[1] He is known for his contributions to single-molecule analysis of chaperone assisted protein folding, molecular topology and medical systems biophysics and bioengineering.

Mashaghi made the first observation of direct chaperone involvement during folding of a protein, using a single molecule force spectroscopy method.

[6][7] In recent years, the team got interested in disease-related biomolecular condensates and thus extended the force spectroscopy and circuit topology approaches to study these complex systems.

[13] Ebola and similar viruses pathologically alter the mechanics of human cells, which is recapitulated in organ chip models.

Moreover, the Mashaghi team developed optical tweezers and acoustic force spectroscopy based assays to probe such mechanical alterations at the single cell level.

He worked and co-authored with Hans Clevers, Cees Dekker, Anthony A. Hyman, Colin Adams, Erica Flapan, Donald E. Ingber, Huib Bakker, Reza Dana, and Petra Schwille.