenvironment of tuberous sclerosis complex-associated angiomyolipoma.

Authors: Watanabe R Fukumoto T Miura N et al.

Source: Scientific reports [Sci Rep] 2025 Nov 27; Vol. 15 (1), pp. 42470. Date of Electronic Publication: 2025 Nov 27.

Publication Type: Case Reports; Journal Article

Journal Info: Publisher: Nature Publishing Group Country of Publication: England NLM ID: 101563288 Publication Model: Electronic Cited Medium: Internet ISSN: 2045-2322 (Electronic) Linking ISSN: 20452322 NLM ISO Abbreviation: Sci Rep Subsets: MEDLINE

MeSH Terms: Tuberous Sclerosis*/complications , Tuberous Sclerosis*/metabolism , Tuberous Sclerosis*/pathology , Angiomyolipoma*/genetics , Angiomyolipoma*/metabolism , Angiomyolipoma*/pathology , Kidney Neoplasms*/genetics , Kidney Neoplasms*/metabolism , Kidney Neoplasms*/pathology , Biomarkers, Tumor*/genetics , Biomarkers, Tumor*/metabolism, Carcinoma, Renal Cell/metabolism ; Carcinoma, Renal Cell/pathology ; Kidney/pathology ; Spatial Transcriptomics ; Tumor Microenvironment ; Humans ; Female ; Aged ; Male ; Adult ; Middle Aged

Integrated Spatial and Single-Cell Transcriptomics Reveals Poor Prognostic Ligand-Receptor Pairs in Glioblastoma.

Authors: Yoshimoto M Sugihara K Tokumura K et al.

Source: Cells [Cells] 2025 Oct 01; Vol. 14 (19). Date of Electronic Publication: 2025 Oct 01.

Publication Type: Journal Article

Journal Info: Publisher: MDPI Country of Publication: Switzerland NLM ID: 101600052 Publication Model: Electronic Cited Medium: Internet ISSN: 2073-4409 (Electronic) Linking ISSN: 20734409 NLM ISO Abbreviation: Cells Subsets: MEDLINE

MeSH Terms: Glioblastoma*/diagnosis , Glioblastoma*/genetics , Glioblastoma*/mortality , Brain Neoplasms*/diagnosis , Brain Neoplasms*/genetics , Brain Neoplasms*/mortality, Cell Communication/genetics ; Receptors, Cell Surface/genetics ; Single-Cell Gene Expression Analysis ; Ligands ; Datasets as Topic ; Spatial Transcriptomics ; Prognosis ; Humans

Decoding Alzheimer's Disease: Single-Cell Sequencing Uncovers Brain Cell Heterogeneity and Pathogenesis.

Authors: Ma YN Xia Y Karako K et al.

Source: Molecular neurobiology [Mol Neurobiol] 2025 Nov; Vol. 62 (11), pp. 14459-14473. Date of Electronic Publication: 2025 Apr 30.

Publication Type: Journal Article; Review

Journal Info: Publisher: Humana Press Country of Publication: United States NLM ID: 8900963 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1559-1182 (Electronic) Linking ISSN: 08937648 NLM ISO Abbreviation: Mol Neurobiol Subsets: MEDLINE

MeSH Terms: Alzheimer Disease*/diagnosis , Alzheimer Disease*/genetics , Alzheimer Disease*/pathology , Single-Cell Analysis*/methods , Brain*/cytology , Brain*/pathology, Humans ; Gene Expression Profiling ; Epigenomics ; Single-Cell Gene Expression Analysis ; Spatial Transcriptomics

Neurobiological subtypes of adolescent depression: a multimodal integration of morphometric similarity network and spatial transcriptomics.

Authors: Wu P Kong L Zhou Y et al.

Source: Molecular psychiatry [Mol Psychiatry] 2025 Nov; Vol. 30 (11), pp. 5448-5462. Date of Electronic Publication: 2025 Aug 02.

