Christopher Churas

textToKnowledgeGraph: Generation of Molecular Interaction Knowledge Graphs Using Large Language Models for Exploration in Cytoscape

The paper introduces textToKnowledgeGraph, a tool using large language models to extract molecular interactions into BEL format for analysis in Cytoscape.

The FAIRSCAPE AI-readiness Framework for Biomedical Research

The paper introduces FAIRSCAPE, a framework for packaging biomedical datasets with metadata to enhance AI-readiness, explainability, and FAIR compliance.

State of the Interactomes: an evaluation of molecular networks for generating biological insights

The paper evaluates 46 human interactomes to identify which are best for disease gene discovery and interaction prediction, finding large networks like HumanNet perform better for disease genes while smaller ones like DIP excel in prediction.

Global siRNA Screen Reveals Critical Human Host Factors of SARS-CoV-2 Multicycle Replication

This study identifies critical human host factors involved in SARS-CoV-2 multicycle replication through a genome-scale siRNA screen and validates potential antiviral targets.

Cell Maps for Artificial Intelligence: AI-Ready Maps of Human Cell Architecture from Disease-Relevant Cell Lines

The paper introduces the CM4AI project, which aims to create AI-ready datasets of human cell architecture using multimodal data from cell lines.

NDEx IQuery: a multi-method network gene set analysis leveraging the Network Data Exchange

NDEx IQuery provides a tool for network-based gene set analysis using diverse pathways and integrates with existing resources to enhance pathway interpretation.

Identifying persistent structures in multiscale 'omics data

This paper introduces a method to identify persistent structures in multiscale omics data, expanding cell type catalogs and revealing SARS-COV-2 protein interactions.