Search Results - Spatial Transcriptomics methods

SpaceBar enables single-cell-resolution clone tracing with imaging-based spatial transcriptomics.

Authors: Kinsler G Fagan C Li H et al.

Source: Nature methods [Nat Methods] 2026 Feb; Vol. 23 (2), pp. 328-333. Date of Electronic Publication: 2025 Dec 18.

Publication Type: Journal Article

Journal Info: Publisher: Nature Pub. Group Country of Publication: United States NLM ID: 101215604 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1548-7105 (Electronic) Linking ISSN: 15487091 NLM ISO Abbreviation: Nat Methods Subsets: MEDLINE

MeSH Terms: Single-Cell Analysis*/methods , Gene Expression Profiling*/methods , Transcriptome*, Animals ; Mice ; Clone Cells ; Humans

Advancing Cardiovascular Research With Single-Cell and Spatial Transcriptomics.

Authors: Li K Samiei S Pikulska D et al.

Source: Circulation research [Circ Res] 2026 Jan 02; Vol. 138 (1), pp. e325795. Date of Electronic Publication: 2026 Jan 02.

Publication Type: Journal Article; Review

Journal Info: Publisher: Lippincott Williams & Wilkins Country of Publication: United States NLM ID: 0047103 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1524-4571 (Electronic) Linking ISSN: 00097330 NLM ISO Abbreviation: Circ Res Subsets: MEDLINE

MeSH Terms: Single-Cell Analysis*/methods , Cardiovascular Diseases*/genetics , Cardiovascular Diseases*/metabolism , Cardiovascular Diseases*/pathology , Gene Expression Profiling*/methods , Transcriptome*, Humans ; Animals

Rigor and Reproducibility of Spatial Transcriptomics Performed on Clinically Sourced Human Tissues.

Authors: Smith KD MacDonald JW Li X et al.

Source: Laboratory investigation; a journal of technical methods and pathology [Lab Invest] 2025 Sep; Vol. 105 (9), pp. 104190. Date of Electronic Publication: 2025 Apr 29.

Publication Type: Journal Article

Journal Info: Publisher: Elsevier Inc Country of Publication: United States NLM ID: 0376617 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1530-0307 (Electronic) Linking ISSN: 00236837 NLM ISO Abbreviation: Lab Invest Subsets: MEDLINE

MeSH Terms: Gene Expression Profiling*/methods , Kidney*/metabolism , Kidney*/pathology , Transcriptome*, Single-Cell Analysis/methods ; Humans ; Reproducibility of Results

Multiplexed spatial transcriptomics methods and the application of expansion microscopy

Authors: Andra Fortner Octavian Bucur

Source: Front Cell Dev Biol
Frontiers in Cell and Developmental Biology, Vol 12 (2024)

Subject Terms: 0301 basic medicine, transcriptomics, ExSeq, Cell and Developmental Biology, 0303 health sciences, 03 medical and health sciences, QH301-705.5, spatial omics, Biology (General), expansion microscopy, MERFISH, FISSEQ

Access URL: https://pubmed.ncbi.nlm.nih.gov/39105173
https://doaj.org/article/23e24aa8140741e89b2cb2a673b0fcec

Technological Innovations and Applications of Spatial Transcriptomics in Livestock and Poultry Research.

Authors: Wang, Mingyu Guo, Ao Zhang, Lin et al.

Source: Animal Research & One Health. Feb2026, Vol. 4 Issue 1, p14-27. 14p.

Development and application of spatial transcriptomics methods

Authors: Andrusivova, Zaneta Lundeberg, Joakim, Professor Shin, Jay W., Doktor

Contributors: Andrusivova, Zaneta Lundeberg, Joakim, Professor Shin, Jay W., Doktor

Source: TRITA-CBH-FOU.

Subject Terms: RNA, Spatial Transcriptomics, RNA sequencing, Biotechnology, Bioteknologi

File Description: electronic

Access URL: https://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-334467
https://kth.diva-portal.org/smash/get/diva2:1789758/FULLTEXT01.pdf

Comparison of spatial transcriptomics technologies using tumor cryosections.

Authors: Rademacher A Huseynov A Bortolomeazzi M et al.

Source: Genome biology [Genome Biol] 2025 Jun 20; Vol. 26 (1), pp. 176. Date of Electronic Publication: 2025 Jun 20.