Publication Type: Journal Article

Journal Info: Publisher: Nature Publishing Group Specialist Journals Country of Publication: England NLM ID: 9607835 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1476-5578 (Electronic) Linking ISSN: 13594184 NLM ISO Abbreviation: Mol Psychiatry Subsets: MEDLINE

MeSH Terms: Major Depressive Disorder*/classification , Major Depressive Disorder*/genetics , Major Depressive Disorder*/metabolism , Major Depressive Disorder*/physiopathology , Nerve Net*/physiopathology , Cerebral Cortex*/diagnostic imaging , Cerebral Cortex*/metabolism , Cerebral Cortex*/physiopathology, Cognition/physiology ; Impulsive Behavior/physiology ; Emotional Regulation/physiology ; GABAergic Neurons/metabolism ; Endocannabinoids/metabolism ; MAP Kinase Signaling System/physiology ; Astrocytes/metabolism ; Microglia/metabolism ; Spatial Transcriptomics ; Neurodevelopment ; Neuroimaging ; Humans ; Male ; Female ; Child ; Adolescent ; Magnetic Resonance Imaging ; Case-Control Studies ; Healthy Volunteers

Progressive fibrosis in human MASLD is associated with spatially linked transcriptomic signatures of metabolic reprogramming and senescence

Authors: Vu, Hani Sun, Yuliangzi Xiong, Zherui et al.

Source: JHEP Reports. 8(2)

Subject Terms: Liver, Senesence, Spatial Transcriptomics, Steatosis, Fibrosis, Metabolism, MASLD, inflammation

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Access URL: https://urn.kb.se/resolve?urn=urn:nbn:se:oru:diva-126223
https://doi.org/10.1016/j.jhepr.2025.101657

Bacterial Systematic Genetics and Integrated Multi-Omics: Beyond Static Genomics Toward Predictive Models.

Authors: Sakaguchi T Irifune Y Kamada R et al.

Source: International journal of molecular sciences [Int J Mol Sci] 2025 Sep 24; Vol. 26 (19). Date of Electronic Publication: 2025 Sep 24.

Publication Type: Journal Article; Review

Journal Info: Publisher: MDPI Country of Publication: Switzerland NLM ID: 101092791 Publication Model: Electronic Cited Medium: Internet ISSN: 1422-0067 (Electronic) Linking ISSN: 14220067 NLM ISO Abbreviation: Int J Mol Sci Subsets: MEDLINE

MeSH Terms: Systems Biology*/methods , Systems Biology*/trends , Multiomics*/methods , Multiomics*/trends , Genomics*/methods , Genomics*/trends , Genome, Bacterial*, Proteomics/methods ; Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; Microfluidics/methods ; Genome-Wide Association Study ; Protein Interaction Mapping ; Spatial Transcriptomics ; Single-Cell Gene Expression Analysis ; Quantitative Trait Loci ; Polymorphism, Single Nucleotide ; Gene Editing ; Machine Learning ; Metabolic Engineering ; Drug Discovery

Charting the single-cell and spatial landscape of IDH-wild-type glioblastoma with GBmap

Authors: Ruiz-Moreno, Cristian Salas, Sergio Marco Samuelsson, Erik et al.

Source: Neuro-Oncology. 27(9):2281-2295

Subject Terms: glioblastoma, hypoxia, spatial transcriptomics, single-cell atlas, tumor organization

File Description: electronic

Access URL: https://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-578346
https://doi.org/10.1093/neuonc/noaf113

CiCLoDS: Joint cell clustering and gene selection for single-cell spatial transcriptomics.

Authors: Wang, Nuozhou He, Yimeng Ray, Edward et al.

Source: Scientific Reports. 2/9/2026, Vol. 16 Issue 1, p1-12. 12p.

Subject Terms: *FEATURE selection, *SPATIAL transcriptomics, *CLUSTERING algorithms, *BIOINFORMATICS, *DATA analysis, *QUANTITATIVE research, *TRANSCRIPTOMES

Long-Read Spatial Transcriptomics of Patient-Derived Clear Cell Renal Cell Carcinoma Organoids Identifies Heterogeneity and Transcriptional Remodelling Following NUC-7738 Treatment.

Authors: Abdullah, Hazem Zhang, Ying Kirkwood, Kathryn et al.

Source: Cancers. Jan2026, Vol. 18 Issue 2, p254. 15p.

Subject Terms: *SPATIAL transcriptomics, *GENE expression profiling, *RENAL cell carcinoma, *CULTURES (Biology)

Multi-omics and high-spatial-resolution omics: deciphering complexity in neurological disorders.

Authors: Liu X Li F Czosnyka M et al.

Source: GigaScience [Gigascience] 2025 Jan 06; Vol. 14.

