Author

David Y. Chen

Washington University in St. LouisORCID 0000-0002-3681-6576Unclaimed ORCID profile · follow to get notified of new preprints

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David Y. Chen1 paper

Biology Disciplines

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Genomics· 3 Bioengineering· 1

Signature Assays, Organisms & Methods

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Organism:human· 4 Research Focus:differential expression· 3 Research Focus:gene regulatory network inference· 3 Research Focus:cell type annotation· 2 Research Focus:cell-cell communication· 2 Research Focus:clustering· 2 Approach:deep learning· 2 Approach:experimental assay· 2

Frequent Co-Authors

Aadel A. ChaudhuriiD· 1 shared Aaron M. NewmaniD· 1 shared Abul UsmaniiD· 1 shared Blake Sparkman· 1 shared Brian D. MueggeiD· 1 shared Caroline Bonmati· 1 shared Clément Collignon· 1 shared Colin HercusiD· 1 shared

Activity by Year

2025-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 12 mutual co-author links

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1 shared paperGenomics

Aadel A. ChaudhuriORCID

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4 papers

Recent·Most cited

SMURF: soft-segmentation for single-cell reconstruction and topological analysis of spatial transcriptomic data

Juanru Guo, Simona Sarafinovska, Ryan A. Hagenson, Mark C. Valentine, David Y. Chen, William H. McCoy IV, Joseph D. Dougherty, Robi David Mitra, Brian D. Muegge

SMURF improves spatial transcriptomic analysis by accurately assigning mRNAs to cells and revealing gene-expression zonation in tissues.

Nature Communications · Jun 26, 2026Peer-reviewedGenomics

The optical origin of the human skin color 'banana' in CIELAB space

Maysoon Harunani, Ye Jin Han, Mutian Shen, Blake Sparkman, David Y. Chen, Zohar Nussinov, Leonid Shmuylovich

The paper develops a physics-based framework to link skin chromophore content to colorimeter-derived skin color coordinates, revealing how melanin and blood contribute to the banana-shaped locus in CIELAB space.

bioRxiv · Jun 18, 2026 · PreprintBioengineering

Mapping single-cell developmental potential in health and disease with interpretable deep learning

Minji Kang, José Juan Almagro Armenteros, Gunsagar Singh Gulati, Rachel Gleyzer, Susanna Avagyan, Erin L. Brown, Wubing Zhang, Abul Usmani, Noah J. Earland, Zhenqin Wu, James Zou, Ryan Courtney Fields, David Y. Chen, Aadel A. Chaudhuri, Aaron M. Newman

The paper introduces CytoTRACE 2, a deep learning framework to assess cell potency from scRNA-seq data, showing improved performance across multiple datasets and applications.

Nature Methods · Oct 27, 2025Peer-reviewedGenomics

Genomic and Immunogenomic Profiling of Extramedullary Acute Myeloid Leukemia Reveals Actionable Clonal Branching and Frequent Immune Editing

Clément Collignon, T H Hansen, Colin Hercus, Marianna B. Ruzinova, Gabrielle Roth Guépin, Caroline Bonmati, Marie‐Thérèse Rubio, Pierre Feugier, Mélanie Gaudfrin, Hervé Sartelet, Marion Divoux, Marc Müller, Sharon E. Heath, Geoffrey L. Uy, David H. Spencer, , Francesca Ferraro

This study profiles genomic and immunogenomic features of eAML, finding clonal branching and immune editing, with FLT3 mutations in relapsed cases.

Blood Cancer Journal · Aug 13, 2025Peer-reviewedGenomics