Author

Dan Yuan

Allen Institute for Brain Science

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

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Biology Disciplines

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Immunology· 1 Neuroscience· 1

Signature Assays, Organisms & Methods

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Approach:statistical model· 2 Research Focus:batch correction / integration· 1 Research Focus:benchmarking· 1 Assay:bulk RNA-seq· 1 Research Focus:cell type annotation· 1 Approach:deep learning· 1 Research Focus:differential expression· 1 Approach:experimental assay· 1

Frequent Co-Authors

Andrew T. MagisiD· 1 shared Andrew WebsteriD· 1 shared Brett SmithiD· 1 shared Brian PieningiD· 1 shared Changkyu LeeiD· 1 shared Christopher CardenasiD· 1 shared Christopher G. LaustediD· 1 shared Daniel G. CheniD· 1 shared

Activity by Year

2025-2025 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 21 mutual co-author links

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1 shared paperImmunology

Andrew T. MagisORCID

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Author profile →

2 papers

Recent·Most cited

Fast Optimization of Robust Transcriptomics Embeddings using Probabilistic Inference Autoencoder Networks for multi-Omics

Ning Wang, David Turner, Hannah Feinberg, Victor Eduardo Nieto Caballero, Dan Yuan, Nathaniel Scott, Christopher Cardenas, Michael DeBerardine, Shu Dan, Lakme Caceres, Jessica Schembri, Zizhen Yao, Changkyu Lee, Jonathan W. Pillow, Fenna M. Krienen

The paper introduces PIANO, a variational autoencoder for multi-omics integration, showing improved performance on single-species and multi-atlas datasets.

bioRxiv · Nov 16, 2025 · PreprintNeuroscience

APMAT analysis reveals the association between CD8 T cell receptors, cognate antigen, and T cell phenotype and persistence

Jingyi Xie, Daniel G. Chen, William Chour, Rachel H. Ng, Rongyu Zhang, Dan Yuan, Jongchan Choi, Michaela McKasson, Pamela Troisch, Brett Smith, Lesley Jones, Andrew Webster, Yusuf Rasheed, Sarah Li, Rick Edmark, , James R. Heath

APMAT analysis links CD8 T cell receptors, cognate antigens, and T cell phenotype/persistence using integrated experimental-computational methods.

Nature Communications · Feb 6, 2025Peer-reviewedImmunology