Publication Type: Journal Article; Systematic Review

Journal Info: Publisher: Oxford University Press Country of Publication: United States NLM ID: 101596872 Publication Model: Print Cited Medium: Internet ISSN: 2047-217X (Electronic) Linking ISSN: 2047217X NLM ISO Abbreviation: Gigascience Subsets: MEDLINE

MeSH Terms: Computational Biology*/trends , Nervous System Diseases*/diagnosis , Nervous System Diseases*/genetics , Nervous System Diseases*/metabolism, Multiomics/trends ; Spatial Transcriptomics/trends ; Animals ; Humans ; Single-Cell Gene Expression Analysis

Spatial Transcriptomic Assessments of Gene Expression Profiles in Human Peri-Implant Lesions

Authors: Dionigi, Carlotta Ericson, Anna-Carin Shikhan, Asal et al.

Source: JOURNAL OF CLINICAL PERIODONTOLOGY. 53(1):137-151

Subject Terms: Clinical Medicine, Klinisk medicin, biopsy, immunohistochemistry, peri-implantitis, RNA-sequencing, spatial transcriptomics

Access URL: https://gup.ub.gu.se/publication/354928

Charting intra-tumoral heterogeneity dynamics through the integration of multi-modal single-cell profiles

Authors: Elosua-Bayés, Marc

Contributors: University/Department: Universitat Pompeu Fabra. Departament de Medicina i Ciències de la Vida

Thesis Advisors: Gut, Ivo Glynne, Heyn, Holger

Source: TDX (Tesis Doctorals en Xarxa)

Subject Terms: single-cell RNA-sequencing, seqüenciació d’ARN de cèl·lules individuals, Spatial Transcriptomics, Transcriptómica Espacial, Cell type deconvolution, Descomposició de tipus cel·lulars, Immuno-oncology, Immuno-oncologia, Tumor Immune Cell Atlas, Atlas de Cèl·lules Immunes, Schwann cells, Cèl·lules de Schwann, Cancer, Càncer, Metastasis, Metàstasi

File Description: application/pdf

Access URL: http://hdl.handle.net/10803/688558

A perspective on developing foundation models for analyzing spatial transcriptomic data.

Authors: Liu, Tianyu Hao, Minsheng Liu, Xinhao et al.

Source: Quantitative Biology. Dec2025, Vol. 13 Issue 4, p1-6. 6p.

Subject Terms: *TRANSCRIPTOMES, *SPATIAL transcriptomics

Spatial transcriptomics iterative hierarchical clustering (stIHC): A novel method for identifying spatial gene co‐expression modules

Authors: Higgins, Catherine Li, Jingyi Jessica Carey, Michelle

Source: Quantitative Biology. 13(4)

Subject Terms: 31 Biological Sciences (for-2020), 3102 Bioinformatics and Computational Biology (for-2020), 3105 Genetics (for-2020), Genetics (rcdc), Biotechnology (rcdc), Human Genome (rcdc), Bioengineering (rcdc), functional data analysis, functionally related genes, gene co-expression modules, spatial transcriptomics, spatially variable genes, 0601 Biochemistry and Cell Biology (for), 3102 Bioinformatics and computational biology (for-2020)

Access URL: https://escholarship.org/uc/item/55r7d8v2

Spatial transcriptomics reveals an unexpected impact of tau and tau pathology on the expression of transthyretin

Authors: Croteau, Deborah L. Fernandez Navarro, Jose Comptdaer, Thomas et al.

Source: Frontiers in Aging Neuroscience. 17

Subject Terms: aggregation, amyloid beta, spatial transcriptomics, tau, tauopathies, transthyretin

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Access URL: https://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-373338
https://doi.org/10.3389/fnagi.2025.1656850

Standalone single- and bi-layered human skin 3D models supported by recombinant silk feature native spatial organization

Authors: Gkouma, Savvini Bhalla, Nayanika Frapard, Solene et al.

Source: Biofabrication. 17(1)

Subject Terms: 3D in vitro model, basement membrane, bilayered skin model, cornification, recombinant silk, spatial transcriptomics, vascularization

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Access URL: https://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-356696
https://doi.org/10.1088/1758-5090/ad8b72

Oligodendroglia vulnerability in the human dorsal striatum in Parkinson’s disease

Authors: Barba-Reyes, Juan M. Harder, Lisbeth Marco Salas, Sergio et al.

Source: Acta Neuropathologica. 149(1)

Subject Terms: Myelin, Neurodegeneration, Oligodendrocyte, Sc-RNA-seq, Spatial transcriptomics, Striatum

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Access URL: https://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-243311
https://doi.org/10.1007/s00401-025-02884-5