Dexter R. Pratt

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

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.

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.

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

reguloGPT constructs a knowledge graph of molecular regulatory pathways using GPT-4 for entity recognition and relationship extraction, improving over existing methods and demonstrating utility in cancer research.

The paper constructs a PPI network of 100 high-confidence ASD genes, identifies novel interactions, and uses AlphaFold-Multimer to prioritize variants for functional validation in organoids.

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

This study maps the SARS-CoV-2 virus-host interactome using BioID in A549 cells and provides a public resource for analyzing host-viral protein associations.

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

This paper introduces DeepSyn, a machine learning method for gene functional enrichment that uses a knowledge graph to infer gene functions based on disease and drug context, achieving high accuracy in various applications.