Evidence map›Paper›PMID 40894635›Full record

ArticlebioRxiv : the preprint server for biology2025

Constructing and Using Cell Type Populations of the Human Reference Atlas.

Andreas Bueckle, Bruce W Herr, Lu Chen, Daniel Bolin, Danial Qaurooni, Michael Ginda, Yashvardhan Jain, Aleix Puig-Barbe, Kristin Ardlie, Fusheng Wang and 1 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

5 · Who and what money

Authors and funding

11 authors.

Andreas BueckleDepartment of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN, 47408, USA.ORCID 0000-0002-8977-498X
Bruce W HerrDepartment of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN, 47408, USA.ORCID 0000-0002-6703-7647
Lu ChenDepartment of Computer Science and Department of Biomedical Informatics, Stony Brook University, Stony Brook, NY, 11794, USA.ORCID 0000-0001-5998-9317
Daniel BolinDepartment of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN, 47408, USA.ORCID 0000-0002-3803-2476
Danial QaurooniDepartment of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN, 47408, USA.ORCID 0000-0001-6190-073X
Michael GindaDepartment of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN, 47408, USA.ORCID 0000-0002-7500-8096
Yashvardhan JainDepartment of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN, 47408, USA.ORCID 0000-0002-6300-5568
Aleix Puig-BarbeEuropean Molecular Biology Laboratory-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.ORCID 0000-0001-6677-8489
Kristin ArdlieBroad Institute, Cambridge, MA, 02142, USA.ORCID 0000-0003-4272-6283
Fusheng WangDepartment of Computer Science and Department of Biomedical Informatics, Stony Brook University, Stony Brook, NY, 11794, USA.ORCID 0000-0002-9369-9361
Katy BörnerDepartment of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN, 47408, USA.ORCID 0000-0002-3321-6137

Funding

SenNet Supplement - Consortium BenchmarkingU24CA268108 · NCI · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI Philip D. Blood, JONATHAN C. SILVERSTEIN · 2021 to 2026
$22.1M
ConProject-002U2CDK114886 · NIDDK · UNIVERSITY OF WASHINGTON · PI KRETZLER, MATTHIAS · 2017 to 2021
$21.0M
Flexible Hybrid Cloud Infrastructure for Seamless Integration and Use of Human Biomolecular Data and Reference Maps [1 of 5]OT2OD033759 · OD · CARNEGIE-MELLON UNIVERSITY · PI BLOOD, PHILIP D., SILVERSTEIN, JONATHAN C. · 2022 to 2025
$20.4M
Developmental GTEx Laboratory, Data Analysis and Coordination CenterU24HG012090 · NHGRI · BROAD INSTITUTE, INC. · PI ARDLIE, KRISTIN, GETZ, GAD A · 2021 to 2025
$12.6M
KPMP Kidney Mapping and Atlas Project (KMAP)U01DK133090 · NIDDK · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI Jonathan Himmelfarb, Matthias Kretzler · 2022 to 2026
$10.4M
Flexible Hybrid Cloud Infrastructure for Seamless Management of HuBMAP Resources, Including Consortium-Wide and External EngagementOT2OD026675 · OD · CARNEGIE-MELLON UNIVERSITY · PI BLOOD, PHILIP D., SILVERSTEIN, JONATHAN C. · 2018 to 2021
$8.9M
3D Multiscale Biomolecular Human Reference Atlas Construction, Visualization and Usage [4 of 5]OT2OD033756 · OD · TRUSTEES OF INDIANA UNIVERSITY · PI BORNER, KATY · 2022 to 2025
$7.4M
The Human Body Atlas: High-Resolution, Functional Mapping of Voxel, Vector, and Meta DatasetsOT2OD026671 · OD · TRUSTEES OF INDIANA UNIVERSITY · PI BORNER, KATY · 2018 to 2021
$3.5M
National Institute of Diabetes and Digestive and Kidney Diseases ATLAS (D2K-ATLAS) Center as an accessible, comprehensive data portfolio for renal and genitourinary development and diseaseU24DK135157 · NIDDK · BRIGHAM AND WOMEN'S HOSPITAL · PI JAIN, SANJAY, VALERIUS, MICHAEL TODD · 2022 to 2023
$3.4M
Amplifying the Value of HuBMAP Data Through Data Interoperability and CollaborationOT2OD030545 · OD · CARNEGIE-MELLON UNIVERSITY · PI BLOOD, PHILIP D., BORNER, KATY · 2020 to 2023
$3.1M
Computational pathology software for integrative cancer research with three-dimensional digital slidesU01CA242936 · NCI · GEORGIA STATE UNIVERSITY · PI KONG, JUN, WANG, FUSHENG · 2019 to 2021
$1.1M
3D Human Reference Body: Multiscale Exploration and Visualization of Biomolecular Data in Virtual RealityR03OD039970 · OD · TRUSTEES OF INDIANA UNIVERSITY · PI BUECKLE, ANDREAS · 2025 to 2025
$317k
NCI NIH HHS U01 CA242936NCI NIH HHS U24 CA268108NHGRI NIH HHS U24 HG012090NIDDK NIH HHS U01 DK133090NIDDK NIH HHS U24 DK135157NIDDK NIH HHS U2C DK114886NIH HHS OT2 OD026671NIH HHS OT2 OD026675NIH HHS OT2 OD030545NIH HHS OT2 OD033756NIH HHS OT2 OD033759NIH HHS R03 OD039970
6 · The paper itself

Abstract

The human body contains ~27-36 trillion cells of up to 10,000 cell types (CTs) within a volume of ~62-120 liters (males) and 52-89 liters (females). The Human Reference Atlas (HRA) v2.3 provides a quantitative 3D framework of CTs across 73 reference organs and 1,283 3D anatomical structures (ASs). The HRA Cell Type Population (HRApop) effort quantifies CTs per AS using high-quality single-cell (sc) data processed through scalable, reproducible workflows and cell type annotation (CTann) tools. HRApop v1.0 includes reference CT populations for 73 ASs (112 when sex-specific) using 662 datasets spatially registered to 230 locations across 17 organs (31 when sex-specific). For 558 sc-transcriptomics datasets (11,042,750 cells), CTs and biomarker expression were computed using Azimuth, CellTypist, and popV. To test generalizability, 104 sc-proteomics datasets (16,576,863 cells) were integrated. In total, HRApop includes 27,619,613 cells. HRApop can be used to predict (1) CT populations for 3D volumes in the human body and (2) the spatial origin of a tissue block, given a CT population. Data and code are at cns-iu.github.io/hra-cell-type-populations-supporting-information.

Identifiers

PMID40894635
PMCPMC12393406

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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.