Ewy A. Mathé

This paper introduces ConcuRx, a statistical framework that improves gene prioritization across heterogeneous CRISPR drug-response datasets by modeling between-study variability, leading to better identification of MOA-associated genes.

GEO-BERT improves dataset retrieval from GEO by using a retrieval-augmented LLM framework with a hierarchical hybrid field-aware system, enhancing semantic search and traditional search performance.

CalFluxTools automates analysis of calcium flux data from high-throughput screens, providing quality control, statistical tests, and machine learning predictions for toxicity assessment.

RD-OMICS integrates and structures rare disease omics data from GEO into a knowledge graph to support research and drug repurposing.

This study uses metabolomics to distinguish Dengue and Zika virus infections in hiPSCs, identifying virus-specific metabolic signatures and pathways that regulate viral replication.

This paper introduces GENN, a method for multi-omic interactome analysis that improves prediction of biomedical outcomes by learning salient associations in a low-dimensional space.

The paper explores NCATS biomedical data to identify drug repurposing candidates through chemical clustering and evidence mining.

The paper develops OMICmAge, a multi-omics biomarker of biological age, and shows it outperforms existing markers in predicting chronic diseases and mortality.

The paper clusters rare diseases using a knowledge graph with node embeddings, identifying 37 clusters with shared genes and semantic similarities.

RaMP-DB 2.0 provides an updated database and tools for functional interpretation of metabolomic and multi-omic data, with enhanced annotations and enrichment analysis capabilities.

The paper presents a workflow for integrating diverse datasets to build a network pharmacology resource for COVID-19 research, resulting in a Neo4j graph database named Neo4COVID19.

ALTRE is an R package and web app for analyzing chromatin accessibility data to identify altered regulatory elements across cell types.