OrthoGather provides a user-friendly platform for comparative proteomic analysis and Gene Ontology enrichment across species, enabling functional interpretation of protein sets without computational expertise.

bioRxiv · Oct 1, 2026 · PreprintSystems Biology

Proteasomal downregulation of the pro-apoptotic MST2 pathway contributes to BRAF inhibitor resistance in melanoma

David Romano, Lucia García-Gutiérrez, Nourhan K. Aboud, David J. Duffy, Keith T. Flaherty, Dennie Tompers Frederick, Walter Kölch, David Matallanas

Life Science Alliance · Aug 29, 2022Peer-reviewedMolecular Biology

BAX and SMAC Regulate Bistable Properties of the Apoptotic Caspase System

Stephanie McKenna, Lucia García-Gutiérrez, David Matallanas, Dirk Fey

This study presents a mathematical model of how BAX and SMAC regulate the bistable properties of the apoptotic caspase system, validated by experimental and computational evidence.

Scientific Reports · Feb 8, 2021Peer-reviewedSystems Biology

Accurate Prediction of Kinase-Substrate Networks Using Knowledge Graphs

Vít Nováček, Gavin McGauran, David Matallanas, Alfonso Blanco, Piero Conca, Emir Muñoz, Luca Costabello, Kamalesh Kanakaraj, Zeeshan Nawaz, Brian Walsh, Sameh K. Mohamed, Pierre-Yves Vandenbussche, Colm J. Ryan, Walter Kölch, Dirk Fey

The paper introduces a model using knowledge graphs to predict kinase-substrate networks, achieving higher coverage and accuracy than existing methods through network-based learning.

PLoS Computational Biology · Dec 3, 2020Peer-reviewedBioinformatics