Joaquim Aguirre‐Plans

Inferring and Evaluating Network Medicine-Based Disease Modules with Nextflow

This paper introduces a Nextflow pipeline to evaluate disease module detection methods, showing variability in results due to method, network, and seed differences.

Structure-based learning to model complex protein-DNA interactions and transcription-factor co-operativity in cis-regulatory elements

The paper introduces a structure-based learning approach to predict TF binding preferences and model TF regulatory complexes, demonstrating its effectiveness over existing methods in cases of remote homology.

TPMS technology to infer biomarkers of macular degeneration prognosis in in silico simulated prototype-patients under the study of heart failure treatment with sacubitril and valsartan

The paper uses TPMS to model drug mechanisms and identify biomarkers linked to macular degeneration as an adverse effect of heart failure treatment with sacubitril/valsartan.

Targeting comorbid diseases via network endopharmacology

This study introduces PxEA, a network-based method to identify drugs targeting common pathways across diseases, demonstrating drug repurposing opportunities for autoimmune disorders and comorbid conditions like type 2 diabetes and Alzheimer's disease.