Author

Peiying Cai

SIB Swiss Institute of BioinformaticsORCID 0009-0001-9229-2244Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Bioinformatics· 4 Genomics· 1

Signature Assays, Organisms & Methods

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Assay:spatial transcriptomics· 4 Approach:statistical model· 4 Research Focus:differential expression· 3 Research Focus:benchmarking· 2 Approach:Bayesian inference· 1 Approach:benchmark study· 1 Assay:bulk RNA-seq· 1 Research Focus:cell type annotation· 1

Frequent Co-Authors

Mark D. RobinsoniD· 5 shared Simone TiberiiD· 4 shared Charlotte SonesoniD· 2 shared Jieran SuniD· 2 shared Martin EmonsiD· 2 shared Raphaël GottardoiD· 2 shared Samuel GunziD· 2 shared Ahmed Essam MahfouziD· 1 shared

Activity by Year

2024-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 37 mutual co-author links

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5 shared papersBioinformatics

Mark D. RobinsonORCID

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5 papers

Recent·Most cited

GenomicsNature MethodsPeer-reviewedAug 24, 2026

Beyond benchmarking: an expert-guided consensus approach to spatially aware clustering

Jieran Sun, Kirti Biharie, Peiying Cai…·Naveed Ishaque

The paper introduces SACCELERATOR, a framework for spatially aware clustering that improves benchmarking by incorporating expert feedback and consensus analysis across diverse datasets.

5 citationstop 3%

humanmouse

𝕏 PostBluesky

BioinformaticsBioinformaticsPeer-reviewedJun 24, 2026

DESpace2: detection of differential spatial patterns in spatial omics data

Peiying Cai, Mark D. Robinson, Simone Tiberi

DESpace2 identifies differential spatial patterns in spatial omics data by comparing gene expression across experimental conditions.

1 citation

spatial transcriptomicsstatistical model

𝕏 PostBluesky

BioinformaticsbioRxivPreprintNov 20, 2025

Orchestrating Spatial Transcriptomics Analysis with Bioconductor

Helena Lucia Crowell, Yixing Dong, Ilaria Billato…·Lukas M. Weber

The paper provides an open-source online book for analyzing spatial transcriptomics data using Bioconductor in R, with reproducible code and datasets.

4 citations

spatial transcriptomicsstatistical model

𝕏 PostBluesky

BioinformaticsBiostatisticsPeer-reviewedMay 22, 2024

DifferentialRegulation: a Bayesian hierarchical approach to identify differentially regulated genes

Simone Tiberi, Joël Meili, Peiying Cai…·Mark D. Robinson

DifferentialRegulation identifies differentially regulated genes by analyzing unspliced mRNA abundance across experimental conditions using a Bayesian hierarchical model.

1 citation

bulk RNA-seqscRNA-seq

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BioinformaticsBioinformaticsPeer-reviewedJan 15, 2024

DESpace: spatially variable gene detection via differential expression testing of spatial clusters

Peiying Cai, Mark D. Robinson, Simone Tiberi

DESpace detects spatially variable genes by testing differential expression between spatial clusters across biological replicates, showing good performance and computational efficiency.

17 citations

spatial transcriptomicsstatistical model

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