To help make this massive dataset more accessible to the research community, we developed interactive exploration tools at @alleninstitute.org
Easily explore DEGs and pathways and view how the whole panel of cytokines affect your favorite genes at:
apps.allenimmunology.org/aifi/resourc...
@parse.bsky.social released an amazing 10M cell dataset for immunologists: they profiled 90 cytokine responses in 12 donors with the GigaLab platform:
www.parsebiosciences.com/datasets/10-...
We have recently uploaded our revised manuscript “Evaluating the role of pre-training dataset size and diversity on single-cell foundation model performance”.
TL;DR: More models, more tasks => same results.
Looking forward to Cytokines 2025! @alleninstitute.org will be there, with posters about plasma cells, Rheumatoid arthritis, neuroimmune signaling, ulcerative colitis, TRM formation, and a new interferon signaling atlas.
Times and details at:
apps.allenimmunology.org/aifi/present...
#cytokines2025
Our colleagues at @benaroyaresearch.bsky.social and @alleninstitute.org collected patient metadata, clinical labs, vaccine serology, plasma proteomics, scRNA-seq, and whole blood RNA-seq data, all curated and openly available for download with consistent metadata from our web portal.
30.10.2025 18:08 — 👍 2 🔁 0 💬 0 📌 0
If you're an Immunologist studying vaccine response or looking for a great control dataset for your study, or if you're looking for a great dataset for large-scale, machine learning, look no further than our Dynamics of Immune Health and Age website.
apps.allenimmunology.org/aifi/insight...
Now that the paper is out, we're proud to support both our team's publication and immunologists through open visualizations, tools, downloads, and a record of analyses, called a Certificate of Reproducibility through the Human Immune System Explorer.
royalsocietypublishing.org/doi/10.1098/...
As we continue to develop the @alleninstitute.org Allen Institute for Immunology web platform, our first big challenge was to build tools to support the release of the amazing longitudinal Immune Health study, published yesterday in Nature:
www.nature.com/articles/s41...
Years before the pain begins, early-warning signs for rheumatoid arthritis (RA) could help doctors catch the disease before it starts. 🧵
24.09.2025 18:49 — 👍 23 🔁 5 💬 3 📌 2
Two #AACR25 posters from Allen Institute for Immunology will be up Tuesday from 9-12.
Medbh Dillon will showcase 3D Multiple Myeloma culture models at Sec. 6, No. 14
Imran McGrath and I have our scRNA-seq and spatial transcriptomics from MM patients at Sec. 28 No. 11
@alleninstitute.bsky.social
The Allen Institute for Immunology is at #AACR25 conference!
Come see my poster to preview our open data and tools for Multiple Myeloma.
2 PM, Section 46, Board 11
More details and where to find us at tinyurl.com/allen-aacr-2...
@alleninstitute.bsky.social @theaacr.bsky.social
Here's a direct link to that Reference tool:
apps.allenimmunology.org/aifi/resourc...
More complement-related gene symbols can be found here, courtesy of the HGNC:
www.genenames.org/data/genegro...
The main way we have to look at Complement System in our atlas is by looking at expression of the genes that are involved. For example, if you select the gene C1QA (serum complement component C1q) in our reference tool, we can see that it's expressed by a specialized C1Q+ monocyte population:
15.01.2025 00:49 — 👍 1 🔁 0 💬 1 📌 0
🩸🔬 Introducing #CryoSCAPE, a groundbreaking technique that keeps blood cells alive in deep freeze. This innovation promises to expand the reach of cutting-edge single-cell technologies to rural or underserved populations. ✨ 🧵
#SingleCellTech #RNAseq
The striatum is a key region involved in substance use disorders and movement disorders, and these new tools provide a way to target specific populations within this important brain region.
Congrats to the Allen Institute for Brain Science team on building this resource!
Amazing new tools for targeting the striatum across species, from mouse to primate from my colleagues in Brain Science at the @alleninstitute.bsky.social .
www.biorxiv.org/content/10.1...
Christian LaFrance overcame a series of technical hurdles to make this beautiful, responsive, and extensible tool that we can build on in future releases.
The data and analyses that went into building this resource are described here:
apps.allenimmunology.org/aifi/resourc...
As part of our Human Immune Health Atlas release from the Allen Institute for Immunology, we built a UMAP viewer for interactive data exploration that can handle millions of cells.
You can find our Human Immune Health Atlas UMAP Explorer here:
apps.allenimmunology.org/aifi/resourc...
The Data-Driven Discovery: AI and Modeling in Biology Workshop is happening now at the Allen Institute.
I saw some great talks yesterday!
More info below, with links to recordings and the live stream, can be found here:
#openscience #machinelearning #modeling
To understand disease, we must understand the healthy immune system, deeply and across the human lifespan.
Thanks to the dedication of ~100 healthy volunteers and many research teams, we are proud to share the Human Immune Health Atlas. 🧵
#OpenScienceWeek
