Author

Philip Fradkin

University of Toronto

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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Genomics· 2 Bioinformatics· 1

Signature Assays, Organisms & Methods

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Research Focus:benchmarking· 1 Assay:bulk RNA-seq· 1 Approach:contrastive learning· 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 Assay:GWAS summary statistics· 1

Frequent Co-Authors

Bo WangiD· 3 shared Brendan J. Frey· 2 shared Leo J. LeeiD· 2 shared Quaid MorrisiD· 2 shared Ruian Shi· 2 shared Taykhoom DalaliD· 2 shared Adamo YoungiD· 1 shared Andrew Jung· 1 shared

Activity by Year

2022-2026 · peak 1/yr

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10 top collaborators · 33 mutual co-author links

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3 shared papersGenomics

Bo WangORCID

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3 papers

Recent·Most cited

Orthrus: Towards Evolutionary and Functional RNA Foundation Models

Philip Fradkin, Ruian Shi, Taykhoom Dalal, Keren Isaev, Brendan J. Frey, Leo J. Lee, Quaid Morris, Bo Wang

Orthrus is a Mamba-based RNA foundation model pre-trained with biological augmentations and contrastive learning, achieving better mRNA property prediction than existing models with less fine-tuning data.

Nature Methods · Apr 17, 2026Peer-reviewedGenomics

mRNABench: A curated benchmark for mature mRNA property and function prediction

Ruian Shi, Taykhoom Dalal, Philip Fradkin, Divya Koyyalagunta, Simran Chhabria, Andrew Jung, Cyrus L. Tam, Defne Ceyhan, Jessica Lin, Kaitlin U. Laverty, Ilyes Baali, Bo Wang, Quaid Morris

The paper introduces mRNABench, a benchmark for evaluating mRNA property and function prediction models using self-supervised learning.

bioRxiv · Jul 5, 2025 · PreprintGenomics

A graph neural network approach to molecule carcinogenicity prediction

Philip Fradkin, Adamo Young, Lazar Atanackovic, Brendan J. Frey, Leo J. Lee, Bo Wang

This paper introduces a graph neural network model for predicting molecule carcinogenicity, showing improved performance over existing methods.

Bioinformatics · Apr 14, 2022Peer-reviewedBioinformatics