Evidence map›Paper›PMID 42146363›Full record

ArticlebioRxiv : the preprint server for biology2026

PHYFUM: Phylogenetic Reconstruction of Normal and Pre-malignant Tissue Evolution Using Fluctuating Methylation.

Pablo Bousquets-Muñoz, Heather E Grant, Darryl Shibata, Trevor A Graham, Carlo C Maley, Calum Gabbutt, Diego Mallo

Abstract readPreprint
PubMed Full text at PMC Publisher
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

7 authors.

Pablo Bousquets-MuñozCentre for Evolution and Cancer, Institute of Cancer Research, London, UK.ORCID 0000-0002-2969-008X
Heather E GrantCentre for Evolution and Cancer, Institute of Cancer Research, London, UK.ORCID 0000-0001-9500-1644
Darryl ShibataDepartment of Pathology, University of Southern California Keck School of Medicine, Los Angeles, CA, USA.ORCID 0000-0002-4567-1639
Trevor A GrahamCentre for Evolution and Cancer, Institute of Cancer Research, London, UK.ORCID 0000-0001-9582-1597
Carlo C MaleyArizona Cancer Evolution Center; Biodesign Center for Biocomputing, Security, and Society and School of Life Sciences, Arizona State University, Tempe, AZ, USA.ORCID 0000-0002-0745-7076
Calum GabbuttCentre for Evolution and Cancer, Institute of Cancer Research, London, UK.ORCID 0000-0003-1946-4780
Diego MalloArizona Cancer Evolution Center; Biodesign Center for Biocomputing, Security, and Society and School of Life Sciences, Arizona State University, Tempe, AZ, USA.ORCID 0000-0002-9046-8859

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

We present PHYFUM, a novel Bayesian phylogenetic method for methylation data that reconstructs the evolutionary history of stem cells and the glandular structures they reside within in normal tissue. Using simulations, we validated this phylogenetic method and confirmed its accuracy. A re-analysis of 22 patients unveiled early gland divergence in the human gut, in contrast to a much later common ancestor in the endometrium, and yielded strong evidence against gland division by segregation of individual stem cells.

Identifiers

PMID42146363
PMCPMC13174555

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-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 OpenQuestion graph.