Evidence map›Paper›PMID 42160174›Full record

ArticleSTAR protocols2026

Protocol for spatially resolved pathology scores using optimal transport on spatial transcriptomics data.

Mohammad Nuwaisir Rahman, James F Martin, M Saifur Rahman, Md Abul Hassan Samee

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In one paragraph

Article in STAR protocols, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
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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

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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

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

4 authors.

Mohammad Nuwaisir RahmanComputer Science and Engineering, Bangladesh University of Engineering and Technology, Dhaka 1000, Bangladesh; Computer Science and Engineering, BRAC University, Dhaka 1212, Bangladesh; Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119077, Singapore. Electronic address: nuwaisir1998@gmail.com.
James F MartinIntegrative Physiology, Baylor College of Medicine, Houston, TX 77030, USA; Texas Heart Institute, Houston, TX 77030, USA.
M Saifur RahmanComputer Science and Engineering, Bangladesh University of Engineering and Technology, Dhaka 1000, Bangladesh. Electronic address: mrahman@cse.buet.ac.bd.
Md Abul Hassan SameeIntegrative Physiology, Baylor College of Medicine, Houston, TX 77030, USA. Electronic address: samee@bcm.edu.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Spatial transcriptomics (ST) integrates gene expression with spatial context to study tissue pathology. We present SPaSE (spatially resolved pathology score), a protocol to quantify pathology by computing an optimal transport plan between ST spots of the diseased and the corresponding healthy tissue. We describe steps for assigning pathology scores to each spot and developing support vector regression models to link gene expression with pathological impact. We demonstrate the utility of SPaSE across multiple human and mouse ST datasets. For complete details on the use and execution of this protocol, please refer to Rahman et al.

Indexed as

Gene Expression ProfilingSpatial TranscriptomicsTranscriptomeAnimalsHumansMiceBioinformaticsCancerCell BiologyComputer sciencesGenomicsSystems biology

Identifiers

PMID42160174
PMCPMC13199767

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.