Author

Patrick F. Cullen

Biogen (United States)

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Bioinformatics· 1 Genomics· 1 Neuroscience· 1

Signature Assays, Organisms & Methods

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Approach:statistical model· 3 Research Focus:cell type annotation· 2 Organism:human· 2 Assay:spatial transcriptomics· 2 Assay:bulk RNA-seq· 1 Research Focus:cell-cell communication· 1 Research Focus:clustering· 1 Organism:mouse· 1

Frequent Co-Authors

Baohong ZhangiD· 3 shared Hui‐Hsin TsaiiD· 2 shared Kejie LiiD· 2 shared Ravi Challa· 2 shared Sarbottam PiyaiD· 2 shared Su Jing ChaniD· 2 shared Taylor L. ReynoldsiD· 2 shared Thomas M. CarlileiD· 2 shared

Activity by Year

2021-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 45 mutual co-author links

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3 shared papersNeuroscience

Baohong ZhangORCID

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Author profile →

3 papers

Recent·Most cited

Spatial transcriptomics reveals heterogeneous cell-cell interactions among brain regions in a cuprizone model consistent with multiple sclerosis lesions

Hui‐Hsin Tsai, Sarbottam Piya, Jing Wang, Jing Zhu, Wenxing Hu, Andrew R. Gehrke, Shaolong Cao, Amanda J. Guise, Su Jing Chan, Mark J. Sheehan, Jenhwa Chu, Zhengyu Ouyang, Matthew M. Ryals, Michelle Lee, Wanli Wang, , Baohong Zhang

The paper uses spatial transcriptomics to analyze cell-cell interactions in a cuprizone model, finding region-specific changes and partial translatability to multiple sclerosis lesions.

Frontiers in Bioinformatics · Aug 6, 2026Peer-reviewedNeuroscience

Scaling up spatial transcriptomics for large-sized tissues: uncovering cellular-level tissue architecture beyond conventional platforms with iSCALE

Amelia R. Schroeder, Melanie Loth, Chunyu Luo, Sicong Yao, Hanying Yan, Daiwei Zhang, Sarbottam Piya, Edward D. Plowey, Wenxing Hu, Jean Rene V. Clemenceau, Inyeop Jang, Minji Kim, Isabel Barnfather, Su Jing Chan, Taylor L. Reynolds, , Mingyao Li

iSCALE predicts super-resolution gene expression and annotates tissue architecture in large tissues, revealing features missed by conventional spatial transcriptomics.

Nature Methods · Sep 1, 2025Peer-reviewedGenomics

CellMap: Characterizing the types and composition of iPSC-derived cells from RNA-seq data

Zhengyu Ouyang, Nathanael Bourgeois, Eugenia Lyashenko, Paige Cundiff, Patrick F. Cullen, Ravi Challa, Kejie Li, Xinmin Zhang, Fergal Casey, Sandi Engle, Baohong Zhang, Maria I. Zavodszky

CellMap infers cell type profiles in bulk RNA-seq data from iPSC-derived cell lines using reference single-cell datasets.

bioRxiv · May 24, 2021 · PreprintBioinformatics