Quinn Dickinson

REPLAY: A reproducible and user-friendly application for DNA replication timing analysis from Repli-seq data

REPLAY automates DNA replication timing analysis from Repli-seq data, providing a reproducible and user-friendly tool without requiring programming expertise.

Cryptic multicellularity in wild yeast brings selective advantages under stress

This study identifies a cryptic multicellular trait in wild yeast that provides survival advantages under stress conditions.

PARTAGE: Parallel analysis of replication timing and gene expression

PARTAGE jointly profiles replication timing, gene expression, and copy number variation from the same sample to better understand their relationships.

Multi-Omic Integration by Machine Learning (MIMaL) Reveals Protein-Metabolite Connections and New Gene Functions

This paper uses machine learning to integrate proteome and metabolome data, revealing new protein-metabolite connections and gene functions in yeast.

Positional SHAP (PoSHAP) for Interpretation of Machine Learning Models Trained from Biological Sequences

This paper introduces PoSHAP, a framework for interpreting machine learning models trained on biological sequences, demonstrating its ability to reproduce known peptide binding motifs and provide insights into amino acid interactions.