Author

Daniel J. Stein

Broad InstituteORCID 0000-0002-9442-2604Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Organism:human· 2 Assay:spatial transcriptomics· 2 Approach:deep learning· 1 Research Focus:differential expression· 1 Organism:mouse· 1 Assay:proteomics· 1 Research Focus:spatial domain detection· 1 Approach:statistical model· 1

Frequent Co-Authors

Ilya KorsunskyiD· 2 shared Andrew D. FileriD· 1 shared Anna Helena JonssoniD· 1 shared Lakshay Sood· 1 shared Laurie RumkeriD· 1 shared Michelle L. CurtisiD· 1 shared Miles TraniD· 1 shared Mukta G. PalshikariD· 1 shared

Activity by Year

2025-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 37 mutual co-author links

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2 shared papersGenomics

Ilya KorsunskyORCID

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2 papers

Recent·Most cited

Powerful and accurate case-control analysis of spatial molecular data

Yakir Reshef, Lakshay Sood, Michelle L. Curtis, Laurie Rumker, Daniel J. Stein, Mukta G. Palshikar, Saba Nayar, Andrew D. Filer, Anna Helena Jonsson, Ilya Korsunsky, Soumya Raychaudhuri

This paper introduces VIMA, a method for analyzing spatial molecular data to identify disease-associated spatial features, showing improved performance over existing methods in simulations and real datasets.

Nature Methods · Oct 6, 2026Peer-reviewedGenomics

Accurate tiling of spatial single-cell data with Tessera

Daniel J. Stein, Miles Tran, Ilya Korsunsky

Tessera improves tissue segmentation in spatial single-cell data by creating accurate, boundary-preserving tiles that capture natural tissue structures in mouse and human tissues.

bioRxiv · Jan 17, 2025 · PreprintBioinformatics