Arda Halu

This paper introduces Pathopticon, a network-based method integrating pharmacogenomics, cheminformatics, and disease phenotypes to prioritize cell lines and drugs for cell type-guided drug discovery.

The paper isolates and analyzes extracellular vesicles from atherosclerotic plaques and aortic valves, identifying shared and distinct molecular pathways involved in calcification.

The paper introduces MuXTalk, a network-based method to detect signaling crosstalk by integrating signaling and regulatory interactions, expanding crosstalk databases and improving prediction performance.

The paper shows vitamin D regulates two chromosomal loci linked to autoimmune and inflammatory diseases by modulating gene expression and immune pathways.

The paper analyzes the robustness of multilayer biological networks by integrating gene regulatory, protein-protein interaction, and metabolic data to assess how perturbations affect system stability.

This study constructs and analyzes a multiplex network of 779 human diseases, revealing connections between genetic and phenotypic layers and identifying new disease associations.

The paper identifies NFATC4 as a key regulator of Type 2 Diabetes genes by analyzing a gene regulatory network in pancreatic islets and linking it to eQTLs and differential expression.

This paper introduces a new disease classification system (NCD) that integrates phenotypic and molecular networks to improve disease specificity and redefine disease boundaries.