Author

Samuel D. Aragones

University of California, Los AngelesORCID 0000-0002-5071-797XUnclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Bioinformatics· 2

Signature Assays, Organisms & Methods

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Research Focus:benchmarking· 2 Research Focus:dimensionality reduction· 2 Assay:scRNA-seq· 2 Approach:statistical model· 2 Research Focus:cell type annotation· 1

Frequent Co-Authors

Breanne SpartaiD· 2 shared Eric J. DeedsiD· 2 shared Timothy HamiltoniD· 2 shared Gunalan Natesan· 1 shared J. Christian J. RayiD· 1 shared Shamus M. CooleyiD· 1 shared

Activity by Year

2024-2026 · peak 1/yr

Co-Author Collaboration Network

6 top collaborators · 13 mutual co-author links

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2 shared papersBioinformatics

Breanne SpartaORCID

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2 papers

Recent·Most cited

A novel metric reveals previously unrecognized distortion in dimensionality reduction of scRNA-Seq data

Timothy Hamilton, Breanne Sparta, Shamus M. Cooley, Samuel D. Aragones, J. Christian J. Ray, Eric J. Deeds

Comparing local point neighborhoods before and after dimensionality reduction reveals that standard scRNA-seq pipelines, t-SNE, and UMAP often distort local neighborhoods by more than 95%, altering downstream clustering.

bioRxiv · May 11, 2026 · PreprintBioinformatics

Binomial models uncover biological variation during feature selection of droplet-based single-cell RNA sequencing

Breanne Sparta, Timothy Hamilton, Gunalan Natesan, Samuel D. Aragones, Eric J. Deeds

The paper introduces a binomial model to identify biologically variable genes in scRNA-seq data, showing it outperforms existing methods in preserving biological structure.

PLoS Computational Biology · Sep 6, 2024Peer-reviewedBioinformatics