Publication Type: Journal Article; Comparative Study

Journal Info: Publisher: BioMed Central Ltd Country of Publication: England NLM ID: 100960660 Publication Model: Electronic Cited Medium: Internet ISSN: 1474-760X (Electronic) Linking ISSN: 14747596 NLM ISO Abbreviation: Genome Biol Subsets: MEDLINE

MeSH Terms: Gene Expression Profiling*/methods , Medulloblastoma*/genetics , Medulloblastoma*/pathology , Transcriptome*, Humans ; Tumor Microenvironment

From spots to cells: Cell segmentation in spatial transcriptomics with BOMS.

Authors: Kamboj O Park J Stegle O et al.

Source: PloS one [PLoS One] 2025 Jun 12; Vol. 20 (6), pp. e0311458. Date of Electronic Publication: 2025 Jun 12 (Print Publication: 2025).

Publication Type: Journal Article

Journal Info: Publisher: Public Library of Science Country of Publication: United States NLM ID: 101285081 Publication Model: eCollection Cited Medium: Internet ISSN: 1932-6203 (Electronic) Linking ISSN: 19326203 NLM ISO Abbreviation: PLoS One Subsets: MEDLINE

MeSH Terms: Gene Expression Profiling*/methods , Image Processing, Computer-Assisted*/methods , Transcriptome*, RNA, Messenger/genetics ; RNA, Messenger/metabolism ; Humans ; Software ; Algorithms

Spatial transcriptomics in breast cancer: providing insight into tumor heterogeneity and promoting individualized therapy.

Authors: An J Lu Y Chen Y et al.

Source: Frontiers in immunology [Front Immunol] 2024 Dec 19; Vol. 15, pp. 1499301. Date of Electronic Publication: 2024 Dec 19 (Print Publication: 2024).

Publication Type: Journal Article; Review

Journal Info: Publisher: Frontiers Research Foundation] Country of Publication: Switzerland NLM ID: 101560960 Publication Model: eCollection Cited Medium: Internet ISSN: 1664-3224 (Electronic) Linking ISSN: 16643224 NLM ISO Abbreviation: Front Immunol Subsets: MEDLINE

MeSH Terms: Breast Neoplasms*/genetics , Precision Medicine*/methods , Tumor Microenvironment*/genetics , Gene Expression Profiling*/methods , Transcriptome*, Biomarkers, Tumor/genetics ; Single-Cell Analysis/methods ; Humans ; Female ; Gene Expression Regulation, Neoplastic ; Genetic Heterogeneity

Homebuilt Imaging-Based Spatial Transcriptomics: Tertiary Lymphoid Structures as a Case Example.

Authors: Defard T Desrentes A Fouillade C et al.

Source: Methods in molecular biology (Clifton, N.J.) [Methods Mol Biol] 2025; Vol. 2864, pp. 77-105.

Publication Type: Journal Article

Journal Info: Publisher: Humana Press Country of Publication: United States NLM ID: 9214969 Publication Model: Print Cited Medium: Internet ISSN: 1940-6029 (Electronic) Linking ISSN: 10643745 NLM ISO Abbreviation: Methods Mol Biol Subsets: MEDLINE

MeSH Terms: Tertiary Lymphoid Structures*/genetics , Tertiary Lymphoid Structures*/pathology , Gene Expression Profiling*/methods , Transcriptome*, Humans ; Software ; Animals

Spatial transcriptomics and the anatomical pathologist: Molecular meets morphology.

Authors: Pang JB Byrne DJ Bergin ART et al.

Source: Histopathology [Histopathology] 2024 Mar; Vol. 84 (4), pp. 577-586. Date of Electronic Publication: 2023 Nov 22.

Publication Type: Journal Article; Review

Journal Info: Publisher: Blackwell Scientific Publications Country of Publication: England NLM ID: 7704136 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1365-2559 (Electronic) Linking ISSN: 03090167 NLM ISO Abbreviation: Histopathology Subsets: MEDLINE

MeSH Terms: Gene Expression Profiling*/methods , Pathologists*, Paraffin Embedding/methods ; Formaldehyde/metabolism ; Humans ; Transcriptome

Disparities in spatially variable gene calling highlight the need for benchmarking spatial transcriptomics methods

Authors: Natalie Charitakis Agus Salim Adam T. Piers et al.

Source: Genome Biology, Vol 24, Iss 1, Pp 1-12 (2023)

Subject Terms: Biology (General), QH301-705.5, Genetics, QH426-470

File Description: electronic resource

Relation: https://doaj.org/toc/1474-760X

Access URL: https://doaj.org/article/1b4f8dd834724091bdaa2bce84d5993b

Accurate single-molecule spot detection for image-based spatial transcriptomics with weakly supervised deep learning.

