Karen Rothfels

Application of Large Language Models for Annotating Genes into Reactome Pathways

This paper applies large language models to assist in gene annotation into Reactome pathways, showing promising results in supporting curation workflows.

Pathway-based, reaction-specific annotation of disease variants for elucidation of molecular phenotypes

The paper annotates disease variants in the context of biological pathways to infer molecular phenotypes and model variant impacts.

ChatGPT usage in the Reactome curation process

This paper explores using ChatGPT in Reactome curation to automate pathway annotation, comparing its outputs to manual curation and identifying challenges and improvements.

Illuminating Dark Proteins using Reactome Pathways

The paper predicts functional interactions of dark proteins with Reactome pathways using a random forest classifier and develops a web portal to visualize these interactions.

COVID-19 Disease Map, a computational knowledge repository of SARS-CoV-2 virus-host interaction mechanisms

The paper describes the development of a computational knowledge repository, the COVID-19 Disease Map, which curates SARS-CoV-2 virus-host interaction mechanisms and provides tools for their analysis and application.