Author

Pen Yuan Chu

Taipei Veterans General HospitalORCID 0009-0003-4693-0887Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Cancer Biology· 2

Signature Assays, Organisms & Methods

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Approach:deep learning· 2 Organism:human· 2 Assay:bulk RNA-seq· 1 Research Focus:cell type annotation· 1 Research Focus:clustering· 1 Research Focus:differential expression· 1 Research Focus:drug response / drug discovery· 1 Assay:spatial transcriptomics· 1

Frequent Co-Authors

Amos StemmeriD· 2 shared Chi‐Ping DayiD· 2 shared Danh-Tai HoangiD· 2 shared Eytan RuppiniD· 2 shared Muh‐Hwa YangiD· 2 shared Saugato Rahman DhrubaiD· 2 shared Sumeet PatiyaliD· 2 shared Sumit MukherjeeiD· 2 shared

Activity by Year

2025-2026 · peak 1/yr

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10 top collaborators · 45 mutual co-author links

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2 shared papersCancer Biology

Amos StemmerORCID

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2 papers

Recent·Most cited

Cancer BiologybioRxivPreprintMay 19, 2026

Histopathology-inferred spatial transcriptomics characterizes the tumor microenvironment in 1,500 head and neck tumors and predicts clinical outcomes

Sumona Biswas, Sumeet Patiyal, T W Chen…·Eytan Ruppin

This paper develops HEiST, a deep learning method to infer spatial transcriptomes from H&E slides, identifies two prognostic Spatiotypes in HNSC, and shows they predict treatment response better than existing biomarkers.

DOI 10.64898/2026.05.16.725687

humanspatial transcriptomics

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Cancer BiologybioRxivPreprintJun 27, 2025

Pan-cancer prediction of tumor immune activation and response to immune checkpoint blockade from tumor transcriptomics and histopathology

Sumit Mukherjee, Sumeet Patiyal, Lipika R. Pal…·Eytan Ruppin

This paper introduces TIME_ACT, a transcriptomic signature predicting immune checkpoint blockade response across cancers, validated using histopathology and multiple cohorts.

DOI 10.1101/2025.06.27.661875

humanbulk RNA-seq

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