Author

Steve R. Quake

Stanford University

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

Biology Disciplines

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Cell Biology· 1 Genetic & Genomic Medicine· 1

Signature Assays, Organisms & Methods

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Organism:human· 2 Research Focus:benchmarking· 1 Research Focus:cell type annotation· 1 Approach:deep learning· 1 Research Focus:differential expression· 1 Assay:DNA methylation· 1 Organism:multiple species· 1 Assay:scRNA-seq· 1

Frequent Co-Authors

Aaron Scott· 1 shared Alan AshworthiD· 1 shared Anna BergamaschiiD· 1 shared Chin‐Jen Ku· 1 shared Chris Ellison· 1 shared Erin McCarthyiD· 1 shared François ColliniD· 1 shared Gita MahmoudabadiiD· 1 shared

Activity by Year

2020-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 29 mutual co-author links

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1 shared paperGenetic & Genomic Medicine

Aaron Scott

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2 papers

Recent·Most cited

Species-specific small models for cell type classification approach the performance of large single cell foundation models

Gita Mahmoudabadi, Lakshmi Krishnan, Tejaswini Ganapathi, James Pearce, Steve R. Quake, Theofanis Karaletsos

The paper introduces CytoType and ESM-CE, species-specific small models for cell type classification that achieve performance comparable to large foundation models with fewer parameters.

bioRxiv · Mar 18, 2026 · PreprintCell Biology

Pilot study demonstrating changes in DNA hydroxymethylation enable detection of multiple cancers in plasma cell-free DNA

Anna Bergamaschi, Yuhong Ning, Chin‐Jen Ku, Chris Ellison, François Collin, Gulfem Dilek Guler, Tierney C. Phillips, Erin McCarthy, Wendy Wang, Michael Antoine, Aaron Scott, Paul Lloyd, Alan Ashworth, Steve R. Quake, Samuel Levy

This study uses 5-hydroxymethyl cytosine (5hmC) profiles in plasma cell-free DNA to detect multiple cancers with high accuracy using machine learning.

medRxiv · Jan 22, 2020 · PreprintGenetic & Genomic Medicine