Author

Ruian Shi

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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Approach:statistical model· 2 Research Focus:benchmarking· 1 Assay:bulk RNA-seq· 1 Approach:contrastive learning· 1 Research Focus:differential expression· 1 Research Focus:gene regulatory network inference· 1 Assay:GWAS summary statistics· 1 Organism:human· 1

Frequent Co-Authors

Quaid MorrisiD· 3 shared Bo WangiD· 2 shared Philip Fradkin· 2 shared Taykhoom DalaliD· 2 shared Amit Deshwar· 1 shared Andrew Jung· 1 shared Brendan J. Frey· 1 shared Caitlin F Harrigan· 1 shared

Activity by Year

2019-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 28 mutual co-author links

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3 shared papersGenomics

Quaid MorrisORCID

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Author profile →

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

TrackSig: reconstructing evolutionary trajectories of mutations in cancer

Yulia Rubanova, Ruian Shi, Caitlin F Harrigan, Roujia Li, Jeff Wintersinger, Nil Sahin, Amit Deshwar, Quaid Morris, PCAWG Evolution and Heterogeneity Working Group, PCAWG network

TrackSig estimates mutation evolutionary trajectories from bulk tumor sequencing data, showing improved accuracy in detecting subclonal populations and signature activity changes compared to baseline methods.

bioRxiv · Sep 30, 2019 · PreprintBioinformatics