Evidence map›Paper›PMID 42465438›Full record

ArticlebioRxiv : the preprint server for biology2026

Scalable 3D cell-interaction analysis via supercell graphs for prostate cancer risk stratification.

Yujie Zhao, Sarah S L Chow, Renao Yan, David Brenes, Robert Serafin, Cristina Almagro-Pérez, Andrew H Song, Priti Lal, Emily Chan, Michelle Downes and 6 more

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

16 authors.

Yujie ZhaoDepartment of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA, USA.
Sarah S L ChowDepartment of Pathology, Stanford University, Stanford, CA, USA.
Renao YanDepartment of Pathology, Stanford University, Stanford, CA, USA.
David BrenesDepartment of Pathology, Stanford University, Stanford, CA, USA.
Robert SerafinDepartment of Medicine, Section of Hematology/Oncology, University of Chicago, Chicago, IL, USA.
Cristina Almagro-PérezDepartment of Pathology, Mass General Brigham, Harvard Medical School, Boston, MA, USA.
Andrew H SongDepartment of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
Priti LalPathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA.
Emily ChanStanford Medical Center, Stanford, CA, USA.
Michelle DownesSunnybrook Health Sciences Centre, University of Toronto, Toronto, ON, Canada.
Elena BaraznenokUC Berkeley-UCSF Graduate Program in Bioengineering, University of California, Berkeley, CA, USA.
Jennifer Salguero LopezWallace H. Coulter Department of Biomedical Engineering, Emory University & Georgia Institute of Technology, Atlanta, GA, USA.
Anant MadabhushWallace H. Coulter Department of Biomedical Engineering, Emory University & Georgia Institute of Technology, Atlanta, GA, USA.
Faisal MahmoodDepartment of Pathology, Mass General Brigham, Harvard Medical School, Boston, MA, USA.
Lawrence D TrueDepartment of Laboratory Medicine & Pathology, University of Washington, Seattle, WA, USA.
Jonathan T C LiuDepartment of Pathology, Stanford University, Stanford, CA, USA.

Funding

TRANSCRIPTOME AND PROTEOME STRATIFICATION OF PROSTATE ADENOCARCINOMA PHENOTYPESP50CA097186 · NCI · FRED HUTCHINSON CANCER RESEARCH CENTER · PI PETER S NELSON · 2002 to 2026
$58.1M
Whole Exome Approaches for Esophageal Adenocarcinoma Susceptibility GenesU54CA163060 · NCI · CASE WESTERN RESERVE UNIVERSITY · PI CHAK, AMITABH, GUDA, KISHORE · 2011 to 2022
$14.0M
Identify and validate novel epigenetic molecular markers for colorectal neoplasmU01CA152756 · NCI · FRED HUTCHINSON CANCER RESEARCH CENTER · PI GRADY, WILLIAM MALLORY, GUDA, KISHORE · 2010 to 2021
$6.7M
Biomarkers for optimizing risk prediction and early detection of cancers of the colon and esophagusU2CCA271902 · NCI · FRED HUTCHINSON CANCER CENTER · PI William Mallory Grady, Cecilia C Yeung · 2022 to 2026
$5.3M
Esophageal Cancer from Cells to Population: A Multiscale ApproachU01CA182940 · NCI · FRED HUTCHINSON CANCER RESEARCH CENTER · PI HUR, CHIN, INADOMI, JOHN MATTHEW · 2013 to 2017
$3.3M
(PQ6) Radiogenomics of colorectal polyps to assess benign proliferative vs. premalignant states.R01CA220004 · NCI · FRED HUTCHINSON CANCER RESEARCH CENTER · PI GRADY, WILLIAM MALLORY, HALBERG, RICHARD BROTT · 2017 to 2021
$3.2M
Prostate cancer risk stratification via computational 3D pathologyR01CA268207 · NCI · UNIVERSITY OF WASHINGTON · PI Jonathan T.C. Liu, Anant Madabhushi · 2022 to 2026
$3.1M
Computational 3D pathology for Barrett's esophagus risk stratificationR01DK138948 · NIDDK · UNIVERSITY OF WASHINGTON · PI William Mallory Grady, Jonathan T.C. Liu · 2024 to 2026
$2.2M
Instrumentation platform for 3D pathology with open-top light-sheet microscopyR01EB031002 · NIBIB · UNIVERSITY OF WASHINGTON · PI LIU, JONATHAN T.C. · 2021 to 2024
$1.9M
NCI NIH HHS P50 CA097186NCI NIH HHS R01 CA220004NCI NIH HHS R01 CA268207NCI NIH HHS U01 CA152756NCI NIH HHS U01 CA182940NCI NIH HHS U2C CA271902NCI NIH HHS U54 CA163060NIBIB NIH HHS R01 EB031002NIDDK NIH HHS R01 DK138948
6 · The paper itself

Abstract

Cellular interactions underlie fundamental biological processes but are not fully represented in conventional 2D histology images. While 3D pathology allows for more-accurate construction of cell-level graphs, machine-learning models are computationally unwieldy and prone to overfitting, especially when dealing with small cohorts. Here, we introduce

Identifiers

PMID42465438
PMCPMC13371040

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.