Code and data analysis from the Rush Alzheimer's Disease Center.
We study the genetics and molecular biology of Alzheimer's disease, Parkinson's disease, and related dementias, using deeply phenotyped autopsy cohorts — chiefly ROSMAP — with matched genomic, transcriptomic, and proteomic data.
Repositories fall into three groups: manuscript releases (analysis code and reproducible reports accompanying published work), pipelines and tools, and teaching material.
Manuscript releases · Pipelines & tools · Teaching
Data underlying these analyses is generally not in the repositories. Requests go through the RADC Resource Sharing Hub or the relevant Synapse project — see each repo's README for specifics.
Analysis code and rendered reports released alongside publications.
Association of structural variants with AD/ADRD clinical and neuropathologic traits. Includes summary statistics.
Vialle RA, et al. Structural variants linked to Alzheimer's disease and other common age-related clinical and neuropathologic traits. Genome Medicine 17, 20 (2025).
Multi-omics factor analysis across ROSMAP omics layers, with GSEA, phenotype association, and clustering into molecular subtypes.
Scheidemantel LP, et al. Integration of aged brain multi-omics reveals cross-system mechanisms underlying Alzheimer's disease heterogeneity. Cell Reports (2026).
Module–trait network analysis of ROSMAP single-nucleus and bulk RNA-seq.
de Paiva Lopes K, et al. Gene module-trait network analysis uncovers cell type specific systems and genes relevant to Alzheimer's disease. Acta Neuropathologica Communications (2025).
Spatial transcriptomics of human AD brain tissue: Seurat and BayesSpace clustering, cell2location deconvolution, plaque–glia niche models.
Avey DR, Ng B, Vialle RA, et al. Uncovering plaque-glia niches in human Alzheimer's disease brains using spatial transcriptomics. Molecular Neurodegeneration Advances (2025).
Cytokine expression in aged cortex: association with AD traits, variance partition, AD-PRS and APOE effects, GSEA, with MSBB and Mayo replication.
Godoy JB, et al. Cytokine expression profile in the human brain of older adults. Journal of Neuroinflammation 22, 224 (2025).
Cell–cell communication across myeloid and microglial populations in the DLPFC.
Santos L, et al. Altered microglial communication in brains with Alzheimer's disease pathology. bioRxiv (2026).
Method and code for genotyping the TOMM40'523 poly-T polymorphism directly from whole-genome sequencing.
Vialle RA, et al. Genotyping TOMM40'523 poly-T polymorphisms using whole-genome sequencing. Human Genetics and Genomics Advances (2025).
| Project | Description | Stack | Last commit |
|---|---|---|---|
| TOMM40_WGS-original | Genotyping the TOMM40 '523 poly-T polymorphism from WGS. — cite Vialle et al., HGG Advances (2025) | Snakemake/R |  |
| CIRI3-fork | circRNA detection, forked from gyjames/CIRI3 and split into decoupled SCAN1 / BUILD_UNIVERSE / SCAN2 / FINALIZE stages so per-sample steps parallelize across a cluster — cite Zheng et al Nat Biotechnol 44, 1463–1469 (2026) | Java |  |
| peer-fork | OpenMP-parallelized PEER (3–10× faster, inference unchanged), forked from stasaki/peer — cite Stegle et al., Nature Protocols 7, 500–507 (2012) | C++ |  |
| Course | Description |
|---|---|
| Intro_Systems_Biology | Introduction to Systems Biology. Systems biology course focused on molecular networks, WGCNA, and network medicine, plus hands-on WGCNA tutorials on bulk RNA-seq. Ministered at IAMSPE-SP Brazil by Katia Lopes. |
| IAMSPE-CS31-Genomica_Computacional | Genômica Computacional (IAMSPE, CS31). Introductory course on computational genomics. Ministered at IAMSPE-SP Brazil by Ricardo Vialle |
Most manuscript repositories are rendered R Markdown: .Rmd sources sit next to
HTML reports, several of which are published to GitHub Pages (links above).
Licenses vary by repository (GPL-2.0, MIT, Apache-2.0) — check before reuse.
If something here is useful but under-documented, open an issue on that repository.
Maintained by the RushAlz team.
