Evidence map›Paper›PMID 40661390›Full record

ArticlebioRxiv : the preprint server for biology2025

PIVOT: an open-source tool for multi-omic spatial data registration.

André Forjaz, Valentina Matos Romero, Ian Reucroft, Margaret Eminizer, Donald Kramer, Daniela Higuera, Hengameh Mojdeganlou, Paola A Guerrero, Jimin Min, Meredith Wetzel and 14 more

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2025. 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
–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

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

24 authors.

André ForjazDepartment of Chemical & Biomolecular Engineering, Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD, USA.ORCID 0009-0002-5115-2293
Valentina Matos RomeroDepartment of Chemical & Biomolecular Engineering, Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD, USA.
Ian ReucroftDepartment of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
Margaret EminizerThe Data Science and Artificial Intelligence Institute, Johns Hopkins University, Baltimore, MD, USA.
Donald KramerDepartment of Chemical & Biomolecular Engineering, Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD, USA.
Daniela HigueraDepartment of Chemical & Biomolecular Engineering, Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD, USA.
Hengameh MojdeganlouDepartment of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
Paola A GuerreroDepartment of Translational Molecular Pathology and Sheikh Ahmed Center for Pancreatic Cancer Research, MD Anderson Cancer Center, Houston, TX.
Jimin MinDepartment of Translational Molecular Pathology and Sheikh Ahmed Center for Pancreatic Cancer Research, MD Anderson Cancer Center, Houston, TX.
Meredith WetzelDepartment of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
Dmitrijs LvovsInstitute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD.
Alens ValentinDepartment of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
Sarah M ShinDepartment of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
Xuan YuanDepartment of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
Rosalie C SearsDepartment of Molecular and Medical Genetics, Oregon Health and Sciences University, Portland, OR.ORCID 0000-0003-1558-2413
Koei ChinCenter for Spatial Systems Biomedicine, Oregon Health and Sciences University, Portland, OR.
Anirban MaitraDepartment of Translational Molecular Pathology and Sheikh Ahmed Center for Pancreatic Cancer Research, MD Anderson Cancer Center, Houston, TX.
Elana J FertigInstitute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD.
Won Jin HoDepartment of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
Luciane T KagoharaDepartment of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
Laura D WoodDepartment of Chemical & Biomolecular Engineering, Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD, USA.
Denis WirtzDepartment of Chemical & Biomolecular Engineering, Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD, USA.
Dimitrios N SidiropoulosDepartment of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
Ashley L KiemenDepartment of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.ORCID 0000-0002-6281-2616

Funding

Tech Core 2U54CA268083 · NCI · JOHNS HOPKINS UNIVERSITY · PI Denis Wirtz, Laura DeLong Wood · 2022 to 2026
$10.2M
Omic and Multidimensional Spatial Atlas of Metastatic Breast CancerU2CCA233280 · NCI · OREGON HEALTH & SCIENCE UNIVERSITY · PI GOECKS, JEREMY · 2018 to 2023
$9.7M
Tumor Microenvironment Crosstalk Drives Early Lesions in Pancreatic CancerU54CA274371 · NCI · UNIVERSITY OF TX MD ANDERSON CAN CTR · PI Elana Fertig · 2022 to 2026
$9.5M
An atlas of pancreatic tumorigenesis in the context of altered DNA repair occurring in high-risk individualsU01CA294548 · NCI · OREGON HEALTH & SCIENCE UNIVERSITY · PI BRODY, JONATHAN, FERTIG, ELANA · 2024 to 2025
$5.1M
PASSCODE (Pancreatic Adenocarcinoma Stromal Reprograming ConSortium COordination, Data Management and Education)U24CA274274 · NCI · UNIVERSITY OF TX MD ANDERSON CAN CTR · PI J. Jack LEE, ANIRBAN MAITRA · 2022 to 2026
$4.9M
Single-cell and imaging data integration software to spatially resolve the tumor microenvironmentU01CA253403 · NCI · JOHNS HOPKINS UNIVERSITY · PI FERTIG, ELANA · 2020 to 2022
$1.2M
NCI NIH HHS U01 CA253403NCI NIH HHS U01 CA294548NCI NIH HHS U24 CA274274NCI NIH HHS U2C CA233280NCI NIH HHS U54 CA268083NCI NIH HHS U54 CA274371
6 · The paper itself

Abstract

Advances in spatial profiling have resulted in the generation of multi-omic atlases that span biological scales. In general, multiple workflows are required for image registration, coordinate registration, and spot deconvolution to integrate modalities. To improve the throughput of registration of multi-omic cohorts, we introduce PIVOT, a user-friendly and open-source interface for streamlined nonlinear registration. We demonstrate PIVOT's strengths through registration of three multi-omic datasets, and show comparison of its performance to existing workflows.

Identifiers

PMID40661390
PMCPMC12259011

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.