Fine-Grained Synonymous Codon Usage Patterns and their Potential Role in Functional Protein Production. - Ashley Babjac; Jun Li 052; Scott J. Emrich (BIBM, 2021)

A comparison of dimensionality reduction methods for large biological data. - Ashley Babjac; Taylor M. Royalty; Andrew D. Steen; Scott J. Emrich (BCB, 2022)

CodonBERT: Using BERT for Sentiment Analysis to Better Predict Genes with Low Expression. - Ashley Nicole Babjac; Zhixiu Lu; Scott J. Emrich (BCB, 2023)

Adapting Protein Language Models for Explainable Fine-Grained Evolutionary Pattern Discovery. - Ashley Babjac; Owen Queen; Shawn-Patrick Barhorst; Kambiz Kalhor; Andrew D. Steen; Scott J. Emrich (BIBM, 2023)

CodonT5: A Multi-task Codon Language Model to Perform Generative Codon Optimization. - Ashley Babjac; Scott J. Emrich (BIBM, 2024)