Evidence map›Paper›PMID 41648423›Full record

ArticlebioRxiv : the preprint server for biology2026

4D multimodal wound healing atlas reveals organ-level controls of repair phase transitions.

Jonathan Chin Cheong, Simon Van Deursen, Dreyton Amador, Shannon Hiner, Yvon Woappi

Abstract readPreprint
In one paragraph

Article in bioRxiv : the preprint server for biology, 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
–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

5 authors.

Jonathan Chin CheongSynthetic Regeneration and Systems Physiology Laboratory, Columbia Stem Cell Initiative, Columbia Data Science Institute, Naomi Berrie Diabetes Center, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, 10032, USA.
Simon Van DeursenSynthetic Regeneration and Systems Physiology Laboratory, Columbia Stem Cell Initiative, Columbia Data Science Institute, Naomi Berrie Diabetes Center, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, 10032, USA.
Dreyton AmadorSynthetic Regeneration and Systems Physiology Laboratory, Columbia Stem Cell Initiative, Columbia Data Science Institute, Naomi Berrie Diabetes Center, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, 10032, USA.ORCID 0009-0004-9270-6330
Shannon HinerSynthetic Regeneration and Systems Physiology Laboratory, Columbia Stem Cell Initiative, Columbia Data Science Institute, Naomi Berrie Diabetes Center, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, 10032, USA.
Yvon WoappiSynthetic Regeneration and Systems Physiology Laboratory, Columbia Stem Cell Initiative, Columbia Data Science Institute, Naomi Berrie Diabetes Center, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, 10032, USA.ORCID 0000-0003-3177-4730

Funding

Training in Cardiovascular Translational ResearchT32HL120826 · NHLBI · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI MARKS, ANDREW ROBERT, TABAS, IRA A · 2014 to 2023
$4.7M
Delineating epigenetic coordination of regenerative cell plasticityR00GM140262 · NIGMS · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI WOAPPI, YVON · 2022 to 2024
$747k
Delineating epigenetic coordination of regenerative cell plasticityK99GM140262 · NIGMS · BRIGHAM AND WOMEN'S HOSPITAL · PI WOAPPI, YVON · 2021 to 2022
$167k
NHLBI NIH HHS T32 HL120826NIGMS NIH HHS K99 GM140262NIGMS NIH HHS R00 GM140262
6 · The paper itself

Abstract

Deep skin wounds demand tightly coordinated communication across diverse tissue systems, yet knowledge of the molecular logic governing organ-scale injury response remains incomplete. Existing wound atlases profile fragments of this process, capturing limited tissue groups and healing phases, obscuring how whole organs synchronize repair. Here, we present the Organ-Scale Wound Healing Atlas (OWHA), a 4D multimodal omnibus that integrates snRNA-seq, scRNA-seq, CITE-seq and high-definition spatial transcriptomics to reconstruct the complete spatial and temporal choreography of mammalian wound healing at single cell resolution. OWHA profiles over 725,000 murine single-cell and spatial transcriptomes encompassing the entire wound healing process from early to late healing phases across the vast skin microanatomical tissue niches. This omnibus overcomes long-standing technical limitations, enabling robust resolution of adipocytes, Schwann cells, fragile epithelial intermediates, and over 100 precisely annotated cell states, including populations missed in prior wound databases. This revealed that wound repair proceeds through sharp transcriptional and cellular inflection points driven by Central Orchestrator populations that coordinate healing via synchronized transcriptional activation and direct cross-tissue signaling. Key among these is a

Indexed as

Diabetic ulcersMultimodal Single-Cell AtlasSema3CSingle-Cell atlasSpatial transcriptomicsWound healing

Identifiers

PMID41648423
PMCPMC12871262

What Socratic holds

Textmetadata
LicenceCC BY-ND
Read underepoch 390

Registered trials

None linked

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 Socratic graph.