Evidence map›Paper›PMID 39147769›Full record

ArticleScientific reports2024

Automated spatial omics landscape analysis approach reveals novel tissue architectures in ulcerative colitis.

Derek R Holman, Samuel J S Rubin, Mariusz Ferenc, Elizabeth A Holman, Alexander N Koron, Robel Daniel, Brigid S Boland, Garry P Nolan, John T Chang, Stephan Rogalla

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Scientific reports, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

2 citing papers in PubMed.

  1. Article
  2. Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

10 authors.

Derek R Holman *Division of Gastroenterology and Hepatology, Department of Medicine, Stanford University, Stanford, CA, USA. drholman@stanford.edu.
Samuel J S Rubin *Division of Gastroenterology and Hepatology, Department of Medicine, Stanford University, Stanford, CA, USA.
Mariusz Ferenc *Nalecz Institute of Biocybernetics and Biomedical Engineering, Polish Academy of Sciences, Warsaw, Poland.
Elizabeth A Holman *Division of Gastroenterology and Hepatology, Department of Medicine, Stanford University, Stanford, CA, USA.
Alexander N KoronDivision of Gastroenterology and Hepatology, Department of Medicine, Stanford University, Stanford, CA, USA.
Robel DanielDivision of Gastroenterology and Hepatology, Department of Medicine, Stanford University, Stanford, CA, USA.
Brigid S BolandDivision of Gastroenterology, Department of Medicine, University of California San Diego, San Diego, CA, USA.
Garry P NolanDepartment of Pathology, Stanford University, Stanford, CA, USA.
John T ChangDivision of Gastroenterology, Department of Medicine, University of California San Diego, San Diego, CA, USA.
Stephan RogallaDivision of Gastroenterology and Hepatology, Department of Medicine, Stanford University, Stanford, CA, USA. srogalla@stanford.edu.

Funding

Stanford Center for Clinical & Translational Education and Research (Spectrum)UL1TR003142 · NCATS · STANFORD UNIVERSITY · PI O'HARA, RUTH M · 2019 to 2023
$45.0M
Kenneth Rainin Foundation 2018-575NCATS NIH HHS UL1 TR003142
6 · The paper itself

Abstract

The utility of spatial omics in leveraging cellular interactions in normal and diseased states for precision medicine is hampered by a lack of strategies for matching disease states with spatial heterogeneity-guided cellular annotations. Here we use a spatial context-dependent approach that matches spatial pattern detection to cell annotation. Using this approach in existing datasets from ulcerative colitis patient colonic biopsies, we identified architectural complexities and associated difficult-to-detect rare cell types in ulcerative colitis germinal-center B cell follicles. Our approach deepens our understanding of health and disease pathogenesis, illustrates a strategy for automating nested architecture detection for highly multiplexed spatial biology data, and informs precision diagnosis and therapeutic strategies.

Indexed as

Colitis, UlcerativeBiopsyColonHumansComputational analysisInflammatory bowel diseaseSpatial omics

Identifiers

PMID39147769
PMCPMC11327370

What OpenQuestion holds

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LicenceCC BY-NC-ND
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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.