Evidence map›Paper›PMID 41125875›Full record

ArticleNature immunology2025

A unified multimodal single-cell framework reveals a discrete state model of hematopoiesis in mice.

Kyle Ferchen, Xuan Zhang, Kairavee Thakkar, Guangyuan Li, David Bernardicius, Sidharth Sen, Priyanka Rawat, Andre Olsson, Sierra N Bennett, Crystal Potter and 6 more

Abstract read
In one paragraph

Article in Nature immunology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing 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

3 citing papers in PubMed.

  1. Review
  2. Article
  3. Multimodal analysis definesbioRxiv : the preprint server for biology · 2025
    Article
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.

Kyle FerchenDivision of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.ORCID http://orcid.org/0000-0002-3470-3623
Xuan ZhangDivision of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.ORCID http://orcid.org/0000-0001-7966-8748
Kairavee ThakkarDivision of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.ORCID http://orcid.org/0000-0003-1397-486X
Guangyuan LiDivision of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.ORCID http://orcid.org/0000-0002-0628-2454
David BernardiciusDivision of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
Sidharth SenDivision of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
Priyanka RawatDivision of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.ORCID http://orcid.org/0000-0003-4248-347X
Andre OlssonDivision of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
Sierra N BennettDivision of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
Crystal PotterDivision of Immunology, Allergy and Rheumatology, Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, USA.
Fred D FinkelmanDivision of Immunology, Allergy and Rheumatology, Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, USA.
Josh CroteauBioLegend, San Diego, CA, USA.ORCID http://orcid.org/0000-0002-8142-0482
Samantha MorrisDivision of Gastroenterology, Hepatology and Endoscopy, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.ORCID http://orcid.org/0000-0001-8561-4340
Harinder SinghDepartments of Immunology, Center for Systems Immunology, University of Pittsburgh, Pittsburgh, PA, USA. harinder@pitt.edu.ORCID http://orcid.org/0000-0002-6330-8526
Nathan SalomonisDivision of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA. nathan.salomonis@cchmc.org.ORCID http://orcid.org/0000-0001-9689-2469
H Leighton GrimesDivision of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA. lee.grimes@cchmc.org.ORCID http://orcid.org/0000-0001-8162-6758

Funding

Training Program in Cancer TherapeuticsT32CA117846 · NCI · UNIVERSITY OF CINCINNATI · PI PRICE, CAROLYN M, TAKIAR, VINITA · 2006 to 2022
$6.5M
Mechanisms of granulocyte homeostasisR01HL122661 · NHLBI · CINCINNATI CHILDRENS HOSP MED CTR · PI H. LEIGHTON GRIMES, Nathan G. Salomonis · 2015 to 2026
$5.3M
A generalizable framework for linking single-cell genomic states with cell fate outcomes in hematopoiesisRC2DK122376 · NIDDK · CINCINNATI CHILDRENS HOSP MED CTR · PI GRIMES, H. LEIGHTON · 2020 to 2024
$5.3M
NHLBI NIH HHS R01 HL122661U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI) T32CA117846U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI) R01HL122661U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases) RC2DK122376
6 · The paper itself

Abstract

Large-scale, unbiased single-cell genomics studies of complex developmental compartments, such as hematopoiesis, have inferred novel cell states and trajectories; however, further characterization has been hampered by difficulty isolating cells corresponding to discrete genomic states. To address this, we present a framework that integrates multimodal single-cell analyses (RNA, surface protein and chromatin) with high-dimensional flow cytometry and enables semiautomated enrichment and functional characterization of diverse cell states. Our approach combines transcription factor expression with chromatin activity to uncover hierarchical gene regulatory networks driving these states. We delineated and isolated rare bone marrow Lin

Indexed as

HematopoiesisHematopoietic Stem CellsSingle-Cell AnalysisAnimalsCell DifferentiationCell LineageChromatinFlow CytometryGene Regulatory NetworksMiceMice, Inbred C57BLTranscription FactorsChromatinTranscription Factors

Identifiers

PMID41125875
PMCPMC12763301

What OpenQuestion holds

Textmetadata
LicenceTDM
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.