mogam-ai/CDS-BART-mRFP-expression

📊 mRFP expression dataset

This dataset comprises E. coli protein expression data for monomeric Red Fluorescent Protein (mRFP). It was generated from a synonymous codon-randomized library with 1,459 gene variants in E. coli, with a measured protein expression level for each. The original dataset is from CodonBERT.

⁉️ Dataset Contents

• Sequence: The mRNA sequence of the mRFP variants.
• Expression: The measured protein expression level.

🎯 Purpose

This dataset serves as a benchmark for fine-tuning models on a regression task, predicting expression behavior from its sequence. We used this dataset to fine-tune CDS-BART, a BART-based foundation model trained on massive mRNA sequences. Demonstrating its ability to perform downstream tasks related to mRNA regulation which are fine-tuned for various mRNA-related downstream task. CDS-BART available at GitHub

🔧Usage

from datasets import load_dataset

dataset = load_dataset('mogam-ai/CDS-BART-mRFP-expression')

📚 Dataset Reference

• Nieuwkoop, Thijs, et al. "Revealing determinants of translation efficiency via whole-gene codon randomization and machine learning." Nucleic acids research 51.5 (2023): 2363-2376.
• Li, Sizhen, et al. "CodonBERT large language model for mRNA vaccines." Genome research 34.7 (2024): 1027-1035.