Author

Huanhuan Wei

Shanghai Jiao Tong UniversityORCID 0000-0001-5741-4114Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Research Focus:benchmarking· 1 Research Focus:gene regulatory network inference· 1 Approach:large language model· 1 Assay:scRNA-seq· 1 Research Focus:spatial domain detection· 1 Assay:spatial transcriptomics· 1 Approach:statistical model· 1

Frequent Co-Authors

Alexandra PopaiD· 1 shared Hongyi YuiD· 1 shared Hongyu ZhaoiD· 1 shared Hui Juan LuiD· 1 shared J Liang· 1 shared Lixing LiniD· 1 shared Luning Yang· 1 shared Maor SauleriD· 1 shared

Activity by Year

2022-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 29 mutual co-author links

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1 shared paperBioinformatics

Alexandra PopaORCID

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2 papers

Recent·Most cited

BioinformaticsbioRxivPreprintJun 26, 2026

SPEAK: Spatial Prompting with Expert Aligned Knowledge for Tissue Domain Identification in Spatial Transcriptomics

Huanhuan Wei, Xiao Luo, Hongyi Yu…·Xiting Yan

SPEAK identifies spatial domains in spatial transcriptomics data using a large language model and expert-aligned prompts, showing improved accuracy and interpretability.

DOI 10.64898/2026.06.22.733750

spatial transcriptomicslarge language model

𝕏 PostBluesky

BioinformaticsInternational Journal of Molecular SciencesPeer-reviewedMar 20, 2022

Inferring time-lagged causality using the derivative of single-cell expression

Huanhuan Wei, Hui Juan Lu, Hongyu Zhao

This paper introduces CITL, a method to infer time-lagged causal relationships from scRNA-seq data by analyzing gene expression changes, and validates it on simulation and real data.

2 citations

scRNA-seqstatistical model

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