ArticleNature methods2025
Human BioMolecular Atlas Program (HuBMAP): 3D Human Reference Atlas construction and usage.
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Article in Nature methods, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers, 1 of them a synthesis that pooled it.
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42citing papers in PubMed, 1 pooled it
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Who cites it
42 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Vasculature segmentation in 3D hierarchical phase-contrast tomography images of human kidneys.Nature communications · 2026Pooled it
- Single-cell Transcriptomics in Autoimmune Diseases: Mechanistic Insights, Cross-disease Convergence, and Translational Challenges in Rheumatoid Arthritis, Systemic Lupus Erythematosus, Type 1 Diabetes, and Multiple Sclerosis.Clinical reviews in allergy & immunology · 2026Review
- 3D multi-omics tumour atlases: from technology to biology and clinical translation.Nature reviews. Cancer · 2026Review
- Reclaiming Anatomy as Method: From Morphological Reasoning to Clinical Relevance.Clinical anatomy (New York, N.Y.) · 2026Review
- Multiscale harmonization, semantic integration, and immersive exploration of single-cell data in support of novel biological insights.bioRxiv : the preprint server for biology · 2026Article
- Depletion of an immature cord blood NK subset reverses trogocytosis-driven CAR NK dysfunction.Cancer cell · 2026Article
- AI semantics for biomedical data integration.bioRxiv : the preprint server for biology · 2026Article
- HuBMAP Data Portal: a resource for multimodal spatial and single-cell data of healthy human tissues.ArXiv · 2026Article
- A Conversational Multi-Agent AI System for Integrated Multi-Omics Analysis and Biomedical Discovery.bioRxiv : the preprint server for biology · 2026Article
- Organism-scale annotation with Pan-human Azimuth.bioRxiv : the preprint server for biology · 2026Article
- Dissecting human organ development using spatial technologies.Developmental cell · 2026Review
- Spatial transcriptomics in ovarian biology technologies: computational challenges, and biological insights.Reproduction (Cambridge, England) · 2026Review
- Ten years of mapping gene expression in tissues.Nature · 2026Article
- Multi-Tiered µDicer Enables Protein-Preserving Microdissection at 10 µm Resolution.Small (Weinheim an der Bergstrasse, Germany) · 2026Article
- SPEAK: Spatial Prompting with Expert Aligned Knowledge for Tissue Domain Identification in Spatial Transcriptomics.bioRxiv : the preprint server for biology · 2026Article
- Generalist biological artificial intelligence in modeling the language of life.Nature biotechnology · 2026Review
- Volumetric Cyclic Immunofluorescence for 3D Spatial Profiling of Immune Structures in Human FFPE Tissue.bioRxiv : the preprint server for biology · 2026Article
- The Cell Ontology in the age of single-cell omics.Scientific data · 2026Article
- An integrated single-cell and spatial proteotranscriptomics atlas of fibroblast-driven immunoregulation within the human adult oral cavity.Cell press blue · 2026Article
- The Common Fund Data Ecosystem (CFDE).bioRxiv : the preprint server for biology · 2026Article
Corrections and comments
- Update of
Authors and funding
21 authors.
Katy BörnerDepartment of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN, USA. katy@iu.edu.ORCID http://orcid.org/0000-0002-3321-6137
Philip D BloodPittsburgh Supercomputing Center, Carnegie Mellon University, Pittsburgh, PA, USA.
Jonathan C SilversteinDepartment of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.ORCID http://orcid.org/0000-0002-9252-6039
Matthew RuffaloRay and Stephanie Lane Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA.ORCID http://orcid.org/0000-0003-2222-6169
Rahul SatijaNew York Genome Center, New York, NY, USA.ORCID http://orcid.org/0000-0001-9448-8833
Sarah A TeichmannCIFAR MacMillan Multiscale Human program, CIFAR, Toronto, Ontario, Canada.ORCID http://orcid.org/0000-0002-6294-6366
Gloria J PryhuberUniversity of Rochester Medical Center, Rochester, NY, USA.ORCID http://orcid.org/0000-0002-9185-3994
Ravi S MisraUniversity of Rochester Medical Center, Rochester, NY, USA.
Jeffrey M PurkersonUniversity of Rochester Medical Center, Rochester, NY, USA.
Jean FanDepartment of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA.ORCID http://orcid.org/0000-0002-0212-5451
John W HickeyDepartment of Biomedical Engineering, Duke University, Durham, NC, USA.
Gesmira MollaNew York Genome Center, New York, NY, USA.
Chuan XuCambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK.ORCID http://orcid.org/0000-0002-6265-999X
Yun ZhangJ. Craig Venter Institute, La Jolla, CA, USA.ORCID http://orcid.org/0000-0003-2707-5881
Griffin M WeberDepartment of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
Yashvardhan JainDepartment of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN, USA.ORCID http://orcid.org/0000-0002-6300-5568
Danial QaurooniDepartment of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN, USA.ORCID http://orcid.org/0000-0001-6190-073X
Yongxin KongDepartment of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN, USA.
