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Related Experiment Video

Updated: Apr 19, 2026

Identification of Footprints of RNA:Protein Complexes via RNA Immunoprecipitation in Tandem Followed by Sequencing RIPiT-Seq

Identification of Footprints of RNA:Protein Complexes via RNA Immunoprecipitation in Tandem Followed by Sequencing RIPiT-Seq

Published on: July 10, 2019

Orthrus: toward evolutionary and functional RNA foundation models.

Philip Fradkin^1,2, Ruian Ian Shi^1,2,3, Taykhoom Dalal³

¹Vector Institute, Toronto, Ontario, Canada.

|April 17, 2026

Summary

This summary is machine-generated.

Orthrus, a novel foundation model for mature RNA, improves prediction of RNA properties. It leverages biological data and outperforms existing models, aiding transcript function and regulation understanding.

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Last Updated: Apr 19, 2026

Identification of Footprints of RNA:Protein Complexes via RNA Immunoprecipitation in Tandem Followed by Sequencing RIPiT-Seq

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Published on: July 10, 2019

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Method for the Isolation and Identification of mRNAs, microRNAs and Protein Components of Ribonucleoprotein Complexes from Cell Extracts using RIP-Chip

Method for the Isolation and Identification of mRNAs, microRNAs and Protein Components of Ribonucleoprotein Complexes from Cell Extracts using RIP-Chip

Published on: September 29, 2012

Area of Science:

Genomics
Bioinformatics
Computational Biology

Background:

Predicting mature RNA properties from genomic data is challenging.
Existing foundation models lack biological domain knowledge for RNA tasks.

Purpose of the Study:

Introduce Orthrus, a Mamba-based foundation model for mature RNA.
Improve prediction of RNA properties and transcript function.

Main Methods:

Pretrained Orthrus using self-supervised contrastive learning with biological augmentations.
Maximized embedding similarity between splice isoforms and orthologous genes.
Utilized data from ten model organisms and 400+ mammalian species.

Main Results:

Orthrus' latent representation clusters RNA sequences by function and evolution.
Outperformed existing foundation models on mRNA property prediction.
Required significantly less fine-tuning data.

Conclusions:

Orthrus effectively captures functional and evolutionary similarities in RNA.
Demonstrates capability in discerning divergent biological functions of transcript isoforms.
Offers a powerful tool for RNA research and genomic data analysis.