STAPLE: automating spatial transcriptomics analysis and AI interpretation.
| Title: | STAPLE: automating spatial transcriptomics analysis and AI interpretation. |
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| Authors: | Lvovs D; Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD USA.; Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD USA.; Department of Medicine, University of Maryland School of Medicine, Baltimore, MD USA.; Quinn J; Department of Computational Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.; Forjaz A; Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, MD.; Santana-Cruz I; Maryland Genomics, Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD USA.; Stapleton O; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.; Vavikolanu K; Maryland Genomics, Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD USA.; Wetzel M; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.; Bernard V; Department of Gastrointestinal Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX.; Herb BR; Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD USA.; Department of Pharmacology and Physiology, University of Maryland School of Medicine, Baltimore, MD USA.; Kahlert Institute for Addiction Medicine, University of Maryland School of Medicine, Baltimore, MD USA.; UM-MIND Institute for Neuroscience Discovery, University of Maryland School of Medicine, Baltimore, MD USA.; Favorov A; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.; Kagohara LT; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.; Kiemen AL; Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, MD.; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.; Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University, Baltimore, MD.; Department of Functional Anatomy & Evolution, Johns Hopkins University, Baltimore, MD, USA.; Maitra A; Department of Medicine, Laura and Isaac Perlmutter Cancer Center and New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.; Department of Pathology, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.; Sidiropoulos DN; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.; Tansey W; Department of Computational Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.; Wood LD; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.; Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University, Baltimore, MD.; Deshpande A; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.; Noble M; Break Through Cancer, Cambridge, MA, USA.; Fertig EJ; Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD USA.; Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD USA.; Department of Medicine, University of Maryland School of Medicine, Baltimore, MD USA.; Department of Epidemiology, University of Maryland School of Medicine, Baltimore, MD USA. |
| Corporate Authors: | Demystifying Pancreatic Cancer Therapies TeamLab; Data Science Hub Teamlab |
| Source: | BioRxiv : the preprint server for biology [bioRxiv] 2026 Apr 01. Date of Electronic Publication: 2026 Apr 01. |
| Publication Type: | Journal Article; Preprint |
| Language: | English |
| 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 |
| Abstract: | Spatial transcriptomics workflows often span separate tools for cell typing, neighborhoods, and cell-cell communication, yielding fragmented outputs that hinder scalability, interpretation, and reproducibility. STAPLE systematizes analyses across distinct methods into a modular framework, unifying data structures and cross-tool interoperability. End-to-end analyses are performed unassisted with a single invocation, fostering rigorous, reproducible spatial transcriptomics analysis. Its novel, AI-enabled reporting layer synthesizes quantitative results into summaries of biological findings, facilitating analysis interpretation. |
| Competing Interests: | Conflicts of interest E.J.F. was a paid consultant to Mestag Therapeutics and on the Scientific Advisory Board of Viosera Therapuetics / Resistance Bio. E.J.F, M.O. are paid consultants to the Fred Hutch Cancer Institute Bio-OCS Open Case Studies. |
| Entry Date(s): | Date Created: 20260410 Date Completed: 20260421 Latest Revision: 20260421 |
| Update Code: | 20260421 |
| PubMed Central ID: | PMC13060245 |
| DOI: | 10.64898/2026.03.30.715127 |
| PMID: | 41959373 |
| Database: | MEDLINE |
Journal Article; Preprint