Authors: Laubscher E Wang X Razin N et al.

Source: Cell systems [Cell Syst] 2024 May 15; Vol. 15 (5), pp. 475-482.e6.

Publication Type: Journal Article

Journal Info: Publisher: Cell Press Country of Publication: United States NLM ID: 101656080 Publication Model: Print Cited Medium: Internet ISSN: 2405-4720 (Electronic) Linking ISSN: 24054712 NLM ISO Abbreviation: Cell Syst Subsets: MEDLINE

MeSH Terms: In Situ Hybridization, Fluorescence*/methods , Transcriptome*/genetics , Gene Expression Profiling*/methods , Deep Learning*, Single-Cell Analysis/methods ; Image Processing, Computer-Assisted/methods ; Single Molecule Imaging/methods ; Software ; Humans ; Animals ; Supervised Machine Learning

SpatioFreq: A Deep Learning Framework for Decoding Cellular and Tissue Landscapes Across Organisms Using Spatial Transcriptomics.

Authors: Wang Z Dai R Wang M et al.

Source: Interdisciplinary sciences, computational life sciences [Interdiscip Sci] 2026 Mar 06. Date of Electronic Publication: 2026 Mar 06.

Publication Type: Journal Article

Journal Info: Publisher: Springer-Verlag Country of Publication: Germany NLM ID: 101515919 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1867-1462 (Electronic) Linking ISSN: 18671462 NLM ISO Abbreviation: Interdiscip Sci Subsets: MEDLINE

Advancing sequencing-based spatial transcriptomics with a comprehensive benchmarking study.

Source: Nature methods [Nat Methods] 2024 Sep; Vol. 21 (9), pp. 1589-1590.

Publication Type: Editorial

Journal Info: Publisher: Nature Pub. Group Country of Publication: United States NLM ID: 101215604 Publication Model: Print Cited Medium: Internet ISSN: 1548-7105 (Electronic) Linking ISSN: 15487091 NLM ISO Abbreviation: Nat Methods Subsets: MEDLINE

MeSH Terms: Gene Expression Profiling*/methods , Benchmarking* , Transcriptome*, Sequence Analysis, RNA/methods ; Humans

SAGE-FM: A lightweight and interpretable spatial transcriptomics foundation model

Authors: Zhan, Xianghao Xu, Jingyu Zheng, Yuanning et al.

Subject Terms: Machine Learning, Genomics, Quantitative Methods

Relation: http://arxiv.org/abs/2601.15504

Availability: http://arxiv.org/abs/2601.15504

Super-resolved, three-dimensional spatial transcriptomics reveals cell-type and brain-region-specific modulation of key epitranscriptomic switches following adolescent alcohol exposure.

Authors: Tandukar J Islam A Malovic E et al.

Source: BioRxiv : the preprint server for biology [bioRxiv] 2026 Jan 23. Date of Electronic Publication: 2026 Jan 23.

Publication Type: Journal Article; Preprint

Journal Info: Country of Publication: United States NLM ID: 101680187 Publication Model: Electronic Cited Medium: Internet ISSN: 2692-8205 (Electronic) Linking ISSN: 26928205 NLM ISO Abbreviation: bioRxiv Subsets: PubMed not MEDLINE

Systems and Methods for Deconvolving Cell Types in Histology Slide Images, Using Super-Resolution Spatial Transcriptomics Data

Benchmarking of computational methods for Spatial Transcriptomics Data analysis

Jämförande analys av beräkningsmetoder för Spatial Transcriptomics data analyser

Authors: Taherpour, Nima

Subject Terms: Spatial Transcriptomics, Scanpy, Squidpy, Giotto, Seurat, Bioinformatics and Systems Biology, Bioinformatik och systembiologi

File Description: application/pdf

Relation: TRITA-CBH-GRU ; 2022:312

Availability: http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-321580

CIPHER: An end-to-end framework for designing optimized aggregated spatial transcriptomics experiments.

Authors: Hemminger Z De Ocampo H Xie F et al.

Source: BioRxiv : the preprint server for biology [bioRxiv] 2026 Jan 21. Date of Electronic Publication: 2026 Jan 21.

Publication Type: Journal Article; Preprint

Journal Info: Country of Publication: United States NLM ID: 101680187 Publication Model: Electronic Cited Medium: Internet ISSN: 2692-8205 (Electronic) Linking ISSN: 26928205 NLM ISO Abbreviation: bioRxiv Subsets: PubMed not MEDLINE