Thanks for attending our talks at the Genomics in Action 2025 conference! You can find the presentations, related web resources, and relevant journal articles below.
Large-scale datasets and resources from the Allen Institute for Immunology
Lucas Graybuck | | |
Related web resources
Human Immune System Explorer: Main Page
The best place to go for the latest data releases from the Allen Institute for Immunology.
Human Immune Health Atlas
An age-spanning healthy PBMC cell type atlas from 108 pediatric, young adult, and older adult subjects.
Dynamics of Human Immune Health and Age
Longitudinal profiling of 96 healthy adult subjects over the course of 2+ years, including >13.5 million cells of scRNA-seq.
Systemic Inflammation in At-Risk Individuals Advancing to Clinical Rheumatoid Arthritis
Longitudinal monitoring of subjects at risk for Rheumatoid Arthritis, including those that convert to RA during the study period.
Related Journal Articles
Meijer P, Howard N, Liang J, Kelsey A, Subramanian S, Johnson E, et al. Provide Proactive Reproducible Analysis Transparency with Every Publication. arXiv [cs.CE]. 2024. Available: http://arxiv.org/abs/2408.09103
Gong Q, Sharma M, Kuan EL, Glass MC, Chander A, Singh M, et al. Longitudinal Multi-omic Immune Profiling Reveals Age-Related Immune Cell Dynamics in Healthy Adults. bioRxiv. 2024. p. 2024.09.10.612119. doi:10.1101/2024.09.10.612119
He Z, Glass MC, Venkatesan P, Feser ML, Lazaro L, Okada LY, et al. Systemic inflammation and lymphocyte activation precede rheumatoid arthritis. bioRxiv. 2024. p. 2024.10.25.620344. doi:10.1101/2024.10.25.620344
Automating Immunology: From Raw Data to Insight
Aishwarya Gogate | | |
Related web resources
PALMO Repository
R package for longitudinal modeling of multiomics data
MOCHA Website
R package for advanced modeling of scATAC-seq data
SPARROW Repository
Python-based variational auto-encoder methods for spatial transcriptomics analysis
BarWare Pipeline Repository
Efficient pipelines for large-scale multiplexed scRNA-seq data preprocessing and assembly
Related Journal Articles
Vasaikar SV, Savage AK, Gong Q, Swanson E, Talla A, Lord C, et al. A comprehensive platform for analyzing longitudinal multi-omics data. Nat Commun. 2023;14: 1684. doi:10.1038/s41467-023-37432-w
Rachid Zaim S, Pebworth M-P, McGrath I, Okada L, Weiss M, Reading J, et al. MOCHA’s advanced statistical modeling of scATAC-seq data enables functional genomic inference in large human cohorts. Nat Commun. 2024;15: 6828. doi:10.1038/s41467-024-50612-6
Zhao PA, Garber J, Gustafson C, Kim J, Malone J, Savage A, et al. SPARROW reveals cell states and functions influenced by microenvironment zones in complex tissues. bioRxiv. 2024. p. 2024.04.05.588159. doi:10.1101/2024.04.05.588159
Swanson E, Reading J, Graybuck LT, Skene PJ. BarWare: efficient software tools for barcoded single-cell genomics. BMC Bioinformatics. 2022;23: 106. doi:10.1186/s12859-022-04620-2
Reina-Campos M, Monell A, Ferry A, Luna V, Cheung KP, Galletti G, et al. Tissue-resident memory CD8 T cell diversity is spatiotemporally imprinted. Nature. 2025; 1–10. doi:10.1038/s41586-024-08466-x
Interactive Visualizations for Big Biological Data
Christian La France | |
Download PresentationDownload Poster
Related web resources
Human Immune Health Atlas UMAP Explorer
Interactive visualization of >1.8 Million PBMCs from 108 healthy subjects
Human Immune Health Atlas Landing Page
The main landing page related to the UMAP Explorer, above
Related Journal Articles
Gong Q, Sharma M, Kuan EL, Glass MC, Chander A, Singh M, et al. Longitudinal Multi-omic Immune Profiling Reveals Age-Related Immune Cell Dynamics in Healthy Adults. bioRxiv. 2024. p. 2024.09.10.612119. doi:10.1101/2024.09.10.612119
Data visualization frameworks
Dash
A flexible framework for reactive web applications in Python, including coupling to interactive plotting with the Plotly graphing library.
Deck.gl
A GPU-centric framework for web-based data visualization, including millions of points.
GeoArrow
Fast, columnar storage of geo/spatial data representations