Author

Sirui Ding

University of California, San FranciscoORCID 0000-0001-5827-8214Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Bioinformatics· 1 Immunology· 1

Signature Assays, Organisms & Methods

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Research Focus:benchmarking· 1 Research Focus:cell type annotation· 1 Research Focus:clustering· 1 Approach:deep learning· 1 Research Focus:differential expression· 1 Research Focus:drug response / drug discovery· 1 Assay:flow cytometry· 1 Organism:human· 1

Frequent Co-Authors

Atul Janardhan ButteiD· 2 shared Sanchita BhattacharyaiD· 2 shared Marina SirotaiD· 1 shared Minnie SarwaliD· 1 shared

Activity by Year

2025-2025 · peak 2/yr

Co-Author Collaboration Network

4 top collaborators · 6 mutual co-author links

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2 shared papersBioinformatics

Atul Janardhan ButteORCID

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2 papers

Recent·Most cited

BioinformaticsbioRxivPreprintJul 10, 2025

Transplant-Agents: A Multi-Agent Artificial Intelligence Framework for Reproducibility Assessment of Post-Transplant Risk Prediction and Rejection Biomarkers

Sirui Ding, Sanchita Bhattacharya, Minnie Sarwal…·Atul Janardhan Butte

Transplant-Agents uses a multi-agent AI framework to identify reproducible biomarkers and predict transplant rejection risk with high AUROC scores across multiple datasets.

DOI 10.1101/2025.07.10.664265

humanmachine learning (classical)

𝕏 PostBluesky

ImmunologybioRxivPreprintJul 9, 2025

ImmuneFM: Pre-training Foundation Model from Cytometry Data for Immunology Research

Sirui Ding, Sanchita Bhattacharya, Atul Janardhan Butte

The paper develops ImmuneFM, a foundation model pre-trained on cytometry data for immunology, showing superior performance on eight downstream tasks with limited labeled samples.

3 citations

flow cytometrydeep learning

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