Author

Yuan Xue

Stanford UniversityORCID 0000-0002-7846-4273Unclaimed ORCID profile · follow to get notified of new preprints

Additional preprints under this name without ORCID

Yuan Xue1 paper · Shanghai Institute of Nutrition and Health

Biology Disciplines

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Developmental Biology· 2 Bioinformatics· 1 Immunology· 1

Signature Assays, Organisms & Methods

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Assay:bulk RNA-seq· 3 Research Focus:cell type annotation· 3 Approach:statistical model· 3 Research Focus:differential expression· 2 Research Focus:cell signaling & trafficking· 1 Research Focus:cell-cell communication· 1 Research Focus:clustering· 1 Research Focus:dimensionality reduction· 1

Frequent Co-Authors

Bo WangiD· 3 shared Stephen R. QuakeiD· 3 shared Alexander J. TarashanskyiD· 2 shared Dania Nanes SarfatiiD· 2 shared Pengyang LiiD· 2 shared Aaron FountainiD· 1 shared Adrien BurlacotiD· 1 shared Ashley ByrneiD· 1 shared

Activity by Year

2019-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 28 mutual co-author links

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3 shared papersDevelopmental Biology

Bo WangORCID

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4 papers

Recent·Most cited

SPIC-dependent erythrophagocytic macrophages drive granuloma formation and pathogen persistence during intracellular bacterial infection

Aaron Fountain, Weixian Lin, Max Lain, Yuan Xue, Trung H.M. Pham

The paper identifies SPIC-dependent VCAM1+ macrophages as drivers of granuloma formation and bacterial persistence during Salmonella infection.

bioRxiv · May 27, 2026 · PreprintImmunology

Coordinated wound responses in a regenerative animal-algal photosymbiotic metaorganism

Dania Nanes Sarfati, Yuan Xue, Eun Sun Song, Ashley Byrne, Daniel Le, Spyros Darmanis, Stephen R. Quake, Adrien Burlacot, James Sikes, Bo Wang

This study shows that injury in the acoel Convolutriloba longifissura triggers coordinated responses between the host and its symbiotic algae, mediated by the runt transcription factor.

Nature Communications · May 13, 2024Peer-reviewedDevelopmental Biology

Single-cell analysis of Schistosoma mansoni reveals a conserved genetic program controlling germline stem cell fate

Pengyang Li, Dania Nanes Sarfati, Yuan Xue, Xi Yu, Alexander J. Tarashansky, Stephen R. Quake, Bo Wang

Nature Communications · Jan 20, 2021Peer-reviewedDevelopmental Biology

Self-assembling Manifolds in Single-cell RNA Sequencing Data

Alexander J. Tarashansky, Yuan Xue, Pengyang Li, Stephen R. Quake, Bo Wang

The paper introduces the self-assembling manifold algorithm to improve gene relevance quantification and dimensionality reduction in single-cell RNA sequencing data, showing it outperforms existing methods in identifying stem cell populations and across multiple datasets.

eLife · Sep 16, 2019Peer-reviewedBioinformatics