Author

Jianfeng Ke

University of Massachusetts LowellORCID 0000-0002-0876-3454Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Bioinformatics· 1 Genetic & Genomic Medicine· 1

Signature Assays, Organisms & Methods

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Assay:bulk RNA-seq· 1 Research Focus:differential expression· 1 Research Focus:drug response / drug discovery· 1 Research Focus:gene regulatory network inference· 1 Approach:graph neural network· 1 Organism:human· 1 Research Focus:imputation· 1 Approach:transformer / foundation model· 1

Frequent Co-Authors

Rachel MelamediD· 2 shared Tingjian GeiD· 1 shared

Activity by Year

2025-2026 · peak 1/yr

Co-Author Collaboration Network

2 top collaborators · 1 mutual co-author link

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2 shared papersGenetic & Genomic Medicine

Rachel MelamedORCID

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2 papers

Recent·Most cited

Genetic & Genomic MedicinemedRxivPreprintMay 13, 2026

A transformer model explaining mechanisms of drug therapeutic and adverse effects

Jianfeng Ke, Rachel Melamed

This paper introduces a transformer-based model, DraPhormer, to explain drug therapeutic and adverse effects by integrating drug molecular data, disease genetics, and known drug effects.

DOI 10.64898/2026.05.11.26352917

transformer / foundation modeldrug response / drug discovery

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BioinformaticsbioRxivPreprintMay 8, 2025

Discovering disease genetic variation impacting gene expression in 103 brain tissues with the Brain Ontology Expression (BRONTE) graph neural network model

Jianfeng Ke, Tingjian Ge, Rachel Melamed

The paper imputes gene expression in 103 brain tissues using BRONTE, a graph neural network, and identifies new genes and tissues affected by genetic variants linked to brain-related traits.

2 citations

humanbulk RNA-seq

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