Online resources from the Allen institute for immunology: the human immune health atlas and human immune system explorer platform 3326
Abstract Description The Allen Institute for Immunology was founded in 2018 to perform deep, longitudinal profiling of the human immune system in health and disease. We established partnerships to profile healthy adults and children as well as patients at risk for rheumatoid arthritis, with inflammatory bowel disease, with multiple myeloma diagnosis, under treatment for melanoma, and with COVID-19. We sampled the same subjects longitudinally for up to two years, then performed immune profiling using scRNA-seq, 4 high-dimensional flow cytometry panels, plasma or serum proteomics, and clinical lab tests. In total, we profiled >2,300 samples from >450 subjects, including >55 million cells profiled by scRNA-seq to date. To process, analyze, and distribute this data, we developed the Human Immune System Explorer (HISE) platform, a flexible, scalable, cloud-based framework to enable storage, interactive analysis, visualization, and generation of Certificates of Reproducibility that enable inspection and replay of any step of an analysis workflow. We joined our robust, large-scale analytical platform to public-facing visualization tools, scientific context, and data releases, starting with the Human Immune Health Atlas: an expertly annotated dataset of > 1.3 million PBMCs from 108 healthy donors from 11 to 65 years of age. We invite immunologists to explore this resource and our expanding library of immunology data, insights, and tools at https://explore.allenimmunology.org/. Topic Categories Computational and Systems Immunology (COMP)
Authors
- Vaishnavi Parthasarathy
- Veronica Hernandez (ORCID: https://orcid.org/0000-0003-2568-2565)
- Vitalii Tereshchenko
- Katherine Henderson (ORCID: https://orcid.org/0000-0001-8682-5051)
- Thomas F. Bumol
- Jörg J. Goronzy (ORCID: https://orcid.org/0000-0001-7670-1856)
- Mansi Singh
- Jane H. Buckner (ORCID: https://orcid.org/0000-0002-9005-1885)
- Sarah E. Henrickson (ORCID: https://orcid.org/0000-0001-5569-4132)
- Paul Meijer (ORCID: https://orcid.org/0000-0001-5535-0399)
- Ernie Coffey
- Cara Lord (ORCID: https://orcid.org/0000-0002-7827-2159)
- Qiuyu Gong (ORCID: https://orcid.org/0009-0006-3885-0862)
- Claire E. Gustafson (ORCID: https://orcid.org/0000-0002-1437-6709)
- Lauren Okada (ORCID: https://orcid.org/0000-0002-5691-3373)
- Nicole Howard
- Aishwarya Chander (ORCID: https://orcid.org/0000-0002-0459-7583)
- Palak C. Genge (ORCID: https://orcid.org/0000-0002-0851-6445)
- Aldan Beaubien
- Adam K. Savage (ORCID: https://orcid.org/0000-0003-1913-5485)
- Marla C. Glass (ORCID: https://orcid.org/0000-0003-3763-0842)
- Erik D. Layton (ORCID: https://orcid.org/0000-0001-6409-290X)
- Charles R. Roll (ORCID: https://orcid.org/0000-0002-0726-2076)
- Elliott Swanson (ORCID: https://orcid.org/0000-0002-0351-6446)
- Ananda W. Goldrath (ORCID: https://orcid.org/0000-0002-5900-508X)
- Lynne A. Becker (ORCID: https://orcid.org/0000-0003-1541-4655)
- Laura A. Vella (ORCID: https://orcid.org/0000-0002-8917-4845)
- E. John Wherry (ORCID: https://orcid.org/0000-0003-0477-1956)
- Alex Heubeck
- Morgan Weiss (ORCID: https://orcid.org/0000-0002-4189-1992)
- Upaasana Krishnan (ORCID: https://orcid.org/0000-0001-8589-7061)
- Troy R. Torgerson (ORCID: https://orcid.org/0000-0003-3489-5036)
- Mehul Sharma (ORCID: https://orcid.org/0000-0002-9591-0415)
- Peter J. Skene (ORCID: https://orcid.org/0000-0001-8965-5326)
- Julian Reading (ORCID: https://orcid.org/0000-0002-8533-3992)
- Lucas T. Graybuck (ORCID: https://orcid.org/0000-0002-8814-6818)
- Zachary Thomson (ORCID: https://orcid.org/0000-0002-3861-9998)
- Samir Rachid Zaim (ORCID: https://orcid.org/0009-0007-9256-2324)
- Elisabeth M. Dornisch (ORCID: https://orcid.org/0009-0009-6969-8690)
- Cate Speake (ORCID: https://orcid.org/0000-0003-1480-4272)
- Cole Phalen (ORCID: https://orcid.org/0000-0002-0196-2805)
- Ed Johnson
- Jessica Garber (ORCID: https://orcid.org/0009-0007-8773-9754)
- Tyanna Stuckey (ORCID: https://orcid.org/0009-0003-3262-8441)
- John B. Johanneson (ORCID: https://orcid.org/0009-0002-7612-1290)
- Xiaojun Li (ORCID: https://orcid.org/0000-0003-0832-9479)
- Kevin Lee (ORCID: https://orcid.org/0000-0002-5606-8683)
- Tao Peng (ORCID: https://orcid.org/0000-0002-5914-0417)
- Peter J. Wittig (ORCID: https://orcid.org/0009-0000-9639-5518)
- Neelima Inala
- Yousef Aggoune
- Stark Pister
- Anne Vetto
- Christian La France
- Paul Mariz
- Madeline Ambrose
- Erin K. Kawelo (ORCID: https://orcid.org/0009-0004-0329-9914)
- Nelson Mukuka
- Sathya Subramanian
- Mackenzie Kopp
- James Harvey
- Melissa Kinsey
- Jessica Liang
- Blessing Musgrove
- R Mettey
- Autumn Kelsey
- Megan Smithmeyer
Institutions
- Children's Hospital of Philadelphia (US)
- University of Washington (US)
- Allen Institute for Immunology (US)
- Benaroya Research Institute
- University of Pennsylvania (US)
- Stanford University (US)
Publication Details
- Journal
- The Journal of Immunology
- Published
- 2025-11-01
- DOI
- https://doi.org/10.1093/jimmun/vkaf283.1142
- Primary Topic
- Single-cell and spatial transcriptomics
- Type
- article
- Field-Weighted Citation Impact
- 0.00