Giacomo B. Marino

The CFDE Workbench: Integrating Metadata and Processed Data from Common Fund Programs

The CFDE Workbench integrates metadata and processed data from Common Fund programs to enable FAIR and AI-ready cross-program knowledge discovery.

A Gene Set Foundation Model Pre-Trained on a Massive Collection of Diverse Gene Sets

The paper introduces a gene set foundation model trained on diverse gene sets to predict gene functions, achieving superior performance compared to existing methods.

RummaGEO: Automatic Mining of Human and Mouse Gene Sets from GEO

RummaGEO automatically mines gene sets from GEO RNA-seq studies for human and mouse, enabling signature search and metadata analysis.

Playbook Workflow Builder: Interactive Construction of Bioinformatics Workflows from a Network of Microservices

The paper introduces a web-based platform for building bioinformatics workflows using APIs, enabling hypothesis generation across multiple data sources.

Rummagene: Mining Gene Sets from Supporting Materials of PMC Publications

Rummagene extracts and provides access to gene sets from PMC publications for search and analysis, revealing trends and enabling functional predictions.

ReproTox-KG: Toxicology Knowledge Graph for Structural Birth Defects

The paper constructs a reproductive toxicity knowledge graph (ReproTox-KG) to link birth defects, drugs, and genes, identifying potential molecular mechanisms for drug-induced birth defects.