Author

Douglas E. Henze

Stanford UniversityORCID 0000-0002-6326-5503Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Research Focus:cell type annotation· 4 Research Focus:benchmarking· 2 Research Focus:differential expression· 2 Approach:experimental assay· 2 Approach:machine learning (classical)· 2 Organism:mouse· 2 Assay:scRNA-seq· 2 Assay:spatial transcriptomics· 2

Frequent Co-Authors

Stephen R. QuakeiD· 3 shared Andy Po‐Yi TsaiiD· 2 shared George CrowleyiD· 2 shared Tony Wyss‐CorayiD· 2 shared A.D. Choudhury· 1 shared Ahmad SalehiiD· 1 shared Alan Gi-Lun ChengiD· 1 shared Ali Reza Rais Sadati· 1 shared

Activity by Year

2025-2026 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 22 mutual co-author links

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3 shared papersNeuroscience

Stephen R. QuakeORCID

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4 papers

Recent·Most cited

Site-dependent transcriptomic signatures of endometriosis are conserved across hormonal states

Douglas E. Henze, George Crowley, Stephen R. Quake

The paper identifies core lesion cells in endometriosis that retain uterine transcriptomic identity across hormonal states and uses them to classify disease status and lesion subtype.

bioRxiv · Jul 16, 2026 · PreprintBioinformatics

Spatial and molecular insights into microglial roles in cerebellar aging

Andy Po‐Yi Tsai, Douglas E. Henze, Eduardo Ramirez Lopez, James Haberberger, Chuanpeng Dong, Nannan Lu, Micaiah Atkins, Emma K. Costa, Amelia Farinas, Hamilton Se‐Hwee Oh, Patricia Morán Losada, Yann Le Guen, Alina Isakova, Stephen R. Quake, Tony Wyss‐Coray

The paper investigates age-related changes in cerebellar microglia using single-nuclei RNA sequencing and MERFISH, finding enhanced neuroprotective immune activation and proximity to granule cells in aged mice.

Cell Reports · Nov 26, 2025Peer-reviewedNeuroscience

Benchmarking Cell Type and Gene Set Annotation by Large Language Models with AnnDictionary

George Crowley, Robert C. Jones, Mark A. Krasnow, Angela Oliveira Pisco, Julia Salzman, Nir Yosef, Siyu He, Madhav Mantri, Jessie Aguirre, Ron Garner, Sal Guerrero, William Harper, Resham Irfan, Sophia Mahfouz, Ravi Ponnusamy, , David Seong

The paper benchmarks large language models for cell-type and gene set annotation using AnnDictionary, finding high accuracy in cell-type annotation and strong functional gene set recovery.

Nature Communications · Oct 28, 2025Peer-reviewedBioinformatics

Simultaneous analysis of single-cell gene expression and morphology provides new insight into how microglia change with age

Douglas E. Henze, Andy Po‐Yi Tsai, Tony Wyss‐Coray, Stephen R. Quake

The paper analyzes single-cell gene expression and morphology in microglia to show how aging changes their spatial transcript organization and functional roles.

bioRxiv · Feb 28, 2025 · PreprintNeuroscience