Author

Ruoxi Yuan

Hospital for Special SurgeryORCID 0000-0002-8719-341XUnclaimed ORCID profile · follow to get notified of new preprints

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Approach:statistical model· 5 Assay:bulk RNA-seq· 4 Organism:human· 4 Assay:scRNA-seq· 4 Research Focus:cell type annotation· 3 Approach:deep learning· 2 Research Focus:differential expression· 2 Approach:experimental assay· 2

Frequent Co-Authors

Lionel B. IvashkiviD· 5 shared Bikash MishraiD· 4 shared Richard D. BelliD· 4 shared Anne R. BassiD· 2 shared Claire K. WingertiD· 2 shared Accelerating Medicines Partnership: RA/SLE Network· 1 shared Amit LakhanpaliD· 1 shared Anne‐Marie MalfaitiD· 1 shared

Activity by Year

2025-2026 · peak 5/yr

Co-Author Collaboration Network

10 top collaborators · 26 mutual co-author links

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5 shared papersImmunology

Lionel B. IvashkivORCID

Mutual co-authors in cluster

Author profile →

6 papers

Recent·Most cited

Synovial transcriptional clusters link cartilage degeneration to cell-type-specific gene expression in knee osteoarthritis

Michael R. Mazzucco, Bella Y. Mehta, Jenelys Ruiz Ortiz, Caryn R. Hale, Fuadur Omi, Purva Singh, Ruoxi Yuan, Samantha G. Lessard, Eun Kyung Song, Mengrui Zhang, Shady Younis, William H. Robinson, Daniel C. Ramirez, Edward F. DiCarlo, Wei Wang, , Dana E. Orange

The paper identifies four synovial transcriptional clusters in knee OA linked to cartilage degeneration severity through bulk and single-cell RNA-seq analyses.

bioRxiv · Apr 24, 2026 · PreprintGenomics

Sexual dimorphism in zymosan-induced arthritis is linked with a higher IFN response in myeloid cell subsets that faithfully recapitulate RA synovial cell clusters

Richard D. Bell, Mary Huang, Ruoxi Yuan, Claire K. Wingert, Bikash Mishra, Seda Seren, Toolika Singh, Susan MacLauchlan, Ellen M. Gravallese, Anvita Singh, Amit Lakhanpal, Anne R. Bass, Laura B. Donlin, Lionel B. Ivashkiv

bioRxiv · Nov 24, 2025 · PreprintImmunology

Pathologic profibrotic activation of distinct myeloid cell subsets in a model of impaired healing after anterior cruciate ligament reconstruction

Wataru Morita, Yuki Suzuki, Ruoxi Yuan, Scott Alan Rodeo, Kyung‐Hyun Park‐Min, Lionel B. Ivashkiv

The paper identifies CX3CR1+ monocytes/macrophages as key drivers of impaired healing after ACLR and suggests they are potential therapeutic targets.

bioRxiv · Jul 31, 2025 · PreprintImmunology

Beyond Antagonism: IL-4 Exploits TNF signaling to Shape Its Gene Expression Signature in Monocytes and Macrophages.

Ruoxi Yuan, Chao Yang, Bikash Mishra, David Oliver, Richard D. Bell, Lionel B. Ivashkiv

The paper shows IL-4 enhances TNF-induced gene expression in monocytes/macrophages through epigenetic mechanisms, revealing cooperative crosstalk between antagonistic cytokines.

bioRxiv · Jul 28, 2025 · PreprintImmunology

Opposing Regulation of TNF Responses by IFN-γ and a PGE2-cAMP Axis that is Apparent in Rheumatoid and Immune Checkpoint Inhibitor-induced Arthritis IL-1β+ Macrophages

Upneet K. Sokhi, Ruoxi Yuan, Bikash Mishra, Yurii V. Chinenov, Anvita Singaraju, Karmela K Chan, Anne R. Bass, Richard D. Bell, Laura T. Donlin, Lionel B. Ivashkiv

This study identifies a PGE2-cAMP axis that opposes IFN-γ regulation of TNF responses in IL-1β+ macrophages in RA and ICI-arthritis, revealing a novel regulatory mechanism for inflammatory gene expression.

eLife · Jul 15, 2025Peer-reviewedImmunology

IL-10 Targets IRFs to Suppress IFN and Inflammatory Response Genes by Epigenetic Mechanisms

Bikash Mishra, Mahesh Bachu, Ruoxi Yuan, Claire K. Wingert, Vidyanath Chaudhary, Caroline Brauner, Richard D. Bell, Lionel B. Ivashkiv

This study identifies how IL-10 suppresses inflammatory gene expression by targeting IRF transcription factors and altering chromatin accessibility and histone marks in human monocytes.

Nature Immunology · Apr 22, 2025Peer-reviewedImmunology