mogam-ai/CDS-BART-Ecoli-proteins

📊 E.coli protein dataset

This dataset comprises E.coli protein expression levels, categorized in low, medium and high. Specifically, it contains 2308 low, 2067 medium and 1973 high expression data facilitating the study of protein production in bacterial cells. The original dataset is from CodonBERT.

⁉️ Dataset Contents

• Sequence: The mRNA sequence of the mRNA degradation
• Expression: The three levels of expression data

🎯 Purpose

This dataset serves as a benchmark for fine-tuning models on a classification 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-Ecoli-proteins')

📚 Dataset Reference

• Ding, Zundan, et al. "MPEPE, a predictive approach to improve protein expression in E. coli based on deep learning." Computational and Structural Biotechnology Journal 20 (2022): 1142-1153.
• Li, Sizhen, et al. "CodonBERT large language model for mRNA vaccines." Genome research 34.7 (2024): 1027-1035.