The Trigger Factor Chaperone Encapsulates and Stabilizes Partial Folds of Substrate Proteins. - Kushagra Singhal; Jocelyne Vreede; Alireza Mashaghi; Sander J. Tans; Peter G. Bolhuis (PLoS Comput. Biol., 2015)

Extended Topological Persistence and Contact Arrangements in Folded Linear Molecules. - Sara Kalisnik Verovsek; Alireza Mashaghi (Frontiers Appl. Math. Stat., 2016)

Disease evolution in reaction networks: Implications for a diagnostic problem. - Abolfazl Ramezanpour; Alireza Mashaghi (PLoS Comput. Biol., 2020)

Coloring Invariant for Topological Circuits in Folded Linear Chains. - Jose Ceniceros; Mohamed Elhamdadi; Alireza Mashaghi (Symmetry, 2021)

Circuit Topology for Bottom-Up Engineering of Molecular Knots. - Anatoly Golovnev; Alireza Mashaghi (Symmetry, 2021)

Polynomial Invariant of Molecular Circuit Topology. - Alireza Mashaghi; Roland van der Veen (Symmetry, 2021)

Biochemical reaction network topology defines dose-dependent Drug-Drug interactions. - Mehrad Babaei; Tom M. J. Evers; Fereshteh Shokri; Lucia Altucci; Elizabeth C. M. de Lange; Alireza Mashaghi (Comput. Biol. Medicine, 2023)

Circuit Topology Approach for the Comparative Analysis of Intrinsically Disordered Proteins. - Barbara Scalvini; Vahid Sheikhhassani; Nadine van de Brug; Laurens W. H. J. Heling; Jeremy D. Schmit; Alireza Mashaghi (J. Chem. Inf. Model., 2023)

Semantic Topology: a New Perspective for Communication Style Characterization. - Barbara Scalvini; Alireza Mashaghi (ACL (Findings), 2025)