RoboGen: Robot Generation through Artificial Evolution. - Joshua Evan Auerbach; Deniz Aydin; Andrea Maesani; Przemyslaw Kornatowski; Titus Cieslewski; Gregoire Heitz; Pradeep Fernando; Ilya Loshchilov; Ludovic Daler; Dario Floreano (ALIFE, 2014)

CLoNe: automated clustering based on local density neighborhoods for application to biomolecular structural ensembles. - Sylvain Träger; Giorgio Tamò; Deniz Aydin; Giulia Fonti; Martina Audagnotto; Matteo Dal Peraro (Bioinform., 2021)

Delineating the Ligand-Receptor Interactions That Lead to Biased Signaling at the μ-Opioid Receptor. - Brendan Kelly; Scott A. Hollingsworth; David C. Blakemore; Robert M. Owen; R. Ian Storer; Nigel A. Swain; Deniz Aydin; Rubben Torella; Joseph S. Warmus; Ron O. Dror (J. Chem. Inf. Model., 2021)

Security Vulnerabilities in AI-Generated JavaScript: A Comparative Study of Large Language Models. - Deniz Aydin; Serif Bahtiyar (CSR, 2025)