Author

Mahua Dey

University of Wisconsin–MadisonORCID 0000-0002-7024-5164Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Bioinformatics· 2

Signature Assays, Organisms & Methods

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Research Focus:cell type annotation· 2 Approach:large language model· 2 Assay:scRNA-seq· 2 Approach:deep learning· 1 Research Focus:differential expression· 1 Research Focus:drug response / drug discovery· 1 Research Focus:gene regulatory network inference· 1 Organism:human· 1

Frequent Co-Authors

Christina M. KendziorskiiD· 2 shared Jack M. ShiremaniD· 2 shared Lingxin ChengiD· 2 shared Yujia CaiiD· 2 shared Akash GOGATE· 1 shared Chitrasen MohantyiD· 1 shared Elliot XieiD· 1 shared Jihua LiuiD· 1 shared

Activity by Year

2024-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 36 mutual co-author links

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2 shared papersBioinformatics

Christina M. KendziorskiORCID

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2 papers

Recent·Most cited

BioinformaticsbioRxivPreprintOct 29, 2026

Agentic Discovery Transfer Enables Cross-Cancer Discovery at Scale

Lingxin Cheng, Jack M. Shireman, Akash GOGATE…·Christina M. Kendziorski

SMART, a multi-agent framework, transfers findings from single-cell RNA-sequencing cancer studies to other cancer types, identifying cross-cancer prognostic signatures and generating new hypotheses.

DOI 10.64898/2026.10.28.762506

humanscRNA-seq

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BioinformaticsbioRxivPreprintDec 4, 2024

CASSIA: a multi-agent large language model for reference free, interpretable, and automated cell annotation of single-cell RNA-sequencing data

Elliot Xie, Lingxin Cheng, Jack M. Shireman…·Christina M. Kendziorski

CASSIA automates and improves cell type annotation in single-cell RNA-sequencing data with interpretability and accuracy.

3 citations

scRNA-seqlarge language model

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