HRA Team
Andreas BueckleDepartment of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN, USA. abueckle@iu.edu.ORCID http://orcid.org/0000-0002-8977-498X
Bruce W HerrDepartment of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN, USA. bherr@iu.edu.ORCID http://orcid.org/0000-0002-6703-7647
Funding
Center for Integrated Cellular Analysis - Valeria A. Sanchez EstradaRM1HG011014 · NHGRI · NEW YORK GENOME CENTER · PI LANDAU, DAN, SATIJA, RAHUL · 2020 to 2025
$22.1MSenNet Supplement - Consortium BenchmarkingU24CA268108 · NCI · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI Philip D. Blood, JONATHAN C. SILVERSTEIN · 2021 to 2026
$22.1MConProject-002U2CDK114886 · NIDDK · UNIVERSITY OF WASHINGTON · PI HIMMELFARB, JONATHAN, IYENGAR, SRINIVAS RAVI V · 2017 to 2021
$21.0MFlexible 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
$20.4MThe Duke Senescent Cell Evaluations in Normal Tissues (SCENT) Mapping CenterU54AG075936 · NIA · DUKE UNIVERSITY · PI NIXON, ANDREW B. · 2021 to 2025
$12.7MSenescent cell mapping, identification and validation for human somatic and reproductive tissuesU54AG075932 · NIA · BUCK INSTITUTE FOR RESEARCH ON AGING · PI Simon Melov, Birgit Schilling · 2021 to 2026
$12.5MKPMP Kidney Mapping and Atlas Project (KMAP)U01DK133090 · NIDDK · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI Jonathan Himmelfarb, Matthias Kretzler · 2022 to 2026
$10.4MBioRepository for INvestigation of Diseases of the Lung (BRINDL) - Phase IIIU01HL148861 · NHLBI · UNIVERSITY OF ROCHESTER · PI GLORIA S PRYHUBER · 2019 to 2026
$9.7MFlexible 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
$8.9MThe Human Lung BioMolecular Multi-Scale Atlas Program (HuBMAP-Lung)U54HL165443 · NHLBI · UNIVERSITY OF ROCHESTER · PI PRYHUBER, GLORIA S · 2022 to 2025
$8.0MKidney single cell and spatial molecular atlas project - KIDSSMAPU54DK134301 · NIDDK · WASHINGTON UNIVERSITY · PI JAIN, SANJAY · 2022 to 2025
$7.8M3D Multiscale Biomolecular Human Reference Atlas Construction, Visualization and Usage [4 of 5]OT2OD033756 · OD · TRUSTEES OF INDIANA UNIVERSITY · PI BORNER, KATY · 2022 to 2025
$7.4MBLRD VA I01 BX007249BLRD VA IK6 BX005244NCI NIH HHS U24 CA268108NCI NIH HHS UH3 CA246594NHGRI NIH HHS RM1 HG011014NHLBI NIH HHS U01 HL148861NHLBI NIH HHS U54 HL165440NHLBI NIH HHS U54 HL165443NIAMS NIH HHS U54 AR081775NIA NIH HHS U54 AG075932NIA NIH HHS U54 AG075936NIDDK NIH HHS U01 DK133090NIDDK NIH HHS U24 DK135157NIDDK NIH HHS U2C DK114886NIDDK NIH HHS U54 DK134301NIH HHS OT2 OD026671NIH HHS OT2 OD026673NIH HHS OT2 OD026675NIH HHS OT2 OD026682NIH HHS OT2 OD033756NIH HHS OT2 OD033759NIH HHS OT2 OD033760NIH HHS OT2 OD033761NIH HHS R03 OD036499U.S. Department of Health & Human Services | National Institutes of Health (NIH) 1OT2OD033761U.S. Department of Health & Human Services | National Institutes of Health (NIH) 1R03OD036499U.S. Department of Health & Human Services | National Institutes of Health (NIH) 3OT2OD026682U.S. Department of Health & Human Services | National Institutes of Health (NIH) 3OT2OD033760U.S. Department of Health & Human Services | National Institutes of Health (NIH) 3U54AG075936U.S. Department of Health & Human Services | National Institutes of Health (NIH) HLU01148861U.S. Department of Health & Human Services | National Institutes of Health (NIH) OT2OD026671U.S. Department of Health & Human Services | National Institutes of Health (NIH) OT2OD026673U.S. Department of Health & Human Services | National Institutes of Health (NIH) OT2OD026675U.S. Department of Health & Human Services | National Institutes of Health (NIH) OT2OD033756U.S. Department of Health & Human Services | National Institutes of Health (NIH) OT2OD033759U.S. Department of Health & Human Services | National Institutes of Health (NIH) OT2OD033760U.S. Department of Health & Human Services | National Institutes of Health (NIH) U24CA268108U.S. Department of Health & Human Services | National Institutes of Health (NIH) U24DK135157U.S. Department of Health & Human Services | National Institutes of Health (NIH) U2CDK114886U.S. Department of Health & Human Services | National Institutes of Health (NIH) U54HL165443U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute (NHGRI) RM1HG011014
Abstract
The Human BioMolecular Atlas Program (HuBMAP) aims to construct a 3D Human Reference Atlas (HRA) of the healthy adult body. Experts from 20+ consortia collaborate to develop a Common Coordinate Framework (CCF), knowledge graphs and tools that describe the multiscale structure of the human body (from organs and tissues down to cells, genes and biomarkers) and to use the HRA to characterize changes that occur with aging, disease and other perturbations. HRA v.2.0 covers 4,499 unique anatomical structures, 1,195 cell types and 2,089 biomarkers (such as genes, proteins and lipids) from 33 ASCT+B tables and 65 3D Reference Objects linked to ontologies. New experimental data can be mapped into the HRA using (1) cell type annotation tools (for example, Azimuth), (2) validated antibody panels or (3) by registering tissue data spatially. This paper describes HRA user stories, terminology, data formats, ontology validation, unified analysis workflows, user interfaces, instructional materials, application programming interfaces, flexible hybrid cloud infrastructure and previews atlas usage applications.
Indexed as
Atlases as TopicImaging, Three-DimensionalSoftwareBiomarkersHumansUser-Computer InterfaceBiomarkers
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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.