Miguél Vázquez

This paper introduces an AI-assisted framework for rapid prototyping of multicellular mechanistic models using LLMs and MCP servers to integrate multiple modeling tools.

CollecTRI-derived signed regulons, spanning 1,183 transcription factors (TFs) and 45,856 TF-gene links, outperform DoRothEA, ChEA3, RegNetwork and Pathway Commons at identifying perturbed TFs in KnockTF data.

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.

The paper predicts drug synergies using a logical modeling framework that combines manual curation with automated parameterization, showing that automated methods can outperform manual models in some cases.

The paper provides a user guide to five online tools for exploring and visualizing PCAWG data, demonstrating their integration with external resources to enhance cancer genomics research.

The paper analyzes non-coding mutations across 2,583 cancer genomes to identify genes and pathways affected, finding clusters of interacting proteins and insights into cancer mechanisms.